Microbial Conditions Ontology contains terms to describe growth conditions in microbiological experiments. The first version is based on gene regulation experiments in Escherichia coli K-12. It is being used in RegulonDB to link growth conditions to gene regulation data. Citlalli Mejía Almonte Víctor Tierrafría Manuel Camacho Socorro Castro Gama Julio Collado Vides composition composition source synonym description Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label example 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status has curation status definition definition textual definition English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> DEFINITION definition definition textual definition English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. NCI DEFINITION PT NCI editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> IAO:0000116 uberon editor_note true editor_note IAO:0000116 uberon editor_note true editor_note editor note editor note definition editor term editor Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor definition editor term editor term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term alternative term definition source formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source definition source curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg IAO:0000232 uberon curator_notes true curator_notes curator note curator notes imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) has axiom label A property created to allow the source NICHD to assign a parent to each concept with the intent of creating a hierarchy that includes only terms in which they are the contributing source. A11 Conceptual Entity Has_NICHD_Parent Has_NICHD_Parent Has_NICHD_Parent A property created to allow the source NICHD to assign a parent to each concept with the intent of creating a hierarchy that includes only terms in which they are the contributing source. NCI Has_NICHD_Parent PT NCI Used to associate the concept defining a particular terminology subset with concepts that belong to this subset. A8 Conceptual Entity Concept Is In Subset Concept_In_Subset Concept_In_Subset Concept_In_Subset Used to associate the concept defining a particular terminology subset with concepts that belong to this subset. NCI Concept_In_Subset PT NCI true NHC0 code code code code PT The semantic type describes the sort of thing or category to which a concept belongs in the context of the UMLS semantic network. P106 Conceptual Entity Semantic Type Semantic_Type In general, applying semantic types aids in allowing users (or computer programs) to draw conclusions about concepts by virtue of the categories to which they have been assigned. We use a set of semantic types developed for the UMLS Metathesaurus. There are currently 134 semantic types in the UMLS. Semantic_Type Semantic_Type The semantic type describes the sort of thing or category to which a concept belongs in the context of the UMLS semantic network. NCI Semantic_Type PT NCI Provides an alternative Preferred Name for use in some NCI systems. P107 Conceptual Entity Display Name Display_Name Display Name Display_Name Display_Name Provides an alternative Preferred Name for use in some NCI systems. NCI Display Name SY NCI Display_Name PT NCI The word or phrase that NCI uses by preference to refer to the concept. P108 Conceptual Entity Preferred Name Preferred_Name Preferred Name Preferred Term Preferred_Name Preferred_Name The word or phrase that NCI uses by preference to refer to the concept. NCI Preferred Name SY NCI Preferred Term SY NCI Preferred_Name PT NCI Concept Unique Identifiers, or CUIs, are concept numbers assigned by the National Library of Medicine (NLM). If a concept in any NCI-maintained knowledgebase exists in the NLM Unified Medical Language System (UMLS), NCI includes the NLM CUI among the information we provide about the concept. P207 Conceptual Entity UMLS CUI UMLS_CUI UMLS_CUI UMLS_CUI Concept Unique Identifiers, or CUIs, are concept numbers assigned by the National Library of Medicine (NLM). If a concept in any NCI-maintained knowledgebase exists in the NLM Unified Medical Language System (UMLS), NCI includes the NLM CUI among the information we provide about the concept. NCI UMLS_CUI PT NCI Contains the FDA Unique Ingredient Identifier, a key component of the new federal drug information model. P319 Conceptual Entity FDA UNII Code FDA_UNII_Code FDA_UNII_Code FDA_UNII_Code Contains the FDA Unique Ingredient Identifier, a key component of the new federal drug information model. NCI FDA_UNII_Code PT NCI This property is used to indicate when a non-EVS entity has contributed to, and has a stake in, a concept. This is used where such entities, within or outside NCI, have indicated the need to be able to track their own concepts. A single concept can have multiple instances of this property if multiple entities have such a defined stake. P322 Conceptual Entity Contributing Source Contributing_Source Contributing_Source Contributing_Source This property is used to indicate when a non-EVS entity has contributed to, and has a stake in, a concept. This is used where such entities, within or outside NCI, have indicated the need to be able to track their own concepts. A single concept can have multiple instances of this property if multiple entities have such a defined stake. NCI Contributing_Source PT NCI English language definitions of what a source other than NCI means by the concept. These are limited to 1024 characters. They include information about the definition's source in a form that can easily be interpreted by software. P325 Conceptual Entity [source] Definition ALT_DEFINITION ALT_DEFINITION ALT_DEFINITION English language definitions of what a source other than NCI means by the concept. These are limited to 1024 characters. They include information about the definition's source in a form that can easily be interpreted by software. NCI ALT_DEFINITION PT NCI The NCBI_Taxon_ID property is used to establish correspondence between the NCI Thesaurus concept representing a taxon (species) and the NCBI/NLM Species Taxonomy ID assigned by the NCBI to that taxon. P331 Conceptual Entity NCBI Taxon ID NCBI_Taxon_ID NCBI_Taxon_ID NCBI_Taxon_ID The NCBI_Taxon_ID property is used to establish correspondence between the NCI Thesaurus concept representing a taxon (species) and the NCBI/NLM Species Taxonomy ID assigned by the NCBI to that taxon. NCI NCBI_Taxon_ID PT NCI true A retired unique concept identifier created and stored as Concept Name by legacy EVS software. Use of these values was long discouraged, but continued as late as 2009 when creation of new values ceased and Concept Name was retired. Legacy values are intended solely to help resolve and update earlier coding. P366 Conceptual Entity Legacy Concept Name Legacy Concept Name Legacy_Concept_Name A retired unique concept identifier created and stored as Concept Name by legacy EVS software. Use of these values was long discouraged, but continued as late as 2009 when creation of new values ceased and Concept Name was retired. Legacy values are intended solely to help resolve and update earlier coding. NCI Legacy Concept Name PT NCI P371 Conceptual Entity NICHD_Hierarchy_Term NICHD NICHD_Hierarchy_Term NICHD_Hierarchy_Term NICHD_Hierarchy_Term PT NCI Design notes are notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept. P98 Conceptual Entity DesignNote DesignNote DesignNote DesignNote Design notes are notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept. NCI DesignNote PT NCI RO:0002604 quality is_opposite_of true true is_opposite_of is opposite_of 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'. UBPROP:0000007 uberon has_relational_adjective true has_relational_adjective has_relational_adjective Notes on the how instances of this class vary across species. UBPROP:0000008 uberon taxon_notes true taxon_notes taxon_notes Notes on the how instances of this class vary across species. 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 UBPROP:0000012 uberon external_ontology_notes true external_ontology_notes external_ontology_notes Notes on how similar or equivalent classes are represented in other ontologies. Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. An account of the content of the resource. Description Description The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a resource from which the present resource is derived. Source Source has_alternative_id has_broad_synonym database_cross_reference Fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software. FULL_SYN Synonym with Source Data has exact synonym has_exact_synonym Fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software. NCI FULL_SYN PT NCI Synonym with Source Data SY NCI has_narrow_synonym has_obo_namespace has_related_synonym in_subset shorthand label label BFO:0000051 chebi_ontology has_part false has_part has part RO:0000087 chebi_ontology has_role false false has_role has role c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) has biological role chebi_ontology has_functional_parent false false has functional parent chebi_ontology has_parent_hydride false false has parent hydride chebi_ontology is_conjugate_acid_of true false is conjugate acid of chebi_ontology is_conjugate_base_of true false is conjugate base of chebi_ontology is_enantiomer_of true false is enantiomer of chebi_ontology is_substituent_group_from false false is substituent group from chebi_ontology is_tautomer_of true is tautomer of has biological role in Escherichia coli a relation between a continuant and a treatment, in which the continuant is a necessary component of the treatment used in treatment a relation between a continuant and a treatment, in which the continuant is a necessary component of the treatment, specifically in Escherichia coli experiments used in Escherichia coli treatment a relation between a culture medium and an organism, in wich the culture medium contains the minimal necessities for growth of the wild-type of that organism and contains only inorganic salts, a carbon source for that organism, and water. is minimal medium for a relation between a culture medium and an organism, in which the medium contains all the elements that the specific organism needs for growth and is non-selective, so it is used for the general cultivation and maintenance of the organism kept in laboratory culture collections is rich medium for entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] occurrent Occurrent BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] s-region SpatialRegion 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. 