]> 06-01-2017 An ontology for linking and integrating open biological and biomedical ontologies Development version Edison Ong OLOBO is a biomedical ontology that aims to link and integrate open biological and biomediacl ontologies (OBO),. OLOBO: Ontology for Linking and Integrating Open Biological and Biomedical Ontologies OWL-DL Vision Release: 1.0.01 Yongqun "Oliver" He BFO OWL specification label bfo.owl obi.owl 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 bfo.owl obi.owl Person:Alan Ruttenberg BFO CLIF specification label 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 label editor preferred term editor preferred term editor preferred term~editor preferred label editor preferred label bfo.owl obi.owl 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 bfo.owl obi.owl 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 A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober example example of usage has curation status OBI_0000281 PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status definition textual definition textual definition definition definition bfo.owl chebi.owl doid.owl go.owl obi.owl pato.owl po.owl pro.owl xao.owl zfa.owl 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. definition editor note editor note IAO:0000116 bfo.owl editor_note editor_note obi.owl true uberon 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 bfo.owl obi.owl 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people PERSON:Daniel Schober term editor alternative term bfo.owl obi.owl 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 bfo.owl obi.owl 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 go.owl obi.owl pato.owl po.owl xao.owl zfa.owl 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 notes curator note IAO:0000232 bfo.owl curator_notes curator_notes obi.owl true uberon An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note imported from bfo.owl obi.owl 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 assertion to go.owl obi.owl 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 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 . go.owl obi.owl 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 elucidation bfo.owl obi.owl 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) bfo.owl obi.owl An axiom associated with a term expressed using natural language Person:Alan Ruttenberg Person:Alan Ruttenberg has associated axiom(nl) has associated axiom(fol) bfo.owl obi.owl An axiom expressed in first order logic using CLIF syntax Person:Alan Ruttenberg Person:Alan Ruttenberg has associated axiom(fol) has axiom label bfo.owl obi.owl 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 term replaced by go.owl obi.owl pato.owl po.owl pro.owl xao.owl zfa.owl 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 term from ontology temporal interpretation https://github.com/oborel/obo-relations/wiki/ROAndTime An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. is opposite_of RO:0002604 is_opposite_of is_opposite_of quality true true external_definition An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000001 external_definition external_definition true uberon axiom_lost_from_external_ontology A textual description of an axiom loss in this ontology compared to an external ontology. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000002 axiom_lost_from_external_ontology axiom_lost_from_external_ontology true uberon homology_notes Notes on the homology status of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000003 homology_notes homology_notes true uberon has_relational_adjective UBPROP:0000007 Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'. has_relational_adjective has_relational_adjective true uberon taxon_notes Notes on the how instances of this class vary across species. UBPROP:0000008 taxon_notes taxon_notes true uberon function_notes Notes on the evolved function of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000009 function_notes function_notes true uberon external_ontology_notes Notes on how similar or equivalent classes are represented in other ontologies. Notes on how similar or equivalent classes are represented in other ontologies. This annotation property may be replaced with an annotation property from an external ontology such as IAO This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000012 external_ontology_notes external_ontology_notes true uberon fma_set_term FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term UBPROP:0000202 fma_set_term fma_set_term true uberon has_rank A metadata relation between a class and its taxonomic rank (eg species, family) ncbi_taxonomy contributor bfo.owl dc-contributor dc-contributor obi.owl true uberon go.owl obi.owl po.owl go.owl obi.owl po.owl bfo.owl obi.owl subset_property chebi.owl doid.owl go.owl pato.owl po.owl xao.owl zfa.owl synonym_type_property chebi.owl go.owl po.owl pro.owl xao.owl zfa.owl doid.owl pato.owl pro.owl xao.owl zfa.owl consider go.owl pato.owl po.owl pro.owl xao.owl zfa.owl doid.owl go.owl pato.owl po.owl xao.owl zfa.owl doid.owl go.owl pato.owl po.owl xao.owl zfa.owl chebi.owl doid.owl pato.owl pro.owl xao.owl zfa.owl chebi.owl doid.owl go.owl pato.owl po.owl pro.owl xao.owl zfa.owl has_alternative_id chebi.owl doid.owl go.owl pato.owl po.owl pro.owl xao.owl zfa.owl has_broad_synonym go.owl pato.owl po.owl pro.owl xao.owl zfa.owl database_cross_reference chebi.owl doid.owl go.owl pato.owl po.owl pro.owl xao.owl zfa.owl has_exact_synonym chebi.owl doid.owl go.owl pato.owl po.owl pro.owl xao.owl zfa.owl has_narrow_synonym doid.owl go.owl pato.owl po.owl pro.owl xao.owl zfa.owl has_obo_format_version chebi.owl doid.owl go.owl pato.owl po.owl pro.owl xao.owl zfa.owl has_obo_namespace chebi.owl doid.owl go.owl pato.owl po.owl pro.owl xao.owl zfa.owl has_related_synonym chebi.owl doid.owl go.owl pato.owl po.owl pro.owl xao.owl zfa.owl has_scope go.owl po.owl pro.owl has_synonym_type chebi.owl go.owl po.owl pro.owl xao.owl zfa.owl chebi.owl doid.owl go.owl pato.owl po.owl pro.owl xao.owl zfa.owl in_subset chebi.owl doid.owl go.owl pato.owl po.owl xao.owl zfa.owl go.owl pato.owl go.owl pato.owl chebi.owl pro.owl chebi.owl doid.owl pato.owl po.owl pro.owl xao.owl zfa.owl shorthand chebi.owl go.owl obi.owl pato.owl po.owl xao.owl zfa.owl po.owl xao.owl zfa.owl bfo.owl chebi.owl doid.owl go.owl obi.owl pato.owl po.owl pro.owl xao.owl zfa.owl bfo.owl obi.owl label bfo.owl chebi.owl doid.owl go.owl obi.owl pato.owl po.owl pro.owl xao.owl zfa.owl bfo.owl obi.owl chebi.owl doid.owl go.owl obi.owl pato.owl po.owl pro.owl xao.owl zfa.owl bfo.owl obi.owl part of go.owl obi.owl pato.owl po.owl pro.owl xao.owl zfa.owl Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. a core relation that holds between a part and its whole is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) part_of this day is part of this year (occurrent parthood) has part chebi.owl go.owl obi.owl pato.owl po.owl pro.owl zfa.owl Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. a core relation that holds between a whole and its part has part has_part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) preceded by obi.owl po.owl An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. http://www.obofoundry.org/ro/#OBO_REL:preceded_by is preceded by preceded by preceded_by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. precedes obi.owl po.owl 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 go.owl obi.owl Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant 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 occurs_in unfolds in unfolds_in participates in obi.owl pro.owl a relation between a continuant and a process, in which the continuant is somehow involved in the process participates in participates_in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation has quality obi.owl pro.owl A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence has_quality this apple has quality this red color has role chebi.owl obi.owl A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence has_role this person has role this investigator role (more colloquially: this person has this role of investigator) derives from obi.owl pro.owl This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. 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 this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) located in doid.owl obi.owl po.owl pro.owl http://www.obofoundry.org/ro/#OBO_REL:located_in Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime a relation between two independent continuants, the target and the location, in which the target is entirely within the location located in located_in my brain is located in my head this rat is located in this cage only in taxon po.owl pro.owl lactation SubClassOf 'only in taxon' some 'Mammalia' x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria Chris Mungall develops from po.owl xao.owl zfa.owl Melissa Haendel David Osumi-Sutherland Terry Meehan x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y This is the transitive form of the develops from relation Chris Mungall adjacent to obi.owl po.owl x adjacent to y if and only if x and y share a boundary. A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. This relation acts as a join point with BSPO Chris Mungall The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. entity bfo.owl obi.owl entity BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf Julius Caesar Verdi’s Requiem entity the Second World War your body mass index continuant bfo.owl obi.owl continuant Continuant (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) occurrent bfo.owl obi.owl (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] 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. (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: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent 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]) independent continuant bfo.owl obi.owl IndependentContinuant (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] 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 heart a spatial region ic a chair a leg a molecule 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 spatial region bfo.owl obi.owl (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. temporal region bfo.owl obi.owl (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]) 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]) 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 bfo.owl obi.owl 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 spatiotemporal region bfo.owl obi.owl (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 process bfo.owl obi.owl 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. disposition bfo.owl obi.owl (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. Disposition (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] an atom of element X has the disposition to decay to an atom of element Y 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]) b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis realizable entity bfo.owl obi.owl (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 zero-dimensional spatial region bfo.owl obi.owl 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]) quality bfo.owl obi.owl pro.owl (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] quality Quality (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril specifically dependent continuant bfo.owl obi.owl (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 role bfo.owl obi.owl 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 fiat object part bfo.owl obi.owl pro.owl 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] BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) 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 one-dimensional spatial region bfo.owl obi.owl (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. object aggregate bfo.owl obi.owl ObjectAggregate 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] 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). 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 defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container object-aggregate 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 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. three-dimensional spatial region bfo.owl obi.owl 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]) ThreeDimensionalSpatialRegion a cube-shaped region of space a sphere-shaped region of space, site bfo.owl obi.owl (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] Manhattan Canyon) a rabbit hole site Site a hole in the interior of a portion of cheese an air traffic control region defined in the airspace above an airport b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) object bfo.owl obi.owl pro.owl object BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 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 atom b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star generically dependent continuant bfo.owl obi.owl gdc (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. function bfo.owl obi.owl (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] Function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar process boundary bfo.owl obi.owl (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] Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) p-boundary ProcessBoundary 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. one-dimensional temporal region bfo.owl obi.owl OneDimensionalTemporalRegion 1d-t-region (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). the temporal region during which a process occurs. material entity material entity BFO:0000040 bfo bfo.owl obi.owl pro.owl 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 continuant fiat boundary bfo.owl obi.owl 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 Every continuant fiat boundary is located at some spatial region at every time at which it exists cf-boundary 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 bfo.owl obi.owl 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 bfo.owl obi.owl 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 process profile bfo.owl obi.owl 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]) relational quality bfo.owl obi.owl 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]) two-dimensional continuant fiat boundary bfo.owl obi.owl (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]) zero-dimensional continuant fiat boundary bfo.owl obi.owl (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. zero-dimensional temporal region bfo.owl obi.owl (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. history bfo.owl obi.owl 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 water 0 18.011 18.01530 An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms. BOUND WATER Beilstein:3587155 CAS:7732-18-5 CHEBI:10743 CHEBI:13352 CHEBI:15377 CHEBI:27313 CHEBI:42043 CHEBI:42857 CHEBI:43228 CHEBI:44292 CHEBI:44701 CHEBI:44819 CHEBI:5585 Gmelin:117 H2O HMDB:HMDB02111 HOH InChI=1S/H2O/h1H2 KEGG:C00001 KEGG:D00001 MetaCyc:WATER MolBase:1 PDBeChem:HOH PDBeChem:MTO Reaxys:3587155 WATER Wasser Water Wikipedia:Water XLYOFNOQVPJJNP-UHFFFAOYSA-N [H]O[H] [OH2] acqua agua aqua chebi.owl chebi_ontology dihydridooxygen dihydrogen oxide eau hydrogen hydroxide obi.owl oxidane water hydron +1 1.00794 1.008 CHEBI:10744 CHEBI:13357 CHEBI:15378 CHEBI:5584 GPRLSGONYQIRFK-UHFFFAOYSA-N H H(+) H+ Hydron InChI=1S/p+1 KEGG:C00080 The general name for the hydrogen nucleus, to be used without regard to the hydrogen nuclear mass (either for hydrogen in its natural abundance or where it is not desired to distinguish between the isotopes). [H+] chebi_ontology hydrogen(1+) hydron biotin (+)-cis-Hexahydro-2-oxo-1H-thieno[3,4]imidazole-4-valeric acid (3aS,4S,6aR)-Hexahydro-2-oxo-1H-thieno[3,4-d]imidazole-4-valeric acid 0 244.088 244.31172 5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanoic acid 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. BIOTIN Beilstein:86838 Biotin C10H16N2O3S CAS:58-85-5 CHEBI:13905 CHEBI:15956 CHEBI:22882 CHEBI:22884 CHEBI:3108 CHEBI:41236 COMe:MOL000144 Coenzyme R D-(+)-biotin D-Biotin DrugBank:DB00121 Drug_Central:373 Gmelin:1918703 HMDB:HMDB00030 InChI=1S/C10H16N2O3S/c13-8(14)4-2-1-3-7-9-6(5-16-7)11-10(15)12-9/h6-7,9H,1-5H2,(H,13,14)(H2,11,12,15)/t6-,7-,9-/m0/s1 KEGG:C00120 KEGG:D00029 KNApSAcK:C00000756 LINCS:LSM-3994 MetaCyc:BIOTIN PDBeChem:BTN PMID:11435506 PMID:11800048 PMID:12055344 PMID:12803839 PMID:15012185 PMID:15202718 PMID:15272000 PMID:15899401 PMID:16419467 PMID:16676358 PMID:16677798 PMID:16769720 PMID:17297119 PMID:18452485 PMID:18509457 PMID:19319844 PMID:19727438 PMID:19928962 PMID:20967359 PMID:20974274 PMID:21248194 PMID:21356565 PMID:21373679 PMID:21596550 PMID:21871906 PMID:25515858 Reaxys:86838 Vitamin H Wikipedia:Biotin YBJHBAHKTGYVGT-ZKWXMUAHSA-N [H][C@]12CS[C@@H](CCCCC(O)=O)[C@@]1([H])NC(=O)N2 biotina biotine biotinum chebi.owl chebi_ontology cis-(+)-Tetrahydro-2-oxothieno[3,4]imidazoline-4-valeric acid cis-Hexahydro-2-oxo-1H-thieno(3,4)imidazole-4-valeric acid cis-Tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid obi.owl vitamin B7 polynucleotide (C5H8O6PR)n.C10H17O10PR2 0 0.0 A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues. C10H17O10PR2(C5H8O6PR)n CHEBI:13672 CHEBI:14859 CHEBI:15986 CHEBI:8312 KEGG:C00419 Polynucleotide chebi_ontology polynucleotides GTP 0 5'-GTP 522.991 523.18062 Beilstein:1201437 Beilstein:74004 C10H16N5O14P3 CAS:86-01-1 CHEBI:13342 CHEBI:15996 CHEBI:24451 CHEBI:42934 CHEBI:5234 DrugBank:DB04137 GTP GUANOSINE-5'-TRIPHOSPHATE Guanosine 5'-triphosphate H4gtp InChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1 KEGG:C00044 KNApSAcK:C00007223 Nc1nc2n(cnc2c(=O)[nH]1)[C@@H]1O[C@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)[C@@H](O)[C@H]1O PDBeChem:GTP XKMLYUALXHKNFT-UUOKFMHZSA-N chebi.owl chebi_ontology guanosine 5'-(tetrahydrogen triphosphate) guanosine 5'-triphosphoric acid guanosine triphosphate pro.owl phospholipid A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides. C5H6O8PR3 CHEBI:14816 CHEBI:16247 CHEBI:26063 CHEBI:8150 KEGG:C00865 Phospholipid chebi_ontology phospholipid derivative phospholipids indole-3-acetic acid (Indol-3-yl)acetate (indol-3-yl)acetic acid 0 175.063 175.18400 1H-indol-3-ylacetic acid 2-(indol-3-yl)ethanoic acid 3-Indolylessigsaeure A monocarboxylic acid that is acetic acid in which one of the methyl hydrogens has been replaced by a 1H-indol-3-yl group. Beilstein:143358 C10H9NO2 CAS:87-51-4 CHEBI:16411 CHEBI:24802 CHEBI:5905 DrugBank:DB07950 Gmelin:143197 HMDB:HMDB00197 IAA IES InChI=1S/C10H9NO2/c12-10(13)5-7-6-11-9-4-2-1-3-8(7)9/h1-4,6,11H,5H2,(H,12,13) Indole-3-acetic acid Indoleacetic acid KEGG:C00954 KNApSAcK:C00000100 OC(=O)Cc1c[nH]c2ccccc12 PDBeChem:IAC PMID:13610897 PMID:23545355 PMID:24285754 Reaxys:143358 SEOVTRFCIGRIMH-UHFFFAOYSA-N Wikipedia:Indole-3-acetic_acid chebi.owl chebi_ontology heteroauxin pro.owl lipopolysaccharide CHEBI:14520 CHEBI:16412 CHEBI:25062 CHEBI:6494 KEGG:C00338 LPS Lipopolysaccharide Liposaccharide natural compounds consisting of a trisaccharide repeating unit (two heptose units and octulosonic acid) with oligosaccharide side chains and 3-hydroxytetradecanoic acid units (they are a major constituent of the cell walls of Gram-negative bacteria). PMID:15589368 PMID:24186868 PMID:24506665 PMID:24642373 PMID:24659348 chebi.owl chebi_ontology lipopolysaccharides pro.owl peptide (C2H2NOR)nC2H3NOR 0 Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. CHEBI:14753 CHEBI:16670 CHEBI:25906 CHEBI:7990 KEGG:C00012 Peptid Peptide chebi.owl chebi_ontology obi.owl peptides peptido peptidos acyl monophosphate 0 124.964 124.99730 Acyl phosphate An organic phosphate ester or anhydride formed by condensation of phosphoric acid with a carboxylic acid. CH2O5PR CHEBI:13246 CHEBI:13725 CHEBI:16826 CHEBI:22222 CHEBI:2454 KEGG:C02133 OP(O)(=O)OC([*])=O acyl monophosphate ester acyl monophosphate esters acyl monophosphates acyl phosphates chebi_ontology deoxyribonucleic acid (Deoxyribonucleotide)m (Deoxyribonucleotide)n (Deoxyribonucleotide)n+m CAS:9007-49-2 CHEBI:13302 CHEBI:16991 CHEBI:21123 CHEBI:33698 CHEBI:4291 DNA DNAn DNAn+1 DNS Deoxyribonucleic acid Desoxyribonukleinsaeure High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. KEGG:C00039 chebi.owl chebi_ontology deoxyribonucleic acids deoxyribonucleic acids desoxyribose nucleic acid obi.owl thymus nucleic acid hydrogensulfite -1 80.965 81.07214 Bisulfite CAS:15181-46-1 CHEBI:13367 CHEBI:17137 CHEBI:5598 Gmelin:1455 HO3S HSO3(-) HSO3- Hydrogen sulfite InChI=1S/H2O3S/c1-4(2)3/h(H2,1,2,3)/p-1 KEGG:C11481 LSNNMFCWUKXFEE-UHFFFAOYSA-M OS([O-])=O PDBeChem:SO3 [SO2(OH)](-) bisulfite bisulphite chebi.owl chebi_ontology hydrogen sulfite(1-) hydrogen(trioxidosulfate)(1-) hydrogensulfite(1-) hydrogentrioxosulfate(1-) hydrogentrioxosulfate(IV) hydrosulfite anion hydroxidodioxidosulfate(1-) monohydrogentrioxosulfate obi.owl nucleoside 5'-monophosphate 0 213.016 C5H10O7PR CHEBI:14676 CHEBI:17188 CHEBI:25607 CHEBI:7439 CHEBI:7653 CHEBI:7654 KEGG:C01329 KEGG:C02520 NMP Nucleoside monophosphate Nucleoside phosphate O[C@H]1[C@H]([*])O[C@H](COP(O)(O)=O)[C@H]1O chebi_ontology nucleoside monophosphate nucleoside monophosphates glucose 0 180.15588 An aldohexose used as a source of energy and metabolic intermediate. C6H12O6 CAS:50-99-7 CHEBI:14313 CHEBI:17234 CHEBI:24277 CHEBI:33929 CHEBI:5418 DL-glucose Glc Glucose Glukose KEGG:C00293 Wikipedia:Glucose chebi.owl chebi_ontology gluco-hexose glucose obi.owl GDP 0 443.024 443.20072 C10H15N5O11P2 CAS:146-91-8 CHEBI:13327 CHEBI:14379 CHEBI:17552 CHEBI:24448 CHEBI:42738 CHEBI:5212 DrugBank:DB04315 GDP Guanosine 5'-diphosphate Guanosine diphosphate InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1 KEGG:C00035 KEGG:G10620 Nc1nc2n(cnc2c(=O)[nH]1)[C@@H]1O[C@H](COP(O)(=O)OP(O)(O)=O)[C@@H](O)[C@H]1O QGWNDRXFNXRZMB-UUOKFMHZSA-N chebi.owl chebi_ontology guanosine 5'-(trihydrogen diphosphate) pro.owl 5'-adenylyl sulfate 0 427.020 427.28562 5'-Adenylyl sulfate 5'-adenylyl hydrogen sulfate ADENOSINE-5'-PHOSPHOSULFATE APS Adenosine 5'-phosphosulfate Adenylylsulfate An adenosine 5'-phosphate having a sulfo group attached to one the phosphate OH groups. C10H14N5O10PS CAS:485-84-7 CHEBI:12059 CHEBI:13741 CHEBI:13743 CHEBI:17709 CHEBI:22247 CHEBI:2486 CHEBI:40562 DrugBank:DB03708 IRLPACMLTUPBCL-KQYNXXCUSA-N InChI=1S/C10H14N5O10PS/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-26(18,19)25-27(20,21)22/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H2,11,12,13)(H,20,21,22)/t4-,6-,7-,10-/m1/s1 KEGG:C00224 KNApSAcK:C00007445 Nc1ncnc2n(cnc12)[C@@H]1O[C@H](COP(O)(=O)OS(O)(=O)=O)[C@@H](O)[C@H]1O PDBeChem:ADX adenosine phosphosulfate chebi.owl chebi_ontology obi.owl ceramide 0 100.040 100.09590 C4H6NO2R3 CHEBI:12487 CHEBI:13954 CHEBI:17761 CHEBI:23074 CHEBI:7242 Cer Ceramide Ceramides (N-acyl-sphingoid bases) are a major subclass of sphingoid base derivatives with an amide-linked fatty acid. The fatty acids are typically saturated or monounsaturated with chain lengths from 14 to 26 carbon atoms; the presence of a hydroxyl group on carbon 2 is fairly common. Ceramides are generally precursors of more complex sphingolipids. In the illustrated generalised structure, R(1) = OH, OX (where X = acyl, glycosyl, phosphate, phosphonate, etc.), or H. KEGG:C00195 LIPID_MAPS_class:LMSP02 N-acylated sphingoid O[C@H]([*])[C@H](C[*])NC([*])=O PMID:7542630 Wikipedia:Ceramide a ceramide ceramides chebi_ontology lipid 'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. CHEBI:14517 CHEBI:18059 CHEBI:25054 CHEBI:6486 KEGG:C01356 Lipid chebi_ontology lipids ribonucleoside 0 133.050 Any nucleoside where the sugar component is D-ribose. C5H9O4R CHEBI:13014 CHEBI:13015 CHEBI:13685 CHEBI:18254 CHEBI:21085 CHEBI:26560 CHEBI:4240 CHEBI:8844 KEGG:C00911 OC[C@H]1O[C@@H]([*])[C@H](O)[C@@H]1O Ribonucleoside a ribonucleoside chebi_ontology ribonucleosides N-acetyl-beta-D-galactosaminyl-(1->3)-alpha-D-galactosyl-(1->4)-beta-D-galactosyl-(1->4)-beta-D-glucosylceramide (Gal)2 (GalNAc)1 (Glc)1 (Cer)1 0 1015.507 1016.10840 A glycotetraosylceramide having N-acetyl-beta-D-galactosaminyl-(1->3)-alpha-D-galactosyl-(1->4)-beta-D-galactosyl-(1->4)-beta-D-glucose as the tetrasaccharide component. C45H79N2O23R CAS:11034-93-8 CCCCCCCCCCCCC\C=C\[C@@H](O)[C@H](CO[C@@H]1O[C@H](CO)[C@@H](O[C@@H]2O[C@H](CO)[C@H](O[C@H]3O[C@H](CO)[C@H](O)[C@H](O[C@@H]4O[C@H](CO)[C@H](O)[C@H](O)[C@H]4NC(C)=O)[C@H]3O)[C@H](O)[C@H]2O)[C@H](O)[C@H]1O)NC([*])=O CHEBI:12452 CHEBI:12557 CHEBI:18259 CHEBI:21508 CHEBI:21513 CHEBI:24252 CHEBI:5388 GalNAc-1->3-Gal-1->4-Gal-1->4-Glc-Cer GalNAcbeta1-3-Galalpha1-4Galbeta1-4Glcbeta1-1Cer Gb4 Globoside Gb4 Globotetraosyl ceramide Gb4Cer Gbose4Cer Globoside GL-4 Globoside I Globotetraosyl ceramide KEGG:C03272 KEGG:G00094 N-Acetyl-D-galactosaminyl-1,3-D-galactosyl-1,4-D-galactosyl-1,4-D-glucosylceramide N-Acetyl-galactosaminyl-1,3-D-galactosyl-1,4-D-galactosyl-1,4-D-glucosylceramide N-[(2S,3R,4E)-1-{[2-acetamido-2-deoxy-beta-D-galactopyranosyl-(1->3)-alpha-D-galactopyranosyl-(1->4)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranosyl]oxy}-3-hydroxyoctadec-4-en-2-yl]alkanamide N-acetyl-D-galactosaminyl-(1->3)-D-galactosyl-(1->4)-D-galactosyl-(1->4)-D-glucosylceramides PMID:1528196 PMID:15495792 PMID:15661151 PMID:1601891 PMID:21252262 PMID:21376640 PMID:2456994 PMID:3220436 PMID:4026313 PMID:7287743 PMID:7690848 PMID:8161226 Slt-iiv receptor VT2vp1 Receptor an N-acetyl-beta-D-galactosaminyl-(1->3)-alpha-D-galactosyl-(1->4)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-N-acylsphing-4-enine beta-D-GalNAc-(1->3)-alpha-D-Gal-(1->4)-beta-D-Gal-(1->4)-beta-D-Glc-(1<->1')-Cer beta-D-GalpNAc-(1->3)-alpha-D-Galp-(1->4)-beta-D-Galp-(1->4)-beta-D-Glcp-(1<->1')-Cer chebi.owl chebi_ontology pro.owl 2'-deoxyribonucleoside 0 117.055 2'-Deoxynucleoside 2'-deoxyribonucleosides 2-Deoxy-D-ribosyl-base C5H9O3R CHEBI:1083 CHEBI:11394 CHEBI:11567 CHEBI:11568 CHEBI:18274 CHEBI:19259 CHEBI:19560 CHEBI:4421 Deoxynucleoside KEGG:C02269 KEGG:C03216 OC[C@H]1O[C@@H]([*])C[C@@H]1O a 2'-deoxyribonucleoside chebi_ontology jasmonic acid (-)-Jasmonic acid (-)-jasmonic acid (1R,2R)-3-oxo-2-(2Z)-2-penten-ylcyclopentanacetic acid (1R,2R)-3-oxo-2-(pent-2Z-enyl)-cyclopentaneacetic acid 0 2-{(1R,2R)-3-oxo-2-[(Z)-pent-2-enyl]cyclopentyl}acetate 210.126 210.26950 An oxo monocarboxylic acid that is (3-oxocyclopentyl)acetic acid substituted by a (2Z)-pent-2-en-1-yl group at position 2 of the cyclopentane ring. C12H18O3 CAS:6894-38-8 CC\C=C/C[C@@H]1[C@@H](CC(O)=O)CCC1=O CHEBI:14486 CHEBI:18292 CHEBI:18487 CHEBI:95 HMDB:HMDB32797 InChI=1S/C12H18O3/c1-2-3-4-5-10-9(8-12(14)15)6-7-11(10)13/h3-4,9-10H,2,5-8H2,1H3,(H,14,15)/b4-3-/t9-,10-/m1/s1 Jasmonate Jasmonic acid KEGG:C08491 KNApSAcK:C00000218 LIPID_MAPS_instance:LMFA02020001 PMID:17470145 PMID:19704561 Reaxys:2692609 Wikipedia:Jasmonic_acid ZNJFBWYDHIGLCU-HWKXXFMVSA-N chebi.owl chebi_ontology pro.owl {(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetic acid 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate 0 1,2-Diacyl-sn-glycero-3-phospho-(1'-myo-inositol-4',5'-bisphosphate) 1-O-(3-sn-phosphatidyl)-1D-myo-inositol 4,5-bis(dihydrogen phosphate) 1-Phosphatidyl-1D-myo-inositol 4,5-bisphosphate 1-Phosphatidyl-D-myo-inositol 4,5-bisphosphate 547.973 548.17840 A phosphatidylinositol bisphosphate in which the two phosphate groups are at C-4 and C-5 of the inositol moiety which has the 1D-myo configuration. C11H19O19P3R2 CHEBI:11282 CHEBI:11288 CHEBI:14796 CHEBI:18348 CHEBI:19087 CHEBI:26028 CHEBI:28910 CHEBI:678 CHEBI:8127 KEGG:C04637 PIP2 PIPP PMID:6095072 Phosphatidyl-myo-inositol 4,5-bisphosphate Phosphatidylinositol-4,5-bisphosphate PtsIns(4,5)P2 PtsIns-4,5-P2 [H][C@@](COC([*])=O)(COP(O)(=O)O[C@@H]1[C@H](O)[C@H](O)[C@@H](OP(O)(O)=O)[C@H](OP(O)(O)=O)[C@H]1O)OC([*])=O chebi.owl chebi_ontology pro.owl pyrimidine 2'-deoxyribonucleoside CHEBI:19255 chebi_ontology pyrimidine 2'-deoxyribonucleosides N-glycosyl compound A glycosyl compound arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to a nitrogen atom, thus creating a C-N bond. CHEBI:21731 N-glycoside N-glycosides N-glycosyl compounds chebi_ontology glycosylamine glycosylamines adenosine phosphate CHEBI:22256 adenosine phosphates chebi_ontology benzopyrrole CHEBI:22728 benzopyrroles chebi_ontology glycotetraosylceramide An oligoglycosylceramide consisting of a glycotetraosyl moiety attached to the ceramide oxygen with an unspecified N-acyl substituent attached to the ceramide nitrogen. CHEBI:23075 chebi_ontology glycotetraosylceramides chloride salt CHEBI:23114 chebi_ontology chloride salts chlorides molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. CHEBI:23367 chebi.owl chebi_ontology entidad molecular entidades moleculares entite moleculaire molecular entities molecular entity molekulare Entitaet obi.owl pro.owl cytochalasin CHEBI:23528 Wikipedia:Cytochalasin chebi.owl chebi_ontology cytochalasins obi.owl deoxyribonucleoside CHEBI:23636 chebi_ontology deoxyribonucleosides monoatomic cation CHEBI:23906 chebi_ontology monoatomic cations N-ethyl-N-nitrosourea 0 1-(Aminocarbonyl)-1-ethyl-2-oxohydrazine 1-Ethyl-1-nitrosourea 1-ethyl-1-nitrosourea 117.054 117.10660 A member of the class of N-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups. Aethylnitroso-harnstoff Beilstein:1761174 C3H7N3O2 CAS:759-73-9 CCN(N=O)C(N)=O CHEBI:23995 ENU Ethyl nitrosourea FUSGACRLAFQQRL-UHFFFAOYSA-N InChI=1S/C3H7N3O2/c1-2-6(5-8)3(4)7/h2H2,1H3,(H2,4,7) KEGG:C19178 N-Ethyl-N-nitroso carbamide N-Ethyl-N-nitroso-urea N-Ethylnitrosourea NEU PMID:11732210 PMID:11853764 PMID:11880538 PMID:16423555 PMID:21861612 PMID:22012195 PMID:22238669 PMID:23551873 PMID:24175309 PMID:8603364 Reaxys:1761174 Wikipedia:ENU chebi.owl chebi_ontology obi.owl glycosphingolipid A glycosphingolipid is a glycolipid that is a carbohydrate-containing derivative of a sphingoid or ceramide. It is understood that the carbohydrate residue is attached by a glycosidic linkage to O-1 of the sphingoid. CHEBI:24402 CHEBI:5498 PMID:18845618 PMID:19303901 PMID:26954668 PMID:26976737 PMID:27253729 PMID:27325407 Wikipedia:Glycosphingolipid chebi_ontology glycosphingolipids chemical entity A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. CHEBI:24431 chebi.owl chebi_ontology chemical entity pro.owl guanosine phosphate CHEBI:24455 chebi_ontology guanosine phosphates halogen molecular entity CHEBI:24471 chebi_ontology halogen compounds halogen molecular entities halogen molecular entity organic heterocyclic compound A cyclic compound having as ring members atoms of carbon and at least of one other element. CHEBI:24532 chebi_ontology organic heterocycle organic heterocyclic compounds proton (1)1H(+) (1)H(+) +1 1.00783 1.008 CAS:12408-02-5 CHEBI:24636 GPRLSGONYQIRFK-FTGQXOHASA-N H InChI=1S/p+1/i/hH KEGG:C00080 Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u. [1H+] chebi.owl chebi_ontology obi.owl p p(+) protium(1+) proton hydroxides CHEBI:24651 Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)). chebi_ontology indoles Any compound containing an indole skeleton. CHEBI:24828 chebi_ontology inorganic molecular entity A molecular entity that contains no carbon. CHEBI:24835 anorganische Verbindungen chebi_ontology inorganic compounds inorganic entity inorganic molecular entities inorganics inorganic phosphate Any phosphate that contains no carbon atom. CHEBI:24838 chebi_ontology inorganic phosphates inorganic salt CHEBI:24839 anorganisches Salz chebi_ontology inorganic salts salt A salt is an assembly of cations and anions. CHEBI:24866 Salz Salze chebi_ontology ionic compound ionic compounds sal sales salt salts sel sels monoatomic ion CHEBI:24867 chebi_ontology monoatomic ions ion A molecular entity having a net electric charge. CHEBI:24870 Ion Ionen chebi_ontology ion iones ions lactone Any cyclic carboxylic ester containing a 1-oxacycloalkan-2-one structure, or an analogue having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. CHEBI:25000 Lacton Lakton Laktone chebi_ontology lactona lactonas lactone lactones luciferin A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase. CHEBI:25078 chebi.owl chebi_ontology obi.owl molecule Any polyatomic entity that is an electrically neutral entity consisting of more than one atom. CHEBI:25367 Molekuel chebi_ontology molecula molecule molecules neutral molecular compounds monocarboxylic acid An oxoacid containing a single carboxy group. CHEBI:25384 chebi_ontology monocarboxylic acid monocarboxylic acids nonmetal atom CHEBI:25585 Nichtmetall Nichtmetalle chebi_ontology no metal no metales non-metal non-metaux nonmetal nonmetal nonmetals nucleoside phosphate A nucleobase-containing molecular entity that is a nucleoside in which one or more of the sugar hydroxy groups has been converted into a mono- or poly-phosphate. The term includes both nucleotides and non-nucleotide nucleoside phosphates. CHEBI:25608 KEGG:C01329 NMP Nucleoside monophosphate chebi_ontology nucleoside phosphates organic heteromonocyclic compound CHEBI:25693 chebi_ontology organic heteromonocyclic compounds organic phosphate CHEBI:25703 chebi_ontology organic phosphate organic phosphate ester organic phosphate esters organic phosphates organophosphate ester organophosphate esters organic sulfate CHEBI:25704 Compounds of the general formula SO3HOR where R is an organyl group chebi_ontology organic sulfates organophosphorus compound An organophosphorus compound is formally a compound containing at least one carbon-phosphorus bond, but the term is often extended to include esters and thioesters. CHEBI:25710 chebi_ontology organophosphorus compound organophosphorus compounds oxide An oxide is a chemical compound of oxygen with other chemical elements. CHEBI:25741 chebi_ontology oxide oxides oxygen molecular entity CHEBI:25806 chebi_ontology oxygen molecular entities oxygen molecular entity aldopentose phosphate CHEBI:25900 aldopentose phosphate aldopentose phosphates chebi_ontology phosphate CHEBI:26020 Salts and esters of phosphoric and oligophosphoric acids and their chalcogen analogues. In inorganic chemistry, the term is also used to describe anionic coordination entities with phosphorus as central atom. chebi_ontology phosphates phosphates phosphoric acid derivative CHEBI:26079 chebi_ontology phosphoric acid derivatives phosphoric acids phosphorus molecular entity CHEBI:26082 chebi_ontology phosphorus molecular entities purine nucleoside CHEBI:26394 chebi_ontology purine nucleoside purine nucleosides purine nucleotide Any nucleotide that has a purine nucleobase. CHEBI:26395 chebi_ontology purine nucleotides purine ribonucleoside monophosphate CHEBI:26397 chebi_ontology purine ribonucleoside monophosphates purine ribonucleoside CHEBI:26399 chebi_ontology purine ribonucleosides purine ribonucleotide Any ribonucleotide that has a purine nucleobase. CHEBI:26400 chebi_ontology purine ribonucleotides purines A class of imidazopyrimidines that consists of purine and its substituted derivatives. CHEBI:13678 CHEBI:26401 chebi_ontology pyrimidine nucleoside CHEBI:26440 KEGG:C03169 N-D-Ribosylpyrimidine chebi_ontology pyrimidine nucleosides reactive oxygen species CHEBI:26523 Molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers. ROS Wikipedia:Reactive_oxygen_species chebi_ontology ribonucleoside monophosphate CHEBI:26558 chebi_ontology ribonucleoside monophosphates ribonucleotide CHEBI:26561 chebi_ontology ribonucleotides sodium chloride 0 57.959 58.44247 An inorganic chloride salt having sodium(1+) as the counterion. Beilstein:3534976 CAS:7647-14-5 CHEBI:26710 ClNa FAPWRFPIFSIZLT-UHFFFAOYSA-M Gmelin:13673 InChI=1S/ClH.Na/h1H;/q;+1/p-1 KEGG:C13563 KEGG:D02056 Kochsalz MetaCyc:NACL NaCl Natriumchlorid Reaxys:3534976 Wikipedia:Sodium_Chloride [Na+].