A formal ontology of phenotypes observed in fission yeast. Fission Yeast Phenotype Ontology (FYPO) OBO-Edit 2.3.1 12:05:2020 14:21 fission_yeast_phenotype 1.2 midori svn version: $Revision: 303 $ definition 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 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.obofoundry.org/obo/obi> IAO:0000116 uberon editor_note true editor_note editor note editor note has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason term replaced by Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by term replaced by If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive Term not to be used for direct annotation Term not to be used for direct manual annotation uberon dc-creator true dc-creator creator subset_property consider has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym in_subset shorthand is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of Used in FYPO to identify phenotypes that are always observed in the context of another, usually larger-scale, phenotype. BFO:0000050 BrendaTissueOBO external fission_yeast_phenotype protein quality uberon part_of part_of part of part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part Used in FYPO to link phenotypes that are collections of features to phenotypes representing the features. BFO:0000051 chebi_ontology external fission_yeast_phenotype protein quality uberon has_part false has_part We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. has part has part has_part Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. PATOC:CJM preceded by X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 is preceded by takes place after uberon preceded_by preceded_by preceded by preceded_by is preceded by SIO:000249 takes place after Allen:precedes precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 uberon precedes precedes precedes precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in Used in FYPO to identify a location, usually a cellular component or cell type, within which a phenotype is observed or relevant. BFO:0000066 external fission_yeast_phenotype occurs_in occurs_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in occurs in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t BFO:0000067 uberon contains_process contains_process Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process contains process Identifies a process, cell cycle stage or life stage during which a phenotype that affects an occurrent, i.e. a biological process or molecular function, is observed or relevant. GOREL:0000001 fission_yeast_phenotype happens_during happens_during happens_during Identifies a process, cell cycle stage or life stage during which a phenotype is observed or relevant. GOREL:0000002 fission_yeast_phenotype during during during Identifies a process, cell cycle stage or life stage during which a phenotype that affects a continuant, such as a cellular component or the level of a substance, is observed or relevant. GOREL:0000032 fission_yeast_phenotype exists_during exists_during exists_during This relation is not constrained with respect to whether the place where an event occurs completely surrounds, or is adjacent to, the location indicated. Example: chromatin silencing at centromere unfolds_around centromere : Repression of transcription of centromeric DNA by the formation of heterochromatin. Used in FYPO to identify a position where a phenotype is observed or relevant, usually a DNA or RNA sequence feature specified by a SO ID. GOREL:0000501 fission_yeast_phenotype occurs_at occurs_at occurs_at This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes inverse of the relation 'denotes' Person: Jie Zheng, Chris Stoeckert, Mike Conlon denoted by inheres in this fragility inheres in this vase this red color inheres in this apple a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in Used in FYPO as described in PATO best practices; identifies an entity that displays a quality in an entity-quality logical definition. Used only in logical definitions (aka xps). RO:0000052 fission_yeast_phenotype inheres_in inheres_in inheres in inheres_in bearer of this apple is bearer of this red color this vase is bearer of this fragility a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of RO:0000053 uberon bearer_of bearer_of bearer of bearer of participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in RO:0000056 protein participates_in false participates_in participates in participates_in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of role of this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality RO:0000086 protein uberon has_quality false has_quality has quality has quality has_quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role RO:0000087 chebi_ontology protein has_role false false has_role has role has role has_role this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. RO:0001000 protein derives_from derives_from derives from derives_from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime location_of RO:0001015 uberon location_of location_of location of location_of contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): Intended meaning: domain: material entity range: spatial region or site (immaterial continuant) contained_in contained in contains RO:0001019 uberon contains contains contains contains located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime located_in Used in FYPO to indicate where a physical quality phenotype is observed. http://www.obofoundry.org/ro/#OBO_REL:located_in RO:0001025 fission_yeast_phenotype protein uberon located_in located_in located in located in located_in This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. dos 2017-05-24T09:30:46Z has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. dos 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. dos 2017-05-24T09:49:21Z has component process A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. dos 2017-07-19T17:30:36Z has ligand dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. GOC:dos Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. dos 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. GOC:dos Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. dos 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. GOC:dos A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. GOC:dos David Osumi-Sutherland Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which ends David Osumi-Sutherland di Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. encompasses David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) David Osumi-Sutherland starts_at_end_of A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. RO:0002087 directly preceded by is directly preceded by is immediately preceded by starts_at_end_of uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by immediately_preceded_by A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. SIO:000251 is immediately preceded by SIO:000251 David Osumi-Sutherland Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which starts David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes David Osumi-Sutherland io X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) starts during David Osumi-Sutherland d during RO:0002092 external happens_during happens_during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during happens during David Osumi-Sutherland o overlaps RO:0002093 external ends_during ends_during X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). ends during ends_during A overlaps B if they share some part in common. x overlaps y if and only if there exists some z such that x has part z and z part of y BFO_0000051 some (BFO_0000050 some ?Y) http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 uberon overlaps overlaps overlaps overlaps true w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. RO:0002180 protein uberon has_component false has_component has component has component has_component x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y Chris Mungall David Osumi-Sutherland Melissa Haendel Terry Meehan This is the transitive form of the develops from relation develops from inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan develops into process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false RO:0002211 external regulates regulates regulates regulates Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall negatively regulates (process to process) RO:0002212 external negatively_regulates negatively_regulates negatively regulates negatively regulates Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall positively regulates (process to process) RO:0002213 external positively_regulates positively_regulates positively regulates positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO_0000053 some (RO_0000054 only ?Y) RO:0002215 uberon capable_of capable_of capable of capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) RO:0002216 uberon capable_of_part_of capable_of_part_of capable of part of capable of part of true OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role x actively participates in y if and only if x participates in y and x realizes some active role Chris Mungall agent in Obsoleted as the inverse property was obsoleted. actively participates in obsolete actively participates in true 'heart development' has active participant some Shh protein x has participant y if and only if x realizes some active role that inheres in y This may be obsoleted and replaced by the original 'has agent' relation Chris Mungall has agent obsolete has active participant true Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes has input p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. Chris Mungall produces has output Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y Chris Mungall has developmental contribution from inverse of has developmental contribution from Chris Mungall developmentally contributes to Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false Chris Mungall In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within Inverse of developmentally preceded by Chris Mungall developmentally succeeded by cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of inheres in part of Chris Mungall Used in FYPO as described in MP/HP logical definition best practices for processes, and in an analogous manner for cell/cell part structure; identifies an entity that displays a quality in an entity-quality logical definition. Used only in logical definitions (aka xps). RO:0002314 fission_yeast_phenotype inheres_in_part_of inheres_in_part_of inheres in part of inheres in part of true A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 uberon functionally_related_to functionally_related_to functionally related to functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false RO:0002329 uberon part_of_structure_that_is_capable_of part_of_structure_that_is_capable_of part of structure that is capable of part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in enables part of RO:0002331 protein involved_in false involved_in involved in involved_in inverse of enables Chris Mungall enabled by inverse of regulates Chris Mungall