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]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith 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]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] t-region TemporalRegion Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] temporal region 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 per discussion with Barry Smith A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] 2d-s-region TwoDimensionalSpatialRegion an infinitely thin plane in space. the surface of a sphere-shaped part of space A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] two-dimensional spatial region A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] st-region SpatiotemporalRegion 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 A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [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]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] spatiotemporal region A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [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 s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] 0d-s-region ZeroDimensionalSpatialRegion A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] zero-dimensional spatial region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality (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] a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] fiat-object-part FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object part b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] 1d-s-region OneDimensionalSpatialRegion an edge of a cube-shaped portion of space. 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]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] one-dimensional spatial 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]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] 3d-s-region ThreeDimensionalSpatialRegion a cube-shaped region of space a sphere-shaped region of space, A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] three-dimensional spatial region A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] site Site Manhattan Canyon) a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] site b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] object Object atom cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 BFO 2 Reference: an object is a maximal causally unified material entity BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) object 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]) gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] p-boundary ProcessBoundary the boundary between the 2nd and 3rd year of your life. 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]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] process boundary 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]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] 1d-t-region OneDimensionalTemporalRegion the temporal region during which a process occurs. BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal region A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] material MaterialEntity material entity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. Examples: collection of random bacteria, a chair, dorsal surface of the body Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] cf-boundary ContinuantFiatBoundary 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]) BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. Every continuant fiat boundary is located at some spatial region at every time at which it exists (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] continuant fiat boundary 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]) 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. (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] immaterial ImmaterialEntity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity 1d-cf-boundary OneDimensionalContinuantFiatBoundary The Equator all geopolitical boundaries all lines of latitude and longitude the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. the median sulcus of your tongue a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] one-dimensional continuant fiat boundary a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] process-profile ProcessProfile 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. 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]) (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] process profile 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]) (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] r-quality RelationalQuality 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. a marriage bond, an instance of love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] relational quality b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] 2d-cf-boundary TwoDimensionalContinuantFiatBoundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] two-dimensional continuant fiat boundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary the geographic North Pole the point of origin of some spatial coordinate system. the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] zero-dimensional continuant fiat boundary 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. requested by Melanie Courtot a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] 0d-t-region ZeroDimensionalTemporalRegion a temporal region that is occupied by a process boundary right now the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. temporal instant. A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] zero-dimensional temporal region A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] history History A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) A monocarboxylic acid comprising 1,8-naphthyridin-4-one substituted by carboxylic acid, ethyl and methyl groups at positions 3, 1, and 7, respectively. An orally administered antibacterial, it is used in the treatment of lower urinary-tract infections due to Gram-negative bacteria, including the majority of E. coli, Enterobacter, Klebsiella, and Proteus species. CHEBI:7456 CAS:389-08-2 DrugBank:DB00779 Drug_Central:1875 KEGG:C05079 KEGG:D00183 LINCS:LSM-5590 PDBeChem:NIX PMID:11321869 PMID:12002106 PMID:12399485 PMID:12702698 PMID:14107587 PMID:16107187 PMID:16423473 PMID:16667857 PMID:16803589 PMID:17132068 PMID:17631104 PMID:18788798 PMID:19071706 PMID:28166217 Patent:BE612258 Patent:US3590036 Reaxys:750515 Wikipedia:Nalidixic_Acid colombos:NALIDIXIC_ACID 1-ethyl-7-methyl-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carboxylic acid NALIDIXIC ACID Nalidixic acid chebi_ontology 0 1,4-dihydro-1-ethyl-7-methyl-4-oxo-1,8-naphthyridine-3-carboxylic acid 1-Aethyl-7-methyl-1,8-naphthyridin-4-on-3-karbonsaeure 1-Ethyl-7-methyl-4-oxo-1,4-dihydro-[1,8]naphthyridine-3-carboxylic acid 1-ethyl-1,4-dihydro-7-methyl-4-oxo-1,8-naphthyridine-3-carboxylic acid 1-ethyl-7-methyl-1,4-dihydro-1,8-naphthyridin-4-one-3-carboxylic acid 232.085 232.23530 3-carboxy-1-ethyl-7-methyl-1,8-naphthyridin-4-one C12H12N2O3 CCn1cc(C(O)=O)c(=O)c2ccc(C)nc12 InChI=1S/C12H12N2O3/c1-3-14-6-9(12(16)17)10(15)8-5-4-7(2)13-11(8)14/h4-6H,3H2,1-2H3,(H,16,17) MHWLWQUZZRMNGJ-UHFFFAOYSA-N acide nalidixique acido nalidixico acidum nalidixicum nalidixic acid CHEBI:100147 nalidixic acid CAS:389-08-2 ChemIDplus CAS:389-08-2 KEGG COMPOUND Drug_Central:1875 DrugCentral PMID:11321869 Europe PMC PMID:12002106 Europe PMC PMID:12399485 Europe PMC PMID:12702698 Europe PMC PMID:14107587 Europe PMC PMID:16107187 Europe PMC PMID:16423473 Europe PMC PMID:16667857 Europe PMC PMID:16803589 Europe PMC PMID:17132068 Europe PMC PMID:17631104 Europe PMC PMID:18788798 Europe PMC PMID:19071706 Europe PMC PMID:28166217 Europe PMC Reaxys:750515 Reaxys 1-ethyl-7-methyl-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carboxylic acid IUPAC NALIDIXIC ACID ChEMBL Nalidixic acid KEGG_COMPOUND 0 ChEBI 1,4-dihydro-1-ethyl-7-methyl-4-oxo-1,8-naphthyridine-3-carboxylic acid ChemIDplus 1-Aethyl-7-methyl-1,8-naphthyridin-4-on-3-karbonsaeure ChemIDplus 1-Ethyl-7-methyl-4-oxo-1,4-dihydro-[1,8]naphthyridine-3-carboxylic acid ChEMBL 1-ethyl-1,4-dihydro-7-methyl-4-oxo-1,8-naphthyridine-3-carboxylic acid ChemIDplus 1-ethyl-7-methyl-1,4-dihydro-1,8-naphthyridin-4-one-3-carboxylic acid ChemIDplus 232.085 KEGG_COMPOUND 232.23530 ChEBI 3-carboxy-1-ethyl-7-methyl-1,8-naphthyridin-4-one ChemIDplus C12H12N2O3 KEGG_COMPOUND CCn1cc(C(O)=O)c(=O)c2ccc(C)nc12 ChEBI InChI=1S/C12H12N2O3/c1-3-14-6-9(12(16)17)10(15)8-5-4-7(2)13-11(8)14/h4-6H,3H2,1-2H3,(H,16,17) ChEBI MHWLWQUZZRMNGJ-UHFFFAOYSA-N ChEBI acide nalidixique ChemIDplus acido nalidixico ChemIDplus acidum nalidixicum ChemIDplus nalidixic acid ChemIDplus A quinolone that is quinolin-4(1H)-one bearing cyclopropyl, carboxylic acid, fluoro and piperazin-1-yl substituents at positions 1, 3, 6 and 7, respectively. CHEBI:102718 CHEBI:3717 CHEBI:41638 Beilstein:3568352 CAS:85721-33-1 DrugBank:DB00537 Drug_Central:659 HMDB:HMDB14677 KEGG:C05349 KEGG:D00186 LINCS:LSM-5226 PDBeChem:CPF PMID:10397494 PMID:10737746 Patent:DE3142854 Patent:US4670444 Reaxys:3568352 Wikipedia:Ciprofloxacin colombos:CIPROFLOXACIN 1-cyclopropyl-6-fluoro-4-oxo-7-(piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylic acid Ciprofloxacin ciprofloxacin chebi_ontology 0 1-CYCLOPROPYL-6-FLUORO-4-OXO-7-PIPERAZIN-1-YL-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC ACID 1-Cyclopropyl-6-fluoro-4-oxo-7-piperazin-1-yl-1,4-dihydro-quinoline-3-carboxylic acid 1-Cyclopropyl-6-fluoro-7-(4-methyl-piperazin-1-yl)-4-oxo-1,4-dihydro-quinoline-3-carboxylic acid 1-cyclopropyl-6-fluoro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid 1-cyclopropyl-6-fluoro-4-oxo-7-(piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylic acid 1-cyclopropyl-6-fluoro-4-oxo-7-piperazin-1-ylquinoline-3-carboxylic acid 1-cyclopropyl-6-fluoro-7-hexahydro-1-pyrazinyl-4-oxo-1,4-dihydro-3-quinolinecarboxylic acid 331.133 331.34150 C17H18FN3O3 InChI=1S/C17H18FN3O3/c18-13-7-11-14(8-15(13)20-5-3-19-4-6-20)21(10-1-2-10)9-12(16(11)22)17(23)24/h7-10,19H,1-6H2,(H,23,24) MYSWGUAQZAJSOK-UHFFFAOYSA-N OC(=O)c1cn(C2CC2)c2cc(N3CCNCC3)c(F)cc2c1=O ciprofloxacin ciprofloxacine ciprofloxacino ciprofloxacinum CHEBI:100241 ciprofloxacin Beilstein:3568352 Beilstein CAS:85721-33-1 ChemIDplus CAS:85721-33-1 KEGG COMPOUND Drug_Central:659 DrugCentral PMID:10397494 ChEMBL PMID:10737746 ChEMBL Reaxys:3568352 Reaxys 1-cyclopropyl-6-fluoro-4-oxo-7-(piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylic acid IUPAC Ciprofloxacin KEGG_COMPOUND ciprofloxacin ChEMBL 0 ChEBI 1-CYCLOPROPYL-6-FLUORO-4-OXO-7-PIPERAZIN-1-YL-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC ACID PDBeChem 1-Cyclopropyl-6-fluoro-4-oxo-7-piperazin-1-yl-1,4-dihydro-quinoline-3-carboxylic acid ChEMBL 1-Cyclopropyl-6-fluoro-7-(4-methyl-piperazin-1-yl)-4-oxo-1,4-dihydro-quinoline-3-carboxylic acid ChEMBL 1-cyclopropyl-6-fluoro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid ChemIDplus 