[Cl-] chebi.owl chebi_ontology chlorure de sodium cloruro sodico common salt halite natrii chloridum obi.owl rock salt salt sodium chloride table salt sodium salt Any alkali metal salt having sodium(1+) as the cation. CHEBI:26714 Natriumsalz Natriumsalze chebi_ontology sodium salts sphingolipid CHEBI:26739 Sphingolipids are a complex family of compounds that share a common structural feature, a sphingoid base backbone. chebi_ontology sphingolipids carbohydrate phosphate CHEBI:26816 carbohydrate phosphates chebi_ontology sulfuric ester 0 95.952 96.06300 An ester of an alcohol and sulfuric acid. CHEBI:26819 O4SR2 [*]OS(=O)(=O)O[*] chebi_ontology sulfate ester sulfuric acid ester sulfuric acid esters sulfur molecular entity CHEBI:26835 chebi_ontology sulfur molecular entities sulfur molecular entity oxolanes Any oxacycle having an oxolane (tetrahydrofuran) skeleton. CHEBI:26912 chebi_ontology organic heterotricyclic compound An organic tricyclic compound in which at least one of the rings of the tricyclic skeleton contains one or more heteroatoms. CHEBI:26979 chebi_ontology heterotricyclic compounds organic heterotricyclic compounds transition element atom An element whose atom has an incomplete d sub-shell, or which can give rise to cations with an incomplete d sub-shell. CHEBI:27081 Uebergangselement Uebergangsmetalle chebi_ontology metal de transicion metal de transition metales de transicion metaux de transition transition element transition element transition elements transition metal transition metals organic heterobicyclic compound CHEBI:27171 chebi_ontology heterobicyclic compounds organic heterobicyclic compounds lead(0) 0 207.20000 207.977 CAS:7439-92-1 CHEBI:27889 CHEBI:6397 InChI=1S/Pb KEGG:C06696 Lead Pb Pb(0) Pbn WABPQHHGFIMREM-UHFFFAOYSA-N [Pb] chebi.owl chebi_ontology lead lead metal lead(0) obi.owl chromium atom 0 24Cr 51.941 51.99610 A chromium group element atom that has atomic number 24. CAS:7440-47-3 CHEBI:23235 CHEBI:28073 CHEBI:3678 Chrom Chromium Cr InChI=1S/Cr KEGG:C06268 VYZAMTAEIAYCRO-UHFFFAOYSA-N WebElements:Cr [Cr] chebi_ontology chrome chromium chromium cromo acrylamide 0 2-Propenamide 71.037 71.07794 A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia. Acrylamide Akrylamid Beilstein:605349 C3H5NO CAS:79-06-1 CHEBI:22215 CHEBI:2441 CHEBI:28619 Gmelin:81842 HMDB:HMDB04296 HRPVXLWXLXDGHG-UHFFFAOYSA-N InChI=1S/C3H5NO/c1-2-3(4)5/h2H,1H2,(H2,4,5) KEGG:C01659 NC(=O)C=C PMID:10719038 PMID:12166997 PMID:15240786 PMID:15901921 PMID:17032038 PMID:17234719 PMID:17484107 PMID:17558658 PMID:17720246 PMID:18469268 PMID:19022940 PMID:19846048 PMID:22136129 PMID:22784192 PMID:7767980 Patent:US2535245 Reaxys:605349 UM-BBD_compID:c0149 Wikipedia:Acrylamide acrylamide chebi.owl chebi_ontology ethylenecarboxamide obi.owl prop-2-enamide phosphorus atom 0 15P 30.97376 30.974 CAS:7723-14-0 CHEBI:26080 CHEBI:28659 CHEBI:8168 Gmelin:16235 InChI=1S/P KEGG:C06262 OAICVXFJPJFONN-UHFFFAOYSA-N P Phosphor Phosphorus WebElements:P [P] chebi_ontology fosforo phosphore phosphorus phosphorus hydroxyl (OH)(.) 0 17.003 17.00734 CAS:3352-57-6 CHEBI:24707 CHEBI:29190 CHEBI:29191 Gmelin:105 HO HO(.) Hydrogen oxide InChI=1S/HO/h1H KEGG:C16844 TUJKJAMUKRIRHC-UHFFFAOYSA-N [O][H] chebi.owl chebi_ontology hydridooxygen(.) hydroxyl hydroxyl radical obi.owl oxidanyl deuterium atom (2)1H (2)H 0 2.01410 CHEBI:29237 D Deuterium InChI=1S/H2/h1H/i1+1 The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second). UFHFLCQGNIYNRP-OUBTZVSYSA-N [2H] chebi.owl chebi_ontology deuterio deuterium deuterium heavy hydrogen hidrogeno pesado hydrogen-2 obi.owl schwerer Wasserstoff alkyl sulfate CHEBI:13810 CHEBI:22325 CHEBI:2583 CHEBI:29281 alkyl sulfates chebi_ontology ruthenium atom 0 101.07000 101.904 44Ru CAS:7440-18-8 CHEBI:30682 InChI=1S/Ru KJTLSVCANCCWHF-UHFFFAOYSA-N Ru Ruthenium WebElements:Ru [Ru] chebi.owl chebi_ontology obi.owl rutenio ruthenium ruthenium alcohol 0 17.003 A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom. Alcohol CHEBI:13804 CHEBI:22288 CHEBI:2553 CHEBI:30879 HOR KEGG:C00069 O[*] alcohols an alcohol chebi_ontology fluorescein 0 3',6'-dihydroxy-3H-spiro[2-benzofuran-1,9'-xanthen]-3-one 3',6'-dihydroxyfluoran 3,6-fluorandiol 332.068 332.307 9-(o-carboxyphenyl)-6-hydroxy-3-isoxanthenone 9-(o-carboxyphenyl)-6-hydroxy-3H-xanthen-3-one A xanthene dye that is highly fluorescent, detectable even when present in minute quantities. Used forensically to detect traces of blood, in analytical chemistry as an indicator in silver nitrate titrations and in microscopy. Beilstein:94324 C.I. 45350 C.I. Solvent Yellow 94 C20H12O5 CAS:2321-07-5 CHEBI:31624 CHEBI:606590 D and C Yellow No. 7 D&C Yellow No. 7 DrugBank:DB00693 Fluoreszein GNBHRKFJIUUOQI-UHFFFAOYSA-N Gmelin:248626 HMDB:HMDB14831 InChI=1S/C20H12O5/c21-11-5-7-15-17(9-11)24-18-10-12(22)6-8-16(18)20(15)14-4-2-1-3-13(14)19(23)25-20/h1-10,21-22H Japan Yellow 201 KEGG:D01261 OC1=CC=C2C3(OC(C4=C3C=CC=C4)=O)C=5C(OC2=C1)=CC(=CC5)O PDB:4FAB PMID:1517825 PMID:15465055 PMID:16195545 PMID:20371259 PMID:2508085 PMID:26756394 PMID:7868912 Reaxys:94324 Solvent Yellow 94 Wikipedia:Fluorescein Yellow fluorescein chebi.owl chebi_ontology fluoresceine obi.owl resorcinolphthalein gadodiamide hydrate 0 591.67000 592.113 C16H28GdN5O9 CAS:122795-43-1 CHEBI:31642 DrugBank:DB00225 Gadodiamide Gadodiamide hydrate Gmelin:898533 InChI=1S/C16H29N5O8.Gd.H2O/c1-17-12(22)7-20(10-15(26)27)5-3-19(9-14(24)25)4-6-21(11-16(28)29)8-13(23)18-2;;/h3-11H2,1-2H3,(H,17,22)(H,18,23)(H,24,25)(H,26,27)(H,28,29);;1H2/q;+3;/p-3 KEGG:C13106 KEGG:D01645 Omniscan The hydrate of gadodiamide. XPCLDSMKWNNKOM-UHFFFAOYSA-K [H]O[H].CNC1=[O][Gd+3]234567[O-]C(=O)C[N]2(CC[N]3(CC(=O)[O-]4)C1)CC[N]5(CC(=O)[O-]6)CC(NC)=[O]7 [N,N-bis(2-{[(carboxy-kappaO)methyl][2-(methylamino)-2-(oxo-kappaO)ethyl]amino-kappaN}ethyl)glycinato(3-)-kappa(2)N,O]gadolinium--water (1/1) chebi.owl chebi_ontology gadodiamida gadodiamidum gadolinium 5,8-bis(carboxylatomethyl)-11-[2-(methylamino)-2-oxoethyl]-3-oxo-2,5,8,11-tetraazatridecan-13-oate hydrate gadolinium [bis(2-{(carboxylatomethyl)[2-(methylamino)-2-oxoethyl]amino}ethyl)amino]acetate--water (1/1) obi.owl gadoteridol 0 558.68000 559.128 A non-ionic gadolinium chelate having a macrocyclic tetraamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). C17H29GdN4O7 C17H29N4O7.Gd CAS:120066-54-8 CHEBI:31643 DPNNNPAKRZOSMO-UHFFFAOYSA-K DrugBank:DB00597 GD-HP-DO 3A Gd-HPDO3A Gmelin:897397 InChI=1S/C17H32N4O7.Gd/c1-14(22)10-18-2-4-19(11-15(23)24)6-8-21(13-17(27)28)9-7-20(5-3-18)12-16(25)26;/h14,22H,2-13H2,1H3,(H,23,24)(H,25,26)(H,27,28);/q;+3/p-3 KEGG:D01137 Patent:EP292689 Patent:US4885363 Wikipedia:Gadoteridol [2,2',2''-{10-[2-(hydroxy-kappaO)propyl]-1,4,7,10-tetraazacyclododecane-1,4,7-triyl-kappa(4)N(1),N(4),N(7),N(10)}triacetato-kappaO(3-)]gadolinium [H][O]1C(C)C[N]23CC[N]45CC[N]67CC[N]8(CC2)CC(=O)[O-][Gd+3]13468([O-]C(=O)C5)[O-]C(=O)C7 chebi.owl chebi_ontology gadolinium 2,2',2''-[10-(2-hydroxypropyl)-1,4,7,10-tetraazacyclododecane-1,4,7-triyl]triacetate gadolinium-HP-DO3A gadoteridol gadoteridol gadoteridolum obi.owl phenol red 0 3,3-bis(p-hydroxyphenyl)-3H-2,1-benzoxathiole 1,1-dioxide 354.056 354.37600 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney. 4,4'-(1,1-dioxido-3H-2,1-benzoxathiole-3,3-diyl)diphenol 4,4'-(3H-2,1-benzoxathiol-3-ylidene)bisphenol S,S-dioxide BELBBZDIHDAJOR-UHFFFAOYSA-N Beilstein:326470 C19H14O5S CAS:143-74-8 CHEBI:31991 Drug_Central:3439 InChI=1S/C19H14O5S/c20-15-9-5-13(6-10-15)19(14-7-11-16(21)12-8-14)17-3-1-2-4-18(17)25(22,23)24-19/h1-12,20-21H KEGG:C12600 KEGG:D01200 Oc1ccc(cc1)C1(OS(=O)(=O)c2ccccc12)c1ccc(O)cc1 PSP Phenol red Phenolsulfonphthalein alpha-hydroxy-alpha,alpha-bis(p-hydroxyphenyl)-o-toluenesulfonic acid gamma-sultone chebi.owl chebi_ontology obi.owl sodium citrate dihydrate 0 2-hydroxy-1,2,3-propanetricarboxylic acid trisodium salt dihydrate 293.994 294.09960 Beilstein:3920956 C6H5O7.3Na.2H2O C6H9Na3O9 CAS:6132-04-3 CHEBI:32142 Citronensaeure,Trinatrium-Salz-Dihydrat InChI=1S/C6H8O7.3Na.2H2O/c7-3(8)1-6(13,5(11)12)2-4(9)10;;;;;/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12);;;;2*1H2/q;3*+1;;/p-3 KEGG:D01781 NLJMYIDDQXHKNR-UHFFFAOYSA-K O.O.[Na+].[Na+].[Na+].OC(CC([O-])=O)(CC([O-])=O)C([O-])=O Sodium citrate Sodium citrate hydrate The dihydrate of trisodium citrate. chebi.owl chebi_ontology obi.owl trisodium 2-hydroxypropane-1,2,3-tricarboxylate--water (1/2) monoatomic entity A monoatomic entity is a molecular entity consisting of a single atom. CHEBI:33238 atomic entity chebi_ontology monoatomic entities oxoacid derivative CHEBI:33241 chebi_ontology oxoacid derivatives inorganic hydride CHEBI:33242 chebi_ontology inorganic hydrides organic group Any substituent group or skeleton containing carbon. CHEBI:33247 chebi.owl chebi_ontology organic groups pro.owl atom A chemical entity constituting the smallest component of an element having the chemical properties of the element. CHEBI:22671 CHEBI:23907 CHEBI:33250 atom atome atomo atoms atomus chebi.owl chebi_ontology element elements obi.owl monoatomic hydrogen 0 1.00794 1.008 CHEBI:33251 H InChI=1S/H YZCKVEUIGOORGS-UHFFFAOYSA-N [H] atomic hydrogen chebi_ontology nucleon CHEBI:33253 Heavy nuclear particle: proton or neutron. Nukleon Nukleonen chebi_ontology nucleon nucleons primary amide A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group. CHEBI:33256 chebi_ontology primary amide primary amides elemental molecular entity A molecular entity all atoms of which have the same atomic number. CHEBI:33259 chebi_ontology homoatomic entity homoatomic molecular entities homoatomic molecular entity elemental hydrogen CHEBI:33260 chebi_ontology organosulfur compound An organosulfur compound is a compound containing at least one carbon-sulfur bond. CHEBI:23010 CHEBI:25714 CHEBI:33261 Wikipedia:Organosulfur_compounds chebi_ontology organosulfur compound organosulfur compounds polyatomic anion An anion consisting of more than one atom. CHEBI:33273 chebi_ontology polyatomic anions heteroorganic entity A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms. CHEBI:33285 chebi_ontology heteroorganic entities organoelement compounds alkali metal molecular entity A molecular entity containing one or more atoms of an alkali metal. CHEBI:33296 alkali metal molecular entities chebi_ontology pnictogen molecular entity A p-block molecular entity containing any pnictogen. CHEBI:33302 chebi_ontology pnictogen molecular entities pnictogen molecular entity chalcogen molecular entity Any p-block molecular entity containing a chalcogen. CHEBI:33304 chalcogen compounds chalcogen molecular entities chalcogen molecular entity chebi_ontology carboxylic ester 0 43.990 An ester of a carboxylic acid, R(1)C(=O)OR(2), where R(1) = H or organyl and R(2) = organyl. CHEBI:13204 CHEBI:23028 CHEBI:33308 CHEBI:3408 CO2R2 Carboxylic ester KEGG:C02391 Wikipedia:Ester [*]C(=O)O[*] a carboxylic ester carboxylic acid esters carboxylic esters chebi_ontology lanthanoid atom CHEBI:33319 Lanthanoid Lanthanoide Lanthanoidengruppe Lanthanoidenreiche Ln chebi_ontology lanthanide lanthanides lanthanoid lanthanoids rare earth metal atom CHEBI:33321 chebi.owl chebi_ontology obi.owl rare earth metal rare earth metals chromium group element atom CHEBI:33350 chebi_ontology chromium group element chromium group elements group 6 elements iron group element atom CHEBI:33356 chebi_ontology group 8 elements iron group element iron group elements cobalt group element atom CHEBI:33358 chebi_ontology cobalt group element cobalt group elements group 9 elements rhodium atom 0 102.90550 102.906 45Rh A cobalt group element atom of atomic number 45. CAS:7440-16-6 CHEBI:33359 InChI=1S/Rh MHOVAHRLVXNVSD-UHFFFAOYSA-N PMID:2936374 Rh WebElements:Rh Wikipedia:Rhodium [Rh] chebi.owl chebi_ontology obi.owl rhodium rhodium rodio gadolinium atom 0 157.25000 157.924 64Gd CAS:7440-54-2 CHEBI:33375 Gd Gmelin:16286 InChI=1S/Gd UIWYJDYFSGRHKR-UHFFFAOYSA-N WebElements:Gd [Gd] chebi.owl chebi_ontology gadolinio gadolinium gadolinium obi.owl terbium atom 0 158.925 158.92534 65Tb CAS:7440-27-9 CHEBI:33376 GZCRRIHWUXGPOV-UHFFFAOYSA-N Gmelin:16311 InChI=1S/Tb Tb WebElements:Tb [Tb] chebi.owl chebi_ontology obi.owl terbio terbium terbium sulfur oxoacid derivative CHEBI:33424 chebi_ontology sulfur oxoacid derivative sulfur oxoacid derivatives phospho sugar Any monosaccharide containing an alcoholic hydroxy group esterified with phosphoric acid. CHEBI:15132 CHEBI:25406 CHEBI:26086 CHEBI:33447 CHEBI:9320 KEGG:C00934 PMID:18186488 chebi_ontology monosaccharide phosphates phospho sugar phospho sugars phosphorylated sugar phosphorylated sugars phosphosugar phosphosugars sulfur oxoanion CHEBI:33482 chebi_ontology oxoanions of sulfur sulfur oxoanion sulfur oxoanions chalcogen oxoanion CHEBI:33485 chalcogen oxoanion chalcogen oxoanions chebi_ontology metal atom An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity. CHEBI:25217 CHEBI:33521 CHEBI:6788 KEGG:C00050 PMID:21784043 Wikipedia:Metal chebi_ontology elemental metal elemental metals metal element metal elements metals organosulfonic acid 0 80.965 81.07100 An organic derivative of sulfonic acid in which the sulfo group is linked directly to carbon. CHEBI:33551 HO3SR OS([*])(=O)=O chebi_ontology organosulfonic acids sulfonic acids sulfonic acid derivative CHEBI:33552 chebi_ontology derivatives of sulfonic acid sulfonic acid derivative sulfonic acid derivatives d-block element atom CHEBI:33561 chebi_ontology d-block element d-block elements f-block element atom CHEBI:33562 chebi_ontology f-block element f-block elements carboxylic acid 0 44.998 45.01740 A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid. CHEBI:13428 CHEBI:13627 CHEBI:23027 CHEBI:33575 CHO2R Carbonsaeure Carbonsaeuren Karbonsaeure OC([*])=O PMID:17147560 PMID:18433345 RC(=O)OH Wikipedia:Carboxylic_acid acide carboxylique acides carboxyliques acido carboxilico acidos carboxilicos carboxylic acid carboxylic acids chebi_ontology main group molecular entity A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table. CHEBI:33579 chebi_ontology main group compounds main group molecular entities carbon group molecular entity CHEBI:33582 carbon group molecular entities carbon group molecular entity chebi_ontology cyclic compound Any molecule that consists of a series of atoms joined together to form a ring. CHEBI:33595 Wikipedia:Cyclic_compound chebi_ontology cyclic compounds hydrogen molecular entity CHEBI:33608 chebi_ontology hydrogen compounds hydrogen molecular entities polycyclic compound CHEBI:33635 chebi_ontology polycyclic compounds organic aromatic compound CHEBI:33659 chebi_ontology organic aromatic compounds heteromonocyclic compound CHEBI:33670 chebi_ontology heteromonocyclic compound heteromonocyclic compounds heteropolycyclic compound CHEBI:33671 chebi_ontology heteropolycyclic compounds polyheterocyclic compounds heterobicyclic compound A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom. CHEBI:33672 chebi_ontology heterobicyclic compounds s-block molecular entity An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element. CHEBI:33674 chebi_ontology s-block compounds s-block molecular entities s-block molecular entity p-block molecular entity A main group molecular entity that contains one or more atoms of a p-block element. CHEBI:33675 chebi_ontology p-block compounds p-block molecular entities p-block molecular entitiy hydrides CHEBI:33692 Hydrides are chemical compounds of hydrogen with other chemical elements. chebi_ontology oxygen hydride CHEBI:33693 chebi_ontology hydrides of oxygen oxygen hydride oxygen hydrides biomacromolecule A macromolecule formed by a living organism. Biopolymere CHEBI:33694 biomacromolecules biopolymer biopolymers chebi_ontology nucleic acid A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. CHEBI:33696 NA Nukleinsaeure Nukleinsaeuren acide nucleique acides nucleiques acido nucleico acidos nucleicos chebi.owl chebi_ontology nucleic acids obi.owl ribonucleic acid CAS:63231-63-0 CHEBI:33697 High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. RNA RNS Ribonukleinsaeure chebi.owl chebi_ontology obi.owl pentosenucleic acids ribonucleic acid ribonucleic acids ribonucleic acids ribose nucleic acid yeast nucleic acid amino-acid residue CHEBI:33708 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 amino-acid residue amino-acid residues chebi.owl chebi_ontology pro.owl amino acid A carboxylic acid containing one or more amino groups. Aminocarbonsaeure Aminokarbonsaeure Aminosaeure CHEBI:13815 CHEBI:22477 CHEBI:33709 Wikipedia:Amino_acid amino acids chebi.owl chebi_ontology obi.owl lanthanoid molecular entity CHEBI:33775 chebi_ontology lanthanoid compounds lanthanoid molecular entities organic hydroxy compound An organic compound having at least one hydroxy group attached to a carbon atom. CHEBI:33822 CHEBI:64710 chebi_ontology hydroxy compounds organic alcohol organic hydroxy compounds organic cyclic compound Any organic molecule that consists of atoms connected in the form of a ring. CHEBI:33832 chebi_ontology organic cyclic compounds heteroarene A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2). CHEBI:33833 chebi_ontology hetarenes heteroarenes nucleoside 0 116.047 116.115 An N-glycosyl compound that has both a nucleobase, normally adenine, guanine, xanthine, thymine, cytosine or uracil, and either a ribose or deoxyribose as functional parents. C5H8O3R2 CHEBI:13661 CHEBI:25611 CHEBI:33838 CHEBI:7647 KEGG:C00801 Nucleoside [C@H]1([C@H]([C@@H](*)[C@@H](O1)*)O)CO a nucleoside chebi_ontology nucleosides nucleosides macromolecule A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. CHEBI:33839 Wikipedia:Macromolecule chebi.owl chebi_ontology macromolecule macromolecules obi.owl polymer polymer molecule polymers phenols Aryl alcohol CHEBI:13664 CHEBI:13825 CHEBI:25969 CHEBI:2857 CHEBI:33853 KEGG:C15584 MetaCyc:Aryl-Alcohol Organic aromatic compounds having one or more hydroxy groups attached to a benzene or other arene ring. Wikipedia:Phenols arenols aryl alcohol chebi_ontology phenols halide salt CHEBI:33958 chebi_ontology halide salts halides benzofurans CHEBI:22721 CHEBI:35259 chebi_ontology steroid 0 259.243 259.450 Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from squalene, so may be considered as triterpenoids. C12C(C3C(C(CC3)*)(C)CC1)CCC4C2(CCCC4)C C19H31R CHEBI:13687 CHEBI:26768 CHEBI:35341 CHEBI:9263 KEGG:C00377 MetaCyc:Steroids Steroid a steroid chebi_ontology steroids 3beta-sterol 0 275.237 275.450 3beta-Hydroxysteroid 3beta-hydroxysteroids 3beta-sterols A sterol that has a hydroxy group at position 3 with beta- configuration. C12C(C3C(C(CC3)*)(C)CC1)CCC4C2(CC[C@@H](C4)O)C C19H31OR CHEBI:13609 CHEBI:1725 CHEBI:20248 CHEBI:35348 KEGG:C02945 a 3beta-hydroxysterol chebi_ontology hydroxy steroid CHEBI:24748 CHEBI:35350 CHEBI:5814 Hydroxysteroid KEGG:C02159 chebi_ontology hydroxy steroids hydroxysteroids organonitrogen compound Any heteroorganic entity containing at least one carbon-nitrogen bond. CHEBI:35352 chebi_ontology organonitrogen compounds organonitrogens oxoanion An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen. CHEBI:33274 CHEBI:33436 CHEBI:35406 chebi_ontology oxoacid anions oxoanion oxoanions alkali metal salt CHEBI:35479 alkali metal salts chebi_ontology hydrate An addition compound that contains water in weak chemical combination with another compound. CHEBI:35505 Hydrat chebi_ontology hidrato hidratos hydrates carbon oxoacid CHEBI:35605 carbon oxoacids chebi_ontology oxoacids of carbon ester A compound formally derived from an oxoacid RkE(=O)l(OH)m (l > 0) and an alcohol, phenol, heteroarenol, or enol by linking with formal loss of water from an acidic hydroxy group of the former and a hydroxy group of the latter. CHEBI:23960 CHEBI:35701 CHEBI:4859 Ester KEGG:C00287 Wikipedia:Ester chebi_ontology esters gadolinium molecular entity CHEBI:35729 chebi.owl chebi_ontology gadolinium compounds gadolinium molecular entities gadolinium molecular entity obi.owl gadolinium coordination entity CHEBI:35730 chebi_ontology gadolinium coordination compounds gadolinium coordination entities gadolinium coordination entity liposaccharide CHEBI:35740 chebi_ontology liposaccharides tetracarboxylic acid An oxoacid containing four carboxy groups. C4H4O8R CHEBI:35742 chebi_ontology tetracarboxylic acids oxo monocarboxylic acid Any monocarboxylic acid having at least one additional oxo functional group. CHEBI:35871 chebi_ontology oxo monocarboxylic acids carboxylic anhydride Anhydrides derived from carboxylic acids. CHEBI:35873 carboxylic anhydride carboxylic anhydrides carboxylic anhydrides chebi_ontology imidazopyrimidine CHEBI:35875 chebi_ontology imidazopyrimidines inorganic chloride CHEBI:36093 chebi_ontology inorganic chloride salt inorganic chloride salts inorganic chlorides baryon Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy). CHEBI:36339 baryons chebi_ontology subatomic particle A particle smaller than an atom. CHEBI:36342 chebi_ontology subatomic particles composite particle A subatomic particle known to have substructure (i.e. consisting of smaller particles). CHEBI:36343 chebi_ontology composite particles nuclear particle A nucleus or any of its constituents in any of their energy states. CHEBI:36347 chebi_ontology nuclear particle polyatomic entity Any molecular entity consisting of more than one atom. CHEBI:36357 chebi_ontology polyatomic entities polyatomic ion An ion consisting of more than one atom. CHEBI:36358 chebi_ontology polyatomic ions phosphorus oxoacid derivative CHEBI:36359 chebi_ontology phosphorus oxoacid derivative oligoglycosylceramide CHEBI:24253 CHEBI:25672 CHEBI:36520 KEGG:C03956 chebi_ontology globosides oligoglycosylceramides oligoglycosylglucosylceramides carbonyl compound Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives. CHEBI:36586 carbonyl compounds chebi_ontology acid anhydride CHEBI:36606 Compounds consisting of two acyl groups bonded to the same oxygen atom acyl-O-acyl. acid anhydride acid anhydrides acid anhydrides anhydride d'acide chebi_ontology acyclic acid anhydride CHEBI:36608 acyclic acid anhydride acyclic acid anhydrides acyclic acid anhydrides acyclic anhydrides chebi_ontology acyclic carboxylic anhydride CHEBI:36631 acyclic carboxylic acid anhydrides acyclic carboxylic anhydride acyclic carboxylic anhydrides chebi_ontology organohalogen compound A compound containing at least one carbon-halogen bond. CHEBI:36684 chebi_ontology organohalogen compounds 3-hydroxy steroid 3-hydroxy steroids Any hydroxy steroid carrying a hydroxy group at position 3. CHEBI:36834 chebi_ontology 3beta-hydroxy steroid 0 275.237 275.450 3beta-hydroxy steroids A 3-hydroxy steroid in which the 3-hydroxy substituent is in the beta-position. C12C(C3C(C(CC3)*)(C)CC1)CCC4C2(CC[C@@H](C4)O)C C19H31OR CHEBI:36836 CHEBI:71195 MetaCyc:3-Beta-Hydroxysterols PMID:10535978 PMID:12829805 a 3beta-hydroxysteroid chebi_ontology inorganic radical CHEBI:36871 chebi_ontology inorganic radicals chalcogen hydride CHEBI:36902 chalcogen hydride chalcogen hydrides chebi_ontology inorganic ion CHEBI:36914 chebi_ontology inorganic ions inorganic cation CHEBI:36915 chebi_ontology inorganic cations cation A monoatomic or polyatomic species having one or more elementary charges of the proton. CHEBI:23058 CHEBI:3473 CHEBI:36916 Cation KEGG:C01373 Kation Kationen cation cationes cations chebi_ontology organochalcogen compound An organochalcogen compound is a compound containing at least one carbon-chalcogen bond. CHEBI:36962 chebi_ontology organochalcogen compound organochalcogen compounds organooxygen compound An organochalcogen compound containing at least one carbon-oxygen bond. CHEBI:36963 PMID:17586126 chebi_ontology organooxygen compound organooxygen compounds nucleotide A nucleotide is a nucleoside phosphate resulting from the condensation of the 3 or 5 hydroxy group of a nucleoside with phosphoric acid. CHEBI:13215 CHEBI:13663 CHEBI:36976 CHEBI:7656 KEGG:C00215 Nucleotide a nucleotide chebi_ontology nucleotides ribonucleoside 5'-monophosphate CHEBI:1976 CHEBI:1977 CHEBI:20500 CHEBI:36996 CHEBI:37010 chebi_ontology ribonucleoside 5'-monophosphates ribonucleoside 5'-phosphate CHEBI:37015 chebi_ontology ribonucleoside 5'-phosphates purine ribonucleoside 5'-monophosphate CHEBI:37021 chebi_ontology purine ribonucleoside 5'-monophosphates purine ribonucleoside 5'-diphosphate CHEBI:37038 chebi_ontology purine ribonucleoside 5'-diphosphates purine ribonucleoside 5'-triphosphate CHEBI:37045 chebi_ontology purine ribonucleoside 5'-triphosphates adenosine 5'-phosphate CHEBI:37096 adenosine 5'-phosphates chebi_ontology guanosine 5'-phosphate CHEBI:37121 chebi_ontology guanosine 5'-phosphates organobromine compound A compound containing at least one carbon-bromine bond. CHEBI:37141 bromoorganic compound chebi_ontology organobromine compounds gadodiamide 0 573.66000 574.102 A non-ionic gadolinium chelate having a macrocyclic triamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). C16H26GdN5O8 CAS:131410-48-5 CHEBI:37333 CNC1=[O][Gd+3]234567[O-]C(=O)C[N]2(CC[N]3(CC(=O)[O-]4)C1)CC[N]5(CC(=O)[O-]6)CC(NC)=[O]7 DrugBank:DB00225 HZHFFEYYPYZMNU-UHFFFAOYSA-K InChI=1S/C16H29N5O8.Gd/c1-17-12(22)7-20(10-15(26)27)5-3-19(9-14(24)25)4-6-21(11-16(28)29)8-13(23)18-2;/h3-11H2,1-2H3,(H,17,22)(H,18,23)(H,24,25)(H,26,27)(H,28,29);/q;+3/p-3 Wikipedia:Gadodiamide [N,N-bis(2-{[(carboxy-kappaO)methyl][2-(methylamino)-2-(oxo-kappaO)ethyl]amino-kappaN}ethyl)glycinato(3-)-kappa(2)N,O]gadolinium chebi.owl chebi_ontology gadolinium 5,8-bis(carboxylatomethyl)-11-[2-(methylamino)-2-oxoethyl]-3-oxo-2,5,8,11-tetraazatridecan-13-oate gadolinium [bis(2-{(carboxylatomethyl)[2-(methylamino)-2-oxoethyl]amino}ethyl)amino]acetate obi.owl heteroatomic molecular entity A molecular entity consisting of two or more chemical elements. CHEBI:37577 chebi_ontology chemical compound heteroatomic molecular entities halide Any heteroatomic molecular entity that is a chemical compound of halogen with other chemical elements. CHEBI:37578 Wikipedia:Halide chebi_ontology halides sodium phosphate CAS:7632-05-5 CHEBI:37586 Wikipedia:Sodium_phosphates chebi.owl chebi_ontology obi.owl phosphoric acid, sodium salt sodium orthophosphate sodium phosphate sodium phosphates sodium salt of phosphoric acid carboxamide 0 41.998 42.01680 An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom. CHEBI:35354 CHEBI:35355 CHEBI:37622 CNOR3 [*]C(=O)N([*])[*] carboxamides carboxamides chebi_ontology primary carboxamide phosphoric ester CHEBI:26019 CHEBI:37734 chebi_ontology phosphate esters phosphoric esters glycerophospholipid Any glycerolipid having a phosphate group ester-linked to a terminal carbon of the glycerol