regulated by (processual) regulated by inverse of negatively regulates Chris Mungall negatively regulated by inverse of positively regulates Chris Mungall positively regulated by inverse of has input Chris Mungall RO:0002352 uberon input_of input_of input of input of inverse of has output Chris Mungall RO:0002353 protein uberon output_of false output_of output of output of output_of A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location Chris Mungall This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall has developmental potential involving x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y Chris Mungall has potential to developmentally contribute to x has the potential to develop into y iff x develops into y or if x is capable of developing into y Chris Mungall has potential to develop into x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y Chris Mungall has potential to directly develop into inverse of upstream of Chris Mungall causally downstream of Chris Mungall immediately causally downstream of This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall immediately causally upstream of p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) affects causally upstream of or within inverse of causally upstream of or within Chris Mungall causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p Chris Mungall involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p Chris Mungall involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. Chris Mungall executes activity in enables activity in is active in c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. GOC:cjm GOC:dos true A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Chris Mungall Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/MI_0914 https://github.com/oborel/obo-relations/wiki/InteractionRelations An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. Chris Mungall binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later Chris Mungall An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. Chris Mungall Vasundra Touré molecularly controls activity directly regulates activity of directly regulates activity of Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Chris Mungall Vasundra Touré directly inhibits inhibits molecularly decreases activity of activity directly negatively regulates activity of directly negatively regulates activity of Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Chris Mungall Vasundra Touré activates directly activates molecularly increases activity of activity directly positively regulates activity of directly positively regulates activity of Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in true Chris Mungall is kinase activity Chris Mungall is ubiquitination A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes Chris Mungall depends on q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. Chris Mungall Relation binding a relational quality or disposition to the relevant type of entity. Used in FYPO as described in PATO best practices; identifies abolished GO processes; identifies substances affected by phenotypes. RO:0002503 fission_yeast_phenotype towards towards towards The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities causal relation between material entities Chris Mungall causally influenced by (entity-centric) causally influenced by (material entity to material entity) causally influenced by Chris Mungall interaction relation helper property https://github.com/oborel/obo-relations/wiki/InteractionRelations Chris Mungall molecular interaction relation helper property Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). Chris Mungall Vasundra Touré causally influences (entity-centric) causally influences (material entity to material entity) causally influences A relation that holds between an attribute or a qualifier and another attribute. Chris Mungall This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. Used in FYPO as described in PATO best practices; placeholder relation to indicate normality/abnormality. RO:0002573 fission_yeast_phenotype qualifier qualifier has modifier qualifier Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Chris Mungall directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. directly positively regulates (process to process) directly positively regulates Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. directly negatively regulates (process to process) directly negatively regulates a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. Melissa Haendel RO:0003000 uberon produces produces Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces produces a produced_by b iff some process that occurs_in b has_output a. Melissa Haendel RO:0003001 uberon produced_by produced_by produced by produced_by Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z enables subfunction cjm 2018-01-26T23:49:30Z acts upstream of or within, positive effect cjm 2018-01-26T23:49:51Z acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive cjm 2018-01-26T23:53:14Z acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative cjm 2018-01-26T23:53:22Z acts upstream of, negative effect cjm 2018-03-13T23:55:05Z causally upstream of or within, negative effect cjm 2018-03-13T23:55:19Z causally upstream of or within, positive effect The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. Vasundra Touré regulates activity of 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 p has output c if either: p has direct output c or p has output input c. Implies that if p happens, c always ensues. Def comes from gorel file. Used in FYPO where one phenotype (p) always results in an additional phenotype (c) as a consequence. There may be other ways to get phenotype (c). fission_yeast_phenotype has_output has_output p has output c if either: p has direct output c or p has output input c. Implies that if p happens, c always ensues. GOC:curators Inverse of has_output. Relation between a structure and a process that forms it, or between one process and a preceding process; A output_of B used where B has_output A isn't always true. Implies that process B is the only way to get output. Used in FYPO where one phenotype (c) always results when another phenotype (p) is present. Phenotype (p) may have other consequences in addition to phenotype (c). formation results from fission_yeast_phenotype output_of output_of formation results from PomBase:mah Used in FYPO when a phenotype is observed after another event, usually a GO biological process, has ended, and where there isn't a suitable process to use with a during relation. fission_yeast_phenotype preceded_by preceded_by Used in FYPO when a phenotype is observed before another event, usually a GO biological process, begins, and where there isn't a suitable process to use with a during relation. fission_yeast_phenotype precedes precedes q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality decreased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. decreased_in_magnitude_relative_to q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality different_in_magnitude_relative_to different_in_magnitude_relative_to q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. quality has_cross_section Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. has_cross_section s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. PATOC:CJM q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality increased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. increased_in_magnitude_relative_to q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. quality reciprocal_of There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. reciprocal_of q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. PATOC:CJM A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap. sequence adjacent_to adjacent_to A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap. PMID:20226267 SO:ke sequence derives_from derives_from Inverse of part_of. sequence has_part Example: operon has_part gene. has_part Inverse of part_of. http://precedings.nature.com/documents/3495/version/1 sequence has_quality The relationship between a feature and an attribute. has_quality sequence member_of A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444. member_of X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y. kareneilbeck 2010-10-14T01:33:15Z sequence overlaps Example: coding_exon overlaps CDS. overlaps X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y. PMID:20226267 X part_of Y if X is a subregion of Y. sequence part_of Example: amino_acid part_of polypeptide. part_of X part_of Y if X is a subregion of Y. http://precedings.nature.com/documents/3495/version/1 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 An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region 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] An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. bfo BFO:0000015 process process A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. realizable entity 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] bfo BFO:0000019 quality quality 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] 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 A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. 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] A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. role bfo BFO:0000024 fiat object part bfo BFO:0000030 object 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. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. 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] An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. bfo BFO:0000040 material entity material entity 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 A structured controlled vocabulary for the source of an enzyme. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. BrendaTissueOBO BTO:0000000 tissues, cell types and enzyme sources A structured controlled vocabulary for the source of an enzyme. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. curators:mgr BrendaTissueOBO BTO:0000001 culture condition:-induced cell BrendaTissueOBO BTO:0000002 culture condition:1,4-dichlorobenzene-grown cell Cells taken from a living organism and grown under controlled conditions (in culture). Methods used to maintain cell lines or strains. BrendaTissueOBO BTO:0000214 cell culture Cells taken from a living organism and grown under controlled conditions (in culture). Methods used to maintain cell lines or strains. Glossary_of_Fermentation_&_Cell_Culture_Terms:http://www.nbsc.com/files/papers/bp0600_gloss_36-44.pdf BrendaTissueOBO BTO:0000216 culture condition A substance, either solid or liquid, used for the cultivation, isolation, identification, or storage of microorganisms. BrendaTissueOBO growth medium medium nutrient medium BTO:0000316 Added as synonym to culture fluid. culture medium true A substance, either solid or liquid, used for the cultivation, isolation, identification, or storage of microorganisms. Biology-Online_Dictionary:http://www.biology-online.org/dictionary/ BrendaTissueOBO BTO:0001479 culture condition:-grown cell Other sources of an enzyme as cell culture or commercial preparation, not related to a specific tissue. BrendaTissueOBO BTO:0001490 other source Other sources of an enzyme as cell culture or commercial preparation, not related to a specific tissue. curators:mgr anatomical entity connected anatomical structure material anatomical entity cell part (CARO) cell part biological entity 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. 