1-cyclopropyl-6-fluoro-4-oxo-7-(piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylic acid ChEMBL 1-cyclopropyl-6-fluoro-4-oxo-7-piperazin-1-ylquinoline-3-carboxylic acid ChEMBL 1-cyclopropyl-6-fluoro-7-hexahydro-1-pyrazinyl-4-oxo-1,4-dihydro-3-quinolinecarboxylic acid ChEMBL 331.133 KEGG_COMPOUND 331.34150 ChEBI C17H18FN3O3 KEGG_COMPOUND InChI=1S/C17H18FN3O3/c18-13-7-11-14(8-15(13)20-5-3-19-4-6-20)21(10-1-2-10)9-12(16(11)22)17(23)24/h7-10,19H,1-6H2,(H,23,24) ChEBI MYSWGUAQZAJSOK-UHFFFAOYSA-N ChEBI OC(=O)c1cn(C2CC2)c2cc(N3CCNCC3)c(F)cc2c1=O ChEBI ciprofloxacin ChemIDplus ciprofloxacine ChemIDplus ciprofloxacino ChemIDplus ciprofloxacinum ChemIDplus A quinolinemonocarboxylic acid with broad-spectrum antibacterial activity against most gram-negative and gram-positive bacteria. Norfloxacin is bactericidal and its mode of action depends on blocking of bacterial DNA replication by binding itself to an enzyme called DNA gyrase. CHEBI:7629 Beilstein:567897 CAS:70458-96-7 DrugBank:DB01059 Drug_Central:1967 Gmelin:1576626 HMDB:HMDB15192 KEGG:C06687 KEGG:D00210 LINCS:LSM-5286 PMID:3317294 PMID:3908074 PMID:6211142 PMID:6224685 PMID:6234465 PMID:6454381 PMID:6461606 Patent:BE863429 Patent:DE2840910 Patent:US4146719 Patent:US4292317 Reaxys:567897 Wikipedia:Norfloxacin colombos:NORFLOXACIN 1-ethyl-6-fluoro-4-oxo-7-(piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylic acid chebi_ontology 0 1,4-Dihydro-1-ethyl-6-fluoro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid 1-Ethyl-6-fluor-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-chinolincarbonsaeure 1-Ethyl-6-fluoro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid 319.133 319.33080 C16H18FN3O3 CCn1cc(C(O)=O)c(=O)c2cc(F)c(cc12)N1CCNCC1 InChI=1S/C16H18FN3O3/c1-2-19-9-11(16(22)23)15(21)10-7-12(17)14(8-13(10)19)20-5-3-18-4-6-20/h7-9,18H,2-6H2,1H3,(H,22,23) NFLX OGJPXUAPXNRGGI-UHFFFAOYSA-N norfloxacin norfloxacine norfloxacino norfloxacinum CHEBI:100246 norfloxacin Beilstein:567897 Beilstein CAS:70458-96-7 ChemIDplus CAS:70458-96-7 KEGG COMPOUND Drug_Central:1967 DrugCentral Gmelin:1576626 Gmelin PMID:3317294 Europe PMC PMID:3908074 Europe PMC PMID:6211142 Europe PMC PMID:6224685 Europe PMC PMID:6234465 Europe PMC PMID:6454381 Europe PMC PMID:6461606 Europe PMC Reaxys:567897 Reaxys 1-ethyl-6-fluoro-4-oxo-7-(piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylic acid IUPAC 0 ChEBI 1,4-Dihydro-1-ethyl-6-fluoro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid ChemIDplus 1-Ethyl-6-fluor-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-chinolincarbonsaeure ChemIDplus 1-Ethyl-6-fluoro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid ChemIDplus 319.133 KEGG_COMPOUND 319.33080 ChEBI C16H18FN3O3 KEGG_COMPOUND CCn1cc(C(O)=O)c(=O)c2cc(F)c(cc12)N1CCNCC1 ChEBI InChI=1S/C16H18FN3O3/c1-2-19-9-11(16(22)23)15(21)10-7-12(17)14(8-13(10)19)20-5-3-18-4-6-20/h7-9,18H,2-6H2,1H3,(H,22,23) ChEBI NFLX KEGG_DRUG OGJPXUAPXNRGGI-UHFFFAOYSA-N ChEBI norfloxacin KEGG_DRUG norfloxacine ChemIDplus norfloxacino ChemIDplus norfloxacinum ChemIDplus A sulfonamide antibacterial with an oxazole substituent. It has antibiotic activity against a wide range of gram-negative and gram-positive organisms. CHEBI:9343 Beilstein:263871 CAS:127-69-5 DrugBank:DB00263 Drug_Central:2529 Gmelin:864477 KEGG:C07318 KEGG:D00450 LINCS:LSM-3120 PMID:1861917 PMID:4960234 PMID:7356572 Patent:US2430094 Wikipedia:Sulfisoxazole colombos:SULFISOXAZOLE colombos:SULFISOXAZOLE:+UNKNOWN 4-amino-N-(3,4-dimethylisoxazol-5-yl)benzenesulfonamide chebi_ontology 0 267.068 267.30400 3,4-Dimethyl-5-sulfanilamidoisoxazole 3,4-Dimethyl-5-sulfonamidoisoxazole 3,4-Dimethyl-5-sulphanilamidoisoxazole 3,4-Dimethyl-5-sulphonamidoisoxazole 3,4-Dimethylisoxazole-5-sulfanilamide 3,4-Dimethylisoxazole-5-sulphanilamide 4-Amino-N-(3,4-dimethyl-5-isoxazolyl)benzenesulfonamide 4-Amino-N-(3,4-dimethyl-5-isoxazolyl)benzenesulphonamide 5-(4-Aminophenylsulfonamido)-3,4-dimethylisoxazole 5-(p-Aminobenzenesulfonamido)-3,4-dimethylisoxazole 5-(p-Aminobenzenesulphonamido)-3,4-dimethylisoxazole 5-Sulfanilamido-3,4-dimethylisoxazole 5-Sulphanilamido-3,4-dimethyl-isoxazole C11H13N3O3S Cc1noc(NS(=O)(=O)c2ccc(N)cc2)c1C InChI=1S/C11H13N3O3S/c1-7-8(2)13-17-11(7)14-18(15,16)10-5-3-9(12)4-6-10/h3-6,14H,12H2,1-2H3 N'-(3,4)Dimethylisoxazol-5-yl-sulphanilamide N(1)-(3,4-dimethyl-5-isoxazolyl)sulfanilamide N(1)-(3,4-dimethyl-5-isoxazolyl)sulphanilamide NHUHCSRWZMLRLA-UHFFFAOYSA-N Sulfadimethylisoxazole Sulfafurazol Sulfaisoxazole Sulfasoxazole Sulfisonazole Sulfisoxasole Sulfisoxazol Sulfofurazole Sulphadimethylisoxazole Sulphafurazol Sulphafurazole Sulphaisoxazole Sulphisoxazol Sulphofurazole sulfafurazole sulfafurazolum CHEBI:102484 sulfisoxazole Beilstein:263871 Beilstein CAS:127-69-5 ChemIDplus CAS:127-69-5 NIST Chemistry WebBook Drug_Central:2529 DrugCentral Gmelin:864477 Gmelin PMID:1861917 Europe PMC PMID:4960234 Europe PMC PMID:7356572 Europe PMC 4-amino-N-(3,4-dimethylisoxazol-5-yl)benzenesulfonamide IUPAC 0 ChEBI 267.068 KEGG_COMPOUND 267.30400 ChEBI 3,4-Dimethyl-5-sulfanilamidoisoxazole ChemIDplus 3,4-Dimethyl-5-sulfonamidoisoxazole ChemIDplus 3,4-Dimethyl-5-sulphanilamidoisoxazole ChemIDplus 3,4-Dimethyl-5-sulphonamidoisoxazole ChemIDplus 3,4-Dimethylisoxazole-5-sulfanilamide ChemIDplus 3,4-Dimethylisoxazole-5-sulphanilamide ChemIDplus 4-Amino-N-(3,4-dimethyl-5-isoxazolyl)benzenesulfonamide NIST_Chemistry_WebBook 4-Amino-N-(3,4-dimethyl-5-isoxazolyl)benzenesulphonamide ChemIDplus 5-(4-Aminophenylsulfonamido)-3,4-dimethylisoxazole ChemIDplus 5-(p-Aminobenzenesulfonamido)-3,4-dimethylisoxazole ChemIDplus 5-(p-Aminobenzenesulphonamido)-3,4-dimethylisoxazole ChemIDplus 5-Sulfanilamido-3,4-dimethylisoxazole ChemIDplus 5-Sulphanilamido-3,4-dimethyl-isoxazole ChemIDplus C11H13N3O3S KEGG_COMPOUND Cc1noc(NS(=O)(=O)c2ccc(N)cc2)c1C ChEBI InChI=1S/C11H13N3O3S/c1-7-8(2)13-17-11(7)14-18(15,16)10-5-3-9(12)4-6-10/h3-6,14H,12H2,1-2H3 ChEBI N'-(3,4)Dimethylisoxazol-5-yl-sulphanilamide ChemIDplus N(1)-(3,4-dimethyl-5-isoxazolyl)sulfanilamide ChemIDplus N(1)-(3,4-dimethyl-5-isoxazolyl)sulphanilamide ChemIDplus NHUHCSRWZMLRLA-UHFFFAOYSA-N ChEBI Sulfadimethylisoxazole DrugBank Sulfafurazol DrugBank Sulfaisoxazole DrugBank Sulfasoxazole DrugBank Sulfisonazole DrugBank Sulfisoxasole DrugBank Sulfisoxazol DrugBank Sulfofurazole DrugBank Sulphadimethylisoxazole NIST_Chemistry_WebBook Sulphafurazol DrugBank Sulphafurazole DrugBank Sulphaisoxazole DrugBank Sulphisoxazol DrugBank Sulphofurazole DrugBank sulfafurazole KEGG_DRUG sulfafurazolum ChemIDplus Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV. KEGG:C05359 PMID:21614077 electron chebi_ontology -1 0.000548579903 [*-] beta beta(-) beta-particle e e(-) e- negatron CHEBI:10545 electron PMID:21614077 Europe PMC electron ChEBI electron IUPAC electron KEGG_COMPOUND -1 ChEBI 0.000548579903 ChEBI [*-] ChEBI beta IUPAC beta(-) ChEBI beta-particle IUPAC e IUPAC e(-) UniProt e- KEGG_COMPOUND negatron IUPAC CHEBI:26614 Beilstein:2206312 CAS:488-59-5 Gmelin:561300 KEGG:C06153 PMID:24352657 Reaxys:2206312 scyllo-Inositol scyllo-inositol chebi_ontology (1r,2r,3r,4r,5r,6r)-cyclohexane-1,2,3,4,5,6-hexol 0 1,3,5/2,4,6-cyclohexanehexol 180.063 180.15588 C6H12O6 CDAISMWEOUEBRE-CDRYSYESSA-N Cocositol InChI=1S/C6H12O6/c7-1-2(8)4(10)6(12)5(11)3(1)9/h1-12H/t1-,2-,3+,4+,5-,6- O[C@H]1[C@H](O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H]1O Quercinitol Scyllitol CHEBI:10642 scyllo-inositol Beilstein:2206312 Beilstein CAS:488-59-5 ChemIDplus CAS:488-59-5 KEGG COMPOUND CAS:488-59-5 NIST Chemistry WebBook Gmelin:561300 Gmelin PMID:24352657 Europe PMC Reaxys:2206312 Reaxys scyllo-Inositol KEGG_COMPOUND scyllo-inositol IUPAC scyllo-inositol UniProt (1r,2r,3r,4r,5r,6r)-cyclohexane-1,2,3,4,5,6-hexol IUPAC 0 ChEBI 1,3,5/2,4,6-cyclohexanehexol IUPAC 180.063 KEGG_COMPOUND 180.15588 ChEBI C6H12O6 KEGG_COMPOUND CDAISMWEOUEBRE-CDRYSYESSA-N ChEBI Cocositol NIST_Chemistry_WebBook InChI=1S/C6H12O6/c7-1-2(8)4(10)6(12)5(11)3(1)9/h1-12H/t1-,2-,3+,4+,5-,6- ChEBI O[C@H]1[C@H](O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H]1O ChEBI Quercinitol ChemIDplus Scyllitol ChemIDplus An organic sodium salt resulting from the replacement of the proton from the carboxy group of benzoic acid by a sodium ion. CAS:532-32-1 KEGG:D02277 PMID:25377186 PMID:25582668 PMID:26585641 PMID:26706697 PMID:26749113 PMID:26870932 PMID:26875563 PMID:26907495 PMID:26951541 PMID:26989415 PMID:27000017 Reaxys:1100243 Wikipedia:Sodium_benzoate colombos:SODIUMBENZOATE colombos:SODIUM_BENZOATE sodium benzoate chebi_ontology 0 144.019 144.103 Benzoic acid, sodium salt C(C=1C=CC=CC1)([O-])=O.[Na+] C7H5NaO2 E211 InChI=1S/C7H6O2.Na/c8-7(9)6-4-2-1-3-5-6;/h1-5H,(H,8,9);/q;+1/p-1 Sodium benzoate WXMKPNITSTVMEF-UHFFFAOYSA-M CHEBI:113455 sodium benzoate CAS:532-32-1 ChemIDplus CAS:532-32-1 KEGG DRUG CAS:532-32-1 NIST Chemistry WebBook PMID:25377186 Europe PMC PMID:25582668 Europe PMC PMID:26585641 Europe PMC PMID:26706697 Europe PMC PMID:26749113 Europe PMC PMID:26870932 Europe PMC PMID:26875563 Europe PMC PMID:26907495 Europe PMC PMID:26951541 Europe PMC PMID:26989415 Europe PMC PMID:27000017 Europe PMC Reaxys:1100243 Reaxys sodium benzoate IUPAC 0 ChEBI 144.019 ChEBI 144.103 ChEBI Benzoic acid, sodium salt ChemIDplus C(C=1C=CC=CC1)([O-])=O.[Na+] ChEBI C7H5NaO2 ChEBI E211 ChEBI InChI=1S/C7H6O2.Na/c8-7(9)6-4-2-1-3-5-6;/h1-5H,(H,8,9);/q;+1/p-1 ChEBI Sodium benzoate KEGG_DRUG WXMKPNITSTVMEF-UHFFFAOYSA-M ChEBI The conjugate base of gamma-amino-beta-hydroxybutyric acid arising from deprotonation of the carboxy group. CAS:352-21-6 KEGG:C03678 4-Amino-3-hydroxybutanoate chebi_ontology -1 118.050 118.11126 C4H8NO3 InChI=1S/C4H9NO3/c5-2-3(6)1-4(7)8/h3,6H,1-2,5H2,(H,7,8)/p-1 NCC(O)CC([O-])=O YQGDEPYYFWUPGO-UHFFFAOYSA-M CHEBI:11955 4-amino-3-hydroxybutanoate CAS:352-21-6 KEGG COMPOUND KEGG:C03678 ChEBI 4-Amino-3-hydroxybutanoate KEGG_COMPOUND -1 ChEBI 118.050 ChEBI 118.11126 ChEBI C4H8NO3 ChEBI InChI=1S/C4H9NO3/c5-2-3(6)1-4(7)8/h3,6H,1-2,5H2,(H,7,8)/p-1 ChEBI NCC(O)CC([O-])=O ChEBI YQGDEPYYFWUPGO-UHFFFAOYSA-M ChEBI D-galacto-hexose D-galactose chebi_ontology 0 180.15588 C6H12O6 D-Gal CHEBI:12936 D-galactose D-galacto-hexose IUPAC D-galactose IUPAC 0 ChEBI 180.15588 ChEBI C6H12O6 ChEBI D-Gal JCBN A 3-hydroxymonocarboxylic acid that is the 3-hydroxy derivative of 3-butenoic acid. Chemspider:8637633 3-hydroxybut-3-enoic acid chebi_ontology 0 102.032 102.089 C4H6O3 InChI=1S/C4H6O3/c1-3(5)2-4(6)7/h5H,1-2H2,(H,6,7) OC(CC(O)=O)=C YMXHTKKMLXGXDC-UHFFFAOYSA-N CHEBI:131367 3-hydroxy-3-butenoic acid 3-hydroxybut-3-enoic acid IUPAC 0 ChEBI 102.032 ChEBI 102.089 ChEBI C4H6O3 ChEBI InChI=1S/C4H6O3/c1-3(5)2-4(6)7/h5H,1-2H2,(H,6,7) ChEBI OC(CC(O)=O)=C ChEBI YMXHTKKMLXGXDC-UHFFFAOYSA-N ChEBI A disaccharide formed by a (1<->1)-glycosidic bond between two hexopyranose units. hexopyranosyl hexopyranoside chebi_ontology CHEBI:131401 hexopyranosyl hexopyranoside hexopyranosyl hexopyranoside IUPAC Any bacterial metabolite