backbone. CHEBI:24362 CHEBI:37739 CHEBI:5456 Glycerophospholipid PMID:17393491 chebi_ontology glycerophospholipids phosphatide phosphatides phosphoglyceride phosphoglycerides acyclic mixed acid anhydride CHEBI:37787 acyclic mixed acid anhydrides chebi_ontology sulfuric acid derivative CHEBI:37826 chebi_ontology sulfuric acid derivative sulfuric acid derivatives acyl sulfate CHEBI:37875 acyl sulfates chebi_ontology cyanine dye CHEBI:37960 Cyanine dyes are synthetic dyes with the general formula R2N[CH=CH]nCH=N(+)R2 <-> R2N(+)=CH[CH=CH]nNR2 (n is a small number) in which the nitrogen and part of the conjugated chain usually form part of a heterocyclic system, such as imidazole, pyridine, pyrrole, quinoline and thiazole. Cyaninfarbstoff Zyaninfarbstoff chebi_ontology cyanine dyes phosphorus-32 atom (32)15P (32)P 0 30.974 31.97391 CAS:14596-37-3 CHEBI:37972 InChI=1S/P/i1+1 KEGG:C19162 OAICVXFJPJFONN-OUBTZVSYSA-N P Phosphorus, isotope of mass 32 The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days. [32P] chebi.owl chebi_ontology obi.owl phosphorus, isotope of mass 32 phosphorus-32 phosphorus-32 phosphorus-33 atom (33)15P (33)P 0 30.974 32.97173 CAS:15749-66-3 CHEBI:37973 InChI=1S/P/i1+2 OAICVXFJPJFONN-NJFSPNSNSA-N P The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2. [33P] chebi.owl chebi_ontology obi.owl phosphorus, isotope of mass 33 phosphorus-33 phosphorus-33 Cy3 dye +1 271.124 271.33580 C19H15N2R2 CHEBI:37987 [H]C(=CC([H])=C1Cc2ccccc2N1[*])C1=[N+]([*])c2ccccc2C1 chebi.owl chebi_ontology obi.owl Cy5 dye +1 297.139 297.37310 C21H17N2R2 CHEBI:37989 [H]C(C=C([H])C1=[N+]([*])c2ccccc2C1)=CC([H])=C1Cc2ccccc2N1[*] chebi.owl chebi_ontology obi.owl benzoxathiole CHEBI:38086 benzoxathioles chebi_ontology 2,1-benzoxathiole 2,1-benzoxathioles CHEBI:38087 chebi_ontology sultone An intramolecular cyclic ester of a hydroxy sulfonic acid, analogous to lactone. CHEBI:38088 chebi_ontology sultones arenesulfonate ester An organosulfonic ester resulting from the formal condensation of an arenesulfonic acid with the hydroxy group of an alcohol, enol, phenol or heteroarenol. CHEBI:38094 arenesulfonate esters chebi_ontology organonitrogen heterocyclic compound Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms. CHEBI:38101 chebi_ontology heterocyclic organonitrogen compounds organonitrogen heterocyclic compounds oxacycle Any organic heterocyclic compound containing at least one ring oxygen atom. CHEBI:38104 PMID:17134300 chebi_ontology heterocyclic organooxygen compounds organooxygen heterocyclic compounds oxacycles organosulfur heterocyclic compound CHEBI:38106 chebi_ontology heterocyclic organosulfur compounds organosulfur heterocyclic compounds organic heteropentacyclic compound CHEBI:38164 chebi_ontology organic heteropentacyclic compounds organic heteropolycyclic compound CHEBI:25429 CHEBI:38075 CHEBI:38166 chebi_ontology organic heteropolycyclic compounds azabicycloalkane CHEBI:38295 azabicycloalkanes chebi_ontology thiabicycloalkane CHEBI:38297 chebi_ontology thiabicycloalkanes diazines Any organic heterocyclic compound containing a benzene ring in which two of the C-H fragments have been replaced by isolobal nitrogens (the diazine parent structure). CHEBI:38313 chebi_ontology inorganic sodium salt CHEBI:38702 chebi_ontology inorganic sodium salts xanthenes CHEBI:38835 chebi_ontology dibenzopyran Any organic heteropolycyclic compound based on a skeleton consisting of a pyran ring fused with two benzene rings. CHEBI:39203 chebi_ontology dibenzopyrans dibenzopyridine CHEBI:39206 chebi_ontology dibenzopyridines digoxigenin 0 390.241 390.51306 3beta,12beta,14-trihydroxy-5beta-card-20(22)-enolide A hydroxy steroid that consists of 5beta-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3beta-, 12beta- and 14beta-positions. It has been isolated from the plant species of the genus Digitalis. C23H34O5 CAS:1672-46-4 CHEBI:38020 CHEBI:42096 CHEBI:42098 HMDB:HMDB60731 InChI=1S/C23H34O5/c1-21-7-5-15(24)10-14(21)3-4-17-18(21)11-19(25)22(2)16(6-8-23(17,22)27)13-9-20(26)28-12-13/h9,14-19,24-25,27H,3-8,10-12H2,1-2H3/t14-,15+,16-,17-,18+,19-,21+,22+,23+/m1/s1 LIPID_MAPS_instance:LMST01120008 PDBeChem:DOG PMID:10438974 PMID:23344238 PMID:23383657 PMID:8080093 PMID:9470094 SHIBSTMRCDJXLN-KCZCNTNESA-N Wikipedia:Digoxigenin [H][C@]12CC[C@]3([H])[C@]([H])(C[C@@H](O)[C@]4(C)[C@]([H])(CC[C@]34O)C3=CC(=O)OC3)[C@@]1(C)CC[C@H](O)C2 chebi.owl chebi_ontology obi.owl ethylenediaminetetraacetic acid (ethane-1,2-diyldinitrilo)tetraacetate (ethane-1,2-diyldinitrilo)tetraacetic acid (ethylenedinitrilo)tetraacetic acid, ion(4-) 0 2,2',2'',2'''-(ethane-1,2-diyldinitrilo)tetraacetate 292.091 292.24272 Acide ethylenediaminetetracetique Beilstein:1716295 Beilstein:3914756 C10H16N2O8 CAS:150-43-6 CAS:60-00-4 CHEBI:30378 CHEBI:42189 CHEBI:42191 CHEBI:4735 DrugBank:DB00974 Drug_Central:987 EDTA EDTA, ion(4-) Edetic acid Ethylenediaminetetraacetic acid Gmelin:144943 H4edta InChI=1S/C10H16N2O8/c13-7(14)3-11(4-8(15)16)1-2-12(5-9(17)18)6-10(19)20/h1-6H2,(H,13,14)(H,15,16)(H,17,18)(H,19,20) KCXVZYZYPLLWCC-UHFFFAOYSA-N KEGG:C00284 KEGG:D00052 N,N'-1,2-Ethane diylbis-(N-(carboxymethyl)glycine) OC(=O)CN(CCN(CC(O)=O)CC(O)=O)CC(O)=O PDBeChem:EDT Wikipedia:Edetate acide edetique acido edetico acidum edeticum chebi.owl chebi_ontology edetic acid edta ethylenediaminetetraacetate ethylenediaminetetraacetic acid obi.owl {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID indolyl carboxylic acid CHEBI:46867 chebi_ontology indolyl carboxylic acids oxazinane CHEBI:46952 chebi_ontology oxazinanes benzoxazine CHEBI:46969 benzoxazines chebi_ontology tetrahydrofuranol CHEBI:47017 chebi_ontology tetrahydrofuranols double-stranded DNA C10H17O8PR2(C5H8O5PR)n.C10H17O7PR2(C5H8O6PR)n CHEBI:4705 Double-stranded DNA KEGG:C00434 chebi.owl chebi_ontology obi.owl pro.owl 5-bromo-2'-deoxyuridine 0 305.985 307.09800 5-Bdu 5-Bromodeoxyuridine 5-Bromodesoxyuridine 5-Bromouracil deoxyriboside 5-Bromouracil-2-deoxyriboside 5-bromo-2'-deoxyuridine A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase. Beilstein:4236087 BrdU Bromodeoxyuridine Bromouracil deoxyriboside C9H11BrN2O5 CAS:59-14-3 CHEBI:31310 CHEBI:472552 CHEBI:47713 Drug_Central:3042 InChI=1S/C9H11BrN2O5/c10-4-2-12(9(16)11-8(4)15)7-1-5(14)6(3-13)17-7/h2,5-7,13-14H,1,3H2,(H,11,15,16)/t5-,6+,7+/m0/s1 OC[C@H]1O[C@H](C[C@@H]1O)n1cc(Br)c(=O)[nH]c1=O PDBeChem:U33 PMID:17325220 PMID:17341060 PMID:3950402 WOVKYSAHUYNSMH-RRKCRQDMSA-N Wikipedia:Bromodeoxyuridine broxuridina broxuridine broxuridinum chebi.owl chebi_ontology obi.owl ureas CHEBI:27220 CHEBI:36947 CHEBI:47857 chebi_ontology urea derivatives hydrogen atom 0 1.00794 1.008 1H CHEBI:24634 CHEBI:49636 CHEBI:49637 H InChI=1S/H Wasserstoff WebElements:H YZCKVEUIGOORGS-UHFFFAOYSA-N [H] chebi_ontology hidrogeno hydrogen hydrogen hydrogene organic amino compound A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups. CHEBI:50047 chebi.owl chebi_ontology organic amino compounds pro.owl chromium-51 (51)24Cr (51)Cr 0 50.94477 51.941 51Cr A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival. CAS:14392-02-0 CHEBI:50076 Chromium, isotope of mass 51 Cr InChI=1S/Cr/i1-1 VYZAMTAEIAYCRO-BJUDXGSMSA-N [51Cr] chebi.owl chebi_ontology chromium-51 obi.owl organic molecular entity Any molecular entity that contains carbon. CHEBI:25700 CHEBI:33244 CHEBI:50860 chebi_ontology organic compounds organic entity organic molecular entities nitrogen molecular entity CHEBI:25556 CHEBI:51143 CHEBI:7594 KEGG:C06061 Nitrogenous compounds chebi_ontology nitrogen compounds nitrogen molecular entities biotins CHEBI:51570 Compounds containing a biotin (5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid) skeleton. chebi_ontology enamide 0 65.998 66.03820 An alpha,beta-unsaturated carboxylic acid amide of general formula R(1)R(2)C=CR(3)-C(=O)NR(4)R(5) in which the amide C=O function is conjugated to a C=C double bond at the alpha,beta position. C3NOR5 CHEBI:51751 [*]\C([*])=C(\[*])C(=O)N([*])[*] chebi_ontology enamides Alexa Fluor 532 0 5-(4-{[(2,5-dioxopyrrolidin-1-yl)oxy]carbonyl}phenyl)-2,3,3,7,7,8-hexamethyl-2,3,7,8-tetrahydro-1H-pyrano[3,2-f:5,6-f']diindole-10,12-disulfonic acid 723.156 723.77144 Alexa Fluor 532 carboxylic acid, succinimidyl ester C34H33N3O11S2 CHEBI:51756 InChI=1S/C34H33N3O11S2/c1-15-33(3,4)21-13-19-25(17-7-9-18(10-8-17)32(40)48-37-23(38)11-12-24(37)39)20-14-22-27(36-16(2)34(22,5)6)31(50(44,45)46)29(20)47-28(19)30(26(21)35-15)49(41,42)43/h7-10,13-16,35H,11-12H2,1-6H3,(H,41,42,43)(H,44,45,46) WHVNXSBKJGAXKU-UHFFFAOYSA-N [H+].[H+].CC1Nc2c(cc3c(Oc4c(c5=NC(C)C(C)(C)c5cc4=C3c3ccc(cc3)C(=O)ON3C(=O)CCC3=O)S([O-])(=O)=O)c2S([O-])(=O)=O)C1(C)C chebi.owl chebi_ontology obi.owl Alexa Fluor 546 0 1078.114 1080.39800 Alexa Fluor 546 carboxylic acid, succinimidyl ester C44H46Cl3N4NaO14S3 CHEBI:51760 InChI=1S/C44H47Cl3N4O14S3.Na/c1-19-16-43(3,4)49-35-21(19)14-23-29(24-15-22-20(2)17-44(5,6)50-36(22)41(68(61,62)63)38(24)64-37(23)40(35)67(58,59)60)30-31(42(56)57)32(45)34(47)39(33(30)46)66-18-25(52)48-13-9-7-8-10-28(55)65-51-26(53)11-12-27(51)54;/h14-15,19-20,49H,7-13,16-18H2,1-6H3,(H,48,52)(H,56,57)(H,58,59,60)(H,61,62,63);/q;+1/p-1 ZAINTDRBUHCDPZ-UHFFFAOYSA-M [H+].[Na+].CC1CC(C)(C)Nc2c1cc1c(Oc3c(c4=NC(C)(C)CC(C)c4cc3=C1c1c(Cl)c(SCC(=O)NCCCCCC(=O)ON3C(=O)CCC3=O)c(Cl)c(Cl)c1C(O)=O)S([O-])(=O)=O)c2S([O-])(=O)=O chebi.owl chebi_ontology obi.owl sodium 6-(2-carboxy-3,4,6-trichloro-5-{[2-({6-[(2,5-dioxopyrrolidin-1-yl)oxy]-6-oxohexyl}amino)-2-oxoethyl]thio}phenyl)-2,2,4,8,10,10-hexamethyl-3,4,5a,8,9,10,11,12a-octahydro-2H-pyrano[3,2-g:5,6-g']diquinolin-1-ium-12,14-disulfonate organic polycyclic compound CHEBI:51958 chebi_ontology organic polycyclic compounds inorganic hydroxy compound CHEBI:52625 chebi_ontology inorganic hydroxides Alexa Fluor 555 0 4-(6-amino-3-imino-4,5-disulfo-3H-xanthen-9-yl)benzene-1,3-dicarboxylic acid 534.004 534.47300 A fluorescent dye of absorption wavelength 555 nm and emission wavelength 565 nm, derived from a 3,6-diaminoxanthene-4,5-disulfate. C21H14N2O11S2 CHEBI:52673 IGAZHQIYONOHQN-UHFFFAOYSA-N InChI=1S/C21H14N2O11S2/c22-13-5-3-10-15(9-2-1-8(20(24)25)7-12(9)21(26)27)11-4-6-14(23)19(36(31,32)33)17(11)34-16(10)18(13)35(28,29)30/h1-7,22H,23H2,(H,24,25)(H,26,27)(H,28,29,30)(H,31,32,33) Nc1ccc2c(-c3ccc(cc3C(O)=O)C(O)=O)c3ccc(=N)c(c3oc2c1S(O)(=O)=O)S(O)(=O)=O chebi.owl chebi_ontology obi.owl tritiated thymidine (3)HTdR (3H)Thymidine CAS:50-88-4 CHEBI:53526 Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis. Thymidine-(H-3) chebi.owl chebi_ontology obi.owl tritiated thymidines heterocyclic compound A cyclic compound having as ring members atoms of at least two different elements. CHEBI:5686 Heterocyclic compound chebi_ontology compuesto heterociclico compuestos heterociclicos heterocycle heterocyclic compounds dimethyl sulfate 0 125.999 126.13200 Beilstein:635994 C2H6O4S CAS:77-78-1 CHEBI:371544 CHEBI:59050 COS(=O)(=O)OC DMS Dimethoxysulfone Dimethyl monosulfate Dimethyl sulphate InChI=1S/C2H6O4S/c1-5-7(3,4)6-2/h1-2H3 KEGG:C19177 PMID:2299638 Sulfate dimethylique Sulfato de dimetilo Sulfuric acid dimethyl ester The dimethyl ester of sulfuric acid. VAYGXNSJCAHWJZ-UHFFFAOYSA-N chebi.owl chebi_ontology dimethyl sulfate obi.owl diethyl pyrocarbonate 0 162.053 162.14060 Beilstein:637031 C6H10O5 CAS:1609-47-8 CCOC(=O)OC(=O)OCC CHEBI:4525 CHEBI:59051 Dicarbonic acid diethyl ester Diethyl oxydiformate Diethyl pyrocarbonate Diethyl pyrocarbonic acid Ethyl pyrocarbonate FFYPMLJYZAEMQB-UHFFFAOYSA-N Gmelin:602268 InChI=1S/C6H10O5/c1-3-9-5(7)11-6(8)10-4-2/h3-4H2,1-2H3 KEGG:C11592 Oxydiformic acid diethyl ester Pyrocarbonate d'ethyle Pyrocarbonic acid diethyl ester Pyrokohlensaeure diaethyl ester The diethyl ester of dicarbonic acid. chebi.owl chebi_ontology diethyl dicarbonate obi.owl 1,1-dihydroxy-3-ethoxy-2-butanone 0 148.074 148.15710 3-Ethoxy-1,1-dihydroxy-2-butanone 3-ethoxy-1,1-dihydroxybutan-2-one A butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position. Beilstein:8677948 C6H12O4 CAS:27762-78-3 CCOC(C)C(=O)C(O)O CHEBI:59052 Chetossale Drug_Central:3202 InChI=1S/C6H12O4/c1-3-10-4(2)5(7)6(8)9/h4,6,8-9H,3H2,1-2H3 KEGG:D04651 YRCRRHNVYVFNTM-UHFFFAOYSA-N beta-Ethoxy-alpha-ketobutyraldehyde chebi.owl chebi_ontology kethoxal ketoxalum obi.owl N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide 0 1-Cmec 1-Cyclohexyl-3-(2-(4-morpholinyl)ethyl)carbodiimide 237.184 237.34120 A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents. Beilstein:196522 C13H23N3O C1CCC(CC1)N=C=NCCN1CCOCC1 CAS:15580-20-8 CHEBI:59053 CMCT InChI=1S/C13H23N3O/c1-2-4-13(5-3-1)15-12-14-6-7-16-8-10-17-11-9-16/h13H,1-11H2 N-cyclohexyl-N'-(2-morpholin-4-ylethyl)methanediimine N-cyclohexyl-N'-[2-(morpholin-4-yl)ethyl]carbodiimide XNPOFXIBHOVFFH-UHFFFAOYSA-N chebi.owl chebi_ontology obi.owl N-methylisatoic anhydride 0 1-methyl-2H-3,1-benzoxazine-2,4(1H)-dione 1-methyl-3,1-benzoxazine-2,4-dione 177.043 177.15680 A 3,1-benzoxazin-1,4-dione having an N-methyl substituent. Beilstein:383957 C9H7NO3 CAS:10328-92-4 CHEBI:59054 Cn1c2ccccc2c(=O)oc1=O InChI=1S/C9H7NO3/c1-10-7-5-3-2-4-6(7)8(11)13-9(10)12/h2-5H,1H3 KJMRWDHBVCNLTQ-UHFFFAOYSA-N Methyl-N-carboxyanthranilic anhydride N-Methyl IA chebi.owl chebi_ontology obi.owl (S)-1-(4-bromoacetamidobenzyl)EDTA 0 1-(para-Bromoacetamidobenzyl)edta 2,2',2'',2'''-{[(2S)-3-{4-[(bromoacetyl)amino]phenyl}propane-1,2-diyl]dinitrilo}tetraacetic acid 2-[[(2S)-1-[bis(carboxymethyl)amino]-3-[4-[(2-bromoacetyl)amino]phenyl] propan-2-yl]-(carboxymethyl)amino]acetic acid 517.070 518.31300 A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration. Beilstein:7236603 C19H24BrN3O9 CAS:81677-64-7 CHEBI:59055 InChI=1S/C19H24BrN3O9/c20-6-15(24)21-13-3-1-12(2-4-13)5-14(23(10-18(29)30)11-19(31)32)7-22(8-16(25)26)9-17(27)28/h1-4,14H,5-11H2,(H,21,24)(H,25,26)(H,27,28)(H,29,30)(H,31,32)/t14-/m0/s1 N-4-(2,3-Bis(bis(carboxymethyl)amino)propyl)phenyl bromoacetamide OC(=O)CN(C[C@H](Cc1ccc(NC(=O)CBr)cc1)N(CC(O)=O)CC(O)=O)CC(O)=O VOQPQBGCWBEYEV-AWEZNQCLSA-N chebi.owl chebi_ontology obi.owl EDTA methidiumpropylamide 0 645.291 645.70550 A combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe. C33H39N7O7 CHEBI:59056 C[n+]1c(-c2ccc(NCCCNC(=O)CN(CCN(CC(O)=O)CC([O-])=O)CC(O)=O)cc2)c2cc(N)ccc2c2ccc(N)cc12 InChI=1S/C33H39N7O7/c1-38-28-16-23(35)6-10-26(28)25-9-5-22(34)15-27(25)33(38)21-3-7-24(8-4-21)36-11-2-12-37-29(41)17-39(18-30(42)43)13-14-40(19-31(44)45)20-32(46)47/h3-10,15-16H,2,11-14,17-20,34H2,1H3,(H6,35,36,37,41,42,43,44,45,46,47) PFGGLNMBUNROLG-UHFFFAOYSA-N [(carboxymethyl){2-[(carboxymethyl){2-[(3-{[4-(3,8-diamino-5-methylphenanthridinium-6-yl)phenyl]amino}propyl)amino]-2-oxoethyl}amino]ethyl}amino]acetate chebi.owl chebi_ontology obi.owl bromophenol blue 0 3',3'',5',5''-tetrabromophenolsulfonephthalein 3',3'',5',5''-tetrabromophenolsulfophthalein 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye. 4,4'-(1,1-dioxido-3H-2,1-benzoxathiole-3,3-diyl)bis(2,6-dibromophenol) 665.698 669.96100 Beilstein:61698 C19H10Br4O5S CAS:115-39-9 CHEBI:59424 InChI=1S/C19H10Br4O5S/c20-12-5-9(6-13(21)17(12)24)19(10-7-14(22)18(25)15(23)8-10)11-3-1-2-4-16(11)29(26,27)28-19/h1-8,24-25H Oc1c(Br)cc(cc1Br)C1(OS(=O)(=O)c2ccccc12)c1cc(Br)c(O)c(Br)c1 UDSAIICHUKSCKT-UHFFFAOYSA-N bromophenol blue, sultone form chebi.owl chebi_ontology obi.owl oxygen radical An inorganic radical in which a free electron resides on one or more oxygen atoms of an oxygen species. CHEBI:61073 chebi_ontology oxygen radicals nucleobase-containing molecular entity Any compound that has a nucleobase as a part. CHEBI:61120 chebi_ontology nucleobase-containing compound nucleobase-containing compounds nucleobase-containing molecular entities guanyl ribonucleotide A purine ribonucleotide where the purine is guanine. CHEBI:61295 chebi_ontology adenyl ribonucleotide A purine riboncleotide where adenine is the purine. CHEBI:61296 adenine ribonucleotide chebi_ontology globoside Any glycosphingolipid where the oligosaccharide component has an N-acetylgalactosaminyl residue at the non-reducing end. CHEBI:61360 Wikipedia:Globoside chebi_ontology globosides carbohydrate derivative Any organooxygen compound derived from a carbohydrate by replacement of one or more hydroxy group(s) by an amino group, a thiol group or similar heteroatomic groups. The term also includes derivatives of these compounds. CHEBI:63299 carbohydrate derivatives chebi_ontology derivatised carbohydrate derivatised carbohydrates derivatized carbohydrate derivatized carbohydrates monosaccharide derivative A carbohydrate derivative that is formally obtained from a monosaccharide. CHEBI:63367 chebi_ontology monosaccharide derivatives polysaccharide derivative A carbohydrate derivative that is any derivative of a polysaccharide. CHEBI:65212 chebi_ontology polysaccharide derivatives double-stranded RNA A ribonucleic acid with two complementary strands, similar to the DNA found in all cells. CHEBI:67208 Wikipedia:RNA#Double-stranded_RNA chebi.owl chebi_ontology double stranded ribonucleic acid dsRNA pro.owl pyrimidine deoxyribonucleoside A deoxyribonucleoside containing a pyrimidine base. CHEBI:68472 MetaCyc:Pyrimidine-Deoxyribonucleosides chebi_ontology pyrimidine deoxyribonucleosides organic molecule Any molecule that consists of at least one carbon atom as part of the electrically neutral entity. CHEBI:72695 chebi_ontology organic compound organic compounds organic molecules N-nitrosoureas A nitroso compound that is any urea in which one of the nitrogens is substituted by a nitroso group CHEBI:76551 chebi_ontology carbohydrates and carbohydrate derivatives Any organooxygen compound that is a polyhydroxy-aldehyde or -ketone, or a compound derived from one. Carbohydrates contain only carbon, hydrogen and oxygen and usually have an empirical formula Cm(H2O)n; carbohydrate derivatives may contain other elements by substitution or condensation. CHEBI:78616 carbohydrates and derivatives carbohydrates and their derivatives chebi_ontology organosulfonic ester 0 79.957 80.06300 An ester resulting from the formal condensation of the hydroxy group of an alcohol, phenol, heteroarenol, or enol with an organosulfonic acid. CHEBI:83347 O3SR2 [*]S(=O)(=O)O[*] chebi_ontology organosulfonate ester organosulfonate esters organosulfonic esters pentose phosphate Any phospho sugar that is the phosphate derivative of pentose. CHEBI:84055 chebi_ontology pentose phosphates N-acetyl-beta-D-galactosaminyl-(1->3)-alpha-D-galactosyl-(1->4)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide 0 806.280 806.719 A glycotetraosylceramide having N-acetyl-beta-D-galactosaminyl-(1->3)-alpha-D-galactosyl-(1->4)-beta-D-galactosyl-(1->4)-beta-D-glucosyl component attached to the primary hydroxy function of a ceramide with undefined sphingoid base. C30H50N2O23R2 CHEBI:88167 N-acetyl-beta-D-galactosaminyl-(1->3)-alpha-D-galactosyl-(1->4)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide [C@H]([C@@H](*)O)(NC(=O)*)CO[C@@H]1O[C@@H]([C@@H](O[C@@H]2O[C@@H]([C@H](O[C@@H]3[C@@H]([C@@H](O[C@H]4[C@@H]([C@H]([C@@H](O)[C@H](O4)CO)O)NC(C)=O)[C@H]([C@@H](CO)O3)O)O)[C@@H]([C@H]2O)O)CO)[C@@H]([C@H]1O)O)CO beta-D-GalNAc-(1->3)-alpha-D-Gal-(1->4)-beta-D-Gal-(1->4)-beta-D-Glc-(1<->1')-Cer beta-D-GalpNAc-(1->3)-alpha-D-Galp-(1->4)-beta-D-Galp-(1->4)-beta-D-Glcp-(1<->1')-Cer chebi_ontology tris 0 1,1,1-tris(hydroxymethyl)methanamine 121.074 121.13500 2-Amino-2-(hydroxymethyl)-1,3-propanediol 2-amino-2-(hydroxymethyl)propane-1,3-diol A primary amino compound that is tert-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC. Beilstein:741883 C4H11NO3 CAS:77-86-1 CHEBI:9754 DrugBank:DB03754 Drug_Central:2771 Gmelin:217857 InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2 KEGG:C07182 KEGG:D00396 LENZDBCJOHFCAS-UHFFFAOYSA-N NC(CO)(CO)CO PDBeChem:TRS PMID:22553829 Reaxys:741883 THAM Tris Tris amino Tris base Tris buffer Tris-base Trizma Trometamol Tromethamine Wikipedia:Tris aminotris(hydroxymethyl)methane chebi.owl chebi_ontology obi.owl tris(hydroxymethyl)aminomethane 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. DOID:4 MESH:D004194 NCI:C2991 SNOMEDCT_US_2016_03_01:64572001 UMLS_CUI:C0012634 disease_ontology phosphopyruvate hydratase complex A multimeric enzyme complex, usually a dimer or an octamer, that catalyzes the conversion of 2-phospho-D-glycerate to phosphoenolpyruvate and water. GO:0000015 cellular_component enolase complex go.owl pro.owl transcription factor TFIIIC complex A heterotrimeric transcription factor complex that is involved in regulating transcription from RNA polymerase III (Pol III) promoters. TFIIIC contains three conserved subunits that associate with the proximal Pol III promoter element, and additional subunits that associate with sequence elements downstream of the promoter and are more diverged among species. It also functions as a boundary element to partition genome content into distinct domains outside Pol III promoter regions. GO:0000127 cellular_component go.owl pro.owl ubiquitin ligase complex A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex. GO:0000151 cellular_component go.owl pro.owl nuclear ubiquitin ligase complex A ubiquitin ligase complex found in the nucleus. GO:0000152 cellular_component cyclin-dependent protein kinase holoenzyme complex CDK holoenzyme Cyclin-dependent protein kinases (CDKs) are enzyme complexes that contain a kinase catalytic subunit associated with a regulatory cyclin partner. GO:0000307 cellular_component go.owl pro.owl DNA-directed RNA polymerase complex A protein complex that possesses DNA-directed RNA polymerase activity. GO:0000428 cellular_component proteasome complex 26S proteasome A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core. GO:0000502 cellular_component go.owl pro.owl proteasome glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex An enzyme complex that catalyzes the transfer of GlcNAc from UDP-GlcNAc to an acceptor phosphatidylinositol, the first step in the production of GPI anchors for cell surface proteins. The complex contains PIG-A, PIG-C, PIG-H, PIG-Q, PIG-P, and DPM2 in human, and Eri1p, Gpi1p, Gpi2p, Gpi15p, Gpi19p, and Spt14p in budding yeast. GO:0000506 GPI-GlcNAc transferase complex GPI-GnT complex GPI-N-acetylglucosaminyltransferase complex Note that this term should not be confused with 'GPI-anchor transamidase complex ; GO:0042765', which represents a distinct complex with a different catalytic activity. cellular_component go.owl pro.owl telomere cap complex A complex of DNA and protein located at the end of a linear chromosome that protects and stabilizes a linear chromosome. GO:0000782 Note that this term can be used in place of the obsolete cellular component term 'telomere ; GO:0005696'. Use with caution because this term refers to a specific protein complex and not a region of the chromosome. cellular_component nuclear telomere cap complex A complex of DNA and protein located at the end of a linear chromosome in the nucleus that protects and stabilizes a linear chromosome. GO:0000783 Note that this term can be used in place of the obsolete cellular component term 'telomere ; GO:0005696'. Use with caution because this term refers to a specific protein complex and not a region of the chromosome. cellular_component regulatory region DNA binding 2010-08-10T10:56:24Z GO:0000975 Interacting selectively and non-covalently with a DNA region that regulates a DNA-based process. Such processes include transcription, DNA replication, and DNA repair. kchris molecular_function core promoter binding 2010-08-27T03:00:52Z GO:0001047 Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. go.owl kchris molecular_function obi.owl regulatory region nucleic acid binding 2010-10-21T04:08:56Z GO:0001067 Interacting selectively and non-covalently with a nucleic acid region that regulates a nucleic acid-based process. Such processes include transcription, DNA replication, and DNA repair. kchris molecular_function cell activation A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand. GO:0001775 biological_process antibody-dependent cellular cytotoxicity ADCC Cytolysis of target cells by natural killer cells, eosinophils, neutrophils, monocytes, or macrophages following engagement of antibodies bound to the target cells by Fc receptors on the effector cells. GO:0001788 Wikipedia:Antibody-dependent_cell-mediated_cytotoxicity Wikipedia:Antibody-dependent_cellular_cytotoxicity antibody dependent cell death antibody dependent cell killing antibody-dependent cell death antibody-dependent cell killing biological_process go.owl obi.owl type VI hypersensitivity type IIa hypersensitivity An inflammatory response resulting in cell death mediated by activation of the classical complement pathway or induction of effector cell phagocytosis or cytolysis mechanisms via complement or Fc receptors following the binding of antibodies to cell surface antigens on a target cell. GO:0001794 Note that some type IIb hypersensitivity responses (GO:0001795) are referred to simply as type II hypersensitivity in the earlier literature, but are mechanistically distinct from type IIa hypersensitivity. biological_process type IV hypersensitivity An inflammatory response driven by T cell recognition of processed soluble or cell-associated antigens leading to cytokine release and leukocyte activation. GO:0001806 GO:0016069 Wikipedia:Type_IV_hypersensitivity biological_process delayed hypersensitivity response delayed-type hypersensitivity go.owl obi.owl cytokine production GO:0001816 Note that this term is intended for use when a gene product is seen to cause apparent increases in intracellular or extracellular cytokine levels, without specific regard as to whether the increase is due to increased biosynthesis, increased secretion of preexisting cytokine molecules, or increased conversion from precursor molecules. The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl interferon production interleukin production obi.owl histamine secretion GO:0001821 The regulated release of histamine by a cell or tissue. It is formed by decarboxylation of histidine and it acts through receptors in smooth muscle and in secretory systems. biological_process cell killing Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions. GO:0001906 biological_process go.owl necrosis obi.owl leukocyte mediated cytotoxicity GO:0001909 The directed killing of a target cell by a leukocyte. This term was improved by GO_REF:0000022. It was moved. Note that this term and its children describe contact-dependent killing of target cells by lymphocytes and myeloid cells of the immune system. biological_process immune cell mediated cell death immune cell mediated cell killing immune cell mediated cytotoxicity leucocyte mediated cytotoxicity T cell mediated cytotoxicity GO:0001913 Note that either or both mechanisms mentioned in the definition may be used in this process. Note that both granule release and the engagement of death receptors on target cells result in the induction of apoptosis in the target cell. Note that both CD4 and CD8 positive T cells can mediate apoptosis of target cells, independently of their definition as 'helper' T cells or not. T cell mediated apoptosis T cell mediated cell death T cell mediated cell killing T cell mediated cytolysis T lymphocyte mediated cytotoxicity T-cell mediated apoptosis T-cell mediated cell death T-cell mediated cell killing T-cell mediated cytotoxicity T-lymphocyte mediated cytotoxicity The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors. biological_process go.owl obi.owl 3-methylcrotonyl-CoA carboxylase complex, mitochondrial 2010-03-15T04:58:08Z 3-methylcrotonyl-CoA carboxylase holoenzyme A mitochondrial protein complex which is capable of 3-methylcrotonyl-CoA carboxylase activity. In mammals, at least, consists as a dodecamer of 6 alpha and 6 beta subunits. MCCC-alpha has a covalently bound biotin essential for the ATP-dependent carboxylation. MCCC-beta possesses carboxyltransferase activity which presumably is essential for binding to 3-methylcrotonyl-CoA. GO:0002169 MCCC complex cellular_component go.owl hjd methylcrotonoyl-CoA carboxylase complex pro.owl palmitoyltransferase complex 2010-12-03T10:49:17Z A protein complex with palmitoyltransferase activity. GO:0002178 cellular_component go.owl hjd pro.owl homodimeric serine palmitoyltransferase complex 2010-12-03T10:50:59Z A homodimeric complex which transfers a palmitoyl group onto serine, forming 3-dehydro-D-sphinganine. GO:0002179 This complex occurs primarily in bacteria. cellular_component go.owl hjd pro.owl 5-lipoxygenase complex 2011-06-09T01:05:53Z An nuclear membrane protein complex having arachidonate 5-lipoxygenase activity. GO:0002180 cellular_component go.owl hjd pro.owl creatine kinase complex 2011-06-14T02:12:19Z A protein complex having creatine kinase activity. GO:0002185 cellular_component go.owl hjd pro.owl cytosolic creatine kinase complex 2011-06-14T02:14:16Z A dimeric protein complex having creatine kinase activity. GO:0002186 cellular_component go.owl hjd pro.owl xanthine dehydrogenase complex 2011-10-03T03:55:57Z A homodimeric protein complex having xanthine dehydrogenase activity. GO:0002197 cellular_component go.owl hjd pro.owl zona pellucida receptor complex 2011-12-23T01:33:23Z A multisubunit complex comprising the chaperonin-containing T-complex and several other components involved in mediating sperm-oocyte Interaction. GO:0002199 cellular_component go.owl hjd pro.owl sperm protein complex I adaptive immune response An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). GO:0002250 This term was added by GO_REF:0000022. Wikipedia:Adaptive_immune_system acquired immune response biological_process go.owl immune memory response obi.owl immune effector process Any process of the immune system that can potentially contribute to an immune response. GO:0002252 This term was added by GO_REF:0000022. biological_process cell activation involved in immune response A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an immune response. GO:0002263 This term was added by GO_REF:0000022. biological_process cell activation during immune response lymphocyte activation involved in immune response A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response. GO:0002285 biological_process lymphocyte activation during immune response T cell activation involved in immune response GO:0002286 T cell activation during immune response T lymphocyte activation during immune response T-cell activation during immune response T-lymphocyte activation during immune response The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response. biological_process leukocyte activation involved in immune response A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response. GO:0002366 biological_process immune cell activation during immune response leucocyte activation during immune response leukocyte activation during immune response cytokine production involved in immune response GO:0002367 The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels. This term was added by GO_REF:0000022. Note that this term is intended for use when a gene product is seen to cause apparent increases in intracellular or extracellular cytokine levels, without specific regard as to whether the increase is due to increased biosynthesis, increased secretion of preexisting cytokine molecules, or increased conversion