0 C12H12N2O3 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 232.23530 232.08479 CCn1cc(C(O)=O)c(=O)c2ccc(C)nc12 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 VSDB:1880 Wikipedia:Nalidixic_Acid 1-ethyl-7-methyl-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carboxylic acid NALIDIXIC ACID Nalidixic acid chebi_ontology 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 3-carboxy-1-ethyl-7-methyl-1,8-naphthyridin-4-one 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 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 3-carboxy-1-ethyl-7-methyl-1,8-naphthyridin-4-one ChemIDplus acide nalidixique ChemIDplus acido nalidixico ChemIDplus acidum nalidixicum ChemIDplus nalidixic acid ChemIDplus A macrolide comprising a fourteen-membered lactone fused to 1,3-dihydroxybenzene; a potent estrogenic metabolite produced by some Giberella species. 0 C18H22O5 InChI=1S/C18H22O5/c1-12-6-5-9-14(19)8-4-2-3-7-13-10-15(20)11-16(21)17(13)18(22)23-12/h3,7,10-12,20-21H,2,4-6,8-9H2,1H3/b7-3+/t12-/m0/s1 MBMQEIFVQACCCH-QBODLPLBSA-N 318.36430 318.14672 C[C@H]1CCCC(=O)CCC\C=C\c2cc(O)cc(O)c2C(=O)O1 CAS:17924-92-4 KEGG:C09981 KNApSAcK:C00003025 LIPID_MAPS_instance:LMPK04000016 PMID:17339071 PMID:18027362 PMID:18221829 PMID:18280460 PMID:18692541 PMID:20654554 Reaxys:4875541 (3S,11E)-14,16-dihydroxy-3-methyl-3,4,5,6,9,10-hexahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione chebi_ontology (-)-Zearalenone (10S)-Zearalenone (S)-(-)-Zearalenone (S)-Zearalenone (S-(E))-3,4,5,6,9,10-Hexahydro-14,16-dihydroxy-3-methyl-1H-2-benzoxacyclotetradecin-1,7(8H)-dione 6-(10-Hydroxy-6-oxo-trans-1-undecenyl)-beta-resorcylic acid lactone trans-Zearalenone CHEBI:10106 zearalenone CAS:17924-92-4 ChemIDplus CAS:17924-92-4 KEGG COMPOUND LIPID_MAPS_instance:LMPK04000016 LIPID MAPS PMID:17339071 Europe PMC PMID:18027362 Europe PMC PMID:18221829 Europe PMC PMID:18280460 Europe PMC PMID:18692541 Europe PMC PMID:20654554 Europe PMC Reaxys:4875541 Reaxys (3S,11E)-14,16-dihydroxy-3-methyl-3,4,5,6,9,10-hexahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione IUPAC (-)-Zearalenone ChemIDplus (10S)-Zearalenone ChemIDplus (S)-(-)-Zearalenone ChemIDplus (S)-Zearalenone ChemIDplus (S-(E))-3,4,5,6,9,10-Hexahydro-14,16-dihydroxy-3-methyl-1H-2-benzoxacyclotetradecin-1,7(8H)-dione ChemIDplus 6-(10-Hydroxy-6-oxo-trans-1-undecenyl)-beta-resorcylic acid lactone ChemIDplus trans-Zearalenone 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. -1 0.000548579903 0.0 KEGG:C05359 PMID:21614077 Wikipedia:Electron electron chebi_ontology Elektron beta beta(-) beta-particle e e(-) e- negatron CHEBI:10545 electron PMID:21614077 Europe PMC PMID:21614077 Europe PMC electron ChEBI electron IUPAC electron KEGG_COMPOUND Elektron ChEBI beta IUPAC beta(-) ChEBI beta-particle IUPAC e IUPAC e(-) UniProt e- KEGG_COMPOUND negatron IUPAC An organophosphate oxoanion that is the trianion of (R)-5-phosphopantothenic acid arising from deprotonation of the carboxy and phosphate OH groups; major species at pH 7.3 -3 C9H15NO8P InChI=1S/C9H18NO8P/c1-9(2,5-18-19(15,16)17)7(13)8(14)10-4-3-6(11)12/h7,13H,3-5H2,1-2H3,(H,10,14)(H,11,12)(H2,15,16,17)/p-3/t7-/m0/s1 XHFVGHPGDLDEQO-ZETCQYMHSA-K 296.19110 296.05517 CC(C)(COP([O-])([O-])=O)[C@@H](O)C(=O)NCCC([O-])=O 3-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonatooxy)butanamido]propanoate chebi_ontology (R)-4'-phosphopantothenate CHEBI:10986 (R)-4'-phosphonatopantothenate(3-) 3-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonatooxy)butanamido]propanoate IUPAC (R)-4'-phosphopantothenate UniProt A glycerophosphocholine having an unspecified O-acyl substituent at the 1-position of the glycerol fragment. +1 C9H20NO7PR 285.232 285.09774 C[N+](C)(C)CCOP(O)(=O)OCC(O)COC([*])=O CHEBI:53029 chebi_ontology 1-O-acylglycerophosphocholines 2-lysophosphatidylcholine CHEBI:11230 1-acylglycerophosphocholine(1+) 1-O-acylglycerophosphocholines ChEBI 2-lysophosphatidylcholine ChEBI A glycerophosphocholine having an unspecified acyl group attached at the 2-position. +1 C9H20NO7PR 285.23140 285.09774 C[N+](C)(C)CCOP(O)(=O)OCC(CO)OC([*])=O PMID:15913955 chebi_ontology 2-acylglycerophosphocholines LPC CHEBI:11502 2-acylglycerophosphocholine PMID:15913955 Europe PMC 2-acylglycerophosphocholines ChEBI LPC ChEBI An alpha,omega dicarboxyacyl-CoA that results from the formal condensation of the thiol group of coenzyme A with one of the carboxy groups of 3-hydroxy-3-methylglutaric acid. 0 C27H44N7O20P3S InChI=1S/C27H44N7O20P3S/c1-26(2,21(40)24(41)30-5-4-15(35)29-6-7-58-17(38)9-27(3,42)8-16(36)37)11-51-57(48,49)54-56(46,47)50-10-14-20(53-55(43,44)45)19(39)25(52-14)34-13-33-18-22(28)31-12-32-23(18)34/h12-14,19-21,25,39-40,42H,4-11H2,1-3H3,(H,29,35)(H,30,41)(H,36,37)(H,46,47)(H,48,49)(H2,28,31,32)(H2,43,44,45)/t14-,19-,20-,21+,25-,27?/m1/s1 CABVTRNMFUVUDM-SJBCKIPMSA-N 911.66072 911.15747 CC(O)(CC(O)=O)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 PMID:20640529 PMID:9160173 3'-phosphoadenosine 5'-{3-[(3R)-4-{[3-({2-[(4-carboxy-3-hydroxy-3-methylbutanoyl)sulfanyl]ethyl}amino)-3-oxopropyl]amino}-3-hydroxy-2,2-dimethyl-4-oxobutyl] dihydrogen diphosphate} chebi_ontology (4-carboxy-3-hydroxy-3-methylbutanoyl)-CoA (4-carboxy-3-hydroxy-3-methylbutanoyl)-coenzyme A 3-hydroxy-3-methylglutaryl-coenzyme A CHEBI:11814 3-hydroxy-3-methylglutaryl-CoA PMID:20640529 Europe PMC PMID:9160173 Europe PMC 3'-phosphoadenosine 5'-{3-[(3R)-4-{[3-({2-[(4-carboxy-3-hydroxy-3-methylbutanoyl)sulfanyl]ethyl}amino)-3-oxopropyl]amino}-3-hydroxy-2,2-dimethyl-4-oxobutyl] dihydrogen diphosphate} IUPAC (4-carboxy-3-hydroxy-3-methylbutanoyl)-CoA ChEBI (4-carboxy-3-hydroxy-3-methylbutanoyl)-coenzyme A ChEBI 3-hydroxy-3-methylglutaryl-coenzyme A ChEBI A ribose diphosphate carrying an additional phosphate group at position 5. chebi_ontology CHEBI:12164 5-phosphoribosyl diphosphate -1 C9H17NO8P InChI=1S/C9H18NO8P/c1-9(2,5-18-19(15,16)17)7(13)8(14)10-4-3-6(11)12/h7,13H,3-5H2,1-2H3,(H,10,14)(H,11,12)(H2,15,16,17)/p-1/t7-/m0/s1 XHFVGHPGDLDEQO-ZETCQYMHSA-M 298.20698 298.06973 CC(C)(COP(O)(O)=O)[C@@H](O)C(=O)NCCC([O-])=O 3-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanamido]propanoate chebi_ontology CHEBI:12886 (R)-4'-phosphopantothenate(1-) 3-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanamido]propanoate IUPAC 0 C6H12O6 180.15588 180.06339 D-galacto-hexose D-galactose chebi_ontology D-Gal CHEBI:12936 D-galactose D-galacto-hexose IUPAC D-galactose IUPAC D-Gal JCBN An antagonist that interferes with the action of the calcium-binding messenger protein calmodulin. PMID:26717596 chebi_ontology CHEBI:130181 calmodulin antagonist PMID:26717596 Europe PMC A disaccharide formed by a (1<->1)-glycosidic bond between two hexopyranose units. hexopyranosyl hexopyranoside chebi_ontology CHEBI:131401 hexopyranosyl hexopyranoside hexopyranosyl hexopyranoside IUPAC A pyridinium ion obtained by protonation of the ring nitrogen of pyridoxal. +1 C8H10NO3 InChI=1S/C8H9NO3/c1-5-8(12)7(4-11)6(3-10)2-9-5/h2,4,10,12H,3H2,1H3/p+1 RADKZDMFGJYCBB-UHFFFAOYSA-O 168.170 168.06552 C1(O)=C(C)[NH+]=CC(CO)=C1C([H])=O 4-formyl-3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-1-ium chebi_ontology pyridoxal cation CHEBI:131530 pyridoxal(1+) 4-formyl-3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-1-ium IUPAC pyridoxal cation ChEBI A pyridinium ion obtained by protonation of both nitrogens of pyridoxamine. +2 C8H14N2O2 InChI=1S/C8H12N2O2/c1-5-8(12)7(2-9)6(4-11)3-10-5/h3,11-12H,2,4,9H2,1H3/p+2 NHZMQXZHNVQTQA-UHFFFAOYSA-P 170.209 170.10443 C1(O)=C(C)[NH+]=CC(CO)=C1C[NH3+] 4-(azaniumylmethyl)-3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-1-ium chebi_ontology pyridoxamine cation pyridoxamine dication CHEBI:131533 pyridoxamine(2+) 4-(azaniumylmethyl)-3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-1-ium IUPAC pyridoxamine cation ChEBI pyridoxamine dication ChEBI 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 carboxylic acid anion resultig from the deprotonation of the carboxy group of a dicarboxylic acid monoester. chebi_ontology CHEBI:131605 dicarboxylic acid monoester(1-) An echinocandin initially isolated as a very minor bioactive fermentation product of Glarea lozoyensis (originally known as Zalerion arboricola). Subsequent random mutagenesis work and optimisation of the fermentation medium permitted the industrial production of pneumocandin B0, which is used as the starting point for the synthesis of the antifungal drug caspofungin. 0 C50H80N8O17 InChI=1S/C50H80N8O17/c1-5-25(2)20-26(3)12-10-8-6-7-9-11-13-37(66)52-31-22-35(64)46(71)56-48(73)41-33(62)18-19-57(41)50(75)39(34(63)23-36(51)65)54-47(72)40(43(68)42(67)28-14-16-29(60)17-15-28)55-45(70)32-21-30(61)24-58(32)49(74)38(27(4)59)53-44(31)69/h14-17,25-27,30-35,38-43,46,59-64,67-68,71H,5-13,18-24H2,1-4H3,(H2,51,65)(H,52,66)(H,53,69)(H,54,72)(H,55,70)(H,56,73)/t25-,26+,27+,30+,31-,32-,33-,34+,35+,38-,39-,40-,41-,42-,43-,46+/m0/s1 DQXPFAADCTZLNL-FXDJFZINSA-N 1065.216 1064.56414 [C@@]12(N(C[C@@H](C1)O)C([C@H]([C@@H](C)O)NC(=O)[C@](C[C@H]([C@@H](O)NC([C@@H]3[C@H](CCN3C([C@H]([C@@H](CC(N)=O)O)NC(=O)[C@H]([C@@H]([C@H](C4=CC=C(C=C4)O)O)O)NC2=O)=O)O)=O)O)(NC(CCCCCCCC[C@H](C[C@H](CC)C)C)=O)[H])=O)[H] CAS:135575-42-7 PMID:24086376 PMID:24270605 PMID:25527531 Reaxys:9316734 Wikipedia:Pneumocandin_Bo (10R,12S)-N-{(2R,6S,9S,11R,12R,14aS,15S,20S,23S,25aS)-20-[(1R)-3-amino-1-hydroxy-3-oxopropyl]-23-[(1S,2S)-1,2-dihydroxy-2-(4-hydroxyphenyl)ethyl]-2,11,12,15-tetrahydroxy-6-[(1R)-1-hydroxyethyl]-5,8,14,19,22,25-hexaoxotetracosahydro-1H-dipyrrolo[2,1-c:2',1'-l][1,4,7,10,13,16]hexaazacyclohenicosin-9-yl}-10,12-dimethyltetradecanamide chebi_ontology L 688,786 L-688,786 L-688786 pneumocandin B(0) pneumocardin B(0) CHEBI:131609 pneumocandin B0 CAS:135575-42-7 ChemIDplus PMID:24086376 Europe PMC PMID:24270605 Europe PMC PMID:25527531 Europe PMC Reaxys:9316734 Reaxys (10R,12S)-N-{(2R,6S,9S,11R,12R,14aS,15S,20S,23S,25aS)-20-[(1R)-3-amino-1-hydroxy-3-oxopropyl]-23-[(1S,2S)-1,2-dihydroxy-2-(4-hydroxyphenyl)ethyl]-2,11,12,15-tetrahydroxy-6-[(1R)-1-hydroxyethyl]-5,8,14,19,22,25-hexaoxotetracosahydro-1H-dipyrrolo[2,1-c:2',1'-l][1,4,7,10,13,16]hexaazacyclohenicosin-9-yl}-10,12-dimethyltetradecanamide IUPAC L 688,786 ChemIDplus L-688,786 ChemIDplus L-688786 ChemIDplus pneumocandin B(0) ChemIDplus pneumocardin B(0) ChemIDplus A 2-acyl-sn-glycero-3-phosphocholine in which the acyl group is specified as tertadecanoyl (myristoyl). 