produced during a metabolic reaction in Mycoplasma genitalium. chebi_ontology Mycoplasma genitalium metabolites CHEBI:131604 Mycoplasma genitalium metabolite Mycoplasma genitalium metabolites ChEBI A steroid compound with a structure based on a 24-carbon (cholane) skeleton. chebi_ontology C24-steroids CHEBI:131620 C24-steroid C24-steroids ChEBI Any steroid (or derivative) based on a cholane skeleton. chebi_ontology cholane derivatives CHEBI:131657 cholane derivative cholane derivatives ChEBI Any steroid acid anion based on a cholanic acid skeleton. chebi_ontology cholanic acid anions cholanoic acid anions CHEBI:131878 cholanic acid anion cholanic acid anions ChEBI cholanoic acid anions ChEBI An organic anion obtained by deprotonation of any cholanic acid conjugate. chebi_ontology cholanic acid conjugate anions cholanoic acid conjugate anion cholanoic acid conjugate anions CHEBI:131879 cholanic acid conjugate anion cholanic acid conjugate anions SUBMITTER cholanoic acid conjugate anion SUBMITTER cholanoic acid conjugate anions ChEBI A class of carbonyl compound encompassing dicarboxylic acids and any derivatives obtained by substitution of either one or both of the carboxy hydrogens. chebi_ontology dicarboxylic acids and derivatives CHEBI:131927 dicarboxylic acids and O-substituted derivatives dicarboxylic acids and derivatives ChEBI Any quinone in which one or more of the carbons making up the quinone moiety is substituted by a hydroxy group. chebi_ontology hydroxyquinones CHEBI:132130 hydroxyquinone hydroxyquinones ChEBI A naphthoquinone in which the oxo groups of the quinone moiety are at positions 1 and 4 of the parent naphthalene ring. chebi_ontology CHEBI:132142 1,4-naphthoquinones Any naphthoquinone in which the naphthaoquinone moiety is substituted by at least one hydroxy group. Wikipedia:Hydroxynaphthoquinone chebi_ontology hydroxynaphthoquinones CHEBI:132155 hydroxynaphthoquinone hydroxynaphthoquinones ChEBI Any member of the class of 1,4-naphthoquinones in which the naphthoquinone moiety is substituted by at least one hydroxy group. chebi_ontology hydroxy-1,4-naphthoquinones CHEBI:132157 hydroxy-1,4-naphthoquinone hydroxy-1,4-naphthoquinones ChEBI A citrate anion obtained by deprotonation of the three carboxy groups as well as the hydroxy group of citric acid. Chemspider:34552020 2-oxidopropane-1,2,3-tricarboxylate chebi_ontology -4 187.996 188.092 2-oxido-1,2,3-propanetricarboxylate C(=O)([O-])C(CC(=O)[O-])(CC(=O)[O-])[O-] C6H4O7 InChI=1S/C6H7O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h1-2H2,(H,7,8)(H,9,10)(H,11,12)/q-1/p-3 KSXLKRAZYZIYCZ-UHFFFAOYSA-K citric acid tetraanion CHEBI:132362 citrate(4-) 2-oxidopropane-1,2,3-tricarboxylate IUPAC -4 ChEBI 187.996 ChEBI 188.092 ChEBI 2-oxido-1,2,3-propanetricarboxylate ChEBI C(=O)([O-])C(CC(=O)[O-])(CC(=O)[O-])[O-] ChEBI C6H4O7 ChEBI InChI=1S/C6H7O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h1-2H2,(H,7,8)(H,9,10)(H,11,12)/q-1/p-3 ChEBI KSXLKRAZYZIYCZ-UHFFFAOYSA-K ChEBI citric acid tetraanion ChEBI Any aromatic amide obtained by acylation of aniline. KEGG:C01402 PMID:23535982 PMID:23968552 PMID:24273122 PMID:6205897 chebi_ontology 0 120.045 120.12860 C7H6NOR N-phenyl amide N-phenyl amides [*]C(=O)Nc1ccccc1 an anilide CHEBI:13248 anilide PMID:23535982 Europe PMC PMID:23968552 Europe PMC PMID:24273122 Europe PMC PMID:6205897 Europe PMC 0 ChEBI 120.045 ChEBI 120.12860 ChEBI C7H6NOR ChEBI N-phenyl amide ChEBI N-phenyl amides ChEBI [*]C(=O)Nc1ccccc1 ChEBI an anilide UniProt A reagent that lightens or whitens a substrate through chemical reaction. Bleaching reactions usually involve oxidative or reductive processes that degrade colour systems. Bleaching can occur by destroying one or more of the double bonds in the conjugated chain, by cleaving the conjugated chain, or by oxidation of one of the other moieties in the conjugated chain. Their reactivity results in many bleaches having strong bactericidal, disinfecting, and sterilising properties. Wikipedia:Bleach chebi_ontology CHEBI:132717 bleaching agent chebi_ontology aspartate anion aspartic acid anion CHEBI:132943 aspartate aspartate anion ChEBI aspartic acid anion ChEBI A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of any tartaric acid. CHEBI:35396 tartrate chebi_ontology tartaric acid anion tartaric acid anions tartrate anion tartrate anions tartrates CHEBI:132950 tartrate tartrate ChEBI tartaric acid anion ChEBI tartaric acid anions ChEBI tartrate anion ChEBI tartrate anions ChEBI tartrates ChEBI A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of maleic acid. chebi_ontology maleate anion maleate anions maleates maleic acid anion maleic acid anions CHEBI:132951 maleate maleate anion ChEBI maleate anions ChEBI maleates ChEBI maleic acid anion ChEBI maleic acid anions ChEBI An oxo fatty acid anion obtained by deprotonation of the carboxy group of any 3-oxo fatty acid. chebi_ontology *C(CC(=O)[O-])=O -1 3-keto fatty acid anion 3-keto fatty acid anions 86.000 86.046 C3H2O3R a 3-oxo fatty acid CHEBI:133292 3-oxo fatty acid anion *C(CC(=O)[O-])=O ChEBI -1 ChEBI 3-keto fatty acid anion SUBMITTER 3-keto fatty acid anions ChEBI 86.000 ChEBI 86.046 ChEBI C3H2O3R ChEBI a 3-oxo fatty acid UniProt An inorganic oxide that is an oxide of any metal. chebi_ontology metal oxides CHEBI:133331 metal oxide metal oxides ChEBI A quaternary ammonium salt with choline cation and chloride anion. Beilstein:3563126 CAS:67-48-1 PMID:12962717 PMID:17596274 PMID:20396712 PMID:24905385 PMID:25037344 PMID:6196640 PMID:8047569 Reaxys:3563126 Wikipedia:Choline_chloride 2-hydroxy-N,N,N-trimethylethanaminium chloride chebi_ontology (2-Hydroxyethyl)trimethylammonium chloride (beta-Hydroxyethyl)trimethylammonium chloride 0 139.076 139.624 2-Hydroxy-N,N,N,-trimethylethanaminium chloride Bilineurin chloride Biocolina Biocoline C5H14ClNO Chloride de choline Chlorure de choline Choline chlorhydrate Choline hydrochloride Cholini chloridum Cholinium chloride Cloruro de colina Hepacholine InChI=1S/C5H14NO.ClH/c1-6(2,3)4-5-7;/h7H,4-5H2,1-3H3;1H/q+1;/p-1 Lipotril Luridin chloride Paresan SGMZJAMFUVOLNK-UHFFFAOYSA-M Trimethyl(2-hydroxyethyl)ammonium chloride [Cl-].[N+](CCO)(C)(C)C choline chloride CHEBI:133341 choline chloride Beilstein:3563126 Beilstein CAS:67-48-1 ChemIDplus CAS:67-48-1 NIST Chemistry WebBook PMID:12962717 Europe PMC PMID:17596274 Europe PMC PMID:20396712 Europe PMC PMID:24905385 Europe PMC PMID:25037344 Europe PMC PMID:6196640 Europe PMC PMID:8047569 Europe PMC Reaxys:3563126 Reaxys 2-hydroxy-N,N,N-trimethylethanaminium chloride IUPAC (2-Hydroxyethyl)trimethylammonium chloride ChemIDplus (beta-Hydroxyethyl)trimethylammonium chloride ChemIDplus 0 ChEBI 139.076 ChEBI 139.624 ChEBI 2-Hydroxy-N,N,N,-trimethylethanaminium chloride ChemIDplus Bilineurin chloride ChemIDplus Biocolina ChemIDplus Biocoline ChemIDplus C5H14ClNO ChEBI Chloride de choline ChemIDplus Chlorure de choline ChemIDplus Choline chlorhydrate ChemIDplus Choline hydrochloride ChemIDplus Cholini chloridum ChemIDplus Cholinium chloride ChemIDplus Cloruro de colina ChemIDplus Hepacholine ChemIDplus InChI=1S/C5H14NO.ClH/c1-6(2,3)4-5-7;/h7H,4-5H2,1-3H3;1H/q+1;/p-1 ChEBI Lipotril ChemIDplus Luridin chloride ChemIDplus Paresan ChemIDplus SGMZJAMFUVOLNK-UHFFFAOYSA-M ChEBI Trimethyl(2-hydroxyethyl)ammonium chloride ChemIDplus [Cl-].[N+](CCO)(C)(C)C ChEBI choline chloride ChEBI An organophosphate oxoanion obtained by the deprotonation of the carboxy and one of the phosphate OH groups as well as protonation of the amino group of glyphosate. It is the major microspecies at pH 7.3 (according to Marvin v 6.2.0.). chebi_ontology -1 168.006 168.065 C3H7NO5P InChI=1S/C3H8NO5P/c5-3(6)1-4-2-10(7,8)9/h4H,1-2H2,(H,5,6)(H2,7,8,9)/p-1 O=C([O-])C[NH2+]CP(=O)(O)[O-] XDDAORKBJWWYJS-UHFFFAOYSA-M glyphosate CHEBI:133673 glyphosate(1-) -1 ChEBI 168.006 ChEBI 168.065 ChEBI C3H7NO5P ChEBI InChI=1S/C3H8NO5P/c5-3(6)1-4-2-10(7,8)9/h4H,1-2H2,(H,5,6)(H2,7,8,9)/p-1 ChEBI O=C([O-])C[NH2+]CP(=O)(O)[O-] ChEBI XDDAORKBJWWYJS-UHFFFAOYSA-M ChEBI glyphosate UniProt A tricarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of citric acid. chebi_ontology citrate citrate anions CHEBI:133748 citrate anion citrate ChEBI citrate anions ChEBI A tricarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of pimelic acid. chebi_ontology heptanedioic acid anion heptanedioic acid anions pimelates pimelic acid anion pimelic acid anions CHEBI:133773 pimelate heptanedioic acid anion ChEBI heptanedioic acid anions ChEBI pimelates ChEBI pimelic acid anion ChEBI pimelic acid anions ChEBI chebi_ontology Cu,Zn-SOD inhibitor Cu,Zn-SOD inhibitors Cu-Zn superoxide dismutase inhibitor Cu-Zn superoxide dismutase inhibitors EC 1.15.1.1 (superoxide dismutase) inhibitors EC 1.15.1.1 inhibitor EC 1.15.1.1 inhibitors Fe-SOD inhibitor Fe-SOD inhibitors Mn-SOD inhibitor Mn-SOD inhibitors SOD inhibitor SOD inhibitors SOD-1 inhibitor SOD-1 inhibitors SOD-2 inhibitor SOD-2 inhibitors SOD-3 inhibitor SOD-3 inhibitors SOD-4 inhibitor SOD-4 inhibitors SODF inhibitor SODF inhibitors SODS inhibitor SODS inhibitors copper-zinc superoxide dismutase inhibitor copper-zinc superoxide dismutase inhibitors cuprein inhibitor cuprein inhibitors cytocuprein inhibitor cytocuprein inhibitors erythrocuprein inhibitor erythrocuprein inhibitors ferrisuperoxide dismutase inhibitor ferrisuperoxide dismutase inhibitors hemocuprein inhibitor hemocuprein inhibitors hepatocuprein inhibitor hepatocuprein inhibitors superoxidase dismutase inhibitor superoxidase dismutase inhibitors superoxide dismutase (EC 1.15.1.1) inhibitor superoxide dismutase (EC 1.15.1.1) inhibitors superoxide dismutase I inhibitor superoxide dismutase I inhibitors superoxide dismutase II inhibitor superoxide dismutase II inhibitors superoxide dismutase inhibitor superoxide dismutase inhibitors superoxide:superoxide oxidoreductase inhibitor superoxide:superoxide oxidoreductase inhibitors CHEBI:134084 EC 1.15.1.1 (superoxide dismutase) inhibitor Cu,Zn-SOD inhibitor ChEBI Cu,Zn-SOD inhibitors ChEBI Cu-Zn superoxide dismutase inhibitor ChEBI Cu-Zn superoxide dismutase inhibitors ChEBI EC 1.15.1.1 (superoxide dismutase) inhibitors ChEBI EC 1.15.1.1 inhibitor ChEBI EC 1.15.1.1 inhibitors ChEBI Fe-SOD inhibitor ChEBI Fe-SOD inhibitors ChEBI Mn-SOD inhibitor ChEBI Mn-SOD inhibitors ChEBI SOD inhibitor ChEBI SOD inhibitors ChEBI SOD-1 inhibitor ChEBI SOD-1 inhibitors ChEBI SOD-2 inhibitor ChEBI SOD-2 inhibitors ChEBI SOD-3 inhibitor ChEBI SOD-3 inhibitors ChEBI SOD-4 inhibitor ChEBI SOD-4 inhibitors ChEBI SODF inhibitor ChEBI SODF inhibitors ChEBI SODS inhibitor ChEBI SODS inhibitors ChEBI copper-zinc superoxide dismutase inhibitor ChEBI copper-zinc superoxide dismutase inhibitors ChEBI cuprein inhibitor ChEBI cuprein inhibitors ChEBI cytocuprein inhibitor ChEBI cytocuprein inhibitors ChEBI erythrocuprein inhibitor ChEBI erythrocuprein inhibitors ChEBI