from precursor molecules. biological_process cytokine production during immune response go.owl obi.owl immune system process Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. GO:0002376 Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501). This term was added by GO_REF:0000022. Wikipedia:Immune_system biological_process platelet activating factor production GO:0002390 The synthesis or release of platelet activating factor following a stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl inflammatory response to antigenic stimulus An inflammatory response to an antigenic stimulus, which can be include any number of T cell or B cell epitopes. GO:0002437 biological_process acute inflammatory response to antigenic stimulus An acute inflammatory response to an antigenic stimulus. An acute inflammatory response occurs within a matter of minutes or hours, and either resolves within a few days or becomes a chronic inflammatory response. GO:0002438 This term was added by GO_REF:0000022. biological_process production of molecular mediator of immune response GO:0002440 The synthesis or release of any molecular mediator of the immune response, resulting in an increase in its intracellular or extracellular levels. This term was added by GO_REF:0000022. biological_process production of cellular mediator of immune response histamine secretion involved in inflammatory response GO:0002441 The regulated release of histamine by a cell as part of an inflammatory response. biological_process histamine secretion involved in acute inflammatory response leukocyte mediated immunity Any process involved in the carrying out of an immune response by a leukocyte. GO:0002443 GO:0019723 GO:0042087 This term was added by GO_REF:0000022. biological_process cell-mediated immune response cellular immune response immune cell effector process immune cell mediated immunity leucocyte immune effector process leucocyte mediated immunity leukocyte immune effector process myeloid leukocyte mediated immunity Any process involved in the carrying out of an immune response by a myeloid leukocyte. GO:0002444 This term was added by GO_REF:0000022. biological_process myeloid leucocyte immune effector process myeloid leucocyte mediated immunity myeloid leukocyte immune effector process type II hypersensitivity An inflammatory response resulting in cell death or dysfunction mediated by activation of the classical complement pathway or induction of effector cell phagocytosis, cytolysis mechanisms via complement or Fc receptors following the binding of antibodies to cell surface antigens on a target cell, or mediated by the direct binding of antibody to cellular receptors. GO:0002445 Wikipedia:Type_II_hypersensitivity biological_process lymphocyte mediated immunity Any process involved in the carrying out of an immune response by a lymphocyte. GO:0002449 This term was added by GO_REF:0000022. biological_process cell-mediated immunity cellular immune response T cell mediated immunity Any process involved in the carrying out of an immune response by a T cell. GO:0002456 T lymphocyte mediated immunity T-cell mediated immunity T-lymphocyte mediated immunity This term was added by GO_REF:0000022. biological_process cell-mediated immunity cellular immune response adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains An immune response mediated by lymphocytes expressing specific receptors for antigen produced through a somatic diversification process that includes somatic recombination of germline gene segments encoding immunoglobulin superfamily domains. Recombined receptors for antigen encoded by immunoglobulin superfamily domains include T cell receptors and immunoglobulins (antibodies) produced by B cells. The first encounter with antigen elicits a primary immune response that is slow and not of great magnitude. T and B cells selected by antigen become activated and undergo clonal expansion. A fraction of antigen-reactive T and B cells become memory cells, whereas others differentiate into effector cells. The memory cells generated during the primary response enable a much faster and stronger secondary immune response upon subsequent exposures to the same antigen (immunological memory). An example of this is the adaptive immune response found in Mus musculus. GO:0002460 biological_process tolerance induction A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it. GO:0002507 This term was added by GO_REF:0000022. biological_process go.owl obi.owl B cell tolerance induction A process involving any mechanism for tolerance induction in B cells. B lymphocyte tolerance induction B-cell tolerance induction B-lymphocyte tolerance induction GO:0002514 biological_process go.owl obi.owl T cell tolerance induction A process involving any mechanism for tolerance induction in T cells. GO:0002517 T lymphocyte tolerance induction T-cell tolerance induction T-lymphocyte tolerance induction biological_process go.owl obi.owl hypersensitivity An inflammatory response to an exogenous environmental antigen or an endogenous antigen initiated by the adaptive immune system. GO:0002524 Wikipedia:Hypersensitivity biological_process go.owl hypersensitivity response obi.owl acute inflammatory response GO:0002526 Inflammation which comprises a rapid, short-lived, relatively uniform response to acute injury or antigenic challenge and is characterized by accumulations of fluid, plasma proteins, and granulocytic leukocytes. An acute inflammatory response occurs within a matter of minutes or hours, and either resolves within a few days or becomes a chronic inflammatory response. This term was added by GO_REF:0000022. biological_process production of molecular mediator involved in inflammatory response GO:0002532 The synthesis or release of any molecular mediator of the inflammatory response following an inflammatory stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process production of cellular mediator of acute inflammation production of molecular mediator involved in acute inflammatory response cytokine production involved in inflammatory response GO:0002534 The synthesis or release of a cytokine following a inflammatory stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. biological_process cytokine production involved in acute inflammatory response go.owl obi.owl regulation of immune system process Any process that modulates the frequency, rate, or extent of an immune system process. GO:0002682 biological_process positive regulation of immune system process Any process that activates or increases the frequency, rate, or extent of an immune system process. GO:0002684 activation of immune system process biological_process stimulation of immune system process up regulation of immune system process up-regulation of immune system process upregulation of immune system process regulation of immune effector process Any process that modulates the frequency, rate, or extent of an immune effector process. GO:0002697 biological_process positive regulation of immune effector process Any process that activates or increases the frequency, rate, or extent of an immune effector process. GO:0002699 activation of immune effector process biological_process stimulation of immune effector process up regulation of immune effector process up-regulation of immune effector process upregulation of immune effector process regulation of leukocyte mediated immunity Any process that modulates the frequency, rate, or extent of leukocyte mediated immunity. GO:0002703 biological_process regulation of immune cell mediated immunity regulation of leucocyte mediated immunity positive regulation of leukocyte mediated immunity Any process that activates or increases the frequency, rate, or extent of leukocyte mediated immunity. GO:0002705 activation of leukocyte mediated immunity biological_process positive regulation of immune cell mediated immunity positive regulation of leucocyte mediated immunity stimulation of leukocyte mediated immunity up regulation of leukocyte mediated immunity up-regulation of leukocyte mediated immunity upregulation of leukocyte mediated immunity regulation of lymphocyte mediated immunity Any process that modulates the frequency, rate, or extent of lymphocyte mediated immunity. GO:0002706 biological_process positive regulation of lymphocyte mediated immunity Any process that activates or increases the frequency, rate, or extent of lymphocyte mediated immunity. GO:0002708 activation of lymphocyte mediated immunity biological_process stimulation of lymphocyte mediated immunity up regulation of lymphocyte mediated immunity up-regulation of lymphocyte mediated immunity upregulation of lymphocyte mediated immunity regulation of T cell mediated immunity Any process that modulates the frequency, rate, or extent of T cell mediated immunity. GO:0002709 biological_process regulation of T lymphocyte mediated immunity regulation of T-cell mediated immunity regulation of T-lymphocyte mediated immunity positive regulation of T cell mediated immunity Any process that activates or increases the frequency, rate, or extent of T cell mediated immunity. GO:0002711 activation of T cell mediated immunity biological_process positive regulation of T lymphocyte mediated immunity positive regulation of T-cell mediated immunity positive regulation of T-lymphocyte mediated immunity stimulation of T cell mediated immunity up regulation of T cell mediated immunity up-regulation of T cell mediated immunity upregulation of T cell mediated immunity regulation of B cell mediated immunity Any process that modulates the frequency, rate, or extent of B cell mediated immunity. GO:0002712 biological_process regulation of B lymphocyte mediated immunity regulation of B-cell mediated immunity regulation of B-lymphocyte mediated immunity positive regulation of B cell mediated immunity Any process that activates or increases the frequency, rate, or extent of B cell mediated immunity. GO:0002714 activation of B cell mediated immunity biological_process positive regulation of B lymphocyte mediated immunity positive regulation of B-cell mediated immunity positive regulation of B-lymphocyte mediated immunity stimulation of B cell mediated immunity up regulation of B cell mediated immunity up-regulation of B cell mediated immunity upregulation of B cell mediated immunity regulation of adaptive immune response Any process that modulates the frequency, rate, or extent of an adaptive immune response. GO:0002819 biological_process positive regulation of adaptive immune response Any process that activates or increases the frequency, rate, or extent of an adaptive immune response. GO:0002821 activation of adaptive immune response biological_process stimulation of adaptive immune response up regulation of adaptive immune response up-regulation of adaptive immune response upregulation of adaptive immune response regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains Any process that modulates the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata. GO:0002822 biological_process positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains Any process that activates or increases the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata. GO:0002824 biological_process tumor necrosis factor receptor superfamily complex 2012-12-20T13:26:39Z A receptor complex that contains one or more members of the tumor necrosis factor (TNF) receptor superfamily. GO:0002947 TNF receptor superfamily complex cellular_component go.owl hjd pro.owl 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. GO:0003674 GO:0005554 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. Note that when this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. go.owl molecular function molecular_function obi.owl nucleic acid binding GO:0003676 Interacting selectively and non-covalently with any nucleic acid. molecular_function DNA binding Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0003677 GO:0043566 microtubule/chromatin interaction molecular_function plasmid binding structure specific DNA binding structure-specific DNA binding antigen binding B cell receptor activity GO:0003823 Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. antibody go.owl immunoglobulin molecular_function obi.owl opsonin activity 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. GO:0003824 Wikipedia:Enzyme enzyme activity go.owl molecular_function obi.owl RNA-directed DNA polymerase activity Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time. DNA nucleotidyltransferase (RNA-directed) activity EC:2.7.7.49 GO:0003964 MetaCyc:RNA-DIRECTED-DNA-POLYMERASE-RXN RNA revertase activity RNA-dependent DNA polymerase activity RNA-dependent deoxyribonucleate nucleotidyltransferase activity RNA-directed DNA polymerase, group II intron encoded RNA-directed DNA polymerase, transposon encoded RNA-instructed DNA polymerase activity RT Reactome:REACT_9039 Reactome:REACT_9049 deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (RNA-directed) activity go.owl molecular_function obi.owl reverse transcriptase activity revertase activity transporter activity Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells. GO:0005215 GO:0005478 Reactome:REACT_6315 molecular_function small-molecule carrier or transporter ion channel activity Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size). GO:0005216 go.owl molecular_function obi.owl binding GO:0005488 Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children. The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. Wikipedia:Binding_(molecular) ligand molecular_function protein binding GO:0005515 GO:0045308 Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules). Reactome:REACT_100287 Reactome:REACT_101129 Reactome:REACT_102084 Reactome:REACT_102457 Reactome:REACT_103972 Reactome:REACT_104029 Reactome:REACT_104599 Reactome:REACT_105776 Reactome:REACT_105895 Reactome:REACT_106168 Reactome:REACT_106189 Reactome:REACT_107402 Reactome:REACT_108283 Reactome:REACT_109392 Reactome:REACT_110419 Reactome:REACT_110570 Reactome:REACT_15321 Reactome:REACT_15325 Reactome:REACT_15355 Reactome:REACT_15417 Reactome:REACT_15419 Reactome:REACT_15506 Reactome:REACT_15541 Reactome:REACT_20509 Reactome:REACT_20539 Reactome:REACT_28794 Reactome:REACT_30571 Reactome:REACT_30672 Reactome:REACT_31305 Reactome:REACT_31537 Reactome:REACT_31641 Reactome:REACT_31648 Reactome:REACT_32973 Reactome:REACT_33135 Reactome:REACT_34719 Reactome:REACT_6923 Reactome:REACT_6945 Reactome:REACT_78382 Reactome:REACT_78466 Reactome:REACT_79634 Reactome:REACT_80470 Reactome:REACT_80778 Reactome:REACT_83147 Reactome:REACT_83165 Reactome:REACT_83532 Reactome:REACT_85250 Reactome:REACT_85858 Reactome:REACT_85975 Reactome:REACT_87187 Reactome:REACT_87374 Reactome:REACT_87652 Reactome:REACT_88068 Reactome:REACT_88138 Reactome:REACT_88223 Reactome:REACT_89261 Reactome:REACT_90027 Reactome:REACT_90105 Reactome:REACT_90666 Reactome:REACT_91560 Reactome:REACT_92029 Reactome:REACT_93175 Reactome:REACT_93938 Reactome:REACT_94522 Reactome:REACT_94808 Reactome:REACT_95241 Reactome:REACT_95561 Reactome:REACT_95647 Reactome:REACT_96236 Reactome:REACT_96264 Reactome:REACT_98028 Reactome:REACT_98807 alpha-2 macroglobulin receptor-associated protein activity molecular_function protein amino acid binding protein degradation tagging activity protein folding chaperone protein tagging activity cellular_component GO:0005575 GO:0008372 NIF_Subcellular:sao-1337158144 NIF_Subcellular:sao1337158144 Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. The part of a cell, extracellular environment or virus 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 cellular_component go.owl obi.owl pro.owl subcellular entity laminin-5 complex A laminin complex composed of alpha3, beta3 and gamma2 polypeptide chains. GO:0005610 cellular_component go.owl laminin-332 complex laminin-3A32 complex laminin-5A complex pro.owl alpha DNA polymerase:primase complex A complex of four polypeptides, comprising large and small DNA polymerase alpha subunits and two primase subunits, which catalyzes the synthesis of an RNA primer on the lagging strand of replicating DNA; the smaller of the two primase subunits alone can catalyze oligoribonucleotide synthesis. DNA polymerase alpha:primase complex GO:0005658 cellular_component go.owl heterotetrameric polymerase alpha holoenzyme pol-prim primosome pro.owl DNA replication factor A complex A conserved heterotrimeric complex that binds nonspecifically to single-stranded DNA and is required for multiple processes in eukaryotic DNA metabolism, including DNA replication, DNA repair, and recombination. In all eukaryotic organisms examined the complex is composed of subunits of approximately 70, 30, and 14 kDa. GO:0005662 RPA Wikipedia:Replication_protein_A cellular_component go.owl pro.owl replication protein A DNA replication factor C complex A complex that loads the DNA polymerase processivity factor proliferating cell nuclear antigen (PCNA) onto DNA, thereby permitting processive DNA synthesis catalyzed by DNA polymerase. In eukaryotes the complex consists of five polypeptides. GO:0005663 RFC complex activator 1 complex cellular_component go.owl pro.owl transcription factor complex A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription. GO:0005667 cellular_component go.owl pro.owl transcription factor TFIID complex A complex composed of TATA binding protein (TBP) and TBP associated factors (TAFs); the total mass is typically about 800 kDa. Most of the TAFs are conserved across species. In TATA-containing promoters for RNA polymerase II (Pol II), TFIID is believed to recognize at least two distinct elements, the TATA element and a downstream promoter element. TFIID is also involved in recognition of TATA-less Pol II promoters. Binding of TFIID to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters. GO:0005669 cellular_component go.owl pro.owl transcription factor TFIIF complex A general transcription initiation factor which in humans consists of a heterodimer of an alpha and a beta subunit. Helps recruit RNA polymerase II to the initiation complex and promotes translation elongation. GO:0005674 cellular_component go.owl pro.owl anaphase-promoting complex A ubiquitin ligase complex that degrades mitotic cyclins and anaphase inhibitory protein, thereby triggering sister chromatid separation and exit from mitosis. Substrate recognition by APC occurs through degradation signals, the most common of which is termed the Dbox degradation motif, originally discovered in cyclin B. APC GO:0005680 Note that the synonym 'APC' should not be confused with the abbreviation for the adenomatous polyposis coli gene and protein. Wikipedia:Anaphase-promoting_complex anaphase promoting complex cellular_component cyclosome go.owl pro.owl chromosome A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. GO:0005694 Wikipedia:Chromosome cellular_component chromatid go.owl interphase chromosome obi.owl prophase chromosome DNA-directed RNA polymerase I complex DNA-directed RNA polymerase I activity GO:0005736 RNA polymerase I, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces rRNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerase III and others of which are also found in RNA polymerases II and III. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template. cellular_component go.owl pro.owl mitochondrion A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. GO:0005739 NIF_Subcellular:sao1860313010 Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.) Wikipedia:Mitochondrion cellular_component go.owl mitochondria obi.owl mitochondrial respiratory chain complex IV A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. Contains the 13 polypeptide subunits of cytochrome c oxidase, including cytochrome a and cytochrome a3. Catalyzes the oxidation of reduced cytochrome c by dioxygen (O2). GO:0005751 GO:0005752 cellular_component go.owl pro.owl signal peptidase complex A protein complex that is located in the endoplasmic reticulum membrane and cleaves the signal sequence from precursor proteins following their transport out of the cytoplasmic space. GO:0005787 cellular_component go.owl pro.owl chaperonin-containing T-complex A multisubunit ring-shaped complex that mediates protein folding in the cytosol without a cofactor. CCT particle GO:0005832 TriC cellular_component go.owl pro.owl heterotrimeric G-protein complex Any of a family of heterotrimeric GTP-binding and hydrolyzing proteins; they belong to a superfamily of GTPases that includes monomeric proteins such as EF-Tu and RAS. Heterotrimeric G-proteins consist of three subunits; the alpha subunit contains the guanine nucleotide binding site and possesses GTPase activity; the beta and gamma subunits are tightly associated and function as a beta-gamma heterodimer; extrinsic plasma membrane proteins (cytoplasmic face) that function as a complex to transduce signals from G-protein coupled receptors to an effector protein. GO:0005834 See also the molecular function term 'G-protein coupled receptor activity ; GO:0004930'. cellular_component go.owl heterotrimeric G-protein GTPase activity heterotrimeric G-protein GTPase, alpha-subunit heterotrimeric G-protein GTPase, beta-subunit heterotrimeric G-protein GTPase, gamma-subunit pro.owl mRNA cap binding complex Any protein complex that binds to an mRNA cap at any time in the lifetime of the mRNA. GO:0005845 cellular_component go.owl mRNA cap complex pro.owl mRNA cleavage stimulating factor complex A protein complex required for mRNA cleavage but not for poly(A) addition. CstF complex GO:0005848 cellular_component cleavage stimulation factor activity go.owl pro.owl mRNA cleavage factor complex Any macromolecular complex involved in cleavage or polyadenylation of mRNA molecules. GO:0005849 cellular_component eukaryotic translation initiation factor 2 complex Complex of three heterogeneous polypeptide chains, that form a ternary complex with initiator methionyl-tRNA and GTP. This ternary complex binds to free 40S subunit, which subsequently binds the 5' end of mRNA. GO:0005850 Wikipedia:EIF-2 cellular_component eIF-2 eIF2 go.owl pro.owl kinesin complex Any complex that includes a dimer of molecules from the kinesin superfamily, a group of related proteins that contain an extended region of predicted alpha-helical coiled coil in the main chain that likely produces dimerization. The native complexes of several kinesin family members have also been shown to contain additional peptides, often designated light chains as all of the noncatalytic subunits that are currently known are smaller than the chain that contains the motor unit. Kinesin complexes generally possess a force-generating enzymatic activity, or motor, which converts the free energy of the gamma phosphate bond of ATP into mechanical work. GO:0005871 cellular_component go.owl pro.owl minus-end kinesin complex Any complex that includes a dimer of molecules from the kinesin superfamily and any associated proteins, and moves towards the minus end of a microtubule. GO:0005872 cellular_component go.owl pro.owl plus-end kinesin complex Any complex that includes a dimer of molecules from the kinesin superfamily and any associated proteins, and moves towards the plus end of a microtubule. GO:0005873 cellular_component go.owl pro.owl microtubule associated complex Any multimeric complex connected to a microtubule. GO:0005875 cellular_component plasma membrane GO:0005886 GO:0005904 NIF_Subcellular:sao1663586795 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. Wikipedia:Cell_membrane bacterial inner membrane cell membrane cellular membrane cellular_component cytoplasmic membrane go.owl inner endospore membrane juxtamembrane plasma membrane lipid bilayer plasmalemma pro.owl acetylcholine-gated channel complex A homo- or hetero-pentameric protein complex that forms a transmembrane channel through which ions may pass in response to acetylcholine binding. GO:0005892 cellular_component go.owl nicotinic acetylcholine receptor nicotinic acetylcholine-gated receptor-channel complex pro.owl connexin complex An assembly of six molecules of connexin, made in the Golgi apparatus and subsequently transported to the plasma membrane, where docking of two connexons on apposed plasma membranes across the extracellular space forms a gap junction. GO:0005922 NIF_Subcellular:sao445019788 cellular_component connexon connexon complex go.owl pro.owl phosphatidylinositol 3-kinase complex 1-phosphatidylinositol 3-kinase complex A protein complex capable of phosphatidylinositol 3-kinase activity and containing subunits of any phosphatidylinositol 3-kinase (PI3K) enzyme. These complexes are divided in three classes (called I, II and III) that differ for their presence across taxonomic groups and for the type of their constituents. Catalytic subunits of phosphatidylinositol 3-kinase enzymes are present in all 3 classes; regulatory subunits of phosphatidylinositol 3-kinase enzymes are present in classes I and III; adaptor proteins have been observed in class II complexes and may be present in other classes too. For discussion of membrane association, please see https://sourceforge.net/p/geneontology/ontology-requests/11559/ GO:0005942 PI3-kinase p85-subunit alpha- PI3-kinase p110 complex PI3K complex PIK3C3-PIK3R4 complex PIK3CA-PIK3R1 complex cellular_component go.owl phosphoinositide 3-kinase complex pro.owl 6-phosphofructokinase complex A protein complex that possesses 6-phosphofructokinase activity; homodimeric, homooctameric, and allosteric homotetrameric forms are known. GO:0005945 cellular_component go.owl pro.owl CAAX-protein geranylgeranyltransferase complex A heterodimeric enzyme, composed of an alpha and a beta subunit. Participates in the post-translational C-terminal modification of several small GTPases, allowing their targeting to the membrane. GO:0005953 cellular_component go.owl pro.owl protein kinase CK2 complex A protein complex that possesses protein serine/threonine kinase activity, and contains two catalytic alpha subunits and two regulatory beta subunits. Protein kinase CK2 complexes are found in nearly every subcellular compartment, and can phosphorylate many protein substrates in addition to casein. GO:0005956 Note that this term represents a location and not a function; the activity possessed by this complex is mentioned in the definition for the purpose of describing and distinguishing the complex. casein kinase II complex cellular_component go.owl pro.owl mitochondrial isocitrate dehydrogenase complex (NAD+) GO:0005962 Mitochondrial complex that possesses isocitrate dehydrogenase (NAD+) activity. Note that this term represents a location and not a function; the activity possessed by this complex is mentioned in the definition for the purpose of describing and distinguishing the complex. The function of this complex is represented by the molecular function term 'isocitrate dehydrogenase (NAD+) activity ; GO:0004449'. cellular_component go.owl pro.owl phosphorylase kinase complex An enzyme complex that catalyzes the phosphorylation of phosphorylase b to form phosphorylase a. GO:0005964 cellular_component go.owl pro.owl protein farnesyltransferase complex A protein complex that possesses protein farnesyltransferase activity. GO:0005965 cellular_component go.owl pro.owl ribonucleoside-diphosphate reductase complex An enzyme complex composed of 2-4 or more subunits, which usually contains nonheme iron and requires ATP for catalysis. Catalyzes the formation of 2'-deoxyribonucleoside diphosphate from ribonucleoside diphosphate, using either thioredoxin disulfide or glutaredoxin disulfide as an acceptor. GO:0005971 RNR complex cellular_component go.owl pro.owl ribonucleotide reductase complex carbohydrate metabolic process GO:0005975 Reactome:REACT_102834 Reactome:REACT_103806 Reactome:REACT_104502 Reactome:REACT_105321 Reactome:REACT_106046 Reactome:REACT_107409 Reactome:REACT_115733 Reactome:REACT_28218 Reactome:REACT_32291 Reactome:REACT_33141 Reactome:REACT_33953 Reactome:REACT_34800 Reactome:REACT_474 Reactome:REACT_77669 Reactome:REACT_81945 Reactome:REACT_83038 Reactome:REACT_83329 Reactome:REACT_88330 Reactome:REACT_88558 Reactome:REACT_90099 Reactome:REACT_96375 Reactome:REACT_98394 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule. Wikipedia:Carbohydrate_metabolism biological_process carbohydrate metabolism monosaccharide metabolic process GO:0005996 The chemical reactions and pathways involving monosaccharides, the simplest carbohydrates. They are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides. biological_process monosaccharide metabolism glucose metabolic process GO:0006006 Reactome:REACT_101127 Reactome:REACT_101310 Reactome:REACT_102479 Reactome:REACT_102806 Reactome:REACT_104683 Reactome:REACT_105053 Reactome:REACT_106618 Reactome:REACT_29390 Reactome:REACT_30713 Reactome:REACT_30754 Reactome:REACT_32548 Reactome:REACT_723 Reactome:REACT_80637 Reactome:REACT_81545 Reactome:REACT_85067 Reactome:REACT_85844 Reactome:REACT_94241 Reactome:REACT_97466 Reactome:REACT_98401 Reactome:REACT_98764 Reactome:REACT_99558 The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides. biological_process cellular glucose metabolic process glucose metabolism go.owl obi.owl nucleobase-containing compound metabolic process Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. GO:0006139 GO:0055134 biological_process cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism nucleobase, nucleoside and nucleotide metabolic process nucleobase, nucleoside, nucleotide and nucleic acid metabolic process nucleobase, nucleoside, nucleotide and nucleic acid metabolism DNA metabolic process Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. DNA metabolism GO:0006259 GO:0055132 biological_process cellular DNA metabolism DNA replication DNA biosynthesis is only part of this process. See also the biological process terms 'DNA-dependent DNA replication ; GO:0006261' and 'RNA-dependent DNA replication ; GO:0006278'. GO:0006260 GO:0055133 Reactome:REACT_100559 Reactome:REACT_101280 Reactome:REACT_101497 Reactome:REACT_102679 Reactome:REACT_103614 Reactome:REACT_104547 Reactome:REACT_105292 Reactome:REACT_105467 Reactome:REACT_105835 Reactome:REACT_106018 Reactome:REACT_106104 Reactome:REACT_106382 Reactome:REACT_106434 Reactome:REACT_106732 Reactome:REACT_107075 Reactome:REACT_107423 Reactome:REACT_108461 Reactome:REACT_108634 Reactome:REACT_108739 Reactome:REACT_108768 Reactome:REACT_108929 Reactome:REACT_109137 Reactome:REACT_112472 Reactome:REACT_113703 Reactome:REACT_29423 Reactome:REACT_29444 Reactome:REACT_29691 Reactome:REACT_29764 Reactome:REACT_30149 Reactome:REACT_31024 Reactome:REACT_31919 Reactome:REACT_32546 Reactome:REACT_32932 Reactome:REACT_33572 Reactome:REACT_33874 Reactome:REACT_50018 Reactome:REACT_53588 Reactome:REACT_6729 Reactome:REACT_6738 Reactome:REACT_6750 Reactome:REACT_6769 Reactome:REACT_6798 Reactome:REACT_6869 Reactome:REACT_6936 Reactome:REACT_6939 Reactome:REACT_77532 Reactome:REACT_79188 Reactome:REACT_79450 Reactome:REACT_80432 Reactome:REACT_80571 Reactome:REACT_80896 Reactome:REACT_80988 Reactome:REACT_81803 Reactome:REACT_83095 Reactome:REACT_84829 Reactome:REACT_85561 Reactome:REACT_86410 Reactome:REACT_86739 