0 C22H46NO7P InChI=1S/C22H46NO7P/c1-5-6-7-8-9-10-11-12-13-14-15-16-22(25)30-21(19-24)20-29-31(26,27)28-18-17-23(2,3)4/h21,24H,5-20H2,1-4H3/t21-/m1/s1 IGZPHNNYPPAPLA-OAQYLSRUSA-N 467.578 467.30119 OC[C@@H](OC(CCCCCCCCCCCCC)=O)COP(=O)([O-])OCC[N+](C)(C)C LIPID_MAPS_instance:LMGP01050073 PMID:21510612 PMID:26860358 Reaxys:9670780 (2R)-3-hydroxy-2-(tetradecanoyloxy)propyl 2-(trimethylazaniumyl)ethyl phosphate 2-tetradecanoyl-sn-glycero-3-phosphocholine chebi_ontology 2-myristoyl-sn-glycero-3-phosphocholine PC(0:0/14:0) CHEBI:131738 2-tetradecanoyl-sn-glycero-3-phosphocholine LIPID_MAPS_instance:LMGP01050073 LIPID MAPS PMID:21510612 Europe PMC PMID:26860358 Europe PMC Reaxys:9670780 Reaxys (2R)-3-hydroxy-2-(tetradecanoyloxy)propyl 2-(trimethylazaniumyl)ethyl phosphate IUPAC 2-tetradecanoyl-sn-glycero-3-phosphocholine UniProt 2-myristoyl-sn-glycero-3-phosphocholine ChEBI PC(0:0/14:0) LIPID_MAPS Any monounsaturated fatty acid carrying one or more hydroxy substituents. chebi_ontology hydroxy MUFA hydroxy monounsaturated fatty acids CHEBI:131869 hydroxy monounsaturated fatty acid hydroxy MUFA SUBMITTER hydroxy monounsaturated fatty acids ChEBI Any monounsaturated fatty acid anion carrying one or more hydroxy substituents. chebi_ontology hydroxy MUFA anion hydroxy MUFA anions hydroxy monounsaturated fatty acid anions CHEBI:131870 hydroxy monounsaturated fatty acid anion hydroxy MUFA anion SUBMITTER hydroxy MUFA anions ChEBI hydroxy monounsaturated fatty acid anions ChEBI Any polyunsaturated fatty acid anion carrying one or more hydroxy substituents. -1 CHO3R 61.017 60.99257 O*C([O-])=O chebi_ontology a hydroxy polyunsaturated fatty acid hydroxy PUFA hydroxy polyunsaturated fatty acid anions CHEBI:131871 hydroxy polyunsaturated fatty acid anion a hydroxy polyunsaturated fatty acid UniProt hydroxy PUFA SUBMITTER hydroxy polyunsaturated fatty acid 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 A lysophosphatidylcholine 20:1 in which the acyl group is located at position 1. 0 C28H56NO7P 549.722 549.37944 [C@@H](COC(=O)*)(COP(OCC[N+](C)(C)C)(=O)[O-])O chebi_ontology 1-eicosenoyl-GPC 1-eicosenoyl-GPC (20:1) 1-eicosenoyl-sn-glycero-3-phosphocholine GPC(20:1) GPC(20:1/0:0) LPC(20:1/0:0) PC(20:1/0:0) lysophosphatidylcholine (20:1/0:0) CHEBI:131982 1-icosenoyl-sn-glycero-3-phosphocholine 1-eicosenoyl-GPC ChEBI 1-eicosenoyl-GPC (20:1) ChEBI 1-eicosenoyl-sn-glycero-3-phosphocholine ChEBI GPC(20:1) ChEBI GPC(20:1/0:0) ChEBI LPC(20:1/0:0) ChEBI PC(20:1/0:0) ChEBI lysophosphatidylcholine (20:1/0:0) ChEBI Any member of the class of benzoquinones that is 1,4-benzoquinone or its C-substituted derivatives. 0 C6O2R4 104.063 103.98983 O=C1C(*)=C(*)C(=O)C(*)=C1* chebi_ontology a quinone p-benzoquinones para-benzoquinones CHEBI:132124 1,4-benzoquinones a quinone UniProt p-benzoquinones ChEBI para-benzoquinones 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. -4 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 188.092 187.99790 C(=O)([O-])C(CC(=O)[O-])(CC(=O)[O-])[O-] Chemspider:34552020 2-oxidopropane-1,2,3-tricarboxylate chebi_ontology 2-oxido-1,2,3-propanetricarboxylate citric acid tetraanion CHEBI:132362 citrate(4-) 2-oxidopropane-1,2,3-tricarboxylate IUPAC 2-oxido-1,2,3-propanetricarboxylate ChEBI citric acid tetraanion ChEBI 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 CHEBI:132943 aspartate An octadecenoate in which the double bond is at C-9. -1 C18H33O2 InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1 ZQPPMHVWECSIRJ-UHFFFAOYSA-M 281.454 281.24860 C(=CCCCCCCCC)CCCCCCCC(=O)[O-] octadec-9-enoate chebi_ontology 9-octadecenoate C18:1, n-9(1-) Delta(9)-octadecenoate CHEBI:132944 octadec-9-enoate octadec-9-enoate IUPAC 9-octadecenoate ChEBI C18:1, n-9(1-) ChEBI Delta(9)-octadecenoate 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 A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of suberic acid. chebi_ontology octanedioic acid anion octanedioic acid anions suberate anion suberate anions suberates suberic acid anion suberic acid anions CHEBI:132953 suberate octanedioic acid anion ChEBI octanedioic acid anions ChEBI suberate anion ChEBI suberate anions ChEBI suberates ChEBI suberic acid anion ChEBI suberic acid anions ChEBI A drug that makes increases the sensitivity of tumour cells to radiation therapy. PMID:12520460 Wikipedia:Radiosensitizer chebi_ontology radiosensitiser radiosensitisers radiosensitising agent radiosensitising agents radiosensitizer radiosensitizers radiosensitizing agents CHEBI:132992 radiosensitizing agent PMID:12520460 Europe PMC radiosensitiser ChEBI radiosensitisers ChEBI radiosensitising agent ChEBI radiosensitising agents ChEBI radiosensitizer ChEBI radiosensitizers ChEBI radiosensitizing agents ChEBI A dipeptide obtained by formal condensation of the gamma-carboxy group of glutamic acid with the amino group of 2-aminobutyric acid. 0 C9H16N2O5 InChI=1S/C9H16N2O5/c1-2-6(9(15)16)11-7(12)4-3-5(10)8(13)14/h5-6H,2-4,10H2,1H3,(H,11,12)(H,13,14)(H,15,16) FUZOZPRKGAXGOB-UHFFFAOYSA-N 232.234 232.10592 NC(C(O)=O)CCC(=O)NC(C(=O)O)CC Reaxys:25853400 N-(1-carboxypropyl)glutamine chebi_ontology gamma-glutamyl-2-aminobutyric acid CHEBI:133092 gamma-Glu-Abu Reaxys:25853400 Reaxys N-(1-carboxypropyl)glutamine IUPAC gamma-glutamyl-2-aminobutyric acid ChEBI A peptide anion that is the conjugate base of gamma-Glu-Abu, obtained by removal of protons from the two carboxy groups as well as protonation of the amino group; major species at pH 7.3. -1 C9H15N2O5 InChI=1S/C9H16N2O5/c1-2-6(9(15)16)11-7(12)4-3-5(10)8(13)14/h5-6H,2-4,10H2,1H3,(H,11,12)(H,13,14)(H,15,16)/p-1 FUZOZPRKGAXGOB-UHFFFAOYSA-M 231.226 231.09865 [NH3+]C(C([O-])=O)CCC(=O)NC(C(=O)[O-])CC 2-azaniumyl-5-[(1-carboxylatopropyl)amino]-5-oxopentanoate chebi_ontology gamma-glutamyl-2-aminobutyrate CHEBI:133093 gamma-Glu-Abu(1-) 2-azaniumyl-5-[(1-carboxylatopropyl)amino]-5-oxopentanoate IUPAC gamma-glutamyl-2-aminobutyrate ChEBI An oxaspiro compound in which a carbon atom of an epoxide ring is the only common member of two rings. chebi_ontology spiro-epoxides spiroepoxide spiroepoxides CHEBI:133131 spiro-epoxide spiro-epoxides ChEBI spiroepoxide ChEBI spiroepoxides ChEBI Any organic heteroolycyclic compound whose skeleton two ortho-fused chromene rings, and their derivatives. chebi_ontology chromenochromenes CHEBI:133135 chromenochromene chromenochromenes ChEBI An acyl-CoA oxoanion obtained by deprotonation of the phosphate, diphosphate and carboxy groups of any omega-carboxyacyl-CoA; major species at pH 7.3. -5 C23H31N7O19P3SR 834.516 834.06083 [C@@H]1(N2C3=C(C(=NC=N3)N)N=C2)O[C@H](COP(OP(OCC(C)([C@H](C(NCCC(NCCSC(=O)*C([O-])=O)=O)=O)O)C)(=O)[O-])(=O)[O-])[C@H]([C@H]1O)OP([O-])([O-])=O chebi_ontology omega-dicarboxyl-CoA CHEBI:133241 omega-carboxyacyl-CoA(5-) omega-dicarboxyl-CoA UniProt A dicarboxylic acid dianion that results from the removal of a proton from both of the carboxylic acid groups of any 3-hydroxydicarboxylic acid. -2 C4H4O5R 132.072 132.00587 C(*C(CC(=O)[O-])O)([O-])=O chebi_ontology 3-hydroxydicarboxylic acid dianion(2-) a 3-hydroxy dicarboxylic acid CHEBI:133251 3-hydroxydicarboxylate(2-) 3-hydroxydicarboxylic acid dianion(2-) SUBMITTER a 3-hydroxy dicarboxylic acid UniProt A carboxylic acid dianion obtained by deprotonation of both carboxy groups of any dicarboxylic acid that contains no carbon-carbon double bonds. -2 C2O4R 88.019 87.97966 [O-]C(*C([O-])=O)=O chebi_ontology a saturated dicarboxylic acid saturated dicarboxylate(2-) CHEBI:133291 saturated dicarboxylic acid dianion(2-) a saturated dicarboxylic acid UniProt saturated dicarboxylate(2-) SUBMITTER A dicarboxylic acid dianion obtained by deprotonation of both carboxy groups of any oxo dicarboxylic acid. chebi_ontology oxo dicarboxylic acid CHEBI:133294 oxo dicarboxylic acid dianion oxo dicarboxylic acid UniProt An L-alpha-amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of L-lysine; major species at pH 7.3. 0 C6H14N2O2 InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/t5-/m0/s1 KDXKERNSBIXSRK-YFKPBYRVSA-N 146.188 146.10553 [O-]C([C@H](CCCCN)[NH3+])=O (2S)-6-amino-2-azaniumylhexanoate chebi_ontology L-lysine Lys lysine zwitterion CHEBI:133538 L-lysine zwitterion (2S)-6-amino-2-azaniumylhexanoate IUPAC L-lysine ChEBI Lys ChEBI lysine zwitterion ChEBI 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 phosphonium ylide that is 2-(triphenylphosphoranylidene)acetamide in which the nitrogen has been converted to the corresponding carbamoyl derivative. By targeting the beta-subunit of fatty acid synthase, it inhibits nuclear envelope expansion and nuclear elongation during the closed mitosis of fission yeast. 0 C21H19N2O2P InChI=1S/C21H19N2O2P/c22-21(25)23-20(24)16-26(17-10-4-1-5-11-17,18-12-6-2-7-13-18)19-14-8-3-9-15-19/h1-16H,(H3,22,23,24,25) HIFJFZSMVLIPEA-UHFFFAOYSA-N 362.362 362.11841 P(=CC(NC(N)=O)=O)(C=1C=CC=CC1)(C=2C=CC=CC2)C=3C=CC=CC3 CAS:53296-08-5 PMID:26869222 Reaxys:2765280 2-(triphenyl-lambda(5)-phosphanylidene)acetamide N-carbamoyl-2-(triphenylphosphoranylidene)acetamide chebi_ontology triphenylphosphonium(carbamoylcarbamoyl)methylylid ureidocarbomethylentriphenylphosphoniumylid CHEBI:133750 Cutin-1 CAS:53296-08-5 ChEBI PMID:26869222 Europe PMC Reaxys:2765280 Reaxys 2-(triphenyl-lambda(5)-phosphanylidene)acetamide IUPAC N-carbamoyl-2-(triphenylphosphoranylidene)acetamide IUPAC triphenylphosphonium(carbamoylcarbamoyl)methylylid ChEBI ureidocarbomethylentriphenylphosphoniumylid ChEBI 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 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. -1 CH2O3SR 94.091 93.97246 C(S([O-])(=O)=O)* CHEBI:22318 MetaCyc:Alkanesulfonates chebi_ontology alkanesulfonate oxoanions alkanesulfonates an alkanesulfonate CHEBI:134249 alkanesulfonate oxoanion alkanesulfonate oxoanions ChEBI alkanesulfonates ChEBI an alkanesulfonate UniProt An alpha-amino-acid cation obtained by protonation of the imidazole ring of ergothioneine. It is the major microspecies at pH 7.3 (according to Marvin v 6.2.0.). +1 C9H16N3O2S InChI=1S/C9H15N3O2S/c1-12(2,3)7(8(13)14)4-6-5-10-9(15)11-6/h5,7H,4H2,1-3H3,(H2-,10,11,13,14,15)/p+1/t7-/m0/s1 SSISHJJTAXXQAX-ZETCQYMHSA-O 230.309 230.09577 C=1([NH+]=C(NC1)S)C[C@@H](C(=O)[O-])[N+](C)(C)C (2S)-3-(2-sulfanylidene-2,3-dihydro-1H-imidazol-3-ium-4-yl)-2-(trimethylazaniumyl)propanoate chebi_ontology ergothioneine ergothioneine cation CHEBI:134344 ergothioneine(1+) (2S)-3-(2-sulfanylidene-2,3-dihydro-1H-imidazol-3-ium-4-yl)-2-(trimethylazaniumyl)propanoate IUPAC ergothioneine UniProt ergothioneine cation ChEBI An alcohol where the hydroxy group is attached to a saturated carbon atom adjacent to a double bond (R groups may be H, organyl, etc.). 0 C3HOR5 53.040 53.00274 C(C(=C(*)*)*)(O)(*)* chebi_ontology allylic alcohols CHEBI:134361 allylic alcohol allylic alcohols ChEBI An aliphatic alcohol where the hydroxy carbon is beta to a double bond. 0 C4HOR7 65.050 65.00274 C(=C(*)*)(C(C(O)(*)*)(*)*)* chebi_ontology homoallylic alcohols CHEBI:134362 homoallylic alcohol homoallylic alcohols ChEBI An allylic alcohol in which the carbon atom that links the double bond to the hydroxy group is also attached to two hydrogens. 0 C3H3OR3 55.055 55.01839 C(C(=C(*)*)*)(O)([H])[H] chebi_ontology primary allylic alcohols CHEBI:134394 primary allylic alcohol primary allylic alcohols ChEBI An allylic alcohol in which the carbon atom that links the double bond to the hydroxy group is also attached to one other carbon and one hydrogen. 