ferrisuperoxide dismutase inhibitor ChEBI ferrisuperoxide dismutase inhibitors ChEBI hemocuprein inhibitor ChEBI hemocuprein inhibitors ChEBI hepatocuprein inhibitor ChEBI hepatocuprein inhibitors ChEBI superoxidase dismutase inhibitor ChEBI superoxidase dismutase inhibitors ChEBI superoxide dismutase (EC 1.15.1.1) inhibitor ChEBI superoxide dismutase (EC 1.15.1.1) inhibitors ChEBI superoxide dismutase I inhibitor ChEBI superoxide dismutase I inhibitors ChEBI superoxide dismutase II inhibitor ChEBI superoxide dismutase II inhibitors ChEBI superoxide dismutase inhibitor ChEBI superoxide dismutase inhibitors ChEBI superoxide:superoxide oxidoreductase inhibitor ChEBI superoxide:superoxide oxidoreductase inhibitors ChEBI An L-threonine derivative obtained by formal condensation of the carboxy group of 4-({4-[(morpholin-4-yl)methyl]phenyl}ethynyl)benzoic acid with the amino group of N-hydroxy-L-threoninamide. PMCID:PMC3197220 PMID:17335290 PMID:18025458 PMID:20516283 PMID:21171638 PMID:22024823 PMID:26833150 PMID:27330072 PMID:27526195 Reaxys:18777591 colombos:CHIR-090 N-[(2S,3R)-3-hydroxy-1-(hydroxyamino)-1-oxobutan-2-yl]-4-({4-[(morpholin-4-yl)methyl]phenyl}ethynyl)benzamide chebi_ontology 0 437.195 437.489 C24H27N3O5 FQYBTYFKOHPWQT-VGSWGCGISA-N InChI=1S/C24H27N3O5/c1-17(28)22(24(30)26-31)25-23(29)21-10-8-19(9-11-21)3-2-18-4-6-20(7-5-18)16-27-12-14-32-15-13-27/h4-11,17,22,28,31H,12-16H2,1H3,(H,25,29)(H,26,30)/t17-,22+/m1/s1 O1CCN(CC1)CC2=CC=C(C=C2)C#CC3=CC=C(C(=O)N[C@@H]([C@H](O)C)C(=O)NO)C=C3 CHEBI:134107 CHIR-090 PMCID:PMC3197220 Europe PMC PMID:17335290 Europe PMC PMID:18025458 Europe PMC PMID:20516283 Europe PMC PMID:21171638 Europe PMC PMID:22024823 Europe PMC PMID:26833150 Europe PMC PMID:27330072 Europe PMC PMID:27526195 Europe PMC Reaxys:18777591 Reaxys N-[(2S,3R)-3-hydroxy-1-(hydroxyamino)-1-oxobutan-2-yl]-4-({4-[(morpholin-4-yl)methyl]phenyl}ethynyl)benzamide IUPAC 0 ChEBI 437.195 ChEBI 437.489 ChEBI C24H27N3O5 ChEBI FQYBTYFKOHPWQT-VGSWGCGISA-N ChEBI InChI=1S/C24H27N3O5/c1-17(28)22(24(30)26-31)25-23(29)21-10-8-19(9-11-21)3-2-18-4-6-20(7-5-18)16-27-12-14-32-15-13-27/h4-11,17,22,28,31H,12-16H2,1H3,(H,25,29)(H,26,30)/t17-,22+/m1/s1 ChEBI O1CCN(CC1)CC2=CC=C(C=C2)C#CC3=CC=C(C(=O)N[C@@H]([C@H](O)C)C(=O)NO)C=C3 ChEBI Any compound that inhibits the biosynthesis of any lipopolysaccharide. chebi_ontology lipopolysaccharide biosynthesis inhibitors CHEBI:134108 lipopolysaccharide biosynthesis inhibitor lipopolysaccharide biosynthesis inhibitors ChEBI An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the action of UDP-3-O-acyl-N-acetylglucosamine deacetylase (EC 3.5.1.108). Wikipedia:UDP-3-O-N-acetylglucosamine_deacetylase chebi_ontology EC 3.5.1.108 (UDP-3-O-acyl-N-acetylglucosamine deacetylase) inhibitors EC 3.5.1.108 inhibitor EC 3.5.1.108 inhibitors LpxC deacetylase inhibitor LpxC deacetylase inhibitors LpxC enzyme inhibitor LpxC enzyme inhibitors LpxC inhibitor LpxC inhibitors UDP-(3-O-(R-3-hydroxymyristoyl))-N-acetylglucosamine deacetylase inhibitor UDP-(3-O-(R-3-hydroxymyristoyl))-N-acetylglucosamine deacetylase inhibitors UDP-(3-O-acyl)-N-acetylglucosamine deacetylase inhibitor UDP-(3-O-acyl)-N-acetylglucosamine deacetylase inhibitors UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase inhibitor UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase inhibitors UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase inhibitor UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase inhibitors UDP-3-O-[(3R)-3-hydroxymyristoyl]-N-acetyl-alpha-D-glucosamine amidohydrolase inhibitor UDP-3-O-[(3R)-3-hydroxymyristoyl]-N-acetyl-alpha-D-glucosamine amidohydrolase inhibitors UDP-3-O-[(3R)-3-hydroxymyristoyl]-N-acetylglucosamine amidohydrolase inhibitor UDP-3-O-[(3R)-3-hydroxymyristoyl]-N-acetylglucosamine amidohydrolase inhibitors UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase inhibitor UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase inhibitors UDP-3-O-acyl-GlcNAc deacetylase inhibitor UDP-3-O-acyl-GlcNAc deacetylase inhibitors deacetylase LpxC inhibitor deacetylase LpxC inhibitors CHEBI:134109 EC 3.5.1.108 (UDP-3-O-acyl-N-acetylglucosamine deacetylase) inhibitor EC 3.5.1.108 (UDP-3-O-acyl-N-acetylglucosamine deacetylase) inhibitors ChEBI EC 3.5.1.108 inhibitor ChEBI EC 3.5.1.108 inhibitors ChEBI LpxC deacetylase inhibitor ChEBI LpxC deacetylase inhibitors ChEBI LpxC enzyme inhibitor ChEBI LpxC enzyme inhibitors ChEBI LpxC inhibitor ChEBI LpxC inhibitors ChEBI UDP-(3-O-(R-3-hydroxymyristoyl))-N-acetylglucosamine deacetylase inhibitor ChEBI UDP-(3-O-(R-3-hydroxymyristoyl))-N-acetylglucosamine deacetylase inhibitors ChEBI UDP-(3-O-acyl)-N-acetylglucosamine deacetylase inhibitor ChEBI UDP-(3-O-acyl)-N-acetylglucosamine deacetylase inhibitors ChEBI UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase inhibitor ChEBI UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase inhibitors ChEBI UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase inhibitor ChEBI UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase inhibitors ChEBI UDP-3-O-[(3R)-3-hydroxymyristoyl]-N-acetyl-alpha-D-glucosamine amidohydrolase inhibitor ChEBI UDP-3-O-[(3R)-3-hydroxymyristoyl]-N-acetyl-alpha-D-glucosamine amidohydrolase inhibitors ChEBI UDP-3-O-[(3R)-3-hydroxymyristoyl]-N-acetylglucosamine amidohydrolase inhibitor ChEBI UDP-3-O-[(3R)-3-hydroxymyristoyl]-N-acetylglucosamine amidohydrolase inhibitors ChEBI UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase inhibitor ChEBI UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase inhibitors ChEBI UDP-3-O-acyl-GlcNAc deacetylase inhibitor ChEBI UDP-3-O-acyl-GlcNAc deacetylase inhibitors ChEBI deacetylase LpxC inhibitor ChEBI deacetylase LpxC inhibitors ChEBI volatile organic compounds Any organic compound having an initial boiling point less than or equal to 250 degreeC (482 degreeF) measured at a standard atmospheric pressure of 101.3 kPa. Wikipedia:Volatile_organic_compound colombos:VOC colombos:VOC:-1+1 chebi_ontology VOC VOCs volatile organic compounds CHEBI:134179 volatile organic compound VOC ChEBI VOCs ChEBI volatile organic compounds ChEBI An alkanesulfonate in which the carbon at position 1 is attached to R, which can represent hydrogens, a carbon chain, or other groups. CHEBI:22318 MetaCyc:Alkanesulfonates chebi_ontology -1 93.972 94.091 C(S([O-])(=O)=O)* CH2O3SR alkanesulfonate oxoanions alkanesulfonates an alkanesulfonate CHEBI:134249 alkanesulfonate oxoanion -1 ChEBI 93.972 ChEBI 94.091 ChEBI C(S([O-])(=O)=O)* ChEBI CH2O3SR ChEBI alkanesulfonate oxoanions ChEBI alkanesulfonates ChEBI an alkanesulfonate UniProt An N-oxide where there are three organic groups bonded to the nitrogen atom. Patent:EP0545208 Patent:EP0757983 Patent:EP0866058 Patent:EP1068179 Patent:US4206204 Patent:WO9950236 chebi_ontology *[N+](*)([O-])* 0 29.998 30.006 NOR3 tertiary amine oxides CHEBI:134363 tertiary amine oxide *[N+](*)([O-])* ChEBI 0 ChEBI 29.998 ChEBI 30.006 ChEBI NOR3 ChEBI tertiary amine oxides ChEBI Any oxo fatty acid in which an oxo substituent is located at position 3. chebi_ontology 3-keto fatty acid 3-keto fatty acids 3-oxo fatty acids CHEBI:134416 3-oxo fatty acid 3-keto fatty acid ChEBI 3-keto fatty acids ChEBI 3-oxo fatty acids ChEBI A class containing any titanium molecular entity that is an oxide of titanium. chebi_ontology titanium oxide CHEBI:134438 titanium oxides titanium oxide ChEBI A nanoparticle composed of any titanium oxide. chebi_ontology CHEBI:134441 titanium oxide nanoparticle A diol in which the two hydroxy groups are on different carbon atoms, usually but not necessarily adjacent. glycols chebi_ontology Glykol a glycol CHEBI:13643 glycol glycols IUPAC Glykol ChEBI a glycol UniProt Organonitrogen compounds that have the general structure R(1)(R(2))C=N(O)OH (R(1),R(2) = H, organyl). They are tautomers of C-nitro compounds. chebi_ontology 0 59.001 59.024 C(*)(=[N+](O)[O-])* CHNO2R2 aci-nitro compounds oxime N-oxide oxime N-oxides CHEBI:136622 aci-nitro compound 0 ChEBI 59.001 ChEBI 59.024 ChEBI C(*)(=[N+](O)[O-])* ChEBI CHNO2R2 ChEBI aci-nitro compounds ChEBI oxime N-oxide ChEBI oxime N-oxides ChEBI An organic group derived from any 3-oxo-Delta(4)-steroid. chebi_ontology 0 94.042 94.111 C1=C(C*)*C(CC1=O)* C6H6O a 3-oxo-Delta4-steroid group CHEBI:136849 3-oxo-Delta(4)-steroid group 0 ChEBI 94.042 ChEBI 94.111 ChEBI C1=C(C*)*C(CC1=O)* ChEBI C6H6O ChEBI a 3-oxo-Delta4-steroid group UniProt A compound that, on administration, undergoes conversion by biochemical (enzymatic), chemical (possibly following an enzymatic step), or physical (e.g. photochemical) activation processes before becoming the active agent for which it is a pro-agent. PMID:26449612 chebi_ontology pro-agents proagent proagents CHEBI:136859 pro-agent PMID:26449612 Europe PMC pro-agents ChEBI proagent ChEBI proagents ChEBI chebi_ontology 5beta steroids 5beta-steroid 5beta-steroids CHEBI:136889 5beta steroid 5beta steroids ChEBI 5beta-steroid ChEBI 5beta-steroids ChEBI A 3-oxo monocarboxylic acid anion that is the conjugate base of acetoacetic acid, arising from deprotonation of the carboxy group. Beilstein:4128534 CAS:141-81-1 KEGG:C00164 MetaCyc:3-KETOBUTYRATE Reaxys:4128534 UM-BBD_compID:c0069 3-oxobutanoate Acetoacetate acetoacetate chebi_ontology -1 101.024 101.08070 Acetoacetate ion(1-) Butanoic acid, 3-oxo-, ion(1-) C4H5O3 CC(=O)CC([O-])=O InChI=1S/C4H6O3/c1-3(5)2-4(6)7/h2H2,1H3,(H,6,7)/p-1 WDJHALXBUFZDSR-UHFFFAOYSA-M CHEBI:13705 acetoacetate Beilstein:4128534 Beilstein CAS:141-81-1 ChemIDplus Reaxys:4128534 Reaxys UM-BBD_compID:c0069 UM-BBD 3-oxobutanoate IUPAC Acetoacetate KEGG_COMPOUND acetoacetate UniProt -1 ChEBI 101.024 ChEBI 101.08070 ChEBI Acetoacetate ion(1-) ChemIDplus Butanoic acid, 3-oxo-, ion(1-) ChemIDplus C4H5O3 ChEBI CC(=O)CC([O-])=O ChEBI InChI=1S/C4H6O3/c1-3(5)2-4(6)7/h2H2,1H3,(H,6,7)/p-1 ChEBI WDJHALXBUFZDSR-UHFFFAOYSA-M ChEBI Water-soluble carbon monoxide-releasing molecule. CAS:475473-26-8 PDBeChem:318487530 colombos:CORM-3 chebi_ontology 0 292.591 292.866 C5H2ClNO5Ru Carbon monoxide releasing molecule 3 InChI=1S/C2H3NO2.3CO.ClH.Ru/c3-1-2(4)5;3*1-2;;/h1H2,(H,4,5);;;;1H;/q;;;;;+2/p-2 Tricarbonylchloro(glycinato)ruthenium UQJJDVOKPPHMJI-UHFFFAOYSA-L [Ru+2]1([Cl-])([O-]C(=O)C[N]1)([C]=O)([C]=O)[C]=O CHEBI:137081 CORM 3 CAS:475473-26-8 SUBMITTER PDBeChem:318487530 SUBMITTER 0 SUBMITTER 292.591 SUBMITTER 292.866 SUBMITTER C5H2ClNO5Ru SUBMITTER Carbon monoxide releasing molecule 3 SUBMITTER InChI=1S/C2H3NO2.3CO.ClH.Ru/c3-1-2(4)5;3*1-2;;/h1H2,(H,4,5);;;;1H;/q;;;;;+2/p-2 ChEBI Tricarbonylchloro(glycinato)ruthenium SUBMITTER UQJJDVOKPPHMJI-UHFFFAOYSA-L ChEBI [Ru+2]1([Cl-])([O-]C(=O)C[N]1)([C]=O)([C]=O)[C]=O ChEBI An atom of an element that exhibits properties that are between those of metals and nonmetals, or that has a mixture of them. The term generally includes boron, silicon, germanium, arsenic, antimony, and tellurium, while