Reactome:REACT_87233 Reactome:REACT_87449 Reactome:REACT_87590 Reactome:REACT_88085 Reactome:REACT_88384 Reactome:REACT_88529 Reactome:REACT_89355 Reactome:REACT_89439 Reactome:REACT_89725 Reactome:REACT_90512 Reactome:REACT_90809 Reactome:REACT_90838 Reactome:REACT_91184 Reactome:REACT_91302 Reactome:REACT_92527 Reactome:REACT_92644 Reactome:REACT_92706 Reactome:REACT_94983 Reactome:REACT_95253 Reactome:REACT_95329 Reactome:REACT_96115 Reactome:REACT_96804 Reactome:REACT_96998 Reactome:REACT_97204 Reactome:REACT_97726 Reactome:REACT_99948 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. Wikipedia:DNA_replication biological_process go.owl obi.owl DNA modification GO:0006304 The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties. biological_process DNA alkylation GO:0006305 The addition of alkyl groups to many positions on all four bases of DNA. Alkylating agents can also modify the bases of incoming nucleotides in the course of DNA synthesis. biological_process DNA methylation GO:0006306 The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. Wikipedia:DNA_methylation biological_process go.owl obi.owl chromatin organization Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin. GO:0006325 GO:0016568 biological_process chromatin modification chromatin organisation establishment or maintenance of chromatin architecture chromatin remodeling Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation. GO:0006338 biological_process chromatin modeling chromatin modelling chromatin remodelling go.owl obi.owl protein complex assembly GO:0006461 The aggregation, arrangement and bonding together of a set of components to form a protein complex. biological_process chaperone activity protein complex formation cellular protein modification process GO:0006464 The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification). biological_process process resulting in protein modification protein modification process protein tagging activity cellular aromatic compound metabolic process GO:0006725 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 aromatic hydrocarbon metabolic process aromatic hydrocarbon metabolism biological_process nitrogen compound metabolic process GO:0006807 Note that amino acid and derivative metabolism should not be annotated here. Instead use the 'amino acid and derivative metabolism' node. The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen, including (but not limited to) nitrogen fixation, nitrification, denitrification, assimilatory/dissimilatory nitrate reduction and the interconversion of nitrogenous organic matter and ammonium. biological_process nitrogen compound metabolism transport GO:0006810 GO:0015457 GO:0015460 The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. auxiliary transport protein activity biological_process small molecule transport solute:solute exchange transport accessory protein activity ion transport GO:0006811 Reactome:REACT_102356 Reactome:REACT_102895 Reactome:REACT_106972 Reactome:REACT_109067 Reactome:REACT_110862 Reactome:REACT_19397 Reactome:REACT_29110 Reactome:REACT_31978 Reactome:REACT_33992 Reactome:REACT_34201 Reactome:REACT_79109 Reactome:REACT_82618 Reactome:REACT_87822 Reactome:REACT_91472 Reactome:REACT_91958 Reactome:REACT_92903 Reactome:REACT_93485 Reactome:REACT_94357 Reactome:REACT_96078 Reactome:REACT_96919 Reactome:REACT_98077 The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process cation transport GO:0006812 GO:0006819 GO:0015674 The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process di-, tri-valent inorganic cation transport exocytosis A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. GO:0006887 GO:0016194 GO:0016195 Wikipedia:Exocytosis biological_process nonselective vesicle exocytosis vesicle exocytosis endocytosis A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle. GO:0006897 GO:0016193 GO:0016196 Wikipedia:Endocytosis biological_process nonselective vesicle endocytosis plasma membrane invagination vesicle endocytosis phagocytosis An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles. GO:0006909 Wikipedia:Phagocytosis biological_process go.owl obi.owl movement of cell or subcellular component GO:0006928 Note that in GO cellular components include whole cells (cell is_a cellular component). The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore. biological_process cell movement cellular component motion cellular component movement response to stress 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 disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). GO:0006950 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. biological_process response to abiotic stress response to biotic stress defense response GO:0002217 GO:0006952 GO:0042829 Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack. antimicrobial peptide activity biological_process defence response defense/immunity protein activity physiological defense response inflammatory response GO:0006954 Inflammation The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. This term was improved by GO_REF:0000022. It was moved. Wikipedia:Inflammation biological_process immune response Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. GO:0006955 This term was improved by GO_REF:0000022. It was redefined and moved. biological_process go.owl obi.owl cellular response to DNA damage 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 indicating damage to its DNA from environmental insults or errors during metabolism. DNA damage response GO:0006974 GO:0034984 biological_process cellular DNA damage response go.owl obi.owl response to DNA damage stimulus response to genotoxic stress organelle organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GO:0006996 biological_process organelle organisation organelle organization and biogenesis actin filament organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking. GO:0007015 actin filament organisation biological_process regulation of actin filament localization cell cycle GO:0007049 The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. Wikipedia:Cell_cycle biological_process cell-division cycle go.owl obi.owl blood coagulation GO:0007596 Reactome:REACT_101311 Reactome:REACT_101372 Reactome:REACT_102544 Reactome:REACT_102650 Reactome:REACT_105166 Reactome:REACT_105212 Reactome:REACT_107268 Reactome:REACT_108583 Reactome:REACT_113650 Reactome:REACT_114152 Reactome:REACT_118351 Reactome:REACT_1439 Reactome:REACT_2051 Reactome:REACT_32530 Reactome:REACT_32765 Reactome:REACT_33270 Reactome:REACT_34525 Reactome:REACT_604 Reactome:REACT_76944 Reactome:REACT_78290 Reactome:REACT_81054 Reactome:REACT_81972 Reactome:REACT_82283 Reactome:REACT_82383 Reactome:REACT_82403 Reactome:REACT_82445 Reactome:REACT_82812 Reactome:REACT_82940 Reactome:REACT_83271 Reactome:REACT_84055 Reactome:REACT_84833 Reactome:REACT_85674 Reactome:REACT_86354 Reactome:REACT_89750 Reactome:REACT_89805 Reactome:REACT_90236 Reactome:REACT_90805 Reactome:REACT_92318 Reactome:REACT_94085 Reactome:REACT_94213 Reactome:REACT_94315 Reactome:REACT_94798 Reactome:REACT_96458 The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers. Wikipedia:Coagulation biological_process blood clotting go.owl obi.owl hemostasis GO:0007599 The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part. Wikipedia:Hemostasis biological_process transcription elongation factor complex Any protein complex that interacts with RNA polymerase II to increase (positive transcription elongation factor) or reduce (negative transcription elongation factor) the rate of transcription elongation. GO:0008023 cellular_component cyclin/CDK positive transcription elongation factor complex A transcription elongation factor complex that facilitates the transition from abortive to productive elongation by phosphorylating the CTD domain of the large subunit of DNA-directed RNA polymerase II, holoenzyme. Contains a cyclin and a cyclin-dependent protein kinase catalytic subunit. GO:0008024 See also the cellular component terms 'cyclin-dependent protein kinase activating kinase holoenzyme complex ; GO:0019907' and 'DNA-directed RNA polymerase II, holoenzyme ; GO:0016591'. cellular_component go.owl positive transcription elongation factor complex b pro.owl biological_process Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. GO:0000004 GO:0007582 GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. Wikipedia:Biological_process biological process biological_process go.owl obi.owl physiological process metabolic process GO:0008152 Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. 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 biological_process metabolic process resulting in cell growth metabolism metabolism resulting in cell growth actin polymerization or depolymerization Assembly or disassembly of actin filaments by the addition or removal of actin monomers from a filament. GO:0008154 biological_process opsonization GO:0008228 The process in which a microorganism (or other particulate material) is rendered more susceptible to phagocytosis by coating with an opsonin, a blood serum protein such as a complement component or antibody. Wikipedia:Opsonin biological_process go.owl obi.owl cohesin complex 14S cohesin 9S cohesin A protein complex that is required for sister chromatid cohesion in eukaryotes. The cohesin complex forms a molecular ring complex, and is composed of structural maintenance of chromosomes (SMC) and kleisin proteins. For example, in yeast, the complex is composed of the SMC proteins Smc1p and Smc3p, and the kleisin protein Scc1p. In vertebrates, the complex is composed of the SMC1 (SMC1A or SMC1B) and SMC3 heterodimer attached via their hinge domains to a kleisin (RAD21, REC8 or RAD21L) which links them, and one STAG protein (STAG1, STAG2 or STAG3). GO:0008278 GO:0008279 GO:0008280 GO:0043222 SMC complex SMC/kleisin ring complex Smc1-Smc3 complex cellular_component cohesin core heterodimer go.owl pro.owl cell proliferation GO:0008283 The multiplication or reproduction of cells, resulting in the expansion of a cell population. This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms. biological_process go.owl obi.owl F-actin capping protein complex A heterodimer consisting of alpha and beta subunits that binds to and caps the barbed ends of actin filaments, thereby regulating the polymerization of actin monomers but not severing actin filaments. GO:0008290 cellular_component go.owl pro.owl caspase complex A protein complex that is located in the cytosol and contains one or more cysteine-type endopeptidases (also called caspases), which give the complex a peptidase activity with specificity for the hydrolysis of aspartyl bonds. These complexes may be involved e.g. in apoptotic or inflammation processes. GO:0008303 Note that this term was reinstated from obsolete. cellular_component cysteine-type endopeptidase complex go.owl pro.owl integrin complex A protein complex that is composed of one alpha subunit and one beta subunit, both of which are members of the integrin superfamily of cell adhesion receptors; the complex spans the plasma membrane and binds to extracellular matrix ligands, cell-surface ligands, and soluble ligands. GO:0008305 cellular_component go.owl laminin receptor protein pro.owl IkappaB kinase complex A trimeric protein complex that phosphorylates inhibitory-kappaB (I-kappaB) proteins. The complex is composed of two kinase subunits (alpha and beta) and a regulatory gamma subunit (also called NEMO). In a resting state, NF-kappaB dimers are bound to inhibitory IKB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription. GO:0008385 IKK complex cellular_component go.owl heterotrimeric IKK complex pro.owl trimeric IKK complex biosynthetic process GO:0009058 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 biological_process biosynthesis formation synthesis macromolecule biosynthetic process GO:0009059 GO:0043284 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. biological_process biopolymer biosynthetic process macromolecule anabolism macromolecule biosynthesis macromolecule formation macromolecule synthesis ornithine carbamoyltransferase complex A homotrimeric protein complex that catalyzes the transfer of a carbamoyl group to ornithine, forming citrulline. GO:0009348 cellular_component go.owl pro.owl riboflavin synthase complex An flavoprotein that catalyzes the reaction the breakdown of dimethyl(ribityl)lumazine to form riboflavin and ribitylamino-amino-dihydroxypyrimidine. GO:0009349 cellular_component go.owl pro.owl fertilization GO:0009566 The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). Wikipedia:Fertilisation biological_process go.owl obi.owl syngamy hormone transport GO:0009914 The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_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. GO:0008151 GO:0009987 GO:0050875 biological_process cell growth and/or maintenance cell physiology cellular physiological process go.owl obi.owl endosome membrane GO:0010008 NIF_Subcellular:sao978443756 The lipid bilayer surrounding an endosome. cellular_component endosomal membrane go.owl pro.owl gene expression GO:0010467 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 or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. Wikipedia:Gene_expression biological_process go.owl obi.owl 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 or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. GO:0010468 This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availability of mRNA or circRNA for translation and thereby regulates the rate of production of the encoded protein via translation. Wikipedia:Regulation_of_gene_expression biological_process regulation of gene product expression regulation of protein expression vascular endothelial growth factor production GO:0010573 The appearance of vascular endothelial growth factor production due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. VEGF production biological_process go.owl obi.owl regulation of hormone levels Any process that modulates the levels of hormone within an organism or a tissue. A hormone is any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. GO:0010817 biological_process ion transmembrane transporter activity Enables the transfer of an ion from one side of a membrane to the other. GO:0015075 ion transporter activity molecular_function channel activity Enables the energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules. GO:0015249 GO:0015267 GO:0015268 TC:1 alpha-type channel activity channel-forming toxin activity channel/pore class transporter activity molecular_function nonselective channel activity pore activity pore class transporter activity ammonium transport GO:0015696 The directed movement of ammonium into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Ammonium is the cation NH4+ which is formed from N2 by root-nodule bacteria in leguminous plants and is an excretory product in ammonotelic animals. ammonia transport biological_process membrane A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. GO:0016020 Wikipedia:Biological_membrane cellular_component cellular component organization A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GO:0016043 GO:0044235 GO:0071842 biological_process cell organisation cell organization and biogenesis cellular component organisation at cellular level cellular component organisation in other organism cellular component organization at cellular level cellular component organization in other organism immunoglobulin mediated immune response An immune response mediated by immunoglobulins, whether cell-bound or in solution. GO:0016064 This term was improved by GO_REF:0000022. It was renamed and redefined. antibody-mediated immune response biological_process go.owl obi.owl vesicle-mediated transport A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. GO:0006899 GO:0016192 biological_process nonselective vesicle transport protein sorting along secretory pathway vesicle trafficking vesicle transport vesicular transport prefoldin complex A multisubunit chaperone that is capable of delivering unfolded proteins to cytosolic chaperonin, which it acts as a cofactor for. In humans, the complex is a heterohexamer of two PFD-alpha and four PFD-beta type subunits. In Saccharomyces cerevisiae, it also acts in the nucleus to regulate the rate of elongation by RNA polymerase II via a direct effect on histone dynamics. GIM complex GO:0016272 Wikipedia:Prefoldin cellular_component go.owl pro.owl mitochondrial fatty acid beta-oxidation multienzyme complex A complex that includes the long-chain 3-hydroxyacyl-CoA dehydrogenase and long-chain enoyl-CoA hydratase activities in two subunits (alpha and beta), catalyzing two steps of the fatty acid beta-oxidation cycle within the mitochondrial matrix. GO:0016507 cellular_component fatty acid beta-oxidation multienzyme complex go.owl pro.owl trifunctional enzyme cyclin-dependent protein kinase 5 holoenzyme complex A protein complex that activates cyclin-dependent kinase 5; composed of regulatory and catalytic subunits. GO:0016533 cellular_component go.owl pro.owl covalent chromatin modification GO:0016569 The alteration of DNA or protein in chromatin by the covalent addition or removal of chemical groups. biological_process chromatin modification histone modification GO:0016570 The covalent alteration of one or more amino acid residues within a histone protein. Wikipedia:Histone#Histone_modifications_in_chromatin_regulation biological_process go.owl obi.owl mediator complex A protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The mediator complex is required for activation of transcription of most protein-coding genes, but can also act as a transcriptional corepressor. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins. CDK8-containing TRAP/mediator complex GO:0000119 GO:0016592 L mediator complex Srb-mediator complex TRAP complex Wikipedia:Mediator_(coactivator) cellular_component go.owl pro.owl transferase activity Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. EC:2 GO:0016740 Reactome:REACT_25050 molecular_function transferase activity, transferring phosphorus-containing groups Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). EC:2.7 GO:0016772 Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. molecular_function nucleotidyltransferase activity Catalysis of the transfer of a nucleotidyl group to a reactant. EC:2.7.7 GO:0016779 molecular_function transcriptional repressor complex A protein complex that possesses activity that prevents or downregulates transcription. GO:0017053 cellular_component transcription factor inhibitor complex serine C-palmitoyltransferase complex An enzyme complex that catalyzes the transfer of a palmitoyl on to serine, forming 3-dehydro-D-sphinganine. GO:0017059 cellular_component go.owl pro.owl aminoacyl-tRNA synthetase multienzyme complex A multienzyme complex found in all multicellular eukaryotes composed of eight proteins with aminoacyl-tRNA synthetase activities (abbreviated as: ArgRS, AspRS, GluProRS, GlnRS, IleRS, LeuRS, LysRS, MetRS where RS is the enzyme, preceded by the amino acid it uses as a substrate) as well as three non-synthetase proteins (p43, p38, and p18) with diverse functions. Several of these subunits are known dimers, so the total polypeptide count in the multisynthetase complex is at least fifteen. All of the enzymes in this assembly catalyze the same reaction, the covalent attachment of an amino acid to either the 2'- or 3'-hydroxyl of the 3'-terminal adenosine of tRNA, but using different substrates. GO:0017101 aminoacyl-tRNA synthetase complex cellular_component go.owl multisynthetase complex pro.owl glutamate-cysteine ligase complex An enzyme complex that catalyzes the ligation of glutamate to cysteine, forming glutamylcysteine. GO:0017109 cellular_component gamma-glutamylcysteine synthetase complex go.owl pro.owl SCF ubiquitin ligase complex A ubiquitin ligase complex in which a cullin from the Cul1 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by a Skp1 adaptor and an F-box protein. SCF complexes are involved in targeting proteins for degradation by the proteasome. The best characterized complexes are those from yeast and mammals (with core subunits named Cdc53/Cul1, Rbx1/Hrt1/Roc1). CDL1 complex CRL1 complex Cul1-RING ubiquitin ligase complex GO:0019005 SCF complex SCF complex substrate recognition subunit Skp1/Cul1/F-box protein complex Wikipedia:SCF_complex cellular_component cullin-RING ligase 1 go.owl pro.owl snRNA-activating protein complex A protein complex that recognizes the proximal sequence element of RNA polymerase II and III snRNA promoters. GO:0019185 SNAPc cellular_component go.owl pro.owl 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. GO:0019219 biological_process regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process 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. GO:0019222 biological_process regulation of metabolism hexose metabolic process GO:0019318 The chemical reactions and pathways involving a hexose, any monosaccharide with a chain of six carbon atoms in the molecule. biological_process hexose metabolism protein metabolic process GO:0006411 GO:0019538 The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification. Wikipedia:Protein_metabolism biological_process protein metabolic process and modification protein metabolism protein metabolism and modification B cell mediated immunity Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells. B lymphocyte mediated immune effector process B lymphocyte mediated immunity B-cell mediated immune effector process B-cell mediated immunity B-lymphocyte mediated immune effector process B-lymphocyte mediated immunity GO:0019724 This term was improved by GO_REF:0000022. It was moved. biological_process immunoglobulin complex A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. GO:0019814 Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. cellular_component go.owl obi.owl B cell receptor complex An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. B cell receptor accessory molecule complex B lymphocyte receptor complex B-cell receptor complex B-lymphocyte receptor complex BCR complex GO:0019815 GO:0042570 Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. antibody cellular_component go.owl immunoglobulin complex, membrane bound obi.owl antigen processing and presentation GO:0019882 GO:0030333 The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. This term was improved by GO_REF:0000022. It was renamed and redefined. Wikipedia:Antigen_presentation antigen presentation antigen processing biological_process go.owl obi.owl protein domain specific binding GO:0019904 Interacting selectively and non-covalently with a specific domain of a protein. go.owl molecular_function obi.owl protein domain-specific binding cyclin-dependent protein kinase activating kinase holoenzyme complex A cyclin-dependent kinase activating kinase complex capable of activating cyclin-dependent kinases by threonine phosphorylation, thus regulating cell cycle progression. consists of a kinase, cyclin and optional assembly factors, in human CDK7, CCNH and MNAT1. CAK activity is itself regulated throughout the cell cycle by T-loop phosphorylation of its kinase component (CDK7 in human). Phosphorylation of serine residues during mitosis inactivates the enzyme. Also capable of CAK phosphorylating the carboxyl-terminal domain (CTD) of RNA polymerase II and other transcription activating proteins, as part of the general transcription factor TFIIH. CAK complex CDK-activating kinase complex GO:0019907 IntAct:EBI-1246076 IntAct:EBI-9868598 cellular_component go.owl pro.owl nuclear cyclin-dependent protein kinase holoenzyme complex CDK holoenzyme Cyclin-dependent protein kinase (CDK) complex found in the nucleus. GO:0019908 cellular_component reproductive process A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. GO:0022414 biological_process cellular component assembly GO:0022607 GO:0071844 The aggregation, arrangement and bonding together of a cellular component. biological_process cell structure assembly cellular component assembly at cellular level passive transmembrane transporter activity Enables the transfer of a solute from one side of the membrane to the other, down the solute's concentration gradient. GO:0022803 Reactome:REACT_118066 Reactome:REACT_118091 Reactome:REACT_118204 Reactome:REACT_118231 Reactome:REACT_118327 Reactome:REACT_118347 Reactome:REACT_118350 Reactome:REACT_118478 Reactome:REACT_118490 Reactome:REACT_118544 Reactome:REACT_19251 molecular_function substrate-specific channel activity Enables the energy-independent facilitated diffusion, mediated by passage of a specific solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules. GO:0022838 molecular_function transmembrane transporter activity Enables the transfer of a substance from one side of a membrane to the other. GO:0005386 GO:0015646 GO:0022857 Reactome:REACT_100033 Reactome:REACT_106735 Reactome:REACT_111088 Reactome:REACT_111933 Reactome:REACT_113047 Reactome:REACT_113116 Reactome:REACT_113829 Reactome:REACT_114161 Reactome:REACT_19288 Reactome:REACT_77235 Reactome:REACT_81225 Reactome:REACT_88503 Reactome:REACT_91849 Reactome:REACT_94185 molecular_function substrate-specific transmembrane transporter activity Enables the transfer of a specific substance or group of related substances from one side of a membrane to the other. GO:0022891 molecular_function substrate-specific transporter activity Enables the directed movement of a specific substance or group of related substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells. GO:0022892 molecular_function signal release 2010-02-16T09:30:50Z GO:0023061 The process in which a signal is secreted or discharged into the extracellular medium from a cellular source. biological_process signal secretion actin filament polymerization Assembly of actin filaments by the addition of actin monomers to a filament. GO:0030041 actin polymerization actin polymerizing activity biological_process go.owl obi.owl mitochondrial tricarboxylic acid cycle enzyme complex Any of the heteromeric enzymes, located in the mitochondrion, that act in the tricarboxylic acid (TCA) cycle. GO:0030062 TCA cycle enzyme complex cellular_component hemopoiesis GO:0030097 The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates. Wikipedia:Haematopoiesis biological_process blood cell biosynthesis blood cell formation go.owl haemopoiesis hematopoiesis obi.owl membrane coat Any of several different proteinaceous coats that can associate with membranes. Membrane coats include those formed by clathrin plus an adaptor complex, the COPI and COPII complexes, and possibly others. They are found associated with membranes on many vesicles as well as other membrane features such as pits and perhaps tubules. GO:0030117 cellular_component vesicle coat A membrane coat found on a coated vesicle. GO:0030120 NIF_Subcellular:sao1177708494 cellular_component COPI vesicle coat GO:0017167 GO:0030126 One of two multimeric complexes that forms a membrane vesicle coat. The mammalian COPI subunits are called alpha-, beta-, beta'-, gamma-, delta-, epsilon- and zeta-COP. Vesicles with COPI coats are found associated with Golgi membranes at steady state. cellular_component coatomer go.owl pro.owl RNA polymerase complex Any complex that possesses RNA polymerase activity; generally comprises a catalytic subunit and one or more additional subunits. GO:0030880 cellular_component go.owl multisubunit RNA polymerase pro.owl ISWI-type complex Any nuclear protein complex that contains an ATPase subunit of the imitation switch (ISWI) family. ISWI ATPases are involved in assembling chromatin and in sliding and spacing nucleosomes to regulate transcription of nuclear RNA polymerases I, II, and III and also DNA replication, recombination and repair. GO:0031010 cellular_component go.owl pro.owl organelle membrane A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. GO:0031090 NIF_Subcellular:sao830981606 cellular_component intracellular membrane endoplasmic reticulum palmitoyltransferase complex A complex of the endoplasmic reticulum that catalyzes S-palmitoylation, the addition of palmitate (C16:0) or other long-chain fatty acids to proteins at a cysteine residue. GO:0031211 cellular_component go.owl pro.owl death-inducing signaling complex A protein complex formed by the association of signaling proteins with a death receptor upon ligand binding. The complex includes procaspases and death domain-containing proteins in addition to the ligand-bound receptor, and may control the activation of caspases 8 and 10. DISC DISC protein complex GO:0031264 Gene products that may be annotated to this term include: 1) ligand-bound receptors such as FAS/CD95 (though care should be taken because FAS can also act as a non-apoptotic signal transducer); 2) signaling molecules such as FADD (FAS-associated protein with a death domain), cIAPs (cellular inhibitor of apoptosis proteins), c-FLIPs and caspases 8 and 10. Wikipedia:Death-inducing_signaling_complex cellular_component death receptor-induced signaling complex death receptor-induced signalling complex death-inducing signalling complex go.owl pro.owl 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. GO:0031323 biological_process regulation of cellular metabolism cullin-RING ubiquitin ligase complex Any ubiquitin ligase complex in which the catalytic core consists of a member of the cullin family and a RING domain protein; the core is associated with one or more additional proteins that confer substrate specificity. CRL complex GO:0031461 cellular_component cullin complex cullin-RING ligase go.owl pro.owl mannosyltransferase complex A complex that posseses mannosyltransferase activity. GO:0031501 cellular_component go.owl pro.owl TORC2 complex A protein complex that contains at least TOR (target of rapamycin) and Rictor (rapamycin-insensitive companion of TOR), or orthologs of, in complex with other signaling components. Mediates the phosphorylation and activation of PKB (also called AKT). In Saccharomyces, the complex contains Avo1p, Avo2p, Tsc11p, Lst8p, Bit61p, Slm1p, Slm2p, and Tor2p. GO:0031932 TOR complex 2 TORC 2 complex TORC2 Wikipedia:MTORC1 cellular_component go.owl mTORC2 pro.owl rapamycin and nutrient-insensitive TOR complex 4-aminobutyrate transaminase complex A homodimeric protein complex that possesses 4-aminobutyrate transaminase activity. ABAT complex GABA transaminase complex GABA-T complex GO:0032144 cellular_component go.owl pro.owl methylation GO:0032259 Reactome:REACT_100463 Reactome:REACT_104378 Reactome:REACT_106986 Reactome:REACT_107353 Reactome:REACT_107808 Reactome:REACT_110691 Reactome:REACT_34638 Reactome:REACT_6946 Reactome:REACT_77304 Reactome:REACT_78116 Reactome:REACT_87183 Reactome:REACT_88148 Reactome:REACT_90436 Reactome:REACT_92149 Reactome:REACT_92596 Reactome:REACT_93357 Reactome:REACT_95391 Reactome:REACT_98332 Reactome:REACT_99471 Reactome:REACT_99529 The process in which a methyl group is covalently attached to a molecule. Wikipedia:Methylation biological_process ribonuclease H2 complex A protein complex that possesses