0 C3H2OR4 54.047 54.01056 C(C(=C(*)*)*)(O)([H])* chebi_ontology secondary allylic alcohols CHEBI:134396 secondary allylic alcohol secondary allylic alcohols ChEBI A furonaphthodioxole that is 4'-demethyldeoxypodophyllotoxin which is substituted at position 4 of the C-ring by a 2-{[2-(dimethylamino)ethyl](methyl)amino}ethyl group. While structurally related to etoposide, TOP-53 is significantly more toxic to non-small cell lung cancer cells, more active at generating chromosomal breaks, and displays improved cellular uptake and pharmacokinetics in animal lung tissues. 0 C28H36N2O7 InChI=1S/C28H36N2O7/c1-29(2)8-9-30(3)7-6-17-18-12-21-22(37-15-36-21)13-19(18)25(26-20(17)14-35-28(26)32)16-10-23(33-4)27(31)24(11-16)34-5/h10-13,17,20,25-26,31H,6-9,14-15H2,1-5H3/t17-,20-,25-,26+/m1/s1 KLCCMMSKRMSMKI-QVNMXXJYSA-N 512.596 512.25225 C12=CC3=C(C=C1[C@H]([C@@]4([C@@]([C@@H]2CCN(CCN(C)C)C)(COC4=O)[H])[H])C=5C=C(C(=C(C5)OC)O)OC)OCO3 CAS:148262-19-5 PMID:11106259 PMID:11170388 PMID:12081147 PMID:15892669 PMID:15992351 PMID:24827545 PMID:8665518 PMID:9106054 Reaxys:6377812 (5R,5aR,8aR,9S)-9-(2-{[2-(dimethylamino)ethyl](methyl)amino}ethyl)-5-(4-hydroxy-3,5-dimethoxyphenyl)-5,8,8a,9-tetrahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol-6(5aH)-one chebi_ontology 4'-demethyl-4beta-(2-{N-[2-(N',N'-dimethylamino)ethyl]-N-methylamino}ethyl)-4-desoxypodophyllotoxin TOP 53 CHEBI:134547 TOP-53 CAS:148262-19-5 ChemIDplus PMID:11106259 Europe PMC PMID:11170388 Europe PMC PMID:12081147 Europe PMC PMID:15892669 Europe PMC PMID:15992351 Europe PMC PMID:24827545 Europe PMC PMID:8665518 Europe PMC PMID:9106054 Europe PMC Reaxys:6377812 Reaxys (5R,5aR,8aR,9S)-9-(2-{[2-(dimethylamino)ethyl](methyl)amino}ethyl)-5-(4-hydroxy-3,5-dimethoxyphenyl)-5,8,8a,9-tetrahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol-6(5aH)-one IUPAC 4'-demethyl-4beta-(2-{N-[2-(N',N'-dimethylamino)ethyl]-N-methylamino}ethyl)-4-desoxypodophyllotoxin ChEBI TOP 53 ChEBI A UDP-amino sugar having alpha-D-glucosamine as the amino-sugar component. 0 C15H25N3O16P2 InChI=1S/C15H25N3O16P2/c16-8-11(23)9(21)5(3-19)32-14(8)33-36(28,29)34-35(26,27)30-4-6-10(22)12(24)13(31-6)18-2-1-7(20)17-15(18)25/h1-2,5-6,8-14,19,21-24H,3-4,16H2,(H,26,27)(H,28,29)(H,17,20,25)/t5-,6-,8-,9-,10-,11-,12-,13-,14-/m1/s1 CYKLRRKFBPBYEI-NQQHDEILSA-N 565.31700 565.07101 N[C@H]1[C@@H](OP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n2ccc(=O)[nH]c2=O)O[C@H](CO)[C@@H](O)[C@@H]1O KEGG:C02200 uridine 5'-[3-(2-amino-2-deoxyglucopyranosyl) dihydrogen diphosphate] chebi_ontology UDPglucosamine CHEBI:13497 UDP-alpha-D-glucosamine uridine 5'-[3-(2-amino-2-deoxyglucopyranosyl) dihydrogen diphosphate] IUPAC UDPglucosamine KEGG_COMPOUND A diol in which the two hydroxy groups are on different carbon atoms, usually but not necessarily adjacent. glycols chebi_ontology Glykol CHEBI:13643 glycol glycols IUPAC Glykol ChEBI A non-proteinogenic amino acid derivative resulting from reaction of homocysteine at the amino group, the carboxy group, or the side-chain amino group, or from the replacement of any hydrogen of homocysteine by a heteroatom. The definition normally excludes peptides containing homocysteine residues. chebi_ontology homocysteine derivatives CHEBI:136505 homocysteine derivative homocysteine derivatives ChEBI 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. 0 CHNO2R2 59.024 59.00073 C(*)(=[N+](O)[O-])* chebi_ontology aci-nitro compounds oxime N-oxide oxime N-oxides CHEBI:136622 aci-nitro compound aci-nitro compounds ChEBI oxime N-oxide ChEBI oxime N-oxides ChEBI 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 An organic cation obtained by protonation of any secondary amino compound; major species at pH 7.3. +1 H2NR2 16.023 16.01872 *[NH+](*)[H] MetaCyc:Secondary-Amines chebi_ontology a secondary amine secondary amine(1+) CHEBI:137419 secondary ammonium ion a secondary amine UniProt secondary amine(1+) 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 An organic cation obtained by protonation of the amino group of any tertiary amino compound. +1 HNR3 15.015 15.01090 [NH+](*)(*)* chebi_ontology a tertiary amine tertiary amine(1+) tertiary ammonium ions CHEBI:137982 tertiary ammonium ion a tertiary amine UniProt tertiary amine(1+) ChEBI tertiary ammonium ions ChEBI 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 Any steroid carrying a 14alpha-methyl substituent. 0 C20H33R 273.477 273.25823 C12C([C@]3(C(C(CC3)*)(C)CC1)C)CCC4C2(CCCC4)C MetaCyc:14-alpha-methylsteroids chebi_ontology a 14alpha-methyl steroid CHEBI:138029 14alpha-methyl steroid MetaCyc:14-alpha-methylsteroids SUBMITTER a 14alpha-methyl steroid UniProt A Bronsted acid derived from one or more inorganic compounds. Inorganic acids (also known as mineral acids) form hydrons and conjugate base ions when dissolved in water. Wikipedia:Mineral_acid chebi_ontology inorganic acids mineral acid mineral acids CHEBI:138103 inorganic acid inorganic acids ChEBI mineral acid ChEBI mineral acids ChEBI A 2-acyl-sn-glycero-3-phospho-D-myo-inositol that has palmitoleoyl as the acyl group. 0 C25H47O12P InChI=1S/C25H47O12P/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-19(27)36-18(16-26)17-35-38(33,34)37-25-23(31)21(29)20(28)22(30)24(25)32/h7-8,18,20-26,28-32H,2-6,9-17H2,1H3,(H,33,34)/b8-7-/t18-,20-,21-,22+,23-,24-,25-/m1/s1 PEWKZKILLSBVNX-YUCDOUPMSA-N 570.608 570.28051 [C@@H]1([C@@H]([C@@H]([C@@H]([C@H]([C@@H]1O)O)O)O)OP(OC[C@@H](CO)OC(CCCCCCC/C=C\CCCCCC)=O)(=O)O)O PMID:28667014 (2R)-1-hydroxy-3-[(hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl)oxy]propan-2-yl (9Z)-hexadec-9-enoate chebi_ontology 2-(9Z-hexadecenoyl)-glycero-3-phospho-(1'-myo-inositol) 2-(9Z-hexadecenoyl)-sn-glycero-3-phospho-D-myo-inositol CHEBI:138108 2-palmitoleoyl-sn-glycero-3-phospho-D-myo-inositol PMID:28667014 Europe PMC (2R)-1-hydroxy-3-[(hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl)oxy]propan-2-yl (9Z)-hexadec-9-enoate IUPAC 2-(9Z-hexadecenoyl)-glycero-3-phospho-(1'-myo-inositol) ChEBI 2-(9Z-hexadecenoyl)-sn-glycero-3-phospho-D-myo-inositol ChEBI Any pathway inhibitor that acts on the carotenoid biosynthesis pathway. chebi_ontology carotenogenesis inhibitor carotenogenesis inhibitors carotenoid biosynthesis inhibitors carotenoid-biosynthesis inhibitor carotenoid-biosynthesis inhibitors CHEBI:138208 carotenoid biosynthesis inhibitor carotenogenesis inhibitor ChEBI carotenogenesis inhibitors ChEBI carotenoid biosynthesis inhibitors ChEBI carotenoid-biosynthesis inhibitor ChEBI carotenoid-biosynthesis inhibitors ChEBI A nucleoside 5'-monophosphate(2-) obtained by deprotonation of the phospohate OH groups of any pyrimidine ribonucleoside 5'-monophosphate; major species at pH 7.3. -2 C9H8N2O7PR4 287.143 287.00691 N1([C@@H]2O[C@H](COP([O-])(=O)[O-])[C@H]([C@H]2O)O)C(=C(C(=NC1=*)*)*)* CHEBI:140282 chebi_ontology a pyrimidine ribonucleoside 5'-phosphate CHEBI:138238 pyrimidine ribonucleoside 5'-monophosphate(2-) a pyrimidine ribonucleoside 5'-phosphate UniProt Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa). Wikipedia:https://en.wikipedia.org/wiki/Gas chebi_ontology gas molecular entities gaseous molecular entities gaseous molecular entity CHEBI:138675 gas molecular entity gas molecular entities ChEBI gaseous molecular entities ChEBI gaseous molecular entity ChEBI A member of the class of imidazoles that is 1,3-dihydroimidazole-2-thione and its derivatives by substitution. 0 C3N2SR4 96.112 95.97822 N1(C(N(C(=C1*)*)*)=S)* chebi_ontology CHEBI:139340 1,3-dihydroimidazole-2-thiones Any molecular entity in which the isotopic ratio of nuclides for at least one element deviates measurably from that occurring in nature. The term includes both isotopically substituted compounds (in which essentially all the molecules of the compound have only the indicated nuclide(s) at each designated position) and isotopically labeled compounds (a formal mixture of an isotopically unmodified compound with one or more analogous isotopically substituted compound(s). chebi_ontology isotopically modified compounds CHEBI:139358 isotopically modified compound isotopically modified compounds ChEBI -1 CH2NO2 InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4)/p-1 KXDHJXZQYSOELW-UHFFFAOYSA-M 60.03212 60.00910 NC([O-])=O Beilstein:3903503 CAS:302-11-4 Gmelin:239604 carbamate chebi_ontology Carbamat Karbamat carbamate ion carbamic acid, ion(1-) CHEBI:13941 carbamate Beilstein:3903503 Beilstein CAS:302-11-4 ChemIDplus Gmelin:239604 Gmelin carbamate IUPAC carbamate UniProt Carbamat ChEBI Karbamat ChEBI carbamate ion ChemIDplus carbamic acid, ion(1-) ChemIDplus An alpha-oxyketone that has a hydroxy group as the alpha-oxy moiety. PMID:15326516 PMID:19908854 PMID:20382022 PMID:23295224 chebi_ontology alpha-hydroxy ketones alpha-hydroxy-ketone alpha-hydroxy-ketones alpha-hydroxyketone alpha-hydroxyketones CHEBI:139588 alpha-hydroxy ketone PMID:15326516 Europe PMC PMID:19908854 Europe PMC PMID:20382022 Europe PMC PMID:23295224 Europe PMC alpha-hydroxy ketones ChEBI alpha-hydroxy-ketone ChEBI alpha-hydroxy-ketones ChEBI alpha-hydroxyketone ChEBI alpha-hydroxyketones ChEBI An alpha-hydroxy ketone in which the carbonyl group and the hydroxy group are linked by a -CH2 (methylene) group. 0 C2H3O2R 59.044 59.01330 *C(C(O)([H])[H])=O chebi_ontology primary alpha-hydroxy ketones primary alpha-hydroxy-ketone primary alpha-hydroxy-ketones primary alpha-hydroxyketone primary alpha-hydroxyketones CHEBI:139590 primary alpha-hydroxy ketone primary alpha-hydroxy ketones ChEBI primary alpha-hydroxy-ketone ChEBI primary alpha-hydroxy-ketones ChEBI primary alpha-hydroxyketone ChEBI primary alpha-hydroxyketones ChEBI An alpha-hydroxy ketone in which the carbonyl group and the hydroxy group are linked by a carbon bearing two organyl groups. 0 C2HO2R3 57.028 56.99765 C(C(=O)*)(O)(*)* chebi_ontology tertiary alpha-hydroxy ketones tertiary alpha-hydroxy-ketone tertiary alpha-hydroxy-ketones tertiary alpha-hydroxyketone tertiary alpha-hydroxyketones CHEBI:139592 tertiary alpha-hydroxy ketone tertiary alpha-hydroxy ketones ChEBI tertiary alpha-hydroxy-ketone ChEBI tertiary alpha-hydroxy-ketones ChEBI tertiary alpha-hydroxyketone ChEBI tertiary alpha-hydroxyketones ChEBI A carboxamide resulting from the formal condensation of a carboxylic acid with ammonia; formula RC(=O)NH2. 0 CH2NOR 44.033 44.01364 N(C(*)=O)([H])[H] chebi_ontology primary carboxamides CHEBI:140324 primary carboxamide primary carboxamides ChEBI A carboxamide resulting from the formal condensation of a carboxylic acid with a primary amine; formula RC(=O)NHR(1). 0 CHNOR2 43.025 43.00581 N(C(*)=O)(*)[H] chebi_ontology secondary carboxamides CHEBI:140325 secondary carboxamide secondary carboxamides ChEBI Any polyunsaturated fatty acid carrying one or more hydroxy substituents. chebi_ontology CHEBI:140345 hydroxy polyunsaturated fatty acid A nucleotide-sugar oxoanion obtained by deprotonation of the phosphate OH groups of any UDP-monosaccharide. This compound class represents generic and unspecified UDP-sugars. -2 C9H11N2O12P2R 401.138 400.97872 [C@@H]1(N2C(NC(C=C2)=O)=O)O[C@H](COP(OP([O-])(O*)=O)([O-])=O)[C@H]([C@H]1O)O MetaCyc:UDP-sugar chebi_ontology UDP-sugar(2-) a UDP-monosaccharide CHEBI:140359 UDP-monosaccharide(2-) MetaCyc:UDP-sugar SUBMITTER UDP-sugar(2-) ChEBI a UDP-monosaccharide UniProt Any saturated fatty acid containing 4 carbons. 