carbon, aluminium, selenium, polonium, and astatine are less commonly included. Wikipedia:Metalloid chebi_ontology metalloid metalloids CHEBI:137980 metalloid atom metalloid ChEBI metalloids ChEBI A compound formally derived from ammonium by replacing three hydrogen atoms by hydrocarbyl groups. chebi_ontology +1 15.011 15.015 HNR3 [NH+](*)(*)* a tertiary amine CHEBI:137982 tertiary amine(1+) +1 SUBMITTER 15.011 SUBMITTER 15.015 SUBMITTER HNR3 SUBMITTER [NH+](*)(*)* ChEBI a tertiary amine UniProt Any compound that can disrupt the functions of the endocrine (hormone) system PMID:27929035 PMID:28356401 PMID:28526231 Wikipedia:Endocrine_disruptor chebi_ontology endocrine disrupting chemical endocrine disrupting chemicals endocrine disrupting compound endocrine disrupting compounds endocrine disruptors endocrine-disrupting chemical endocrine-disrupting chemicals hormonally active agent hormonally active agents CHEBI:138015 endocrine disruptor PMID:27929035 Europe PMC PMID:28356401 Europe PMC PMID:28526231 Europe PMC endocrine disrupting chemical ChEBI endocrine disrupting chemicals ChEBI endocrine disrupting compound ChEBI endocrine disrupting compounds ChEBI endocrine disruptors ChEBI endocrine-disrupting chemical ChEBI endocrine-disrupting chemicals ChEBI hormonally active agent ChEBI hormonally active agents ChEBI Beilstein:3903503 CAS:302-11-4 Gmelin:239604 carbamate chebi_ontology -1 60.009 60.03212 CH2NO2 Carbamat InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4)/p-1 KXDHJXZQYSOELW-UHFFFAOYSA-M Karbamat NC([O-])=O carbamate ion carbamic acid, ion(1-) CHEBI:13941 carbamate Beilstein:3903503 Beilstein CAS:302-11-4 ChemIDplus Gmelin:239604 Gmelin carbamate IUPAC carbamate UniProt -1 ChEBI 60.009 ChEBI 60.03212 ChEBI CH2NO2 ChEBI Carbamat ChEBI InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4)/p-1 ChEBI KXDHJXZQYSOELW-UHFFFAOYSA-M ChEBI Karbamat ChEBI NC([O-])=O ChEBI carbamate ion ChemIDplus carbamic acid, ion(1-) ChemIDplus A D-glucose monophosphate in which the phosphate group is attached to position 6. chebi_ontology 0 260.13578 6-O-phosphono-D-glucose C6H13O9P D-glucose 6-(dihydrogen phosphate) CHEBI:14314 D-glucose 6-phosphate 0 ChEBI 260.13578 ChEBI 6-O-phosphono-D-glucose IUPAC C6H13O9P ChEBI D-glucose 6-(dihydrogen phosphate) IUPAC A glycerol monophosphate having the phosphate group located at position 1. CAS:57-03-4 HMDB:HMDB00126 KEGG:C03189 MetaCyc:Glycerol-1-phosphate PMID:1694860 PMID:22770225 PMID:6083437 Reaxys:1723974 Wikipedia:Glycerol_1-phosphate 2,3-dihydroxypropyl dihydrogen phosphate Glycerol 1-phosphate glycerol 1-(dihydrogen phosphate) chebi_ontology 0 1,2,3-propanetriol, 1-(dihydrogen phosphate) 1-glycerophosphate 1-glycerophosphoric acid 1-phosphoglycerol 172.014 172.07370 2,3-dihydroxypropyl dihydrogen phosphate 2,3-hydroxy-1-propyl dihydrogen phosphate 3-glycerophosphate AWUCVROLDVIAJX-UHFFFAOYSA-N C3H9O6P D,L-alpha-glycerol-phosphate DL-Glycerol 3-phosphate DL-Glyceryl 1-phosphate DL-glycerol 1-phosphate InChI=1S/C3H9O6P/c4-1-3(5)2-9-10(6,7)8/h3-5H,1-2H2,(H2,6,7,8) OCC(O)COP(O)(O)=O PG alpha-glycerophosphoric acid alpha-phosphoglycerol glycerol alpha-phosphate rac-Glycerol 1-phosphate CHEBI:14336 glycerol 1-phosphate CAS:57-03-4 ChemIDplus CAS:57-03-4 KEGG COMPOUND PMID:1694860 Europe PMC PMID:22770225 Europe PMC PMID:6083437 Europe PMC Reaxys:1723974 Reaxys 2,3-dihydroxypropyl dihydrogen phosphate IUPAC Glycerol 1-phosphate KEGG_COMPOUND glycerol 1-(dihydrogen phosphate) IUPAC 0 ChEBI 1,2,3-propanetriol, 1-(dihydrogen phosphate) ChemIDplus 1-glycerophosphate ChemIDplus 1-glycerophosphoric acid ChemIDplus 1-phosphoglycerol ChEBI 172.014 ChEBI 172.07370 ChEBI 2,3-dihydroxypropyl dihydrogen phosphate ChEBI 2,3-hydroxy-1-propyl dihydrogen phosphate ChemIDplus 3-glycerophosphate ChemIDplus AWUCVROLDVIAJX-UHFFFAOYSA-N ChEBI C3H9O6P ChEBI D,L-alpha-glycerol-phosphate MetaCyc DL-Glycerol 3-phosphate HMDB DL-Glycerol 3-phosphate KEGG_COMPOUND DL-Glyceryl 1-phosphate KEGG_COMPOUND DL-glycerol 1-phosphate MetaCyc InChI=1S/C3H9O6P/c4-1-3(5)2-9-10(6,7)8/h3-5H,1-2H2,(H2,6,7,8) ChEBI OCC(O)COP(O)(O)=O ChEBI PG ChEBI alpha-glycerophosphoric acid ChemIDplus alpha-phosphoglycerol ChemIDplus glycerol alpha-phosphate ChemIDplus rac-Glycerol 1-phosphate KEGG_COMPOUND A divalent inorganic anion obtained by removal of both protons from hydrogen sulfide. CAS:18496-25-8 UM-BBD_compID:c0569 sulfanediide sulfide(2-) chebi_ontology -2 31.972 32.06600 InChI=1S/S/q-2 S S(2-) Sulfide UCKMPCXJQFINFW-UHFFFAOYSA-N [S--] sulfide sulphide CHEBI:15138 sulfide(2-) CAS:18496-25-8 ChemIDplus UM-BBD_compID:c0569 UM-BBD sulfanediide IUPAC sulfide(2-) IUPAC -2 ChEBI 31.972 ChEBI 32.06600 ChEBI InChI=1S/S/q-2 ChEBI S ChEBI S(2-) IUPAC Sulfide ChemIDplus UCKMPCXJQFINFW-UHFFFAOYSA-N ChEBI [S--] ChEBI sulfide UniProt sulphide ChEBI Beilstein:5740673 rel-(2R,3R)-2,3-dihydroxybutanedioate chebi_ontology -2 148.07096 C4H4O6 CHEBI:15193 tartrate(2-) Beilstein:5740673 Beilstein rel-(2R,3R)-2,3-dihydroxybutanedioate IUPAC -2 ChEBI 148.07096 ChEBI C4H4O6 ChEBI A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity. CHEBI:13699 CHEBI:2377 KEGG:C00028 KEGG:C16722 Acceptor acceptor chebi_ontology A Akzeptor Hydrogen-acceptor Oxidized donor accepteur CHEBI:15339 acceptor Acceptor KEGG_COMPOUND acceptor UniProt A KEGG_COMPOUND Akzeptor ChEBI Hydrogen-acceptor KEGG_COMPOUND Oxidized donor KEGG_COMPOUND accepteur ChEBI A 3-oxo monocarboxylic acid that is butyric acid bearing a 3-oxo substituent. CHEBI:22172 CHEBI:2391 CHEBI:40507 Beilstein:1747690 CAS:541-50-4 DrugBank:DB01762 HMDB:HMDB00060 KEGG:C00164 KNApSAcK:C00007458 LIPID_MAPS_instance:LMFA01060003 MetaCyc:3-KETOBUTYRATE PMID:17190852 PMID:20444635 PMID:21806064 PMID:22382897 PMID:3884391 Reaxys:1747690 UM-BBD_compID:c0069 Wikipedia:Acetoacetic_acid 3-oxobutanoic acid Acetoacetic acid chebi_ontology 0 102.032 102.08864 3-Ketobutyric acid 3-Oxobutanoic acid 3-Oxobutyric acid 3-ketobutanoic acid C4H6O3 CC(=O)CC(O)=O InChI=1S/C4H6O3/c1-3(5)2-4(6)7/h2H2,1H3,(H,6,7) WDJHALXBUFZDSR-UHFFFAOYSA-N beta-Ketobutyric acid CHEBI:15344 acetoacetic acid Beilstein:1747690 Beilstein CAS:541-50-4 ChemIDplus CAS:541-50-4 KEGG COMPOUND LIPID_MAPS_instance:LMFA01060003 LIPID MAPS PMID:17190852 Europe PMC PMID:20444635 Europe PMC PMID:21806064 Europe PMC PMID:22382897 Europe PMC PMID:3884391 Europe PMC Reaxys:1747690 Reaxys UM-BBD_compID:c0069 ChEBI 3-oxobutanoic acid IUPAC Acetoacetic acid KEGG_COMPOUND 0 ChEBI 102.032 KEGG_COMPOUND 102.08864 ChEBI 3-Ketobutyric acid HMDB 3-Oxobutanoic acid KEGG_COMPOUND 3-Oxobutyric acid ChemIDplus 3-ketobutanoic acid ChEBI C4H6O3 KEGG_COMPOUND CC(=O)CC(O)=O ChEBI InChI=1S/C4H6O3/c1-3(5)2-4(6)7/h2H2,1H3,(H,6,7) ChEBI WDJHALXBUFZDSR-UHFFFAOYSA-N ChEBI beta-Ketobutyric acid KEGG_COMPOUND A thiol comprising a panthothenate unit in phosphoric anhydride linkage with a 3',5'-adenosine diphosphate unit; and an aminoethanethiol unit. CHEBI:13294 CHEBI:13295 CHEBI:13298 CHEBI:23355 CHEBI:3771 CHEBI:41597 CHEBI:41631 CHEBI:741566 Beilstein:77809 CAS:85-61-0 DrugBank:DB01992 KEGG:C00010 KNApSAcK:C00007258 PDBeChem:COA PDBeChem:COZ PMID:11923312 PMID:13025483 PMID:15014152 PMID:15893380 PMID:18407920 PMID:19666462 PMID:20351285 PMID:2981478 PMID:7310833 Wikipedia:Coenzyme_A 3'-phosphoadenosine 5'-{3-[(3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)butyl] dihydrogen diphosphate} COENZYME A Coenzyme A chebi_ontology 0 3'-phosphoadenosine-(5')diphospho(4')pantatheine 767.115 767.53540 C21H36N7O16P3S CC(C)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n1cnc2c(N)ncnc12)[C@@H](O)C(=O)NCCC(=O)NCCS CoA CoA-SH CoASH Coenzym A HSCoA InChI=1S/C21H36N7O16P3S/c1-21(2,16(31)19(32)24-4-3-12(29)23-5-6-48)8-41-47(38,39)44-46(36,37)40-7-11-15(43-45(33,34)35)14(30)20(42-11)28-10-27-13-17(22)25-9-26-18(13)28/h9-11,14-16,20,30-31,48H,3-8H2,1-2H3,(H,23,29)(H,24,32)(H,36,37)(H,38,39)(H2,22,25,26)(H2,33,34,35)/t11-,14-,15-,16+,20-/m1/s1 Koenzym A RGJOEKWQDUBAIZ-IBOSZNHHSA-N [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R)-3-hydroxy-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate CHEBI:15346 coenzyme A Beilstein:77809 Beilstein CAS:85-61-0 ChemIDplus CAS:85-61-0 KEGG COMPOUND PMID:11923312 Europe PMC PMID:13025483 Europe PMC PMID:15014152 Europe PMC PMID:15893380 Europe PMC PMID:18407920 Europe PMC PMID:19666462 Europe PMC PMID:20351285 Europe PMC PMID:2981478 Europe PMC PMID:7310833 ChEMBL 3'-phosphoadenosine 5'-{3-[(3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)butyl] dihydrogen diphosphate} IUPAC COENZYME A PDBeChem Coenzyme A KEGG_COMPOUND 0 ChEBI 3'-phosphoadenosine-(5')diphospho(4')pantatheine ChEBI 767.115 KEGG_COMPOUND 767.53540 ChEBI C21H36N7O16P3S KEGG_COMPOUND CC(C)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n1cnc2c(N)ncnc12)[C@@H](O)C(=O)NCCC(=O)NCCS ChEBI CoA KEGG_COMPOUND CoA-SH KEGG_COMPOUND CoASH ChEBI Coenzym A ChEBI HSCoA ChEBI InChI=1S/C21H36N7O16P3S/c1-21(2,16(31)19(32)24-4-3-12(29)23-5-6-48)8-41-47(38,39)44-46(36,37)40-7-11-15(43-45(33,34)35)14(30)20(42-11)28-10-27-13-17(22)25-9-26-18(13)28/h9-11,14-16,20,30-31,48H,3-8H2,1-2H3,(H,23,29)(H,24,32)(H,36,37)(H,38,39)(H2,22,25,26)(H2,33,34,35)/t11-,14-,15-,16+,20-/m1/s1 ChEBI Koenzym A ChEBI RGJOEKWQDUBAIZ-IBOSZNHHSA-N ChEBI [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R)-3-hydroxy-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate ChEBI An acyl-CoA having acetyl as its S-acetyl component. CHEBI:13712 CHEBI:22192 CHEBI:2408 CHEBI:40470 CAS:72-89-9 ECMDB:ECMDB01206 HMDB:HMDB01206 KEGG:C00024 KNApSAcK:C00007259 PDBeChem:ACO PMID:12527305 PMID:12739170 PMID:15247244 PMID:16101314 PMID:16667687 PMID:16708165 PMID:17189273 PMID:17242360 PMID:17631502 PMID:18613815 PMID:19356710 PMID:19596230 PMID:19914586 PMID:3950616 Reaxys:78145 UM-BBD_compID:c0031 Wikipedia:Acetyl-CoA YMDB:YMDB00312 3'-phosphoadenosine 5'-(3-{(3R)-4-[(3-{[2-(acetylsulfanyl)ethyl]amino}-3-oxopropyl)amino]-3-hydroxy-2,2-dimethyl-4-oxobutyl} dihydrogen diphosphate) Acetyl-CoA chebi_ontology 0 809.126 809.57208 AcCoA Acetyl coenzyme A C23H38N7O17P3S CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n1cnc2c(N)ncnc12 InChI=1S/C23H38N7O17P3S/c1-12(31)51-7-6-25-14(32)4-5-26-21(35)18(34)23(2,3)9-44-50(41,42)47-49(39,40)43-8-13-17(46-48(36,37)38)16(33)22(45-13)30-11-29-15-19(24)27-10-28-20(15)30/h10-11,13,16-18,22,33-34H,4-9H2,1-3H3,(H,25,32)(H,26,35)(H,39,40)(H,41,42)(H2,24,27,28)(H2,36,37,38)/t13-,16-,17-,18+,22-/m1/s1 S-acetyl-CoA S-acetyl-coenzyme A ZSLZBFCDCINBPY-ZSJPKINUSA-N CHEBI:15351 acetyl-CoA CAS:72-89-9 ChemIDplus CAS:72-89-9 KEGG COMPOUND PMID:12527305 Europe PMC PMID:12739170 Europe PMC PMID:15247244 Europe PMC PMID:16101314 Europe PMC PMID:16667687 Europe PMC PMID:16708165 Europe PMC PMID:17189273 Europe PMC PMID:17242360 Europe PMC PMID:17631502 Europe PMC PMID:18613815 Europe PMC PMID:19356710 Europe PMC PMID:19596230 Europe PMC PMID:19914586 Europe PMC PMID:3950616 