ribonuclease H activity, in which the catalytic subunit is a member of the RNase H2 (or HII) class. For example, in Saccharomyces the complex contains Rnh201p, Rnh202p and Rnh203p. GO:0032299 RNase H2 complex cellular_component go.owl pro.owl multicellular organismal process Any biological process, occurring at the level of a multicellular organism, pertinent to its function. GO:0032501 GO:0050874 biological_process organismal physiological process developmental process A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. GO:0032502 biological_process development connective tissue growth factor production CCN2 production CTGF production Fisp12 production GO:0032601 Hcs24 production IGFBP8 production The appearance of connective tissue growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl hypertrophic chondrocyte-specific gene product 24 production obi.owl chemokine production GO:0032602 The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl granulocyte macrophage colony-stimulating factor production GM-CSF production GO:0032604 The appearance of granulocyte macrophage colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl granulocyte macrophage colony stimulating factor production obi.owl hepatocyte growth factor production GO:0032605 The appearance of hepatocyte growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl type I interferon production GO:0032606 The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. biological_process go.owl interferon type I production obi.owl type I IFN production interferon-beta production GO:0032608 IFN-beta production IFNB production The appearance of interferon-beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interferon-gamma production GO:0032609 IFNG production The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon. biological_process go.owl obi.owl type II IFN production type II interferon production interleukin-1 alpha production GO:0032610 IL-1 alpha production The appearance of interleukin-1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-1 beta production GO:0032611 IL-1 beta production The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-1 production GO:0032612 IL-1 production The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-10 production GO:0032613 IL-10 production The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-11 production GO:0032614 IL-11 production The appearance of interleukin-11 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-12 production GO:0032615 IL-12 production The appearance of interleukin-12 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-13 production GO:0032616 IL-13 production The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-14 production GO:0032617 IL-14 production The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-15 production GO:0032618 IL-15 production The appearance of interleukin-15 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-16 production GO:0032619 IL-16 production The appearance of interleukin-16 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-17 production GO:0032620 IL-17 production The appearance of any member of the interleukin-17 family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-18 production GO:0032621 IL-18 production The appearance of interleukin-18 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-19 production GO:0032622 IL-19 production The appearance of interleukin-19 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-2 production GO:0032623 IL-2 production The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-20 production GO:0032624 IL-20 production The appearance of interleukin-20 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-21 production GO:0032625 IL-21 production The appearance of interleukin-21 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-22 production GO:0032626 IL-22 production The appearance of interleukin-22 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-23 production GO:0032627 IL-23 production The appearance of interleukin-23 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-24 production GO:0032628 IL-24 production The appearance of interleukin-24 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-25 production GO:0032629 IL-25 production The appearance of interleukin-25 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-26 production GO:0032630 IL-26 production The appearance of interleukin-26 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-27 production GO:0032631 IL-27 production The appearance of interleukin-27 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-3 production GO:0032632 IL-3 production The appearance of interleukin-3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-4 production GO:0032633 IL-4 production The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-5 production GO:0032634 IL-5 production The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-6 production GO:0032635 IL-6 production The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-7 production GO:0032636 IL-7 production The appearance of interleukin-7 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-8 production GO:0032637 IL-8 production The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl interleukin-9 production GO:0032638 IL-9 production The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl TRAIL production GO:0032639 The appearance of TRAIL due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl tumor necrosis factor production GO:0032640 Note that this term refers only to the specific, original 'tumor necrosis factor' protein (TNF) and not other members of the tumor necrosis factor superfamily (those with the gene symbol root 'TNFSF'). TNF production TNF-alpha production The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl tumor necrosis factor-alpha production lymphotoxin A production GO:0032641 LTA production TNF-beta production The appearance of lymphotoxin A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl lymphotoxin-alpha production obi.owl tumor necrosis factor-beta production carboxy-terminal domain protein kinase complex A protein complex that phosphorylates amino acid residues of RNA polymerase II C-terminal domain repeats; phosphorylation occurs mainly on Ser2 and Ser5. CTDK complex GO:0032806 cellular_component transforming growth factor beta1 production GO:0032905 TGF-B1 production TGFB1 production The appearance of transforming growth factor-beta1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl transforming growth factor-beta1 production transforming growth factor beta2 production GO:0032906 TGF-B2 production TGFB2 production The appearance of transforming growth factor-beta2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl transforming growth factor-beta2 production transforming growth factor beta3 production GO:0032907 TGF-B3 production TGFB3 production The appearance of transforming growth factor-beta3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl transforming growth factor-beta3 production secretion by cell GO:0032940 The controlled release of a substance by a cell. Wikipedia:Secretion biological_process cellular secretion mononuclear cell proliferation GO:0032943 PBMC proliferation The expansion of a mononuclear cell population by cell division. A mononuclear cell is a leukocyte with a single non-segmented nucleus in the mature form. biological_process peripheral blood mononuclear cell proliferation macromolecular complex A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. GO:0032991 cellular_component go.owl macromolecule complex pro.owl protein containing complex protein-DNA complex A macromolecular complex containing both protein and DNA molecules. DNA-protein complex GO:0032993 Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here. cellular_component go.owl pro.owl Bcl3-Bcl10 complex A protein complex containing Bcl3 and Bcl10, which forms when Akt1 is activated by TNF-alpha to phosphorylate Bcl10; the Bcl3-Bcl10 complex is translocated to the nucleus. GO:0032996 cellular_component go.owl pro.owl macromolecule localization Any process in which a macromolecule is transported to, or maintained in, a specific location. GO:0033036 biological_process go.owl macromolecule localisation obi.owl dolichol-phosphate-mannose synthase complex A protein complex that possesses dolichyl-phosphate beta-D-mannosyltransferase activity; contains a catalytic subunit, a regulatory subunit, and a third subunit that stabilizes the complex. In human and several other metazoa, the subunits are named DPM1, DPM2 and DPM3, respectively. DPM synthase complex GO:0033185 cellular_component dolichyl-phosphate beta-D-mannosyltransferase complex go.owl pro.owl amide binding GO:0033218 Interacting selectively and non-covalently with an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group. molecular_function cellular response to stress 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 indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). GO:0033554 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. biological_process mitotic checkpoint complex A multiprotein complex that functions as a mitotic checkpoint inhibitor of the anaphase-promoting complex/cyclosome (APC/C). In budding yeast this complex consists of Mad2p, Mad3p, Bub3p and Cdc20p, and in mammalian cells it consists of MAD2, BUBR1, BUB3, and CDC20. GO:0033597 MCC cellular_component go.owl pro.owl DNA polymerase activity Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group. DNA nucleotidyltransferase activity GO:0034061 Reactome:REACT_115680 Reactome:REACT_115778 Reactome:REACT_115899 Reactome:REACT_115932 Reactome:REACT_116106 Reactome:REACT_116167 deoxynucleate polymerase activity deoxyribonucleate nucleotidyltransferase activity deoxyribonucleic acid polymerase activity deoxyribonucleic polymerase activity go.owl molecular_function obi.owl type III interferon production GO:0034343 Note that IL-28A, IL-28B, and IL-29 are types of interferon-lambda. The appearance of type III interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon lambda is the only member of the type III interferon found so far. biological_process go.owl obi.owl type III IFN production RNA cap binding complex Any protein complex that binds to a specialized RNA cap structure at any time in the lifetime of the RNA. GO:0034518 cellular_component cellular macromolecular complex assembly GO:0034622 The aggregation, arrangement and bonding together of a set of macromolecules to form a complex, carried out at the cellular level. biological_process cellular macromolecule complex assembly cellular nitrogen compound metabolic process GO:0034641 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. biological_process cellular nitrogen compound metabolism cellular macromolecule biosynthetic process GO:0034645 GO:0034961 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. biological_process cellular biopolymer biosynthetic process cellular macromolecule anabolism cellular macromolecule biosynthesis cellular macromolecule formation cellular macromolecule synthesis integrin alphaM-beta2 complex An integrin complex that comprises one alphaM subunit and one beta2 subunit. GO:0034688 Itgam-Itgb2 complex alphaM-beta2 integrin complex cellular_component go.owl pro.owl ion channel complex A protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient. GO:0034702 cellular_component go.owl pro.owl methyltransferase complex A protein complex that possesses methyltransferase activity. GO:0034708 cellular_component go.owl pro.owl Toll-like receptor 1-Toll-like receptor 2 protein complex 2010-03-04T04:35:44Z A heterodimeric protein complex containing Toll-like receptor 1 (TLR1) and Toll-like receptor 2 (TLR2). GO:0035354 GO:0038125 Reactome:REACT_8486.1 TLR1-TLR2 protein complex TLR1:TLR2 complex TLR2:TLR1 heterodimer cellular_component go.owl pro.owl rfoulger toll-like receptor TLR1:TLR2 heterodimeric complex Toll-like receptor 2-Toll-like receptor 6 protein complex 2010-03-04T04:37:00Z A heterodimeric protein complex containing Toll-like receptor 2 (TLR2) and Toll-like receptor 6 (TLR6). GO:0035355 GO:0038126 Reactome:REACT_8554.1 TLR2-TLR6 protein complex TLR2:TLR6 heterodimer TLR6:TLR2 complex cellular_component go.owl pro.owl rfoulger toll-like receptor TLR6:TLR2 heterodimeric complex chemokine (C-X-C motif) ligand 9 production 2010-03-23T10:03:20Z CXCL9 production GO:0035393 MIG production Monokine induced by gamma interferon production The appearance of chemokine (C-X-C motif) ligand 9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl rfoulger helper T cell enhancement of adaptive immune response 2010-03-23T10:38:31Z GO:0035397 Positive regulation of an adaptive immune response mediated via cytokine production by helper T cell. biological_process go.owl obi.owl provision of T cell help rfoulger helper T cell enhancement of T cell mediated immune response 2010-03-23T10:40:00Z GO:0035398 Positive regulation of a T cell mediated immune response mediated via cytokine production by a helper T cell. biological_process go.owl helper T cell enhancement of T cell mediated immunity obi.owl provision of T cell help to T cell rfoulger helper T cell enhancement of B cell mediated immune response 2010-03-23T10:41:46Z GO:0035399 Positive regulation of a B cell mediated immune response mediated via cytokine production by a helper T cell. biological_process go.owl helper T cell enhancement of B cell mediated immunity obi.owl provision of T cell help to B cell rfoulger NF-kappaB p50/p65 complex 2010-05-05T10:45:13Z A heterodimer of NF-kappa B p50 and p65 subunits. GO:0035525 NF-kappa B1/RelA complex NF-kappa B1/p65 complex NF-kappa p105/RelA complex NF-kappa p105/p65 complex NF-kappa p50/RelA complex Note that the p50 subunit is encoded by NFKB1 gene in human and the p65 subunit is encoded by the RELA gene in human. Similar nomenclature is used in other vertebrate species. The p50 subunit has a precursor form p105 in some publications. cellular_component go.owl pro.owl rfoulger granzyme A production 2011-03-17T02:39:11Z GO:0035746 The appearance of granzyme A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl rfoulger perforin production 2011-07-27T11:44:21Z GO:0035944 The appearance of a perforin protein due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl rfoulger fatty acid beta-oxidation multienzyme complex 2012-02-28T02:10:39Z A multienzyme complex possessing three kinds of enzymes that catalyze the chain reactions in the fatty acid beta-oxidation cycle, enoyl-CoA hydratase (ECH), 3-hydroxyacyl-CoA dehydrogenase (HACD), and acetyl-CoA C-acyltransferase (KACT). For fatty acid beta-oxidation multienzyme complexes located in the mitochondrial matrix, consider instead the term 'mitochondrial fatty acid beta-oxidation multienzyme complex ; GO:0016507'. GO:0036125 cellular_component rfoulger protein modification process 2012-04-26T01:47:12Z GO:0036211 The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification). biological_process protein modification rfoulger granulysin production 2012-06-18T02:11:15Z GO:0036262 The appearance of granulysin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl rfoulger growth factor complex 2013-11-07T11:27:16Z A protein complex that has growth factor activity. GO:0036454 cellular_component rfoulger TOR complex 2013-12-09T14:38:09Z A protein complex that contains at least TOR (target of rapamycin) in complex with other signaling components. Mediates the phosphorylation and activation of downstream signaling components including PKB (AKT) or S6K. GO:0038201 TOR signaling complex cellular_component mTOR complex rfoulger target of rapamycin complex locomotion GO:0040011 Self-propelled movement of a cell or organism from one location to another. biological_process regulation of gene expression, epigenetic Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence. GO:0040029 biological_process go.owl obi.owl regulation of molecular function, epigenetic Any heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya. GO:0040030 biological_process go.owl obi.owl regulation of protein activity, epigenetic T cell proliferation GO:0042098 GO:0042111 T lymphocyte proliferation T-cell proliferation T-lymphocyte proliferation The expansion of a T cell population by cell division. Follows T cell activation. biological_process go.owl obi.owl T cell receptor complex A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains. GO:0042101 T lymphocyte receptor complex T-cell receptor complex T-lymphocyte receptor complex TCR TCR complex Wikipedia:T_cell_receptor cellular_component go.owl obi.owl T cell activation GO:0042110 T lymphocyte activation T-cell activation T-lymphocyte activation The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. biological_process go.owl obi.owl peptide binding GO:0042277 Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds. molecular_function MCM complex A hexameric protein complex required for the initiation and regulation of DNA replication. GO:0042555 cellular_component go.owl mini-chromosome maintenance complex pro.owl immunoglobulin complex, circulating An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component. GO:0042571 Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. Wikipedia:Antibody antibody cellular_component go.owl obi.owl DNA polymerase complex A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA. GO:0042575 cellular_component go.owl obi.owl peptide antigen binding GO:0042605 GO:0042606 GO:0042607 Interacting selectively and non-covalently with an antigen peptide. Note that this term can be used to describe the binding of a peptide to an MHC molecule. endogenous peptide antigen binding exogenous peptide antigen binding go.owl molecular_function obi.owl MHC protein complex A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen. GO:0042611 cellular_component go.owl obi.owl succinate-CoA ligase complex A heterodimeric enzyme complex, usually composed of an alpha and beta chain. Functions in the TCA cycle, hydrolyzing succinyl-CoA into succinate and CoA, thereby forming ATP or GTP. GO:0042709 cellular_component go.owl pro.owl GPI-anchor transamidase complex An enzyme complex which in humans and yeast consists of at least five proteins; for example, the complex contains GAA1, GPI8, PIG-S, PIG-U, and PIG-T in human, and Gaa1p, Gab1p, Gpi8p, Gpi16p, and Gpi17p in yeast. Catalyzes the posttranslational attachment of the carboxyl-terminus of a precursor protein to a GPI-anchor. GO:0042765 GPIT complex Note that this term should not be confused with 'glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex ; GO:0000506', which represents a distinct complex with a different catalytic activity. cellular_component go.owl pro.owl macromolecule metabolic process GO:0043170 GO:0043283 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. biological_process biopolymer metabolic process macromolecule metabolism organelle GO:0043226 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 cellular_component membrane-bounded organelle GO:0043227 NIF_Subcellular:sao414196390 Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. cellular_component go.owl membrane-enclosed organelle obi.owl non-membrane-bounded organelle GO:0043228 NIF_Subcellular:sao1456184038 Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. cellular_component non-membrane-enclosed organelle intracellular organelle GO:0043229 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. cellular_component intracellular membrane-bounded organelle GO:0043231 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. cellular_component intracellular membrane-enclosed organelle intracellular non-membrane-bounded organelle GO:0043232 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. cellular_component intracellular non-membrane-enclosed organelle protein complex A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical. GO:0043234 Wikipedia:Protein_complex cellular_component go.owl obi.owl pro.owl protein-protein complex receptor complex Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. GO:0043235 cellular_component go.owl pro.owl Fanconi anaemia nuclear complex A protein complex composed of the Fanconi anaemia (FA) proteins including A, C, E, G and F (FANCA-F). Functions in the activation of the downstream protein FANCD2 by monoubiquitylation, and is essential for protection against chromosome breakage. FA complex FA core complex FA nuclear complex Fanconi anaemia complex GO:0043240 cellular_component go.owl pro.owl laminin complex A large, extracellular glycoprotein complex composed of three different polypeptide chains, alpha, beta and gamma. Provides an integral part of the structural scaffolding of basement membranes. GO:0043256 cellular_component go.owl pro.owl leukocyte degranulation GO:0043299 The regulated exocytosis of secretory granules by a leukocyte. This term was improved by GO_REF:0000022. It was moved. biological_process immune cell degranulation immune cell granule exocytosis leucocyte degranulation leukocyte granule exocytosis cytotoxic T cell degranulation GO:0043316 The regulated exocytosis of secretory granules containing preformed mediators such as perforin and granzymes by a cytotoxic T cell. biological_process cytotoxic T cell granule exocytosis cytotoxic T lymphocyte degranulation cytotoxic T lymphocyte granule exocytosis cytotoxic T-cell degranulation cytotoxic T-cell granule exocytosis cytotoxic T-lymphocyte degranulation cytotoxic T-lymphocyte granule exocytosis go.owl obi.owl macromolecule modification GO:0043412 The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties. biological_process macromolecule methylation GO:0043414 The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule. biological_process interleukin-12 complex A protein complex that is composed of an interleukin-12 alpha (p35, product of the IL12A gene) and an interleukin-12 beta subunit (p40, product of the IL12B gene) and is secreted into the extracellular space. GO:0043514 IL-12 complex IL12A IL12B Note that this heterodimeric cytokine utilizes the IL-12p35 subunit as its alpha chain, which is also used by IL-35 as its alpha chain, and utilizes the IL-12p40 subunit as its beta chain, which is also used by IL-23 as its beta chain. cellular_component go.owl p35 p40 pro.owl 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase complex 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 complex 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 complex 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 complex 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 complex A homodimeric, bifunctional enzyme complex which catalyzes the synthesis and degradation of fructose 2,6-bisphosphate, and is required for both glycolysis and gluconeogenesis. GO:0043540 Note that we use this single class to represent all 4 isoforms of this complex. We decided to do this because the isoforms do not differ in function, rather in expression and regulation. We may want to revisit this in future. cellular_component go.owl pro.owl sequence-specific DNA binding GO:0043565 Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. go.owl molecular_function obi.owl sequence specific DNA binding cellular protein complex assembly GO:0043623 The aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell. biological_process PCNA complex A protein complex composed of three identical PCNA monomers, each comprising two similar domains, which are joined in a head-to-tail arrangement to form a homotrimer. Forms a ring-like structure in solution, with a central hole sufficiently large to accommodate the double helix of DNA. Originally characterized as a DNA sliding clamp for replicative DNA polymerases and as an essential component of the replisome, and has also been shown to be involved in other processes including Okazaki fragment processing, DNA repair, translesion DNA synthesis, DNA methylation, chromatin remodeling and cell cycle regulation. GO:0043626 PCNA homotrimer cellular_component go.owl pro.owl proliferating cell nuclear antigen complex sliding clamp 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. GO:0034600 GO:0034621 GO:0043933 biological_process cellular macromolecular complex organization cellular macromolecular complex subunit organisation cellular macromolecular complex subunit organization macromolecular complex organization macromolecular complex subunit organisation regulation of DNA methylation Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. GO:0044030 biological_process go.owl obi.owl transcription regulatory region DNA binding 2009-11-04T12:58:25Z GO:0044212 Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. The word "promoter" is used variously in the literature to describe the core promoter specifically or the entire proximal regulatory region (excluding any distal enhancers) including both the core promoter and the upstream region where activating transcription factors such as Gal4 in S. cerevisiae or catabolite activator protein (CAP) in E. coli bind. To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" in order to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind, and "enhancer" regions which are typically more distal from the core promoter. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription. ANNOTATION NOTE: Regarding annotation to "transcription regulatory region DNA binding" (GO:0044212) and any of its is_a children, note that annotation to these terms specifies DNA binding only without any statement about transcription factor activity. To make an annotation about a function of transcription factor activity, consider "sequence-specific DNA binding transcription factor activity" (GO:0003700) or its is_a children which have has_part relationships to the appropriate kind of "transcription regulatory region DNA binding". jane molecular_function cellular metabolic process GO:0044237 The chemical reactions and pathways by which individual cells transform chemical substances. biological_process cellular metabolism intermediary metabolism primary metabolic process GO:0044238 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. biological_process primary metabolism cellular biosynthetic process GO:0044249 The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. biological_process cellular anabolism cellular biosynthesis cellular formation cellular synthesis cellular macromolecule metabolic process GO:0034960 GO:0044260 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. biological_process cellular biopolymer metabolic process cellular macromolecule metabolism cellular protein metabolic process GO:0044267 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. biological_process cellular protein metabolism small molecule metabolic process 2010-01-26T12:05:20Z GO:0044281 Reactome:REACT_111217 Reactome:REACT_112077 Reactome:REACT_112140 Reactome:REACT_112621 Reactome:REACT_112912 Reactome:REACT_113131 Reactome:REACT_113305 Reactome:REACT_113457 Reactome:REACT_113568 Reactome:REACT_113610 Reactome:REACT_113934 Reactome:REACT_114081 Reactome:REACT_114137 Reactome:REACT_114421 Reactome:REACT_114473 Reactome:REACT_114495 Reactome:REACT_114668 Reactome:REACT_114983 Reactome:REACT_115063 Reactome:REACT_115388 Reactome:REACT_115420 Reactome:REACT_115655 Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule. biological_process jane small molecule metabolism extracellular matrix component Any constituent part of the extracellular matrix, the structure lying external to one or more cells, which provides structural support for cells or tissues; may be completely external to the cell (as in animals) or be part of the cell (as often seen in plants). GO:0044420 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component extracellular matrix part extracellular region part Any constituent part of the extracellular region, the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers constituent parts of the host cell environment outside an intracellular parasite. GO:0044421 NIF_Subcellular:sao9117790637 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component extracellular structure 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. GO:0044422 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component 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. GO:0044424 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component membrane part Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. GO:0044425 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component chromosomal part Any constituent part of a chromosome, a structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. GO:0044427 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component chromosomal component chromosome component chromosome part nuclear part Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. GO:0044428 NIF_Subcellular:sao1499850686 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component nuclear subcomponent nucleus component mitochondrial part Any constituent part of a mitochondrion, a semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. GO:0044429 NIF_Subcellular:sao666410040 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component mitochondrial subcomponent mitochondrion component cytoskeletal part Any constituent part of the cytoskeleton, a cellular scaffolding or skeleton that maintains cell shape, enables some cell motion (using structures such as flagella and cilia), and plays important roles in both intra-cellular transport (e.g. the movement of vesicles and organelles) and cellular division. Includes constituent parts of intermediate filaments, microfilaments, microtubules, and the microtrabecular lattice. GO:0044430 NIF_Subcellular:sao1635329413 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component cytoskeletal element cytoskeleton component Golgi apparatus part Any constituent part of the Golgi apparatus, a compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. GO:0044431 Golgi component Golgi subcomponent NIF_Subcellular:sao624292949 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component endoplasmic reticulum part Any constituent part of the endoplasmic reticulum, the irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. ER component GO:0044432 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component cytoplasmic vesicle part Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell. GO:0044433 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component endosomal part Any constituent part of an endosome, a membrane-bounded organelle to which materials ingested by endocytosis are delivered. GO:0044440 NIF_Subcellular:sao1683772610 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component endosomal subcomponent endosome 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. GO:0044444 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component cytoplasm component cytosolic part Any constituent part of cytosol, that part of the cytoplasm that does not contain membranous or particulate subcellular components. GO:0044445 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component cytosol 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. GO:0044446 