0 CHO2R 45.017 44.99765 *C(O)=O chebi_ontology CHEBI:140601 fatty acid 4:0 A primary ammonium ion resulting from the protonation of the amino group of L-tyrosinal. +1 C9H12NO2 InChI=1S/C9H11NO2/c10-8(6-11)5-7-1-3-9(12)4-2-7/h1-4,6,8,12H,5,10H2/p+1/t8-/m0/s1 DXGAIOIQACHYRK-QMMMGPOBSA-O 166.197 166.08626 O=C[C@@H]([NH3+])CC=1C=CC(=CC1)O MetaCyc:CPD-21526 PMID:23281040 (2S)-1-(4-hydroxyphenyl)-3-oxopropan-2-aminium chebi_ontology (2S)-1-(p-hydroxyphenyl)-3-oxopropan-2-aminium L-tyrosinal CHEBI:141668 L-tyrosinal(1+) PMID:23281040 SUBMITTER (2S)-1-(4-hydroxyphenyl)-3-oxopropan-2-aminium IUPAC (2S)-1-(p-hydroxyphenyl)-3-oxopropan-2-aminium ChEBI L-tyrosinal UniProt Any carbobycyclic compound that is an hexahydronaphthalene or a compound obtained from an hexahydronaphthalene by formal substitution of one or more hydrogens. chebi_ontology CHEBI:142348 hexahydronaphthalenes A purine ribonucleoside that is a purine derivative attached to a beta-D-ribofuranosyl residue at position 9 via a glycosidic (N-glycosyl) linkage. 0 C10H11N4O4R2 251.219 251.07803 C1(=*)NC(=NC2=C1N=CN2[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)* chebi_ontology a purine D-ribonucleoside CHEBI:142355 purines D-ribonucleoside a purine D-ribonucleoside UniProt A purine derivative attached to a beta-D-2'-deoxy-ribofuranosyl residue at position 9 via a glycosidic (N-glycosyl) linkage. 0 C10H11N4O3R2 235.220 235.08312 C1(=*)NC(=NC2=C1N=CN2[C@@H]3O[C@H](CO)[C@@H](O)C3)* chebi_ontology a purine 2'-deoxy-D-ribonucleoside CHEBI:142361 purines 2'-deoxy-D-ribonucleoside a purine 2'-deoxy-D-ribonucleoside UniProt A organic ion resulting from the deprotonation of the hydroxy group of any oxime. -1 CNO 42.017 41.99799 C(*)(=N[O-])* oxime anion chebi_ontology oximate oximates oxime anions CHEBI:142513 oxime anion oxime anion ChEBI oximate ChEBI oximates ChEBI oxime anions ChEBI A benzoate ester resulting from the formal condensation of the carboxy group of vanillic acid with the hydroxy group of (-)-borneol. A metabolite isolated from Ferula dissecta. 0 C18H24O4 InChI=1S/C18H24O4/c1-17(2)12-7-8-18(17,3)15(10-12)22-16(20)11-5-6-13(19)14(9-11)21-4/h5-6,9,12,15,19H,7-8,10H2,1-4H3/t12-,15+,18+/m0/s1 KTOAGBIQQPGNIR-WBHUJUFNSA-N 304.381 304.16746 C(C1=CC(=C(C=C1)O)OC)(=O)O[C@@H]2C[C@@]3(CC[C@]2(C3(C)C)C)[H] PMID:20350297 PMID:21589808 PMID:23521895 PMID:29900664 PMID:29912155 Reaxys:26876325 (1S,2R,4S)-1,7,7-trimethylbicyclo[2.2.1]heptan-2-yl 4-hydroxy-3-methoxybenzoate tschimganine chebi_ontology chimganin tschimganin CHEBI:142517 tschimganine PMID:20350297 Europe PMC PMID:21589808 Europe PMC PMID:23521895 Europe PMC PMID:29900664 Europe PMC PMID:29912155 Europe PMC Reaxys:26876325 Reaxys (1S,2R,4S)-1,7,7-trimethylbicyclo[2.2.1]heptan-2-yl 4-hydroxy-3-methoxybenzoate IUPAC tschimganine ChEBI chimganin ChEBI tschimganin ChEBI A triazinoindole that is 5H-[1,2,4]triazino[5,6-b]indole which is substituted at position 3 by a (2-methylprop-2-en-1-yl)thio group. A potent inhibitor of midasin which is an essential protein for eukaryotic ribosome biogenesis. 0 C13H12N4S InChI=1S/C13H12N4S/c1-8(2)7-18-13-15-12-11(16-17-13)9-5-3-4-6-10(9)14-12/h3-6H,1,7H2,2H3,(H,14,15,17) LPCWHNSRTRBKBO-UHFFFAOYSA-N 256.328 256.07827 C12=CC=CC=C1NC3=C2N=NC(=N3)SCC(C)=C CAS:328023-11-6 PMID:27667686 PMID:30318141 3-[(2-methylprop-2-en-1-yl)thio]-5H-[1,2,4]triazino[5,6-b]indole ribozinoindole-1 chebi_ontology 3-((2-methylallyl)thio)-5H-[1,2,4]triazino[5,6-b]indole 3-(2-methylprop-2-enylsulfanyl)-5H-[1,2,4]triazino[5,6-b]indole 3-[(2-methyl-2-propenyl)sulfanyl]-5H-[1,2,4]triazino[5,6-b]indole Rbin-1 CHEBI:142676 ribozinoindole-1 CAS:328023-11-6 ChEBI PMID:27667686 Europe PMC PMID:30318141 Europe PMC 3-[(2-methylprop-2-en-1-yl)thio]-5H-[1,2,4]triazino[5,6-b]indole IUPAC ribozinoindole-1 ChEBI 3-((2-methylallyl)thio)-5H-[1,2,4]triazino[5,6-b]indole ChEBI 3-(2-methylprop-2-enylsulfanyl)-5H-[1,2,4]triazino[5,6-b]indole ChEBI 3-[(2-methyl-2-propenyl)sulfanyl]-5H-[1,2,4]triazino[5,6-b]indole ChEBI Rbin-1 ChEBI Any heterotricyclic compound whose skeleton consists of an indole fused to a triazine ring. triazinoindole chebi_ontology triazinoindoles CHEBI:142677 triazinoindole triazinoindole ChEBI triazinoindoles ChEBI An organic anion arising from deprotonation of the hydroxy group of an enol. -1 C2OR3 40.021 39.99491 [O-]C(=C(*)*)* chebi_ontology enolate anion enolate anions enolates CHEBI:142839 enolate enolate anion ChEBI enolate anions ChEBI enolates ChEBI A polar amino acid zwitterion restulting from the transfer of a proton from the carboxy group to the alpha-amino group of D-histidine. The major species at pH 7.3. 0 C6H9N3O2 InChI=1S/C6H9N3O2/c7-5(6(10)11)1-4-2-8-3-9-4/h2-3,5H,1,7H2,(H,8,9)(H,10,11)/t5-/m1/s1 HNDVDQJCIGZPNO-RXMQYKEDSA-N 155.155 155.06948 C=1(N=CNC1)C[C@H](C(=O)[O-])[NH3+] MetaCyc:CPD-12151 PMID:27230378 (2R)-2-ammonio-3-(1H-imidazol-4-yl)propanoate (2R)-2-azaniumyl-3-(1H-imidazol-4-yl)propanoate chebi_ontology D-histidine CHEBI:142967 D-histidine zwitterion PMID:27230378 SUBMITTER (2R)-2-ammonio-3-(1H-imidazol-4-yl)propanoate IUPAC (2R)-2-azaniumyl-3-(1H-imidazol-4-yl)propanoate IUPAC D-histidine UniProt A D-alpha-amino acid zwitterion arising from the transfer of a proton from the carboxy to the amino group of D-leucine; major species at pH 7.3. 0 C6H13NO2 InChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/t5-/m1/s1 ROHFNLRQFUQHCH-RXMQYKEDSA-N 131.173 131.09463 [O-]C([C@@H](CC(C)C)[NH3+])=O MetaCyc:CPD-12150 PMID:24419381 (2R)-2-azaniumyl-4-methylpentanoate chebi_ontology D-leu D-leucine CHEBI:143079 D-leucine zwitterion PMID:24419381 SUBMITTER (2R)-2-azaniumyl-4-methylpentanoate IUPAC D-leu SUBMITTER D-leucine UniProt A D-alpha-amino acid zwitterion arising from transfer of a proton from the carboxy to the amino group of D-homoserine; major species at pH 7.3. 0 C4H9NO3 InChI=1S/C4H9NO3/c5-3(1-2-6)4(7)8/h3,6H,1-2,5H2,(H,7,8)/t3-/m1/s1 UKAUYVFTDYCKQA-GSVOUGTGSA-N 119.119 119.05824 C([C@H](C([O-])=O)[NH3+])CO MetaCyc:CPD-12255 PMID:24419381 (2R)-2-azaniumyl-4-hydroxybutanoate chebi_ontology D-homoserine CHEBI:143081 D-homoserine zwitterion PMID:24419381 SUBMITTER (2R)-2-azaniumyl-4-hydroxybutanoate IUPAC D-homoserine UniProt An alpha-amino-acid anion that is the conjugate base of glutamic acid, having anionic carboxy groups and a cationic amino group -1 C5H8NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-1 WHUUTDBJXJRKMK-UHFFFAOYSA-M 146.12136 146.04588 [NH3+]C(CCC([O-])=O)C([O-])=O Gmelin:327908 glutamate(1-) hydrogen glutamate chebi_ontology 2-ammoniopentanedioate glutamate glutamic acid monoanion CHEBI:14321 glutamate(1-) Gmelin:327908 Gmelin glutamate(1-) JCBN hydrogen glutamate IUPAC 2-ammoniopentanedioate IUPAC glutamate UniProt glutamic acid monoanion JCBN A phosphatidylinositol where R1 can be an alkyl or an acyl chain and 2R2 is an acyl chain. -1 C10H16O12PR2 359.201 359.03794 [C@@H]1([C@@H]([C@@H]([C@@H]([C@H]([C@@H]1O)O)O)O)OP(OC[C@H](CO*)OC(=O)*)(=O)[O-])O PMID:9463366 chebi_ontology 1-radyl,2-acyl-sn-glycero-3-phospho-(1D-myo-2-acyl-inositol) CHEBI:143813 1-radyl,2-acyl-sn-glycero-3-phospho-(1D-myo-2-acyl-inositol)(1-) PMID:9463366 SUBMITTER 1-radyl,2-acyl-sn-glycero-3-phospho-(1D-myo-2-acyl-inositol) UniProt 0 C21H17N2O7R5 409.370 409.10358 C12=C(C=C(C(=C1C(C=3[C@]([C@@H]([C@]4([C@@H](C([O-])=C(C([C@@]4(O)C3O)=O)C(N)=O)[NH+](C)C)[H])*)(C2(*)*)[H])=O)O)*)* chebi_ontology a tetracycline CHEBI:144644 a tetracycline zwittterion a tetracycline UniProt -1 C10H15N4O7S InChI=1S/C10H16N4O7S/c11-5(10(19)20)1-2-7(15)13-6(4-22-14-21)9(18)12-3-8(16)17/h5-6H,1-4,11H2,(H,12,18)(H,13,15)(H,16,17)(H,19,20)/p-1/t5-,6-/m0/s1 HYHSBSXUHZOYLX-WDSKDSINSA-M 335.310 335.06669 [NH3+][C@@H](CCC(=O)N[C@@H](CSN=O)C(=O)NCC(=O)[O-])C(=O)[O-] (2S)-2-ammonio-5-{[(2S)-1-[(carboxylatomethyl)amino]-3-(nitrosothio)-1-oxopropan-2-yl]amino}-5-oxopentanoate chebi_ontology S-nitrosoglutathione CHEBI:145544 S-nitrosoglutathione(1-) (2S)-2-ammonio-5-{[(2S)-1-[(carboxylatomethyl)amino]-3-(nitrosothio)-1-oxopropan-2-yl]amino}-5-oxopentanoate IUPAC S-nitrosoglutathione UniProt Any nitroso compound in which a carbon atom of an organyl group is attached to the sulfur atom of a nitrosothio group: R-S-N=O. 0 NOSR 62.072 61.97006 *SN=O chebi_ontology S-nitrosothiol compound S-nitrosothiols SNO compound nitrosothio compounds CHEBI:145545 nitrosothio compound S-nitrosothiol compound ChEBI S-nitrosothiols SUBMITTER SNO compound SUBMITTER nitrosothio compounds ChEBI Macrolides (macrocyclic lactones) in which the macrocyclic ring contains more than one ester linkage. Macropolylides include macrodiolides, macrotriolides, macrotetrolides and macropentolides, each containing di-, tri-, tetra-, and penta- ester linkages, respectively, in one macrocyclic ring. Macrocyclic lactones containing nitrogen in their skeletons (azamacrolides and macrolide lactams) and also containing oxazole or thiazole in their skeletons are known in nature. chebi_ontology macropolylides CHEBI:145555 macropolylide macropolylides ChEBI A macropolylide which contains two ester linkages in one macrocyclic ring. PMID:17446696 PMID:29624065 PMID:29671776 PMID:31247219 chebi_ontology macrodiolides CHEBI:145556 macrodiolide PMID:17446696 Europe PMC PMID:29624065 Europe PMC PMID:29671776 Europe PMC PMID:31247219 Europe PMC macrodiolides ChEBI A macrolide in which the macrocyclic lactone ring includes an amide group. PMID:11678663 PMID:12227772 PMID:15248618 PMID:17378533 PMID:31226284 chebi_ontology macrolide lactams CHEBI:145565 macrolide lactam PMID:11678663 Europe PMC PMID:12227772 Europe PMC PMID:15248618 Europe PMC PMID:17378533 Europe PMC PMID:31226284 Europe PMC macrolide lactams ChEBI A branched-chain saturated fatty acid anion resulting from the deprotonation of the carboxy group of (S)-2-methylbutanoic acid. The major species at pH 7.3. -1 C5H9O2 InChI=1S/C5H10O2/c1-3-4(2)5(6)7/h4H,3H2,1-2H3,(H,6,7)/p-1/t4-/m0/s1 WLAMNBDJUVNPJU-BYPYZUCNSA-M 101.126 101.06080 [O-]C([C@H](CC)C)=O PMID:16819884 (2S)-2-methylbutanoate (S)-2-methylbutanoate chebi_ontology (2S)-2-methylbutyrate (2S)-2-methylbutyric acid anion (S)-2-methylbutyrate (S)-alpha-methylbutyrate CHEBI:145932 (S)-2-methylbutanoate PMID:16819884 Europe PMC (2S)-2-methylbutanoate IUPAC (S)-2-methylbutanoate UniProt (2S)-2-methylbutyrate ChEBI (2S)-2-methylbutyric acid anion ChEBI (S)-2-methylbutyrate ChEBI (S)-alpha-methylbutyrate ChEBI A phosphatidylinositol anion where the inositol is either not phosphorylated or phosphorylated at position 4 and/or position 5; major species at pH 7.3. -1 C11H14O13PR4 385.195 385.01720 [C@@H]1([C@@H]([C@@H]([C@@H]([C@H]([C@@H]1O*)O*)O)O)OP(OC[C@@H](COC(=O)*)OC(=O)*)(=O)[O-])O chebi_ontology 1,2-diacyl-sn-glycero-3-phospho-1D-myo-inositol anion derivative a 1,2-diacyl-sn-glycero-3-phospho-1D-myo-inositol derivative CHEBI:147334 1-phosphatidyl-1D-myo-inositol anion derivative 1,2-diacyl-sn-glycero-3-phospho-1D-myo-inositol anion derivative SUBMITTER a 1,2-diacyl-sn-glycero-3-phospho-1D-myo-inositol derivative UniProt A phosphatidylinositol anion where the inositol is phosphorylated at position 3 and either phosphorylated or not at position 4 and/or position 5; major species at pH 7.3. -3 C11H13O16P2R4 463.159 462.96788 [C@@H]1([C@@H]([C@@H]([C@@H]([C@H]([C@@H]1O*)O*)OP(=O)([O-])[O-])O)OP(OC[C@@H](COC(=O)*)OC(=O)*)(=O)[O-])O chebi_ontology 