Europe PMC Reaxys:78145 Reaxys UM-BBD_compID:c0031 ChEBI 3'-phosphoadenosine 5'-(3-{(3R)-4-[(3-{[2-(acetylsulfanyl)ethyl]amino}-3-oxopropyl)amino]-3-hydroxy-2,2-dimethyl-4-oxobutyl} dihydrogen diphosphate) IUPAC Acetyl-CoA KEGG_COMPOUND 0 ChEBI 809.126 KEGG_COMPOUND 809.57208 ChEBI AcCoA ChEBI Acetyl coenzyme A KEGG_COMPOUND C23H38N7O17P3S KEGG_COMPOUND CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n1cnc2c(N)ncnc12 ChEBI InChI=1S/C23H38N7O17P3S/c1-12(31)51-7-6-25-14(32)4-5-26-21(35)18(34)23(2,3)9-44-50(41,42)47-49(39,40)43-8-13-17(46-48(36,37)38)16(33)22(45-13)30-11-29-15-19(24)27-10-28-20(15)30/h10-11,13,16-18,22,33-34H,4-9H2,1-3H3,(H,25,32)(H,26,35)(H,39,40)(H,41,42)(H2,24,27,28)(H2,36,37,38)/t13-,16-,17-,18+,22-/m1/s1 ChEBI S-acetyl-CoA ChEBI S-acetyl-coenzyme A ChEBI ZSLZBFCDCINBPY-ZSJPKINUSA-N ChEBI A choline that is the parent compound of the cholines class, consisting of ethanolamine having three methyl substituents attached to the amino function. CHEBI:13985 CHEBI:23212 CHEBI:3665 CHEBI:41524 Beilstein:1736748 CAS:62-49-7 DrugBank:DB00122 Drug_Central:3097 ECMDB:ECMDB00097 Gmelin:324597 HMDB:HMDB00097 KEGG:C00114 KEGG:D07690 KNApSAcK:C00007298 MetaCyc:CHOLINE PDBeChem:CHT PMID:10930630 PMID:12826235 PMID:12946691 PMID:14972364 PMID:16210714 PMID:17087106 PMID:17283071 PMID:17344490 PMID:18204095 PMID:18230680 PMID:18786517 PMID:18786520 PMID:19246089 PMID:20038853 PMID:20446114 PMID:22770225 PMID:22961562 PMID:23095202 PMID:23616508 PMID:23637565 PMID:23733158 PMID:6420466 PMID:7590654 PMID:9517478 Reaxys:1736748 Wikipedia:Choline YMDB:YMDB00227 2-hydroxy-N,N,N-trimethylethanaminium Choline choline chebi_ontology +1 104.108 104.17080 Bilineurine C5H14NO CHOLINE ION C[N+](C)(C)CCO InChI=1S/C5H14NO/c1-6(2,3)4-5-7/h7H,4-5H2,1-3H3/q+1 N,N,N-trimethylethanol-ammonium N-trimethylethanolamine OEYIOHPDSNJKLS-UHFFFAOYSA-N trimethylethanolamine CHEBI:15354 choline Beilstein:1736748 Beilstein CAS:62-49-7 ChemIDplus CAS:62-49-7 KEGG COMPOUND Drug_Central:3097 DrugCentral Gmelin:324597 Gmelin PMID:10930630 Europe PMC PMID:12826235 Europe PMC PMID:12946691 Europe PMC PMID:14972364 Europe PMC PMID:16210714 Europe PMC PMID:17087106 Europe PMC PMID:17283071 Europe PMC PMID:17344490 Europe PMC PMID:18204095 Europe PMC PMID:18230680 Europe PMC PMID:18786517 Europe PMC PMID:18786520 Europe PMC PMID:19246089 Europe PMC PMID:20038853 Europe PMC PMID:20446114 Europe PMC PMID:22770225 Europe PMC PMID:22961562 Europe PMC PMID:23095202 Europe PMC PMID:23616508 Europe PMC PMID:23637565 Europe PMC PMID:23733158 Europe PMC PMID:6420466 Europe PMC PMID:7590654 Europe PMC PMID:9517478 Europe PMC Reaxys:1736748 Reaxys 2-hydroxy-N,N,N-trimethylethanaminium IUPAC Choline KEGG_COMPOUND choline UniProt +1 ChEBI 104.108 ChEBI 104.17080 ChEBI Bilineurine KEGG_COMPOUND C5H14NO ChEBI CHOLINE ION PDBeChem C[N+](C)(C)CCO ChEBI InChI=1S/C5H14NO/c1-6(2,3)4-5-7/h7H,4-5H2,1-3H3/q+1 ChEBI N,N,N-trimethylethanol-ammonium ChEBI N-trimethylethanolamine ChEBI OEYIOHPDSNJKLS-UHFFFAOYSA-N ChEBI trimethylethanolamine ChEBI A sulfur-containing amino acid that is propanoic acid with an amino group at position 2 and a sulfanyl group at position 3. CHEBI:14061 CHEBI:23508 CHEBI:4050 Beilstein:1721406 CAS:3374-22-9 Gmelin:2933 KEGG:C00736 KNApSAcK:C00001351 KNApSAcK:C00007323 PMID:17439666 PMID:25181601 Reaxys:1721406 Wikipedia:Cysteine colombos:CYSTEINE colombos:CYSTEINE:+UNKNOWNg/L Cysteine cysteine chebi_ontology 0 121.020 121.15922 2-Amino-3-mercaptopropionic acid 2-amino-3-mercaptopropanoic acid 2-amino-3-sulfanylpropanoic acid C C3H7NO2S Cys Cystein Hcys InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6) NC(CS)C(O)=O XUJNEKJLAYXESH-UHFFFAOYSA-N Zystein cisteina CHEBI:15356 cysteine Cystein ChEBI Hcys IUPAC InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6) ChEBI NC(CS)C(O)=O ChEBI XUJNEKJLAYXESH-UHFFFAOYSA-N ChEBI Zystein ChEBI cisteina ChEBI Beilstein:1721406 Beilstein CAS:3374-22-9 ChemIDplus CAS:3374-22-9 KEGG COMPOUND CAS:3374-22-9 NIST Chemistry WebBook Gmelin:2933 Gmelin PMID:17439666 Europe PMC PMID:25181601 Europe PMC Reaxys:1721406 Reaxys Cysteine KEGG_COMPOUND cysteine ChEBI cysteine IUPAC 0 ChEBI 121.020 KEGG_COMPOUND 121.15922 ChEBI 2-Amino-3-mercaptopropionic acid KEGG_COMPOUND 2-amino-3-mercaptopropanoic acid JCBN 2-amino-3-sulfanylpropanoic acid IUPAC C ChEBI C3H7NO2S KEGG_COMPOUND Cys ChEBI A 2-oxo monocarboxylic acid anion that is the conjugate base of pyruvic acid, arising from deprotonation of the carboxy group. CHEBI:14987 CHEBI:26462 Beilstein:3587721 CAS:57-60-3 Gmelin:2502 KEGG:C00022 PMID:17190852 PMID:21603897 PMID:21823181 PMID:21854850 PMID:22006570 PMID:22016370 PMID:22215378 PMID:22311625 PMID:22451307 PMID:22458763 Reaxys:3587721 UM-BBD_compID:c0159 colombos:PYRUVATE 2-oxopropanoate pyruvate chebi_ontology -1 2-oxopropanoate 2-oxopropanoic acid, ion(1-) 87.008 87.05412 C3H3O3 CC(=O)C([O-])=O InChI=1S/C3H4O3/c1-2(4)3(5)6/h1H3,(H,5,6)/p-1 LCTONWCANYUPML-UHFFFAOYSA-M CHEBI:15361 pyruvate Beilstein:3587721 Beilstein CAS:57-60-3 ChemIDplus Gmelin:2502 Gmelin KEGG:C00022 ChEBI PMID:17190852 Europe PMC PMID:21603897 Europe PMC PMID:21823181 Europe PMC PMID:21854850 Europe PMC PMID:22006570 Europe PMC PMID:22016370 Europe PMC PMID:22215378 Europe PMC PMID:22311625 Europe PMC PMID:22451307 Europe PMC PMID:22458763 Europe PMC Reaxys:3587721 Reaxys UM-BBD_compID:c0159 ChEBI 2-oxopropanoate IUPAC pyruvate UniProt -1 ChEBI 2-oxopropanoate ChEBI 2-oxopropanoic acid, ion(1-) ChemIDplus 87.008 ChEBI 87.05412 ChEBI C3H3O3 ChEBI CC(=O)C([O-])=O ChEBI InChI=1S/C3H4O3/c1-2(4)3(5)6/h1H3,(H,5,6)/p-1 ChEBI LCTONWCANYUPML-UHFFFAOYSA-M ChEBI A simple monocarboxylic acid containing two carbons. CHEBI:22169 CHEBI:2387 CHEBI:40486 Beilstein:506007 CAS:64-19-7 Drug_Central:4211 Gmelin:1380 HMDB:HMDB00042 KEGG:C00033 KEGG:D00010 KNApSAcK:C00001176 LIPID_MAPS_instance:LMFA01010002 MetaCyc:ACET PDBeChem:ACT PDBeChem:ACY PMID:12005138 PMID:15107950 PMID:16630552 PMID:16774200 PMID:17190852 PMID:19416101 PMID:19469536 PMID:22153255 PMID:22173419 Reaxys:506007 Wikipedia:Acetic_acid ACETIC ACID Acetic acid acetic acid chebi_ontology 0 60.021 60.05200 AcOH C2H4O2 CC(O)=O CH3-COOH CH3CO2H E 260 E-260 E260 Essigsaeure Ethanoic acid Ethylic acid HOAc INS No. 260 InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4) MeCO2H MeCOOH Methanecarboxylic acid QTBSBXVTEAMEQO-UHFFFAOYSA-N acide acetique ethoic acid CHEBI:15366 acetic acid Beilstein:506007 Beilstein CAS:64-19-7 ChemIDplus CAS:64-19-7 KEGG COMPOUND CAS:64-19-7 NIST Chemistry WebBook Drug_Central:4211 DrugCentral Gmelin:1380 Gmelin LIPID_MAPS_instance:LMFA01010002 LIPID MAPS PMID:12005138 Europe PMC PMID:15107950 Europe PMC PMID:16630552 Europe PMC PMID:16774200 Europe PMC PMID:17190852 Europe PMC PMID:19416101 Europe PMC PMID:19469536 Europe PMC PMID:22153255 Europe PMC PMID:22173419 Europe PMC Reaxys:506007 Reaxys ACETIC ACID PDBeChem Acetic acid KEGG_COMPOUND acetic acid IUPAC 0 ChEBI 60.021 KEGG_COMPOUND 60.05200 ChEBI AcOH ChEBI C2H4O2 KEGG_COMPOUND CC(O)=O ChEBI CH3-COOH IUPAC CH3CO2H ChEBI E 260 ChEBI E-260 ChEBI E260 ChEBI Essigsaeure ChEBI Ethanoic acid KEGG_COMPOUND Ethylic acid ChemIDplus HOAc ChEBI INS No. 260 ChEBI InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4) ChEBI MeCO2H ChEBI MeCOOH ChEBI Methanecarboxylic acid ChemIDplus QTBSBXVTEAMEQO-UHFFFAOYSA-N ChEBI acide acetique ChemIDplus ethoic acid ChEBI CHEBI:10745 CHEBI:13416 CHEBI:23833 CHEBI:25366 CHEBI:30491 CHEBI:44742 CHEBI:7860 CAS:7782-44-7 Gmelin:485 HMDB:HMDB01377 KEGG:C00007 KEGG:D00003 MetaCyc:OXYGEN-MOLECULE MolBase:750 PDBeChem:OXY PMID:10906528 PMID:16977326 PMID:18210929 PMID:18638417 PMID:19840863 PMID:7710549 PMID:9463773 Wikipedia:Oxygen colombos:OXYGEN dioxygen chebi_ontology 0 31.990 31.99880 Disauerstoff E 948 E-948 E948 InChI=1S/O2/c1-2 MYMOFIZGZYHOMD-UHFFFAOYSA-N O2 O=O OXYGEN MOLECULE Oxygen [OO] dioxygene molecular oxygen CHEBI:15379 dioxygen CAS:7782-44-7 ChemIDplus CAS:7782-44-7 KEGG COMPOUND CAS:7782-44-7 NIST Chemistry WebBook Gmelin:485 Gmelin PMID:10906528 Europe PMC PMID:16977326 Europe PMC PMID:18210929 Europe PMC PMID:18638417 Europe PMC PMID:19840863 Europe PMC PMID:7710549 Europe PMC PMID:9463773 Europe PMC dioxygen IUPAC 0 ChEBI 31.990 KEGG_COMPOUND 31.99880 ChEBI Disauerstoff ChEBI E 948 ChEBI E-948 ChEBI E948 ChEBI InChI=1S/O2/c1-2 ChEBI MYMOFIZGZYHOMD-UHFFFAOYSA-N ChEBI O2 IUPAC O2 KEGG_COMPOUND O2 KEGG_COMPOUND O2 UniProt O=O ChEBI OXYGEN MOLECULE PDBeChem Oxygen KEGG_COMPOUND [OO] MolBase dioxygene ChEBI molecular oxygen ChEBI A sulfonium compound that is the S-adenosyl derivative of L-methionine. It is an intermediate in the metabolic pathway of methionine. CHEBI:10786 CHEBI:10833 CHEBI:12742 CHEBI:12757 CHEBI:12760 CHEBI:22036 CHEBI:45607 CHEBI:527887 CHEBI:8946 Beilstein:3576439 CAS:29908-03-0 COMe:MOL000172 DrugBank:DB00118 HMDB:HMDB01185 KEGG:C00019 KNApSAcK:C00007347 MetaCyc:S-ADENOSYLMETHIONINE PMID:11017945 PMID:17439666 Reaxys:3919754 Wikipedia:S-Adenosyl_methionine S-Adenosyl-L-methionine S-adenosyl-L-methionine [(3S)-3-amino-3-carboxypropyl](5'-deoxyadenosin-5'-yl)(methyl)sulfonium chebi_ontology (3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt +1 399.145 399.44500 Acylcarnitine AdoMet C15H23N6O5S C[S+](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n1cnc2c(N)ncnc12 InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/p+1/t7-,8+,10+,11+,14+,27?/m0/s1 MEFKEPWMEQBLKI-AIRLBKTGSA-O S-(5'-deoxyadenosin-5'-yl)-L-methionine S-Adenosylmethionine S-adenosylmethionine SAM SAMe [1-(adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium CHEBI:15414 S-adenosyl-L-methionine Beilstein:3576439 Beilstein CAS:29908-03-0 ChemIDplus CAS:29908-03-0 KEGG COMPOUND PMID:11017945 Europe PMC PMID:17439666 Europe PMC Reaxys:3919754 Reaxys S-Adenosyl-L-methionine KEGG_COMPOUND S-adenosyl-L-methionine ChEBI [(3S)-3-amino-3-carboxypropyl](5'-deoxyadenosin-5'-yl)(methyl)sulfonium IUPAC (3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt ChemIDplus +1 ChEBI 399.145 ChEBI 399.44500 ChEBI Acylcarnitine KEGG_COMPOUND AdoMet JCBN C15H23N6O5S ChEBI C[S+](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n1cnc2c(N)ncnc12 ChEBI InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/p+1/t7-,8+,10+,11+,14+,27?