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component nucleoplasm part Any constituent part of the nucleoplasm, that part of the nuclear content other than the chromosomes or the nucleolus. GO:0044451 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component nucleolar part Any constituent part of a nucleolus, a small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. GO:0044452 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component nucleolus component nuclear membrane part Any constituent part of the nuclear membrane, the envelope that surrounds the nucleus of eukaryotic cells. GO:0044453 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component nuclear chromosome part Any constituent part of a nuclear chromosome, a chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact. GO:0044454 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component mitochondrial membrane part Any constituent part of a mitochondrial membrane, either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope. GO:0044455 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component plasma membrane part Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0044459 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component cell part Any constituent part of a cell, the basic structural and functional unit of all organisms. GO:0044464 NIF_Subcellular:sao628508602 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular subcomponent cellular_component protoplast single-organism process 2012-09-19T15:05:24Z A biological process that involves only one organism. GO:0044699 biological_process janelomax single organism process single organism reproductive process 2012-09-19T15:56:06Z A biological process that directly contributes to the process of producing new individuals, involving a single organism. GO:0044702 biological_process janelomax single-multicellular organism process 2012-09-19T16:07:47Z A biological process occurring within a single, multicellular organism. GO:0044707 biological_process janelomax single-organism metabolic process 2012-10-17T15:46:40Z A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves a single organism. GO:0044710 biological_process janelomax single-organism carbohydrate metabolic process 2012-10-23T15:40:34Z GO:0044723 The chemical reactions and pathways involving carbohydrates, occurring within a single organism. biological_process janelomax DNA methylation or demethylation 2012-10-24T14:49:41Z GO:0044728 The process of adding or removing a methyl group from one or more nucleotides within an DNA molecule. biological_process changes in DNA methylation janelomax single-organism cellular process 2012-12-11T16:56:55Z Any process that is carried out at the cellular level, occurring within a single organism. GO:0044763 biological_process janelomax single-organism transport 2012-12-13T16:25:32Z GO:0044765 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. biological_process janelomax single-organism developmental process 2012-12-19T12:21:31Z A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition, involving only one organism. GO:0044767 biological_process janelomax DNA polymerase processivity factor complex 2013-08-28T11:16:14Z A protein complex which is capable of increasing the processivity of nucleotide polymerization by DNA polymerase as a part of DNA replication. GO:0044796 cellular_component janelomax nuclear transcription factor complex 2013-08-28T12:12:27Z A protein complex, located in the nucleus, that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription. GO:0044798 cellular_component janelomax macrophage migration inhibitory factor production 2013-09-11T12:04:09Z GO:0044807 MIF production The appearance of macrophage migration inhibitory factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl janelomax obi.owl Oncostatin M production 2013-09-11T12:18:00Z GO:0044808 OSM production The appearance of Oncostatin M due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl janelomax obi.owl chemokine (C-C motif) ligand 17 production 2013-09-11T12:21:31Z CCL17 production GO:0044809 TARC production The appearance of chemokine (C-C motif) ligand 17 (CCL17) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl janelomax obi.owl thymus and activation regulated chemokine production regulated exocytosis A process of exocytosis in which soluble proteins and other substances are initially stored in secretory vesicles for later release. It is found mainly in cells that are specialized for secreting products such as hormones, neurotransmitters, or digestive enzymes rapidly on demand. GO:0045055 biological_process regulated secretory pathway azole transport GO:0045117 The directed movement of azoles, heterocyclic compounds found in many biologically important substances, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process tricarboxylic acid cycle enzyme complex Any of the heteromeric enzymes that act in the TCA cycle. GO:0045239 TCA cycle enzyme complex cellular_component isocitrate dehydrogenase complex (NAD+) Complex that possesses isocitrate dehydrogenase (NAD+) activity. GO:0045242 cellular_component succinate-CoA ligase complex (GDP-forming) A heterodimeric enzyme complex, usually composed of an alpha and beta chain. Functions in the TCA cycle, hydrolyzing succinyl-CoA into succinate and CoA, thereby forming GTP. GO:0008325 GO:0045244 GO:0045245 cellular_component go.owl pro.owl succinyl-CoA synthetase, GDP-forming respiratory chain complex IV A part of the respiratory chain, containing the 13 polypeptide subunits of cytochrome c oxidase, including cytochrome a and cytochrome a3. Catalyzes the oxidation of reduced cytochrome c by dioxygen (O2). GO:0045277 GO:0045287 cellular_component cytochrome c oxidase complex electron transport complex IV go.owl pro.owl leukocyte activation A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor. GO:0045321 Wikipedia:Immunologic_activation biological_process immune cell activation leucocyte activation heterocycle metabolic process GO:0046483 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). biological_process heterocycle metabolism lymphocyte activation A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor. GO:0046649 biological_process lymphocyte proliferation GO:0046651 The expansion of a lymphocyte population by cell division. biological_process lipopolysaccharide receptor complex A multiprotein complex that consists of at least three proteins, CD14, TLR4, and MD-2, each of which is glycosylated and which functions as a lipopolysaccharide (LPS) receptor that primes the innate immune response against bacterial pathogens. GO:0046696 LPS receptor complex Note that this term should not be used to refer to CD14 alone, but the multiprotein receptor complex that it is part of. cellular_component go.owl pro.owl hormone secretion GO:0046879 The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells. biological_process secretion GO:0046903 The controlled release of a substance by a cell or a tissue. biological_process animal organ development Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. GO:0048513 Wikipedia:Organogenesis biological_process development of an organ organogenesis 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. GO:0043119 GO:0048518 activation of biological process biological_process positive regulation of physiological process stimulation of biological process up regulation of biological process up-regulation of biological process upregulation of biological process hematopoietic or lymphoid organ development GO:0048534 The process whose specific outcome is the progression of any organ involved in hematopoiesis (also known as hemopoiesis) or lymphoid cell activation over time, from its formation to the mature structure. Such development includes differentiation of resident cell types (stromal cells) and of migratory cell types dependent on the unique microenvironment afforded by the organ for their proper differentiation. biological_process haematopoietic or lymphoid organ development haemopoietic or lymphoid organ development hemopoietic or lymphoid organ development 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. GO:0048583 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. biological_process 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. GO:0048584 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. activation of response to stimulus biological_process stimulation of response to stimulus up regulation of response to stimulus up-regulation of response to stimulus upregulation of response to stimulus anatomical structure development GO:0048856 The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. This term was added by GO_REF:0000021. biological_process development of an anatomical structure cellular developmental process A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. GO:0048869 biological_process go.owl obi.owl cell motility Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. GO:0048870 biological_process cell locomotion cell movement movement of a cell regulation of immune response Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. GO:0050776 Reactome:REACT_101484 Reactome:REACT_106667 Reactome:REACT_107426 Reactome:REACT_11152 Reactome:REACT_81657 Reactome:REACT_82803 Reactome:REACT_87475 Reactome:REACT_94152 Reactome:REACT_95389 Reactome:REACT_97860 biological_process positive regulation of immune response Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. GO:0050778 biological_process stimulation of immune response up regulation of immune response up-regulation of immune response upregulation of immune response 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. GO:0050789 GO:0050791 biological_process 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. GO:0050794 GO:0051244 biological_process regulation of cellular physiological process coagulation GO:0050817 The process in which a fluid solution, or part of it, changes into a solid or semisolid mass. biological_process clotting regulation of body fluid levels Any process that modulates the levels of body fluids. GO:0050878 biological_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. GO:0050896 GO:0051869 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. biological_process go.owl obi.owl physiological response to stimulus regulation of DNA metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA. GO:0051052 biological_process regulation of DNA metabolism 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. GO:0051171 biological_process regulation of nitrogen metabolic process regulation of nitrogen metabolism localization Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. GO:0051179 biological_process establishment and maintenance of cellular component location establishment and maintenance of localization establishment and maintenance of position establishment and maintenance of substance location establishment and maintenance of substrate location localisation establishment of localization Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. GO:0051234 biological_process establishment of localisation protein polymerization GO:0051258 The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein. biological_process protein polymer biosynthesis protein polymer biosynthetic process protein polymer formation chromosome organization A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. GO:0007001 GO:0051276 GO:0051277 biological_process chromosome organisation chromosome organization and biogenesis go.owl maintenance of genome integrity nuclear genome maintenance obi.owl histamine transport GO:0051608 The directed movement of histamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Histamine is a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans. biological_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. GO:0051716 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. biological_process nuclear DNA-directed RNA polymerase complex A protein complex, located in the nucleus, that possesses DNA-directed RNA polymerase activity. GO:0055029 cellular_component 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. GO:0060255 biological_process transferase complex, transferring phosphorus-containing groups 2015-05-06T11:22:38Z A transferase complex capable of catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). GO:0061695 cellular_component dph macromolecular complex assembly GO:0065003 The aggregation, arrangement and bonding together of a set of macromolecules to form a complex. biological_process macromolecule complex assembly biological regulation Any process that modulates a measurable attribute of any biological process, quality or function. GO:0065007 biological_process regulation regulation of biological quality Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc. GO:0065008 biological_process regulation of biological attribute regulation of biological characteristic regulation of molecular function Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GO:0065009 biological_process regulation of a molecular function transforming growth factor beta type I receptor homodimeric complex A receptor complex that consists of two transforming growth factor beta (TGF-beta) type I receptor monomers. TGF-beta type I receptor dimers form in the presence or absence of ligand, and can associate with ligand-bound TGF-beta type II receptor dimers. GO:0070018 TGF-beta type I receptor complex TGF-beta type I receptor dimer TGFBR1 homodimer cellular_component go.owl pro.owl transforming growth factor beta type I receptor complex transforming growth factor beta type II receptor homodimeric complex A receptor complex that consists of two transforming growth factor beta (TGF-beta) type II receptor monomers. TGF-beta type II receptor dimers form in the presence or absence of ligand, and upon ligand binding can associate with TGF-beta type I receptor dimers. GO:0070019 TGF-beta type II receptor complex TGF-beta type II receptor dimer TGFBR2 homodimer cellular_component go.owl pro.owl transforming growth factor beta type II receptor complex transforming growth factor beta receptor complex A homodimeric receptor complex that consists of two TGF-beta receptor monomers. GO:0070022 TGF-beta receptor complex cellular_component go.owl pro.owl transforming growth factor beta receptor complex cytochrome complex A protein complex in which at least one of the proteins is a cytochrome, i.e. a heme-containing protein involved in catalysis of redox reactions. GO:0070069 cellular_component shelterin complex A nuclear telomere cap complex that is formed by the association of telomeric ssDNA- and dsDNA-binding proteins with telomeric DNA, and is involved in telomere protection and recruitment of telomerase. The complex is known to contain TERF1, TERF2, POT1, RAP1, TINF2 and ACD in mammalian cells, and Pot1, Tpz1, Rap1, Rif1, Rif2 and Taz1 in Schizosaccharomyces. Taz1 and Rap1 (or their mammalian equivalents) form a dsDNA-binding subcomplex, Pot1 and Tpz1 form an ssDNA-binding subcomplex, and the two subcomplexes are bridged by Poz1, which acts as an effector molecule along with Ccq1. GO:0070187 Pot1 complex Pot1-Tpz1 complex cellular_component go.owl pro.owl telosome actin polymerization-dependent cell motility A process involved in the controlled movement of a bacterial cell powered by the continuous polymerization of actin at one pole of the cell. GO:0070358 biological_process cell motility by actin tail formation go.owl obi.owl Mad-Max complex A transcriptional repressor complex that consists of a heterodimer of the bHLH-ZIP proteins Mad and Max. GO:0070443 cellular_component go.owl pro.owl SWI/SNF superfamily-type complex 2009-04-29T12:55:46Z A protein complex that contains an ortholog of the Saccharomyces ATPase Swi2/Snf2 as one of the core components and mediates assembly of nucleosomes, changes to the spacing or structure of nucleosomes, or some combination of those activities in a manner that requires ATP. GO:0070603 SWI-SNF global transcription activator complex SWI-SNF-type complex SWI/SNF-type complex SWI2/SNF2 superfamily ATP-dependent chromatin remodeling complex cellular_component go.owl midori pro.owl leukocyte proliferation 2009-05-28T05:25:28Z GO:0070661 The expansion of a leukocyte population by cell division. biological_process midori P-TEFb complex 2009-06-03T03:12:56Z A dimeric positive transcription elongation factor complex b that comprises a cyclin-dependent kinase containing the catalytic subunit, Cdk9, and a regulatory subunit, cyclin T. Bur1/Bur2 complex GO:0070691 Sgv1/Bur2 complex cellular_component dimeric positive transcription elongation factor complex b go.owl midori pro.owl interleukin-23 complex 2009-06-23T01:06:02Z A protein complex that is composed of an interleukin-23 alpha (p19, product of the IL23A gene) and an interleukin-12 beta (p40, product of the IL12B gene) subunit and is secreted into the extracellular space. GO:0070743 IL-23 complex IL12B IL23A Note that this heterodimeric cytokine utilizes the same beta subunit as IL-12. cellular_component go.owl midori p19 p40 pro.owl SMAD protein complex 2009-11-16T02:28:59Z A protein complex that consists of only SMAD proteins; may be homomeric or heteromeric. GO:0071141 SMAD complex cellular_component go.owl midori pro.owl SMAD2-SMAD4 protein complex 2009-11-16T02:47:15Z A heteromeric SMAD protein complex that contains SMAD2 and SMAD4. GO:0071145 SMAD2-SMAD4 heteromer complex cellular_component go.owl midori pro.owl NF-kappaB complex 2009-11-17T02:03:34Z A protein complex that consists of a homo- or heterodimer of members of a family of structurally related proteins that contain a conserved N-terminal region called the Rel homology domain (RHD). In the nucleus, NF-kappaB complexes act as transcription factors. In unstimulated cells, NF-kappaB dimers are sequestered in the cytoplasm by IkappaB monomers; signals that induce NF-kappaB activity cause degradation of IkappaB, allowing NF-kappaB dimers to translocate to the nucleus and induce gene expression. GO:0071159 cellular_component go.owl midori pro.owl transforming growth factor beta production 2010-02-05T03:56:57Z GO:0071604 TGF-B production TGF-beta production TGFB production TGFb production The appearance of any member of the transforming growth factor-beta family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Transforming growth factor-beta family members include TGF-B1, TGF-B2, and TGF-B3. biological_process go.owl midori obi.owl transforming growth factor-beta production monocyte chemotactic protein-1 production 2010-02-05T04:09:53Z CCL2 production GO:0071605 MCP-1 production The appearance of monocyte chemotactic protein-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl midori obi.owl chemokine (C-C motif) ligand 4 production 2010-02-05T04:16:42Z CCL4 production GO:0071606 MIP-1b production The appearance of chemokine (C-C motif) ligand 4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl macrophage inflammatory protein production midori obi.owl macrophage inflammatory protein-1 gamma production 2010-02-05T04:19:52Z CCL9 production GO:0071607 MIP-1g production The appearance of macrophage inflammatory protein-1 gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process chemokine (C-C motif) ligand 9 production go.owl midori obi.owl macrophage inflammatory protein-1 alpha production 2010-02-05T04:24:17Z CCL3 production GO:0071608 MIP-1a production The appearance of macrophage inflammatory protein 1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process chemokine (C-C motif) ligand 3 production go.owl macrophage inflammatory protein production midori obi.owl chemokine (C-C motif) ligand 5 production 2010-02-05T04:32:35Z CCL5 production GO:0071609 RANTES production Regulated upon Activation, Normal T-cell Expressed, and Secreted production The appearance of chemokine (C-C motif) ligand 5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl midori obi.owl chemokine (C-C motif) ligand 1 production 2010-02-05T04:35:00Z CCL1 production GO:0071610 T cell activation 3 production TCA-3 production The appearance of chemokine (C-C motif) ligand 1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl midori obi.owl granulocyte colony-stimulating factor production 2010-02-05T04:38:11Z CSF3 production G-CSF production GO:0071611 The appearance of granulocyte colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process colony stimulating factor 3 (granulocyte) production filgrastim production go.owl granulocyte colony stimulating factor production lenograstim production midori obi.owl pluripoietin production IP-10 production 2010-02-05T04:43:56Z CXCL10 production GO:0071612 The appearance of IP-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process chemokine (C-C motif) ligand 10 production go.owl midori obi.owl granzyme B production 2010-02-05T04:47:15Z GO:0071613 The appearance of granzyme B due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl midori obi.owl organic substance transport 2010-03-08T02:15:14Z GO:0071702 The directed movement of organic substances 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. An organic substance is a molecular entity that contains carbon. biological_process midori organic substance metabolic process 2010-03-08T03:32:18Z GO:0071704 The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. biological_process midori organic molecular entity metabolic process organic molecular entity metabolism organic substance metabolism nitrogen compound transport 2010-03-08T03:56:28Z GO:0071705 The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process midori tumor necrosis factor superfamily cytokine production 2010-03-09T02:40:35Z GO:0071706 TNF superfamily production TNFSF cytokine production The appearance of any member of the TNF superfamily due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl midori obi.owl protein complex subunit organization 2010-09-08T10:01:42Z Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. GO:0071822 biological_process midori protein complex subunit organisation cellular component organization or biogenesis 2010-09-10T01:39:16Z A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. GO:0071840 GO:0071841 biological_process cellular component organisation or biogenesis cellular component organisation or biogenesis at cellular level cellular component organization or biogenesis at cellular level midori chemokine (C-C motif) ligand 22 production 2010-09-28T11:33:13Z C-C motif chemokine 22 production CCL-22 production CCL22 production GO:0071924 The appearance of chemokine (C-C motif) ligand 22 (CCL22) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl midori obi.owl Myc-Max complex 2010-10-01T11:56:17Z A transcription factor complex that consists of a heterodimer of the bHLH-ZIP proteins Myc and Max. GO:0071943 cellular_component go.owl midori pro.owl tumor necrosis factor (ligand) superfamily member 11 production 2011-01-14T01:42:23Z GO:0072535 RANKL production TNFSF11 production The appearance of tumor necrosis factor superfamily member 11 (TNFSF11; RANKL) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl midori obi.owl tumor necrosis factor ligand superfamily member 11 production Cul4-RING E3 ubiquitin ligase complex A ubiquitin ligase complex in which a cullin from the Cul4 family and a RING domain protein form the catalytic core; substrate specificity is conferred by an adaptor protein. GO:0080008 cellular_component go.owl pro.owl regulation of primary metabolic process 2009-04-22T04:30:52Z 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. GO:0080090 biological_process donghui nucleic acid metabolic process 2010-04-07T10:18:47Z Any cellular metabolic process involving nucleic acids. GO:0090304 biological_process tanyaberardini nuclear transcriptional repressor complex 2014-05-09T13:23:51Z A protein complex, located in the nucleus, that possesses activity that prevents or downregulates transcription. GO:0090568 cellular_component tanyaberardini RNA polymerase II transcription repressor complex 2014-05-09T13:26:16Z A protein complex, located in the nucleus, that possesses activity that prevents or downregulates transcription from a RNA polymerase II promoter. GO:0090571 cellular_component tanyaberardini RNA polymerase II transcription factor complex 2014-05-09T14:04:37Z A transcription factor complex that acts at promoters of genes transcribed by RNA polymerase II. GO:0090575 cellular_component tanyaberardini RNA polymerase III transcription factor complex 2014-05-09T14:04:37Z A transcription factor complex that acts at promoters of genes transcribed by RNA polymerase III. GO:0090576 cellular_component tanyaberardini interferon regulatory factor complex 2011-06-15T04:22:30Z A protein complex that consists of two interferon regulatory proteins (IRFs); may be homodimeric or heterodimeric. The activation of a latent closed conformation of IRF in the cytoplasm is triggered by phosphorylation of Ser/Thr residues in a C-terminal region. Phosphorylation stimulates the C-terminal autoinhibitory domain to attain a highly extended conformation triggering dimerization through extensive contacts to a second subunit. GO:0097071 IRF complex cellular_component go.owl paola pro.owl interferon regulatory factor 5 complex 2011-06-15T04:28:57Z An interferon regulatory factor complex that consists of a homodimer of interferon regulatory factor 5. GO:0097073 IRF5:IRF5 complex cellular_component go.owl paola pro.owl interleukin-17A production 2011-06-23T11:31:10Z GO:0097087 IL-17A production The appearance of interleukin-17A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl paola interleukin-17F production 2011-06-23T11:32:59Z GO:0097088 IL-17F production The appearance of interleukin-17F due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl paola organic cyclic compound binding 2011-09-23T02:31:01Z GO:0097159 Interacting selectively and non-covalently with an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure. molecular_function paola complement-dependent cytotoxicity 2012-03-22T05:04:04Z GO:0097278 Lysis of a cell resulting from triggering of the complement cascade. An example can be seen with complement activation and subsequent lysis of a bacterial cell as a result of the binding of IgM to the cell surface followed by the binding of complement proteins to that antibody. biological_process go.owl obi.owl paola histamine secretion mediated by immunoglobulin 2012-03-26T01:30:25Z GO:0097280 Histamine release triggered by the binding of an antigen to an immunoglobulin bound to the cell surface. biological_process go.owl obi.owl paola immune complex formation 2012-03-26T01:35:21Z GO:0097281 The process that gives rise to an immune complex. Immune complexes are clusters of antibodies bound to antigen, to which complement may also be fixed, and which may precipitate or remain in solution. Examples are the clumping of cells such as bacteria or red blood cells in the presence of an antibody, precipitation of a toxin after an antibody binds to it, and clumping of viral particles as a result of antibody binding to the virus. antibody-mediated agglutination biological_process go.owl obi.owl paola immunoglobulin-mediated neutralization 2012-03-26T01:55:24Z GO:0097282 The inhibition of an antigen's biological effects by antibody binding to it. An example is neutralization of diphtheria toxin by preventing its entry into human cells via the binding of antibody specific for diphtheria toxin. antibody-mediated neutralization biological_process go.owl obi.owl paola chemokine (C-C motif) ligand 19 production 2012-10-23T07:54:10Z CCL19 production EBI1 ligand chemokine production ELC production GO:0097388 MIP-3-beta production The appearance of chemokine (C-C motif) ligand 19 (CCL19) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl macrophage inflammatory protein-3-beta production obi.owl paola chemokine (C-C motif) ligand 21 production 2012-10-23T07:56:26Z CCL21 production GO:0097389 The appearance of chemokine (C-C motif) ligand 21 (CCL21) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl paola chemokine (C-X-C motif) ligand 12 production 2012-10-23T07:57:28Z CXCL12 production GO:0097390 The appearance of chemokine (C-X-C motif) ligand 12 (CXCL12) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl paola chemokine (C-X-C motif) ligand 13 production 2012-10-23T07:58:28Z CXCL13 production GO:0097391 The appearance of chemokine (C-X-C motif) ligand 13 (CXCL13) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl paola chemokine (C-X-C motif) ligand 16 production 2012-10-23T07:59:43Z CXCL16 production GO:0097392 The appearance of chemokine (C-X-C motif) ligand 16 (CXCL16) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. biological_process go.owl obi.owl paola supramolecular fiber organization 2012-11-27T15:46:25Z A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a supramolecular fiber, a polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure. GO:0043206 GO:0097435 biological_process extracellular fibril organisation extracellular fibril organization extracellular fibril organization and biogenesis fibril organisation fibril organization paola GAIT complex 2012-12-19T09:32:25Z A protein complex which mediates interferon-gamma-induced transcript-selective translation inhibition in inflammation processes. The complex binds to stem loop-containing GAIT elements in the 3'-UTR of diverse inflammatory mRNAs and suppresses their translation by blocking the recruitment of the 43S ribosomal complex to m7G cap-bound eIF4G. In humans it includes RPL13A, EPRS, SYNCRIP and GAPDH; mouse complexes lack SYNCRIP. GO:0097452 IFN-gamma-activated inhibitor of translation complex cellular_component gamma interferon-activated inhibitor of translation complex go.owl paola pro.owl bounding membrane of organelle 2014-02-26T13:41:31Z Examples include the outer membranes of double membrane bound organelles such as mitochondria as well as the bounding membranes of single-membrane bound organelles such as lysosomes. GO:0098588 The lipid bilayer that forms the outer-most layer of an organelle. cellular_component davidos protein complex involved in cell adhesion Any protein complex that is capable of carrying out some part of the process of cell adhesion to the cell matrix or to another cell. GO:0098636 GO:1990307 cell adhesion complex cellular_component membrane protein complex Any protein complex that is part of a membrane. GO:0098796 cellular_component plasma membrane protein complex Any protein complex that is part of the plasma membrane. GO:0098797 cellular_component mitochondrial protein complex A protein complex that is part of a mitochondrion. GO:0098798 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component inner mitochondrial membrane protein complex Any protein complex that is part of the inner mitochondrial membrane. GO:0098800 cellular_component plasma membrane receptor complex Any protein complex that is part of the plasma membrane and which functions as a receptor. GO:0098802 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component respiratory chain complex Any protein complex that is part of a respiratory chain GO:0098803 cellular_component whole membrane Any lipid bilayer that