1,2-diacyl-sn-glycero-3-phospho-1D-myo-inositol-3-phosphate anion derivative a 1,2-diacyl-sn-glycero-3-phospho-1D-myo-inositol-3-phosphate derivative CHEBI:147335 1-phosphatidyl-1D-myo-inositol-3-phosphate anion derivative 1,2-diacyl-sn-glycero-3-phospho-1D-myo-inositol-3-phosphate anion derivative SUBMITTER a 1,2-diacyl-sn-glycero-3-phospho-1D-myo-inositol-3-phosphate derivative UniProt Any agent that induces nausea and vomiting. chebi_ontology emetics CHEBI:149552 emetic emetics ChEBI Any antiviral agent which inhibits the activity of coronaviruses. Wikipedia:Coronavirus anticoronaviral agent chebi_ontology anti-coronaviral agent anti-coronaviral agents anti-coronavirus agent anti-coronavirus agents anticoronaviral agents anticoronaviral drug anticoronaviral drugs anticoronavirus agent anticoronavirus agents CHEBI:149553 anticoronaviral agent anticoronaviral agent ChEBI anti-coronaviral agent ChEBI anti-coronaviral agents ChEBI anti-coronavirus agent ChEBI anti-coronavirus agents ChEBI anticoronaviral agents ChEBI anticoronaviral drug ChEBI anticoronaviral drugs ChEBI anticoronavirus agent ChEBI anticoronavirus agents ChEBI A divalent inorganic anion obtained by removal of both protons from selenic acid. -2 O4Se InChI=1S/H2O4Se/c1-5(2,3)4/h(H2,1,2,3,4)/p-2 QYHFIVBSNOWOCQ-UHFFFAOYSA-L 142.95760 143.89728 [O-][Se]([O-])(=O)=O CAS:14124-68-6 PDBeChem:SE4 Selenate selenate tetraoxidoselenate(2-) chebi_ontology SELENATE ION [SeO4](2-) CHEBI:15075 selenate CAS:14124-68-6 ChemIDplus Selenate ChemIDplus selenate IUPAC selenate UniProt tetraoxidoselenate(2-) IUPAC SELENATE ION PDBeChem [SeO4](2-) IUPAC A divalent inorganic anion obtained by removal of both protons from hydrogen sulfide. -2 S InChI=1S/S/q-2 UCKMPCXJQFINFW-UHFFFAOYSA-N 32.06600 31.97317 [S--] CAS:18496-25-8 UM-BBD_compID:c0569 sulfanediide sulfide(2-) chebi_ontology S(2-) Sulfide sulphide CHEBI:15138 sulfide(2-) CAS:18496-25-8 ChemIDplus UM-BBD_compID:c0569 UM-BBD sulfanediide IUPAC sulfide(2-) IUPAC S(2-) IUPAC Sulfide ChemIDplus sulphide ChEBI A purine nucleobase found in humans and other organisms. 0 C5H4N4O2 152.111 152.03343 ECMDB:ECMDB00292 KNApSAcK:C00019660 PMID:1557408 PMID:24629268 PMID:9007687 YMDB:YMDB00263 xanthine chebi_ontology 2,6-dioxopurine 2,6-dioxopurines xanthines CHEBI:15318 xanthine PMID:1557408 Europe PMC PMID:24629268 Europe PMC PMID:9007687 Europe PMC xanthine ChEBI 2,6-dioxopurine ChEBI 2,6-dioxopurines ChEBI xanthines 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 chebi_ontology A Akzeptor Hydrogen-acceptor Oxidized donor accepteur CHEBI:15339 acceptor Acceptor KEGG_COMPOUND A KEGG_COMPOUND Akzeptor ChEBI Hydrogen-acceptor KEGG_COMPOUND Oxidized donor KEGG_COMPOUND accepteur ChEBI The aldehyde formed from acetic acid by reduction of the carboxy group. It is the most abundant carcinogen in tobacco smoke. 0 C2H4O InChI=1S/C2H4O/c1-2-3/h2H,1H3 IKHGUXGNUITLKF-UHFFFAOYSA-N 44.05256 44.02621 [H]C(C)=O CHEBI:13703 CHEBI:22158 CHEBI:2383 CHEBI:40533 Beilstein:505984 CAS:75-07-0 Gmelin:779 HMDB:HMDB0000990 KEGG:C00084 KNApSAcK:C00007392 LINCS:LSM-37193 PDBeChem:ACE PMID:11058591 PMID:110589 PMID:11087437 PMID:11290854 PMID:15239123 PMID:15833031 PMID:16404561 PMID:16485909 PMID:18001279 PMID:19396661 PMID:2233695 PMID:24282063 PMID:24326678 PMID:24503565 PMID:4239189 PMID:5526694 PMID:6036728 PMID:7163973 PMID:9171333 Reaxys:505984 UM-BBD_compID:c0160 Wikipedia:Acetaldehyde ACETALDEHYDE Acetaldehyde acetaldehyde chebi_ontology Acetaldehyd Azetaldehyd Ethanal acetaldehydes acetic aldehyde ethyl aldehyde CHEBI:15343 acetaldehyde Beilstein:505984 Beilstein CAS:75-07-0 ChemIDplus CAS:75-07-0 KEGG COMPOUND CAS:75-07-0 NIST Chemistry WebBook Gmelin:779 Gmelin PMID:11058591 Europe PMC PMID:110589 Europe PMC PMID:11087437 Europe PMC PMID:11290854 Europe PMC PMID:15239123 Europe PMC PMID:15833031 Europe PMC PMID:16404561 Europe PMC PMID:16485909 Europe PMC PMID:18001279 Europe PMC PMID:19396661 Europe PMC PMID:2233695 Europe PMC PMID:24282063 Europe PMC PMID:24326678 Europe PMC PMID:24503565 Europe PMC PMID:4239189 Europe PMC PMID:5526694 Europe PMC PMID:6036728 Europe PMC PMID:7163973 Europe PMC PMID:9171333 Europe PMC Reaxys:505984 Reaxys UM-BBD_compID:c0160 UM-BBD ACETALDEHYDE PDBeChem Acetaldehyde KEGG_COMPOUND acetaldehyde IUPAC acetaldehyde UniProt Acetaldehyd NIST_Chemistry_WebBook Azetaldehyd ChEBI Ethanal KEGG_COMPOUND acetaldehydes ChEBI acetic aldehyde NIST_Chemistry_WebBook ethyl aldehyde NIST_Chemistry_WebBook A thiol comprising a panthothenate unit in phosphoric anhydride linkage with a 3',5'-adenosine diphosphate unit; and an aminoethanethiol unit. 0 C21H36N7O16P3S 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 RGJOEKWQDUBAIZ-IBOSZNHHSA-N 767.53540 767.11521 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: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 3'-phosphoadenosine-(5')diphospho(4')pantatheine CoA CoA-SH CoASH Coenzym A HSCoA Koenzym A [(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 3'-phosphoadenosine-(5')diphospho(4')pantatheine ChEBI CoA KEGG_COMPOUND CoA-SH KEGG_COMPOUND CoASH ChEBI Coenzym A ChEBI HSCoA ChEBI Koenzym A 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. 0 C23H38N7O17P3S 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 ZSLZBFCDCINBPY-ZSJPKINUSA-N 809.57208 809.12577 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:13712 CHEBI:22192 CHEBI:2408 CHEBI:40470 CAS:72-89-9 ECMDB:ECMDB01206 HMDB:HMDB0001206 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 AcCoA Acetyl coenzyme A S-acetyl-CoA S-acetyl-coenzyme A 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 UM-BBD 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 AcCoA ChEBI Acetyl coenzyme A KEGG_COMPOUND S-acetyl-CoA ChEBI S-acetyl-coenzyme A ChEBI A choline that is the parent compound of the cholines class, consisting of ethanolamine having three methyl substituents attached to the amino function. +1 C5H14NO InChI=1S/C5H14NO/c1-6(2,3)4-5-7/h7H,4-5H2,1-3H3/q+1 OEYIOHPDSNJKLS-UHFFFAOYSA-N 104.17080 104.10699 C[N+](C)(C)CCO CHEBI:13985 CHEBI:23212 CHEBI:3665 CHEBI:41524 Beilstein:1736748 CAS:62-49-7 DrugBank:DB00122 Drug_Central:3097 ECMDB:ECMDB00097 Gmelin:324597 HMDB:HMDB0000097 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 Bilineurine CHOLINE ION N,N,N-trimethylethanol-ammonium N-trimethylethanolamine 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 Bilineurine KEGG_COMPOUND CHOLINE ION PDBeChem N,N,N-trimethylethanol-ammonium ChEBI N-trimethylethanolamine 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. 0 C3H7NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6) XUJNEKJLAYXESH-UHFFFAOYSA-N 121.15922 121.01975 NC(CS)C(O)=O 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 Cysteine cysteine chebi_ontology 2-Amino-3-mercaptopropionic acid 2-amino-3-mercaptopropanoic acid 2-amino-3-sulfanylpropanoic acid C Cys Cystein Hcys Zystein cisteina CHEBI:15356 cysteine 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 2-Amino-3-mercaptopropionic acid KEGG_COMPOUND 2-amino-3-mercaptopropanoic acid JCBN 2-amino-3-sulfanylpropanoic acid IUPAC C ChEBI Cys ChEBI Cystein ChEBI Hcys IUPAC Zystein ChEBI cisteina ChEBI A simple monocarboxylic acid containing two carbons. 0 C2H4O2 InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4) QTBSBXVTEAMEQO-UHFFFAOYSA-N 60.05200 60.02113 CC(O)=O CHEBI:22169 CHEBI:2387 CHEBI:40486 Beilstein:506007 CAS:64-19-7 Drug_Central:4211 Gmelin:1380 HMDB:HMDB0000042 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 PPDB:1333 Reaxys:506007 Wikipedia:Acetic_acid ACETIC ACID Acetic acid acetic acid chebi_ontology AcOH CH3-COOH CH3CO2H E 260 E-260 E260 Essigsaeure Ethanoic acid Ethylic acid HOAc INS No. 260 MeCO2H MeCOOH Methanecarboxylic acid 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 AcOH 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 MeCO2H ChEBI MeCOOH ChEBI Methanecarboxylic acid ChemIDplus acide acetique ChemIDplus ethoic acid ChEBI A large group of antibiotics isolated from various species of Streptomyces and characterised by having a substituted phenoxazine ring linked to two cyclic heterodetic peptides. CHEBI:13723 CHEBI:22220 CHEBI:2445 CAS:1402-38-6 KEGG:C01775 Actinomycin chebi_ontology actinomycins CHEBI:15369 actinomycin CAS:1402-38-6 ChemIDplus CAS:1402-38-6 KEGG COMPOUND Actinomycin KEGG_COMPOUND actinomycins ChEBI An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms. 0 H2O InChI=1S/H2O/h1H2 XLYOFNOQVPJJNP-UHFFFAOYSA-N 18.01530 18.01056 [H]O[H] CHEBI:10743 CHEBI:13352 CHEBI:27313 CHEBI:42043 CHEBI:42857 CHEBI:43228 CHEBI:44292 CHEBI:44701 CHEBI:44819 CHEBI:5585 Beilstein:3587155 CAS:7732-18-5 Gmelin:117 HMDB:HMDB0002111 KEGG:C00001 KEGG:D00001 MetaCyc:WATER MolBase:1 PDBeChem:HOH Reaxys:3587155 Wikipedia:Water WATER Water oxidane water chebi_ontology BOUND WATER H2O HOH Wasser [OH2] acqua agua aqua dihydridooxygen dihydrogen oxide eau hydrogen hydroxide CHEBI:15377 water Beilstein:3587155 Beilstein CAS:7732-18-5 ChemIDplus CAS:7732-18-5 KEGG COMPOUND CAS:7732-18-5 NIST Chemistry WebBook Gmelin:117 Gmelin Reaxys:3587155 Reaxys WATER PDBeChem Water KEGG_COMPOUND oxidane IUPAC water IUPAC BOUND WATER PDBeChem H2O KEGG_COMPOUND H2O UniProt HOH ChEBI Wasser ChEBI [OH2] IUPAC acqua ChEBI agua ChEBI aqua ChEBI dihydridooxygen IUPAC dihydrogen oxide IUPAC eau ChEBI hydrogen hydroxide ChEBI 0 C10H18O InChI=1S/C10H18O/c1-9(2)7-4-5-10(9,3)8(11)6-7/h7-8,11H,4-6H2,1-3H3/t7-,8+,10+/m1/s1 DTGKSKDOIYIVQL-WEDXCCLWSA-N 154.24932 154.13577 CC1(C)[C@@H]2CC[C@@]1(C)[C@@H](O)C2 CHEBI:10756 CHEBI:14 CHEBI:18440 Beilstein:2038056 CAS:464-43-7 KEGG:C01765 KNApSAcK:C00011023 (+)-Borneol (1R,2S,4R)-1,7,7-trimethylbicyclo[2.2.1]heptan-2-ol chebi_ontology (1R,2S,4R)-(+)-Borneol (1R,2S,4R)-borneol (1R-endo)-1,7,7-trimethylbicyclo[2.2.1]heptan-2-ol Borneocamphor D-borneol Sumatra camphor d-Borneol d-borneol endo-2-Bornanol CHEBI:15393 (+)-borneol Beilstein:2038056 Beilstein CAS:464-43-7 ChemIDplus CAS:464-43-7 KEGG COMPOUND (+)-Borneol KEGG_COMPOUND (1R,2S,4R)-1,7,7-trimethylbicyclo[2.2.1]heptan-2-ol IUPAC (1R,2S,4R)-(+)-Borneol KEGG_COMPOUND (1R,2S,4R)-borneol ChemIDplus (1R,2S,4R)-borneol UniProt (1R-endo)-1,7,7-trimethylbicyclo[2.2.1]heptan-2-ol ChemIDplus Borneocamphor KEGG_COMPOUND D-borneol ChemIDplus Sumatra camphor KEGG_COMPOUND d-Borneol KEGG_COMPOUND d-borneol ChemIDplus endo-2-Bornanol KEGG_COMPOUND 0 C10H18O InChI=1S/C10H18O/c1-9(2)7-4-5-10(9,3)8(11)6-7/h7-8,11H,4-6H2,1-3H3/t7-,8+,10+/m0/s1 DTGKSKDOIYIVQL-QXFUBDJGSA-N 154.24932 154.13577 CC1(C)[C@H]2CC[C@]1(C)[C@H](O)C2 CHEBI:10773 CHEBI:18478 CHEBI:83 Beilstein:2038053 Beilstein:3587558 CAS:464-45-9 KEGG:C01766 KNApSAcK:C00011024 (-)-Borneol (1S,2R,4S)-1,7,7-trimethylbicyclo[2.2.1]heptan-2-ol chebi_ontology (1S,2R,4S)-(-)-Borneol (1S,2R,4S)-(-)-borneol (1S,2R,4S)-borneol (1S-endo)-1,7,7-trimethylbicyclo[2.2.1]heptan-2-ol L-Borneol L-borneol Linderol l-borneol CHEBI:15394 (-)-borneol Beilstein:2038053 Beilstein Beilstein:3587558 Beilstein CAS:464-45-9 ChemIDplus CAS:464-45-9 KEGG COMPOUND CAS:464-45-9 NIST Chemistry WebBook (-)-Borneol KEGG_COMPOUND (1S,2R,4S)-1,7,7-trimethylbicyclo[2.2.1]heptan-2-ol IUPAC (1S,2R,4S)-(-)-Borneol KEGG_COMPOUND (1S,2R,4S)-(-)-borneol NIST_Chemistry_WebBook (1S,2R,4S)-borneol UniProt (1S-endo)-1,7,7-trimethylbicyclo[2.2.1]heptan-2-ol NIST_Chemistry_WebBook L-Borneol KEGG_COMPOUND L-borneol NIST_Chemistry_WebBook Linderol KEGG_COMPOUND l-borneol ChemIDplus A sulfonium compound that is the S-adenosyl derivative of L-methionine. It is an intermediate in the metabolic pathway of methionine. +1 C15H23N6O5S 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 399.44500 399.14452 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: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:HMDB0001185 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 Acylcarnitine AdoMet 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 Acylcarnitine KEGG_COMPOUND AdoMet JCBN 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 The simplest (and the only achiral) proteinogenic amino acid, with a hydrogen atom as its side chain. 