/m0/s1 ChEBI MEFKEPWMEQBLKI-AIRLBKTGSA-O ChEBI S-(5'-deoxyadenosin-5'-yl)-L-methionine JCBN S-Adenosylmethionine KEGG_COMPOUND S-adenosylmethionine ChEBI SAM JCBN SAMe ChemIDplus [1-(adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium IUPAC An adenosine 5'-phosphate in which the 5'-phosphate is a triphosphate group. It is involved in the transportation of chemical energy during metabolic pathways. CHEBI:10789 CHEBI:10841 CHEBI:13236 CHEBI:22249 CHEBI:2359 CHEBI:40938 Beilstein:73010 CAS:56-65-5 DrugBank:DB00171 Drug_Central:91 Gmelin:34857 HMDB:HMDB00538 KEGG:C00002 KEGG:D08646 KNApSAcK:C00001491 PDBeChem:ATP Patent:US3079379 Reaxys:73010 Wikipedia:Adenosine_triphosphate ATP adenosine 5'-(tetrahydrogen triphosphate) chebi_ontology 0 506.996 507.18100 ADENOSINE-5'-TRIPHOSPHATE Adenosine 5'-triphosphate Adenosine triphosphate C10H16N5O13P3 H4atp InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1 Nc1ncnc2n(cnc12)[C@@H]1O[C@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)[C@@H](O)[C@H]1O ZKHQWZAMYRWXGA-KQYNXXCUSA-N CHEBI:15422 ATP Beilstein:73010 Beilstein CAS:56-65-5 ChemIDplus CAS:56-65-5 KEGG COMPOUND Drug_Central:91 DrugCentral Gmelin:34857 Gmelin Reaxys:73010 Reaxys ATP KEGG_COMPOUND adenosine 5'-(tetrahydrogen triphosphate) IUPAC 0 ChEBI 506.996 KEGG_COMPOUND 507.18100 ChEBI ADENOSINE-5'-TRIPHOSPHATE PDBeChem Adenosine 5'-triphosphate KEGG_COMPOUND Adenosine triphosphate ChemIDplus C10H16N5O13P3 KEGG_COMPOUND H4atp IUPAC InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1 ChEBI Nc1ncnc2n(cnc12)[C@@H]1O[C@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)[C@@H](O)[C@H]1O ChEBI ZKHQWZAMYRWXGA-KQYNXXCUSA-N ChEBI The simplest (and the only achiral) proteinogenic amino acid, with a hydrogen atom as its side chain. CHEBI:10792 CHEBI:14344 CHEBI:24368 CHEBI:42964 CHEBI:5460 Beilstein:635782 CAS:56-40-6 DrugBank:DB00145 Drug_Central:1319 ECMDB:ECMDB00123 Gmelin:1808 HMDB:HMDB00123 KEGG:C00037 KEGG:D00011 KNApSAcK:C00001361 MetaCyc:GLY PDBeChem:GLY PMID:10930630 PMID:11019925 PMID:11174716 PMID:11542461 PMID:11806864 PMID:12631515 PMID:12754315 PMID:12770151 PMID:12921899 PMID:15331688 PMID:15388434 PMID:15710237 PMID:16105183 PMID:16151895 PMID:16214212 PMID:16417482 PMID:16444815 PMID:16664855 PMID:16901953 PMID:16918424 PMID:16986325 PMID:16998855 PMID:17154252 PMID:17383967 PMID:17582620 PMID:17970719 PMID:18079355 PMID:18396796 PMID:18440992 PMID:18593588 PMID:18816054 PMID:18840508 PMID:19028609 PMID:19120667 PMID:19449910 PMID:19526731 PMID:19544666 PMID:19738917 PMID:19916621 PMID:19924257 PMID:21751272 PMID:22044190 PMID:22079563 PMID:22234938 PMID:22264337 PMID:22293292 PMID:22401276 PMID:22434786 Reaxys:635782 Wikipedia:Glycine YMDB:YMDB00016 GLYCINE Glycine aminoacetic acid glycine chebi_ontology 0 75.032 75.06664 Aminoacetic acid Aminoessigsaeure C2H5NO2 DHMQDGOQFOQNFH-UHFFFAOYSA-N G Gly Glycin Glycocoll Glykokoll Glyzin H2N-CH2-COOH Hgly InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) Leimzucker NCC(O)=O aminoethanoic acid CHEBI:15428 glycine Beilstein:635782 Beilstein CAS:56-40-6 ChemIDplus CAS:56-40-6 KEGG COMPOUND CAS:56-40-6 NIST Chemistry WebBook Drug_Central:1319 DrugCentral Gmelin:1808 Gmelin PMID:10930630 Europe PMC PMID:11019925 Europe PMC PMID:11174716 Europe PMC PMID:11542461 Europe PMC PMID:11806864 Europe PMC PMID:12631515 Europe PMC PMID:12754315 Europe PMC PMID:12770151 Europe PMC PMID:12921899 Europe PMC PMID:15331688 Europe PMC PMID:15388434 Europe PMC PMID:15710237 Europe PMC PMID:16105183 Europe PMC PMID:16151895 Europe PMC PMID:16214212 Europe PMC PMID:16417482 Europe PMC PMID:16444815 Europe PMC PMID:16664855 Europe PMC PMID:16901953 Europe PMC PMID:16918424 Europe PMC PMID:16986325 Europe PMC PMID:16998855 Europe PMC PMID:17154252 Europe PMC PMID:17383967 Europe PMC PMID:17582620 Europe PMC PMID:17970719 Europe PMC PMID:18079355 Europe PMC PMID:18396796 Europe PMC PMID:18440992 Europe PMC PMID:18593588 Europe PMC PMID:18816054 Europe PMC PMID:18840508 Europe PMC PMID:19028609 Europe PMC PMID:19120667 Europe PMC PMID:19449910 Europe PMC PMID:19526731 Europe PMC PMID:19544666 Europe PMC PMID:19738917 Europe PMC PMID:19916621 Europe PMC PMID:19924257 Europe PMC PMID:21751272 Europe PMC PMID:22044190 Europe PMC PMID:22079563 Europe PMC PMID:22234938 Europe PMC PMID:22264337 Europe PMC PMID:22293292 Europe PMC PMID:22401276 Europe PMC PMID:22434786 Europe PMC Reaxys:635782 Reaxys GLYCINE PDBeChem Glycine KEGG_COMPOUND aminoacetic acid IUPAC glycine IUPAC 0 ChEBI 75.032 KEGG_COMPOUND 75.06664 ChEBI Aminoacetic acid KEGG_COMPOUND Aminoessigsaeure ChEBI C2H5NO2 KEGG_COMPOUND DHMQDGOQFOQNFH-UHFFFAOYSA-N ChEBI G ChEBI Gly KEGG_COMPOUND Glycin ChemIDplus Glycocoll ChemIDplus Glykokoll ChEBI Glyzin ChEBI H2N-CH2-COOH IUPAC Hgly IUPAC InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) ChEBI Leimzucker ChemIDplus NCC(O)=O ChEBI aminoethanoic acid ChEBI aminoethanoic acid JCBN KEGG:C03834 3-Hydroxymonocarboxylic acid chebi_ontology 0 89.024 89.070 C3H5O3R OC([*])CC(O)=O CHEBI:1549 3-hydroxymonocarboxylic acid 3-Hydroxymonocarboxylic acid KEGG_COMPOUND 0 KEGG_COMPOUND 89.024 KEGG_COMPOUND 89.070 KEGG_COMPOUND C3H5O3R KEGG_COMPOUND OC([*])CC(O)=O ChEBI An acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of phenylacetic acid. CHEBI:14780 CHEBI:25980 CHEBI:8086 CAS:7532-39-0 HMDB:HMDB06503 KEGG:C00582 KNApSAcK:C00007536 PMID:11260461 PMID:2009287 PMID:2553650 PMID:6142928 PMID:666745 PMID:6838224 PMID:8352646 PMID:9297469 Reaxys:8399067 3'-phosphoadenosine 5'-{3-[(3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-{[3-oxo-3-({2-[(phenylacetyl)sulfanyl]ethyl}amino)propyl]amino}butyl] dihydrogen diphosphate} Phenylacetyl-CoA Phenylacetyl-coa chebi_ontology 0 885.157 885.66804 C29H42N7O17P3S CC(C)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n1cnc2c(N)ncnc12)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)Cc1ccccc1 Coenzyme A, S-(benzeneacetate) InChI=1S/C29H42N7O17P3S/c1-29(2,24(40)27(41)32-9-8-19(37)31-10-11-57-20(38)12-17-6-4-3-5-7-17)14-50-56(47,48)53-55(45,46)49-13-18-23(52-54(42,43)44)22(39)28(51-18)36-16-35-21-25(30)33-15-34-26(21)36/h3-7,15-16,18,22-24,28,39-40H,8-14H2,1-2H3,(H,31,37)(H,32,41)(H,45,46)(H,47,48)(H2,30,33,34)(H2,42,43,44)/t18-,22-,23-,24+,28-/m1/s1 Phenylacetyl coenzyme A Phenylacetyl-coenzyme A ZIGIFDRJFZYEEQ-CECATXLMSA-N CHEBI:15537 phenylacetyl-CoA CAS:7532-39-0 ChemIDplus PMID:11260461 Europe PMC PMID:2009287 Europe PMC PMID:2553650 Europe PMC PMID:6142928 Europe PMC PMID:666745 Europe PMC PMID:6838224 Europe PMC PMID:8352646 Europe PMC PMID:9297469 Europe PMC Reaxys:8399067 Reaxys 3'-phosphoadenosine 5'-{3-[(3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-{[3-oxo-3-({2-[(phenylacetyl)sulfanyl]ethyl}amino)propyl]amino}butyl] dihydrogen diphosphate} IUPAC Phenylacetyl-CoA KEGG_COMPOUND Phenylacetyl-coa ChemIDplus 0 ChEBI 885.157 KEGG_COMPOUND 885.66804 ChEBI C29H42N7O17P3S KEGG_COMPOUND CC(C)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n1cnc2c(N)ncnc12)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)Cc1ccccc1 ChEBI Coenzyme A, S-(benzeneacetate) ChemIDplus InChI=1S/C29H42N7O17P3S/c1-29(2,24(40)27(41)32-9-8-19(37)31-10-11-57-20(38)12-17-6-4-3-5-7-17)14-50-56(47,48)53-55(45,46)49-13-18-23(52-54(42,43)44)22(39)28(51-18)36-16-35-21-25(30)33-15-34-26(21)36/h3-7,15-16,18,22-24,28,39-40H,8-14H2,1-2H3,(H,31,37)(H,32,41)(H,45,46)(H,47,48)(H2,30,33,34)(H2,42,43,44)/t18-,22-,23-,24+,28-/m1/s1 ChEBI Phenylacetyl coenzyme A KEGG_COMPOUND Phenylacetyl-coenzyme A ChemIDplus ZIGIFDRJFZYEEQ-CECATXLMSA-N ChEBI The D-enantiomer of alanine. CHEBI:10840 CHEBI:12899 CHEBI:20893 CHEBI:4087 CHEBI:41756 CHEBI:41798 CHEBI:41848 CHEBI:41877 Beilstein:1720249 CAS:338-69-2 DrugBank:DB01786 ECMDB:ECMDB01310 Gmelin:82157 HMDB:HMDB01310 KEGG:C00133 KNApSAcK:C00019654 MetaCyc:D-ALANINE PDBeChem:DAL PMID:10977898 PMID:1450921 PMID:22005737 PMID:22075031 PMID:22123251 PMID:22313760 PMID:3275662 Reaxys:1720249 YMDB:YMDB00993 D-Alanine D-alanine chebi_ontology (2R)-2-aminopropanoic acid (R)-2-aminopropanoic acid (R)-alanine 0 89.048 89.09322 C3H7NO2 C[C@@H](N)C(O)=O D-2-Aminopropionic acid D-Ala D-Alanin D-alpha-alanine D-alpha-aminopropionic acid DAL InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m1/s1 QNAYBMKLOCPYGJ-UWTATZPHSA-N CHEBI:15570 D-alanine Beilstein:1720249 Beilstein CAS:338-69-2 ChemIDplus CAS:338-69-2 KEGG COMPOUND CAS:338-69-2 NIST Chemistry WebBook Gmelin:82157 Gmelin PMID:10977898 Europe PMC PMID:1450921 Europe PMC PMID:22005737 Europe PMC PMID:22075031 Europe PMC PMID:22123251 Europe PMC PMID:22313760 Europe PMC PMID:3275662 Europe PMC Reaxys:1720249 Reaxys D-Alanine KEGG_COMPOUND D-alanine IUPAC (2R)-2-aminopropanoic acid IUPAC (R)-2-aminopropanoic acid ChEBI (R)-alanine NIST_Chemistry_WebBook 0 ChEBI 89.048 KEGG_COMPOUND 89.09322 ChEBI C3H7NO2 KEGG_COMPOUND C[C@@H](N)C(O)=O ChEBI D-2-Aminopropionic acid KEGG_COMPOUND D-Ala KEGG_COMPOUND D-Alanin ChEBI D-alpha-alanine NIST_Chemistry_WebBook D-alpha-aminopropionic acid ChEBI DAL PDBeChem InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m1/s1 ChEBI QNAYBMKLOCPYGJ-UWTATZPHSA-N ChEBI An optically active form of malate having (R)-configuration. CHEBI:11002 CHEBI:18685 KEGG:C00497 MetaCyc:CPD-660 (2R)-2-hydroxybutanedioate chebi_ontology (R)-malate -2 132.006 132.07156 BJEPYKJPYRNKOW-UWTATZPHSA-L C4H4O5 D-malate InChI=1S/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H,1H2,(H,6,7)(H,8,9)/p-2/t2-/m1/s1 O[C@H](CC([O-])=O)C([O-])=O CHEBI:15588 (R)-malate(2-) KEGG:C00497 ChEBI (2R)-2-hydroxybutanedioate IUPAC (R)-malate UniProt -2 ChEBI 132.006 ChEBI 132.07156 ChEBI BJEPYKJPYRNKOW-UWTATZPHSA-L ChEBI C4H4O5 ChEBI D-malate ChEBI InChI=1S/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H,1H2,(H,6,7)(H,8,9)/p-2/t2-/m1/s1 ChEBI O[C@H](CC([O-])=O)C([O-])=O ChEBI An optically active form of malate having (S)-configuration. CHEBI:11066 CHEBI:13140 CHEBI:18784 Beilstein:4133558 KEGG:C00149 MetaCyc:MAL Reaxys:4133558 (2S)-2-hydroxybutanedioate chebi_ontology (S)-malate -2 132.006 132.07156 BJEPYKJPYRNKOW-REOHCLBHSA-L C4H4O5 InChI=1S/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H,1H2,(H,6,7)(H,8,9)/p-2/t2-/m0/s1 L-malate O[C@@H](CC([O-])=O)C([O-])=O CHEBI:15589 (S)-malate(2-) Beilstein:4133558 Beilstein KEGG:C00149 ChEBI Reaxys:4133558 Reaxys (2S)-2-hydroxybutanedioate IUPAC (S)-malate UniProt -2 ChEBI 132.006 ChEBI 132.07156 ChEBI BJEPYKJPYRNKOW-REOHCLBHSA-L ChEBI C4H4O5 ChEBI InChI=1S/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H,1H2,(H,6,7)(H,8,9)/p-2/t2-/m0/s1 ChEBI L-malate ChEBI O[C@@H](CC([O-])=O)C([O-])=O ChEBI A C4-dicarboxylate resulting from deprotonation of both carboxy groups of malic acid. CHEBI:14556 CHEBI:25114 Beilstein:3664410 CAS:149-61-1 Gmelin:327305 KEGG:C00711 PMID:17190852 Reaxys:3664410 2-hydroxybutanedioate chebi_ontology -2 132.006 132.07156 BJEPYKJPYRNKOW-UHFFFAOYSA-L C4H4O5 InChI=1S/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H,1H2,(H,6,7)(H,8,9)/p-2 OC(CC([O-])=O)C([O-])=O hydroxybutanedioic acid, ion(2-) mal malate anion malate dianion CHEBI:15595 malate(2-) Beilstein:3664410 Beilstein CAS:149-61-1 ChemIDplus Gmelin:327305 Gmelin KEGG:C00711 ChEBI PMID:17190852 Europe PMC Reaxys:3664410 Reaxys 2-hydroxybutanedioate IUPAC -2 ChEBI 132.006 ChEBI 132.07156 ChEBI BJEPYKJPYRNKOW-UHFFFAOYSA-L ChEBI C4H4O5 ChEBI InChI=1S/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H,1H2,(H,6,7)(H,8,9)/p-2 ChEBI OC(CC([O-])=O)C([O-])=O ChEBI hydroxybutanedioic acid, ion(2-) ChemIDplus mal IUPAC malate anion ChEBI malate dianion ChEBI