completely encloses some structure, and all the proteins embedded in it or attached to it. Examples include the plasma membrane and most organelle membranes. GO:0098805 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular_component chaperone complex A protein complex required for the non-covalent folding or unfolding, maturation, stabilization or assembly or disassembly of macromolecular structures. Usually active during or immediately after completion of translation. Many chaperone complexes contain heat shock proteins. An example of this is HSP90AB1 in human (P08238) in PMID:21855797 (inferred from direct assay). GO:0101031 cellular_component organic cyclic compound metabolic process 2012-09-14T09:03:51Z GO:1901360 The chemical reactions and pathways involving organic cyclic compound. bf biological_process organic cyclic compound metabolism heterocyclic compound binding 2012-09-14T13:53:50Z GO:1901363 Interacting selectively and non-covalently with heterocyclic compound. bf molecular_function organonitrogen compound metabolic process 2012-11-04T15:17:52Z GO:1901564 The chemical reactions and pathways involving organonitrogen compound. biological_process organonitrogen compound metabolism pr organic substance biosynthetic process 2012-11-05T11:04:40Z GO:1901576 The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. biological_process 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 pr catalytic complex 2013-11-13T16:18:47Z A protein complex which is capable of catalytic activity. GO:1902494 bhm cellular_component enzyme complex transmembrane transporter complex 2013-11-13T16:23:04Z A transmembrane protein complex which enables the transfer of a substance from one side of a membrane to the other. GO:1902495 bhm cellular_component serine/threonine protein kinase complex 2013-12-06T16:06:12Z A protein complex which is capable of protein serine/threonine kinase activity. An example is IRE1 in S. cerevisiae (UniProt ID P32361) in PMID:18191223 (inferred from direct assay). GO:1902554 PDR16 complex dimer PDR16 complex homodimer bhm cellular_component single-organism localization 2013-12-18T13:51:04Z A localization which involves only one organism. GO:1902578 biological_process jl single organism localization protein kinase complex 2014-04-17T13:52:40Z A protein complex which is capable of protein kinase activity. An example of this is PKM2 in human (P14618) in PMID:24606918 (inferred from direct assay). GO:1902911 bhm cellular_component methylcrotonoyl-CoA carboxylase complex 2016-05-16T11:03:20Z A protein complex which is capable of methylcrotonoyl-CoA carboxylase activity. GO:1905202 bf cellular_component GTPase complex 2016-08-11T15:34:44Z A protein complex which is capable of GTPase activity. An example of this is HRAS in human (P01112) in PMID:9178006 (inferred from direct assay). GO:1905360 HRAS-SOS1 complex RASH-SOS1 complex bhm cellular_component peptidase complex 2016-08-16T12:49:36Z A protein complex which is capable of peptidase activity. An example of this is PLAU in human (UniProt symbol P00749) in PMID:1689240 (inferred from direct assay). GO:1905368 bhm cellular_component endopeptidase complex 2016-08-16T12:52:16Z A protein complex which is capable of endopeptidase activity. An example of this is PLAU in human (UniProt symbol P00749) in PMID:1689240 (inferred from direct assay). GO:1905369 bhm cellular_component oxidoreductase complex 2013-10-07T08:24:47Z Any protein complex that possesses oxidoreductase activity. GO:1990204 bhm cellular_component oxidation-reduction complex redox complex transferase complex 2013-11-12T13:20:12Z A protein complex capable of catalyzing the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). GO:1990234 bhm cellular_component platelet-derived growth factor complex 2014-01-09T16:09:11Z A protein complex consisting of two chains of platelet-derived growth factor (PDGF) subunits. PDGF dimers bind to PDGF receptors in the plasma membrane and induce receptor dimerisation and activation. PDGFs are involved in a wide variety of signalling processes. PDGFs are found in all vertebrates where at least 2 different chains (A and B) exist. In human (and other mammals), four types of PDGF chains (A, B, C, and D) are known which form five different dimers (AA, AB, BB, CC and DD). An example of this is PDGFA in human (P04085) in PMID:20534510 (inferred from direct assay). GO:1990265 IntAct:EBI-2881436 IntAct:EBI-2881443 IntAct:EBI-2881451 PDGF complex PDGF-AA dimer PDGF-AB dimer PDGF-BB dimer PDGF-CC dimer PDGF-DD dimer bhm cellular_component go.owl pro.owl transporter complex 2014-03-26T14:23:27Z A protein complex facilitating transport of molecules (proteins, small molecules, nucleic acids) into, out of or within a cell, or between cells. An example of this is GTR1 in human (UniProt symbol P11166) in PMID:15449578 (inferred from direct assay). GO:1990351 bhm cellular_component Mus musculus GC_ID:1 Mus muscaris NCBITaxon:85055 house mouse mice C57BL/6xCBA/CaJ hybrid mouse ncbi_taxonomy obi.owl pro.owl Rattus norvegicus GC_ID:1 Gunn rats NCBITaxon:36465 Norway rat Rattus norvegicus8 Rattus norwegicus Rattus rattiscus Rattus sp. strain Wistar brown rat ncbi_taxonomy obi.owl pro.owl rat rats Viruses GC_ID:1 Vira Viridae ncbi_taxonomy obi.owl pro.owl viruses Euteleostomi GC_ID:1 NCBITaxon:40673 bony vertebrates ncbi_taxonomy Ecdysozoa GC_ID:1 ncbi_taxonomy Clupeocephala GC_ID:1 ncbi_taxonomy Bacteria GC_ID:11 Monera PMID:10425795 PMID:10425796 PMID:10425797 PMID:10490293 PMID:10843050 PMID:10939651 PMID:10939673 PMID:10939677 PMID:11211268 PMID:11321083 PMID:11321113 PMID:11411719 PMID:11540071 PMID:11542017 PMID:11542087 PMID:11760965 PMID:12054223 PMID:2112744 PMID:270744 PMID:8123559 PMID:8590690 PMID:9103655 PMID:9336922 Procaryotae Prokaryota Prokaryotae bacteria eubacteria ncbi_taxonomy not Bacteria Haeckel 1894 obi.owl pro.owl prokaryote prokaryotes Archaea Archaebacteria GC_ID:11 Mendosicutes Metabacteria Monera PMID:10425795 PMID:10425796 PMID:10425797 PMID:10490293 PMID:10843050 PMID:10939651 PMID:10939673 PMID:10939677 PMID:11211268 PMID:11321083 PMID:11321113 PMID:11411719 PMID:11540071 PMID:11541975 PMID:11542064 PMID:11542149 PMID:11760965 PMID:12054223 PMID:2112744 PMID:25527841 PMID:270744 PMID:8123559 PMID:8590690 PMID:9103655 PMID:9336922 Procaryotae Prokaryota Prokaryotae archaea ncbi_taxonomy obi.owl pro.owl prokaryote prokaryotes Eukaryota Eucarya Eucaryotae Eukarya Eukaryotae GC_ID:1 PMID:23020233 eucaryotes eukaryotes eukaryotes ncbi_taxonomy obi.owl pro.owl Euarchontoglires GC_ID:1 PMID:11214319 PMID:12082125 PMID:12878460 PMID:15522813 ncbi_taxonomy Amniota GC_ID:1 amniotes ncbi_taxonomy Viridiplantae Chlorobionta Chlorophyta/Embryophyta group GC_ID:1 chlorophyte/embryophyte group green plants green plants ncbi_taxonomy po.owl pro.owl Opisthokonta Fungi/Metazoa group GC_ID:1 ncbi_taxonomy obi.owl opisthokonts pro.owl Bilateria GC_ID:1 ncbi_taxonomy Arabidopsis thaliana Arabidopsis thaliana (thale cress) Arabidopsis_thaliana Arbisopsis thaliana GC_ID:1 mouse-ear cress ncbi_taxonomy obi.owl pro.owl thale cress thale-cress Murinae GC_ID:1 NCBITaxon:109679 ncbi_taxonomy Mammalia GC_ID:1 mammals mammals ncbi_taxonomy obi.owl pro.owl Dictyostelium discoideum GC_ID:1 ncbi_taxonomy obi.owl pro.owl Ascomycota GC_ID:1 PMID:17572334 ascomycetes ascomycetes ncbi_taxonomy sac fungi Schizosaccharomyces pombe GC_ID:1 NCBITaxon:45042 Schizosaccharomyces malidevorans Schizosaccharomyces pombeP fission yeast ncbi_taxonomy obi.owl pro.owl Saccharomyces cerevisiae Candida robusta GC_ID:1 Saccaromyces cerevisiae Saccharomyce cerevisiae Saccharomyces capensis Saccharomyces italicus Saccharomyces oviformis Saccharomyces uvarum var. melibiosus Saccharomyes cerevisiae Sccharomyces cerevisiae baker's yeast brewer's yeast lager beer yeast ncbi_taxonomy obi.owl pro.owl yeast Plasmodium falciparum GC_ID:1 Plasmodium (Laverania) falciparum doid.owl malaria parasite P. falciparum ncbi_taxonomy pro.owl Caenorhabditis elegans GC_ID:1 Rhabditis elegans ncbi_taxonomy obi.owl pro.owl roundworm Drosophila melanogaster Drosophila melangaster GC_ID:1 Sophophora melanogaster fruit fly ncbi_taxonomy obi.owl pro.owl Danio rerio Brachidanio rerio Brachydanio rerio Brachydanio rerio frankei Cyprinus rerio Danio frankei Danio rerio frankei GC_ID:1 NCBITaxon:27702 NCBITaxon:37966 doid.owl leopard danio ncbi_taxonomy obi.owl pro.owl zebra danio zebra fish zebrafish Salmo salar Atlantic salmon GC_ID:1 doid.owl ncbi_taxonomy pro.owl Gallus gallus GC_ID:1 Gallus domesticus Gallus gallus domesticus bantam chicken chickens ncbi_taxonomy obi.owl pro.owl Homo sapiens GC_ID:1 human man ncbi_taxonomy obi.owl pro.owl Rodentia GC_ID:1 ncbi_taxonomy obi.owl pro.owl rodent rodents 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') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch obi.owl pro.owl 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 age A time quality inhering in a bearer by virtue of how long the bearer has existed. PATO:0000011 obi.owl pato.owl quality fluorescence A luminous flux quality inhering in a bearer by virtue of the bearer's emitting longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together. PATO:0000018 obi.owl pato.owl quality biological sex An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. PATO:0000047 obi.owl pato.owl quality morphology A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. PATO:0000051 quality size A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. PATO:0000117 quality length A 1-D extent quality which is equal to the distance between two points. PATO:0000122 obi.owl pato.owl quality mass A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. PATO:0000125 obi.owl pato.owl quality position A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. PATO:0000140 PATO:0001032 PATO:0001631 location placement quality relational spatial quality structure A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. PATO:0000141 PATO:0001452 conformation quality relational structural quality temperature A physical quality of the thermal energy of a system. PATO:0000146 obi.owl pato.owl quality viability An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population. PATO:0000169 quality behavioral quality An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation. PATO:0000186 PATO:0001722 behavioural quality obi.owl pato.owl quality female A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. PATO:0000383 obi.owl pato.owl quality male A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. PATO:0000384 obi.owl pato.owl quality volume A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. PATO:0000918 obi.owl pato.owl quality physical quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATO:0001018 PATO:0002079 Wikipedia:Physical_property quality relational physical quality pressure A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts. PATO:0001025 obi.owl pato.owl quality diluted A concentration which relatively low. PATO:0001161 obi.owl pato.owl quality damaged A structural quality inhering in a bearer by virtue of the bearer being harmed or injured or spoiled, such that its functionality is impaired. PATO:0001167 obi.owl pato.owl quality lateral to A spatial quality inhering in a bearer by virtue of the bearer's being located toward the side relative to another entity. PATO:0001193 lateral obi.owl pato.owl quality ventral to A spatial quality inhering in a bearer by virtue of the bearer's being located toward the abdomen of an organism relative to another entity. PATO:0001196 anterior_ to obi.owl pato.owl quality dorsal to A spatial quality inhering in a bearer by virtue of the bearer's being located toward the back or upper surface of an organism relative to another entity. PATO:0001233 dorsal obi.owl pato.owl posterior_to (human torso) quality superior_to (human head) obi.owl pato.owl true obi.owl pato.owl true physical object quality A quality which inheres in a continuant. PATO:0001237 PATO:0001238 PATO:0001241 Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. monadic quality of a continuant monadic quality of an object monadic quality of continuant multiply inhering quality of a physical entity quality quality of a continuant quality of a single physical entity quality of an object quality of continuant snap:Quality bacterial mating type A mating type that indicates whether the F plasmid has integrated into the chromosome. PATO:0001335 quality yeast mating type A yeast mating type. PATO:0001337 quality mixed sex A biological sex quality inhering in a population of multiple sexes. For example a mixture of females and male or males and hermaphrodites. PATO:0001338 obi.owl pato.owl quality biomaterial purity A composition quality inhering in an bearer by virtue of the bearer's homogeneity of a biomaterial. PATO:0001339 obi.owl pato.owl quality hermaphrodite A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual. PATO:0001340 intersex obi.owl pato.owl quality a mating type (yeast) A S. cerevisiae mating type cells that secrete a pheromone that in alpha haploids stimulates processes that lead to mating. PATO:0001341 a obi.owl pato.owl quality Saccharomyces cerevisiae mating type A S. cerevisiae mating type. PATO:0001342 quality Schizosaccharomyces pombe mating type A S. pombe mating type determined by the gene configuration on the mat1 locus. PATO:0001343 quality alpha mating type (yeast) A S. cerevisiae mating type cells that secrete a pheromone that stimulates a haploids. PATO:0001344 alpha obi.owl pato.owl quality h minus A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus. M PATO:0001345 h - obi.owl pato.owl quality h plus A S. pombe mating type determined by the mat1-Pc and mat1-Pi on the mat1 locus. P PATO:0001346 h+ obi.owl pato.owl quality F mating type A bacterial mating type indicating the presence of F plasmid in a bacterial cell. PATO:0001347 obi.owl pato.owl quality F minus mating type A bacterial mating type indicating the absence of F plasmid in a bacterial cell. F- PATO:0001348 obi.owl pato.owl quality ploidy A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism. PATO:0001374 obi.owl pato.owl quality haploid A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes. PATO:0001375 obi.owl pato.owl quality polyploid A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes. PATO:0001377 obi.owl pato.owl quality aneuploid A ploidy quality inhering in a bearer by virtue of the bearer's containing a non-integral multiple of the monoploid number, due to extra or missing chromosomes. PATO:0001385 obi.owl pato.owl quality euploid A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes. PATO:0001393 quality diploid A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father. PATO:0001394 The exact number may be one or two different from the 2n number and still be classified as diploidy (although with aneuploidy). Nearly all mammals are diploid organisms, although all individuals have some small fracton of cells that are polyploidy. obi.owl pato.owl quality cellular quality A monadic quality of continuant that exists at the cellular level of organisation. PATO:0001396 obi.owl pato.owl quality alive A viability quality inhering in a bearer by virtue of the bearer's condition before death. PATO:0001421 obi.owl pato.owl quality dead A viability quality inhering in a bearer by virtue of the cessation of the bearer's life. PATO:0001422 obi.owl pato.owl quality quality of a solid A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable. PATO:0001546 obi.owl pato.owl quality solidity quality of a gas A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape. PATO:0001547 gaseous obi.owl pato.owl quality quality of a liquid A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape. PATO:0001548 liquidity obi.owl pato.owl quality obi.owl pato.owl true anterior to A spatial quality inhering in a bearer by virtue of the bearer's being located toward the front of an organism relative to another entity. PATO:0001632 obi.owl pato.owl preceding quality ventral_to radiation quality A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. PATO:0001739 quality radioactive A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity. PATO:0001741 obi.owl pato.owl quality left side of A spatial quality inhering in a bearer by virtue of the bearer's being located on left side of from the a another entity. PATO:0001792 obi.owl pato.owl quality right side of A spatial quality inhering in a bearer by virtue of the bearer's being located on right side of a another entity. PATO:0001793 obi.owl pato.owl quality phenotypic sex PATO:0001894 quality mating type A biological sex quality inhering in an individual or a population that undergo sexual reproduction. PATO:0001895 quality frozen A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point. PATO:0001985 obi.owl pato.owl quality organismal quality A quality that inheres in an entire organism or part of an organism. PATO:0001995 obi.owl pato.owl quality quality of a substance 2010-03-15T04:35:27Z A quality inhering in a bearer by virtue of its constitution. George Gkoutos PATO:0002198 quality handedness 2010-03-22T05:48:33Z A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet. Adapted from Wikipedia and the birnlex term that is dbxref'd. Added on behalf of OBI at March 2010 workshop. PATO:0002201 haendel obi.owl pato.owl quality left handedness 2010-03-22T05:49:06Z Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. PATO:0002202 haendel obi.owl pato.owl quality right handedness 2010-03-22T05:49:19Z Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. PATO:0002203 haendel obi.owl pato.owl quality ambidextrous handedness 2010-03-22T05:49:30Z Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot. PATO:0002204 haendel obi.owl pato.owl quality fluid flow rate 2010-07-28T03:00:20Z A physical quality inhering in a fluid (liquid or gas) by virtue of the amount of fluid which passes through a given surface per unit time. PATO:0002243 george obi.owl pato.owl quality volume flow rate volumetric flow rate plant structure development stage A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes. Arabidopsis growth (related) PO:0007021 PO:0009012 PO_GIT:185 Refers to GO:0032502 (developmental process), including growth, differentiation, and senescence. etapa de desarrollo de estructura vegetal (Spanish, exact) plant growth and development stage (exact) plant_structure_development_stage plant anatomical entity 2010-11-15T11:41:38Z An anatomical entity that is or was part of a plant. Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 anatomical entity is defined as: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. PO:0025131 PO_GIT:224 entidad anat&#243mica vegetal (Spanish, exact) plant_anatomy rwalls 植物 解剖学（形態）的実体 (Japanese, exact) protein An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA. PR:000000001 Proteins descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. obi.owl pro.owl protein CD4 molecule A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence. CD4 Category=gene. Requested by=CL. PIRSF:PIRSF001977 PR:000001004 T-cell differentiation antigen L3T4 T-cell surface antigen T4/Leu-3 T-cell surface glycoprotein CD4 obi.owl pro.owl protein CD3 subunit with immunoglobulin domain A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response. CD3 subunit with Ig-like domain Category=family. PIRSF:PIRSF001993 PR:000001018 obi.owl pro.owl protein antithrombin-III A serpin that is a translation product of the human SERPINC1 gene or a 1:1 ortholog thereof. AT3 ATIII Category=gene. PR:000003252 SERPINC1 obi.owl pro.owl protein serpin C1 double-stranded RNA-specific adenosine deaminase 136 kDa double-stranded RNA-binding protein A protein that is a translation product of the human ADAR gene or a 1:1 ortholog thereof. ADAR ADAR1 Category=gene. DRADA DSRAD G1P1 IFI-4 IFI4 K88DSRBP PR:000003745 RNA adenosine deaminase 1 interferon-inducible protein 4 obi.owl p136 pro.owl protein deoxyribonuclease-1 A protein that is a translation product of the human DNASE1 gene or a 1:1 ortholog thereof. Category=gene. DNASE1 DNL1 DNase I DRNI PR:000006592 deoxyribonuclease I dornase alfa obi.owl pro.owl protein glial cell line-derived neurotrophic factor A protein that is a translation product of the human GDNF gene or a 1:1 ortholog thereof. ATF Category=gene. GDNF PR:000007928 astrocyte-derived trophic factor obi.owl pro.owl protein ribonuclease T2 A protein that is a translation product of the human RNASET2 gene or a 1:1 ortholog thereof. Category=gene. PR:000014060 RNASE6PL RNASET2 obi.owl pro.owl protein ribonuclease 6 DNA ligase A protein that is a translation product of the Escherichia coli K-12 ligA gene or a 1:1 ortholog thereof. Category=gene. PR:000023089 dnaL lig ligA lop obi.owl pdeC polydeoxyribonucleotide synthase [NAD(+)] pro.owl protein T cell receptor co-receptor CD8 A protein complex that is a membrane-bound heterodimeric co-receptor for MHC class-I antigen/T-cell receptor interaction. CD8alphabeta Category=complex. Requested by=CL. PR:000025402 TCR co-receptor CD8 obi.owl pro.owl protein guanyl-specific ribonuclease T1 A protein that is a translation product of the Aspergillus oryzae rntA gene or a 1:1 ortholog thereof. Category=gene. PR:000025467 RNase T1 obi.owl pro.owl protein rntA nuclease S1 A protein that is a translation product of the Aspergillus oryzae nucS gene or a 1:1 ortholog thereof. Category=gene. PR:000025471 deoxyribonuclease S1 endonuclease S1 nucS obi.owl pro.owl protein single-stranded-nucleate endonuclease ribonuclease U2 A protein that is a translation product of the Ustilago sphaerogena RNU2 gene or a 1:1 ortholog thereof. Category=gene. PR:000025475 RNU2 RNase U2 obi.owl pro.owl protein ribonuclease V1 A protein with ribonuclease activity that is a constituent of cobra venom. Category=gene. PR:000025477 RNase V1 obi.owl pro.owl protein ribonuclease CL3 A protein with ribonuclease activity that is purified from chicken liver. Category=gene. PR:000025478 RNase CL3 obi.owl pro.owl protein vessel A tubular structure that contains, conveys body fluid, such as blood or lymph. UBERON:0000055 uberon anatomical structure AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FBbt:00007001 FMA:305751 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 UBERON:0000061 VHOG:0001759 WBbt:0000100 XAO:0003000 ZFA:0000037 biological structure connected biological structure uberon organ Anatomical structure that performs a specific function or group of functions [WP]. CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4 CARO:0020004 EFO:0000634 EMAPA:35949 ENVO:01000162 FMA:67498 MA:0003001 OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. UBERON:0000062 UMLS:C0178784 WBbt:0003760 anatomical unit body organ element uberon life cycle stage A spatiotemporal region encompassing some part of the life cycle of an organism. BILS:0000105 EFO:0000399 FBdv:00007012 FMA:24120 HsapDv:0000000 MmusDv:0000000 OlatDv:0000010 PdumDv:0000090 UBERON:0000105 WBls:0000002 XAO:1000000 ZFS:0000000 ZFS:0100000 developmental stage ncithesaurus:Developmental_Stage stage the WBls class 'all stages' belongs here as it is the superclass of other WBls stages this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here uberon we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage breast BTO:0000149 CALOHA:TS-2083 EV:0100124 FMA:9601 GAID:33 MESH:D001940 OpenCyc:Mx4rvVjV7ZwpEbGdrcN5Y29ycA The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's. The upper ventral region of an animal's torso. UBERON:0000310 UMLS:C0006141 doid.owl galen:Breast mamma mammary part of chest mammary region obi.owl uberon heart A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. AAO:0010210 As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] BILA:0000020 BTO:0000562 Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] CALOHA:TS-0445 EFO:0000815 EHDAA2:0000738 EHDAA:420 EMAPA:16105 EV:0100018 FMA:7088 GAID:174 Herz@de MA:0000072 MAT:0000036 MESH:D006321 MIAA:0000036 OpenCyc:Mx4rvVjvDpwpEbGdrcN5Y29ycA Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] TAO:0000114 Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" http://dx.doi.org/10.1101/gad.1485706 UBERON:0000948 UMLS:C0018787 VHOG:0000276 XAO:0000064 ZFA:0000114 branchial heart cardiac cardium chambered heart doid.owl galen:Heart obi.owl relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] uberon vertebrate heart brain (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] AAO:0010478 ABA:Brain BAMS:Br BAMS:Brain BILA:0000135 BTO:0000142 CALOHA:TS-0095 Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO] DHBA:10155 EFO:0000302 EHDAA2:0000183 EHDAA:2641 EHDAA:6485 EMAPA:16894 EV:0100164 FBbt:00005095 FMA:50801 GAID:571 HBA:4005 MA:0000168 MAT:0000098 MBA:8 MBA:997 MESH:D001921 MIAA:0000098 OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA PBA:3999 Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO] TAO:0000008 The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO) UBERON:0000955 UMLS:C0006104 UMLS:C1269537 VHOG:0000157 XAO:0000010 ZFA:0000008 doid.owl encephalon galen:Brain http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21 obi.owl requires review for applicability to invertebrate structures, e.g. synganglion suprasegmental levels of nervous system suprasegmental structures synganglion the brain uberon anatomical entity AAO:0010841 AEO:0000000 BILA:0000000 Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. CARO:0000000 EHDAA2:0002229 FBbt:10000000 FBbt_root:00000000 FMA:62955 HAO:0000000 MA:0000001 TAO:0100000 TGMA:0001822 UBERON:0001062 UMLS:C1515976 XAO:0000000 ZFA:0100000 uberon skeletal muscle tissue EMAPA:32716 FMA:14069 MA:0002439 Muscle tissue that consists primarily of skeletal muscle fibers. Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO] TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle. This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG] Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA] UBERON:0001134 UMLS:C0242692 doid.owl obi.owl skeletal muscle skeletal muscle system somatic muscle uberon tibial nerve EMAPA:36512 FMA:19035 GAID:854 MA:0001173 MESH:D013979 OpenCyc:Mx4rwNya8JwpEbGdrcN5Y29ycA The tibial nerve is a branch of the sciatic nerve. The tibial nerve passes through the popliteal fossa to pass below the arch of soleus. In the popliteal fossa the nerve gives off branches to gastrocnemius, popliteus, soleus and plantaris muscles, an articular branch to the knee joint, and a cutaneous branch that will become the sural nerve. The sural nerve is joined by fibres from the common peroneal nerve and runs down the calf to supply the lateral side of the foot. Below the soleus muscle the nerve lies close to the tibia and supplies the tibialis posterior, the flexor digitorum longus and the flexor hallucis longus. The nerve passes into the foot running posterior to the medial malleolus. Here it is bound down by the flexor retinaculum in company with the posterior tibial artery. [WP,unvetted]. UBERON:0001323 UMLS:C0040186 doid.owl medial popliteal nerve n. tibialis obi.owl uberon coronary artery An artery that supplies the myocardium. BTO:0000290 CALOHA:TS-0176 EFO:0002551 EMAPA:19160 EMAPA:25968 EV:0100383 FMA:49893 MA:0002453 OpenCyc:Mx4rvoL56ZwpEbGdrcN5Y29ycA UBERON:0001621 UMLS:C0205042 VHOG:0001557 ZFA:0005812 coronary arterial tree coronary vessel doid.owl galen:CoronaryArtery obi.owl uberon blood vessel A vessel through which blood circulates in the body. AAO:0011004 AEO:0000207 Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] Any of the vessels through which blood circulates in the body.[AAO] BTO:0001102 CALOHA:TS-0080 EFO:0000817 EHDAA2:0003252 EHDAA:240 EMAPA:32743 EMAPA:35993 FMA:50722 FMA:63183 FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX GAID:169 MA:0000060 MAT:0000393 MESH:D001808 OpenCyc:Mx4rvVjxlpwpEbGdrcN5Y29ycA TAO:0002137 The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] UBERON:0001981 UMLS:C0005847 VHOG:0001250 XAO:0001011 ZFA:0005314 annelids have blood vessels, but this class is not applicable to annelids. consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus region of vascular tree organ uberon vas sanguineum vascular element vascular tree organ region liver AAO:0010111 All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG] An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003). BTO:0000759 CALOHA:TS-0564 EFO:0000887 EHDAA2:0000997 EHDAA:2197 EMAPA:16846 EV:0100089 FMA:7197 GAID:288 MA:0000358 MAT:0000097 MESH:D008099 MIAA:0000097 Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function. OpenCyc:Mx4rvVimppwpEbGdrcN5Y29ycA Organ which secretes bile and participates in formation of certain blood proteins.[AAO] TAO:0000123 The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates. UBERON:0002107 UMLS:C0023884 VHOG:0000257 XAO:0000133 ZFA:0000123 doid.owl galen:Liver hepatic iecur jecur obi.owl relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO] secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. uberon muscle tissue AAO:0000306 AEO:0000122 CALOHA:TS-0642 EHDAA2:0003122 EMAPA:32715 FMA:9641 MA:0002437 MESH:D009132 Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] UBERON:0002385 UMLS:C2328219 Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach. galen:MuscleTissue muscular tissue portion of muscle tissue textus muscularis uberon gland AAO:0000212 AEO:0000096 BTO:0000522 Druese EFO:0000797 EHDAA2:0003096 EHDAA:2161 EHDAA:4475 EHDAA:6522 EMAPA:18425 FBbt:00100317 FMA:7146 FMA:86294 HAO:0000375 MA:0003038 MAT:0000021 MIAA:0000021 OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA UBERON:0002530 UBERON:MIAA_0000021 UMLS:C1285092 WikipediaCategory:Glands an organ that functions as a secretory or excretory organ galen:Gland glandula glandular glandular organ uberon heart blood vessel A blood vessel that is part of a heart [Automatically generated definition]. EMAPA:35397 MA:0002483 UBERON:0003498 blood vessel of heart cardiac blood vessel uberon mesoderm-derived structure An anatomical structure that develops (entirely or partially) from the mesoderm. FBbt:00025998 Grouping term for query purposes UBERON:0004120 mesodermal derivative uberon trunk region element An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions. MA:0000516 UBERON:0005177 trunk organ uberon coronary vessel Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation MESH:D003331 TODO - change relation from part_of UBERON:0005985 uberon digestive gland A gland, such as the liver or pancreas, that secretes into the alimentary canal substances necessary for digestion. AAO:0000130 BTO:0000345 UBERON:0006925 digestive system gland uberon multicellular anatomical structure An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 UBERON:0010000 multicellular structure uberon Xenopus anatomical entity CARO:0000000 Entity that is either an individual member of Xenopus or constitutes the structural organization of an individual member Xenopus. XAO:0000000 xenopus_anatomy Xenopus developmental stage A temporal interval that defines Xenopus life from unfertilized egg to adult and death stages. XAO:1000000 xenopus_developmental_stage zebrafish anatomical entity ZFA:0100000 zebrafish_anatomy Stages ZFS:0100000 zebrafish_stages