0 C2H5NO2 InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) DHMQDGOQFOQNFH-UHFFFAOYSA-N 75.06664 75.03203 NCC(O)=O 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:HMDB0000123 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 Aminoacetic acid Aminoessigsaeure G Gly Glycin Glycocoll Glykokoll Glyzin H2N-CH2-COOH Hgly Leimzucker 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 Aminoacetic acid KEGG_COMPOUND Aminoessigsaeure ChEBI G ChEBI Gly KEGG_COMPOUND Glycin ChemIDplus Glycocoll ChemIDplus Glykokoll ChEBI Glyzin ChEBI H2N-CH2-COOH IUPAC Hgly IUPAC Leimzucker ChemIDplus aminoethanoic acid ChEBI aminoethanoic acid JCBN The simplest hydroxylamine, consisting of ammonia bearing a hydroxy substituent. It is an intermediate in the biological nitrification by microbes like bacteria. 0 H3NO InChI=1S/H3NO/c1-2/h2H,1H2 AVXURJPOCDRRFD-UHFFFAOYSA-N 33.02996 33.02146 NO CHEBI:10793 CHEBI:14421 CHEBI:24708 CHEBI:43221 CHEBI:5806 CAS:7803-49-8 Gmelin:478 HMDB:HMDB0003338 KEGG:C00192 MetaCyc:HYDROXYLAMINE PDBeChem:HOA PMID:11053303 PMID:11160411 PMID:11226629 PMID:11750265 PMID:12962703 PMID:17385063 PMID:18399918 PMID:18515490 PMID:21185448 Reaxys:3587190 Wikipedia:Hydroxylamine Hydroxylamine dihydridohydroxidonitrogen hydroxylamine chebi_ontology H2NHO HYDROXYAMINE Hydroxylamin [NH2OH] oxyammonia CHEBI:15429 hydroxylamine CAS:7803-49-8 ChemIDplus CAS:7803-49-8 KEGG COMPOUND CAS:7803-49-8 NIST Chemistry WebBook Gmelin:478 Gmelin PMID:11053303 Europe PMC PMID:11160411 Europe PMC PMID:11226629 Europe PMC PMID:11750265 Europe PMC PMID:12962703 Europe PMC PMID:17385063 Europe PMC PMID:18399918 Europe PMC PMID:18515490 Europe PMC PMID:21185448 Europe PMC Reaxys:3587190 Reaxys Hydroxylamine KEGG_COMPOUND dihydridohydroxidonitrogen IUPAC hydroxylamine IUPAC hydroxylamine UniProt H2NHO IUPAC HYDROXYAMINE PDBeChem Hydroxylamin ChEBI [NH2OH] IUPAC oxyammonia NIST_Chemistry_WebBook A triterpene consisting of 2,6,10,15,19,23-hexamethyltetracosane having six double bonds at the 2-, 6-, 10-, 14-, 18- and 22-positions with (all-E)-configuration. 0 C30H50 InChI=1S/C30H50/c1-25(2)15-11-19-29(7)23-13-21-27(5)17-9-10-18-28(6)22-14-24-30(8)20-12-16-26(3)4/h15-18,23-24H,9-14,19-22H2,1-8H3/b27-17+,28-18+,29-23+,30-24+ YYGNTYWPHWGJRM-AAJYLUCBSA-N 410.71800 410.39125 CC(C)=CCC\C(C)=C\CC\C(C)=C\CC\C=C(/C)CC\C=C(/C)CCC=C(C)C CHEBI:10795 CHEBI:10843 CHEBI:15104 CHEBI:26746 CHEBI:9245 Beilstein:1728920 CAS:111-02-4 KEGG:C00751 KNApSAcK:C00003755 LIPID_MAPS_instance:LMPR0106010002 PMID:16341241 PMID:24362891 (6E,10E,14E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene Squalene squalene chebi_ontology (all-E)-2,6,10,15,19,23-hexamethyl-2,6,10,14,18,22-tetracosahexaene Spinacene Supraene CHEBI:15440 squalene Beilstein:1728920 Beilstein CAS:111-02-4 ChemIDplus CAS:111-02-4 KEGG COMPOUND CAS:111-02-4 NIST Chemistry WebBook LIPID_MAPS_instance:LMPR0106010002 LIPID MAPS PMID:16341241 Europe PMC PMID:24362891 Europe PMC (6E,10E,14E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene IUPAC Squalene KEGG_COMPOUND squalene UniProt (all-E)-2,6,10,15,19,23-hexamethyl-2,6,10,14,18,22-tetracosahexaene NIST_Chemistry_WebBook Spinacene KEGG_COMPOUND Supraene KEGG_COMPOUND An omega-carboxyacyl-CoA that results from the formal condensation of the thiol group of coenzyme A with one of the carboxy groups of glutaric acid. 0 C26H42N7O19P3S InChI=1S/C26H42N7O19P3S/c1-26(2,21(39)24(40)29-7-6-15(34)28-8-9-56-17(37)5-3-4-16(35)36)11-49-55(46,47)52-54(44,45)48-10-14-20(51-53(41,42)43)19(38)25(50-14)33-13-32-18-22(27)30-12-31-23(18)33/h12-14,19-21,25,38-39H,3-11H2,1-2H3,(H,28,34)(H,29,40)(H,35,36)(H,44,45)(H,46,47)(H2,27,30,31)(H2,41,42,43)/t14-,19-,20-,21+,25-/m1/s1 SYKWLIJQEHRDNH-CKRMAKSASA-N 881.63474 881.14690 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)CCCC(O)=O CHEBI:14326 CHEBI:24332 CHEBI:5436 CAS:3131-84-8 HMDB:HMDB0001339 KEGG:C00527 PDBeChem:GRA PMID:11024031 PMID:3971969 PMID:6547838 PMID:853337 PMID:8722121 UM-BBD_compID:c0222 3'-phosphoadenosine 5'-{3-[(3R)-4-{[3-({2-[(4-carboxybutanoyl)sulfanyl]ethyl}amino)-3-oxopropyl]amino}-3-hydroxy-2,2-dimethyl-4-oxobutyl] dihydrogen diphosphate} Glutaryl-CoA chebi_ontology 4-carboxybutanoyl-CoA 4-carboxybutanoyl-coenzyme A coenzyme A, S-(hydrogen pentanedioate) glutaryl-coenzyme A CHEBI:15524 glutaryl-CoA CAS:3131-84-8 ChemIDplus CAS:3131-84-8 KEGG COMPOUND PMID:11024031 Europe PMC PMID:3971969 Europe PMC PMID:6547838 Europe PMC PMID:853337 Europe PMC PMID:8722121 Europe PMC UM-BBD_compID:c0222 UM-BBD 3'-phosphoadenosine 5'-{3-[(3R)-4-{[3-({2-[(4-carboxybutanoyl)sulfanyl]ethyl}amino)-3-oxopropyl]amino}-3-hydroxy-2,2-dimethyl-4-oxobutyl] dihydrogen diphosphate} IUPAC Glutaryl-CoA KEGG_COMPOUND 4-carboxybutanoyl-CoA ChEBI 4-carboxybutanoyl-coenzyme A ChEBI coenzyme A, S-(hydrogen pentanedioate) ChemIDplus glutaryl-coenzyme A ChEBI The S-malonyl derivative of coenzyme A. 0 C24H38N7O19P3S InChI=1S/C24H38N7O19P3S/c1-24(2,19(37)22(38)27-4-3-13(32)26-5-6-54-15(35)7-14(33)34)9-47-53(44,45)50-52(42,43)46-8-12-18(49-51(39,40)41)17(36)23(48-12)31-11-30-16-20(25)28-10-29-21(16)31/h10-12,17-19,23,36-37H,3-9H2,1-2H3,(H,26,32)(H,27,38)(H,33,34)(H,42,43)(H,44,45)(H2,25,28,29)(H2,39,40,41)/t12-,17-,18-,19+,23-/m1/s1 LTYOQGRJFJAKNA-DVVLENMVSA-N 853.58158 853.11560 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)CC(O)=O CHEBI:14565 CHEBI:25135 CHEBI:43979 CHEBI:6661 CAS:524-14-1 DrugBank:DB04524 KEGG:C00083 KNApSAcK:C00007260 LIPID_MAPS_instance:LMFA07050031 MetaCyc:MALONYL-COA PDBeChem:MLC PMID:11117381 PMID:11934665 PMID:16651524 PMID:17126822 PMID:17522981 PMID:18294446 PMID:21199367 PMID:21508288 PMID:21763447 Reaxys:78309 Wikipedia:Malonyl-CoA 3'-phosphoadenosine 5'-{3-[(3R)-4-{[3-({2-[(3-carboxyacetyl)sulfanyl]ethyl}amino)-3-oxopropyl]amino}-3-hydroxy-2,2-dimethyl-4-oxobutyl] dihydrogen diphosphate} Malonyl-CoA chebi_ontology Coenzyme A, S-(hydrogen propanedioate) Malonyl coenzyme A S-(Hydrogen malonyl)coenzyme A CHEBI:15531 malonyl-CoA CAS:524-14-1 ChemIDplus CAS:524-14-1 KEGG COMPOUND LIPID_MAPS_instance:LMFA07050031 LIPID MAPS PMID:11117381 Europe PMC PMID:11934665 Europe PMC PMID:16651524 Europe PMC PMID:17126822 Europe PMC PMID:17522981 Europe PMC PMID:18294446 Europe PMC PMID:21199367 Europe PMC PMID:21508288 Europe PMC PMID:21763447 Europe PMC Reaxys:78309 Reaxys 3'-phosphoadenosine 5'-{3-[(3R)-4-{[3-({2-[(3-carboxyacetyl)sulfanyl]ethyl}amino)-3-oxopropyl]amino}-3-hydroxy-2,2-dimethyl-4-oxobutyl] dihydrogen diphosphate} IUPAC Malonyl-CoA KEGG_COMPOUND Coenzyme A, S-(hydrogen propanedioate) ChemIDplus Malonyl coenzyme A KEGG_COMPOUND S-(Hydrogen malonyl)coenzyme A ChemIDplus The D-enantiomer of alanine. 0 C3H7NO2 InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m1/s1 QNAYBMKLOCPYGJ-UWTATZPHSA-N 89.09322 89.04768 C[C@@H](N)C(O)=O 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:HMDB0001310 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 D-2-Aminopropionic acid D-Ala D-Alanin D-alpha-alanine D-alpha-aminopropionic acid DAL 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 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 A peptide zwitterion obtained from the tranfer of a proton from the carboxy group to the amino group of any tripeptide. It contains an equal number of positively-charged and negatively-charged functional groups. Major structure at pH 7.3. 0 C6H8N3O4R3 186.146 186.05148 C(=O)([C@@H]([NH3+])*)N[C@H](C(=O)N[C@H](C(=O)[O-])*)* chebi_ontology L-amino acid tripeptide zwitterion L-amino acid tripeptide zwitterions amino acid tripeptide zwitterion amino acid tripeptide zwitterions an L-amino acid tripeptide CHEBI:155837 tripeptide zwitterion L-amino acid tripeptide zwitterion ChEBI L-amino acid tripeptide zwitterions ChEBI amino acid tripeptide zwitterion ChEBI amino acid tripeptide zwitterions ChEBI an L-amino acid tripeptide UniProt The L-enantiomer of leucine. 0 C6H13NO2 InChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/t5-/m0/s1 ROHFNLRQFUQHCH-YFKPBYRVSA-N 131.17296 131.09463 CC(C)C[C@H](N)C(O)=O CHEBI:10866 CHEBI:13131 CHEBI:21348 CHEBI:43646 CHEBI:43695 CHEBI:43733 CHEBI:43814 CHEBI:6260 Beilstein:1721722 CAS:61-90-5 DrugBank:DB00149 Drug_Central:1557 ECMDB:ECMDB00687 Gmelin:50204 HMDB:HMDB0000687 KEGG:C00123 KEGG:D00030 KNApSAcK:C00001377 MetaCyc:LEU PDBeChem:LEU_LFOH PMID:17609475 PMID:22735334 PMID:24206068 PMID:24333966 PMID:8798704 Reaxys:1721722 Wikipedia:Leucine YMDB:YMDB00387 L-Leucine L-leucine chebi_ontology (2S)-2-amino-4-methylpentanoic acid (2S)-alpha-2-Amino-4-methylvaleric acid (2S)-alpha-Leucine (S)-(+)-leucine (S)-leucine 2-Amino-4-methylvaleric acid L L-Leucin L-Leuzin LEUCINE Leu CHEBI:15603 L-leucine Beilstein:1721722 Beilstein CAS:61-90-5 ChemIDplus CAS:61-90-5 KEGG COMPOUND CAS:61-90-5 NIST Chemistry WebBook Drug_Central:1557 DrugCentral Gmelin:50204 Gmelin PMID:17609475 Europe PMC PMID:22735334 Europe PMC PMID:24206068 Europe PMC PMID:24333966 Europe PMC PMID:8798704 Europe PMC Reaxys:1721722 Reaxys L-Leucine KEGG_COMPOUND L-leucine IUPAC (2S)-2-amino-4-methylpentanoic acid IUPAC (2S)-alpha-2-Amino-4-methylvaleric acid KEGG_COMPOUND (2S)-alpha-Leucine KEGG_COMPOUND (S)-(+)-leucine NIST_Chemistry_WebBook (S)-leucine NIST_Chemistry_WebBook 2-Amino-4-methylvaleric acid KEGG_COMPOUND L ChEBI L-Leucin ChEBI L-Leuzin ChEBI LEUCINE PDBeChem Leu ChEBI Aldehydic parent sugars (polyhydroxy aldehydes H[CH(OH)]nC(=O)H, n >= 2) and their intramolecular hemiacetals. 0 C2H4O2(CH2O)n CHEBI:13755 CHEBI:22305 CHEBI:2561 KEGG:C01370 Wikipedia:Aldose Aldose chebi_ontology aldoses an aldose CHEBI:15693 aldose Aldose KEGG_COMPOUND aldoses ChEBI an aldose UniProt The L-enantiomer of homoserine. 0 C4H9NO3 InChI=1S/C4H9NO3/c5-3(1-2-6)4(7)8/h3,6H,1-2,5H2,(H,7,8)/t3-/m0/s1 UKAUYVFTDYCKQA-VKHMYHEASA-N 119.11920 119.05824 N[C@@H](CCO)C(O)=O CHEBI:13123 CHEBI:21330 CHEBI:43131 CHEBI:6246 Beilstein:1721681 CAS:672-15-1 DrugBank:DB04193 HMDB:HMDB0000719 KEGG:C00263 KNApSAcK:C00001366 MetaCyc:HOMO-SER PDBeChem:HSE PMID:22770225 Reaxys:1721681 Wikipedia:Homoserine L-HOMOSERINE L-Homoserine L-homoserine chebi_ontology (2S)-2-amino-4-hydroxybutanoic acid 2-Amino-4-hydroxybutanoic acid 2-Amino-4-hydroxybutyric acid Homoserine CHEBI:15699 L-homoserine Beilstein:1721681 Beilstein CAS:672-15-1 ChemIDplus CAS:672-15-1 KEGG COMPOUND PMID:22770225 Europe PMC Reaxys:1721681 Reaxys L-HOMOSERINE PDBeChem L-Homoserine KEGG_COMPOUND L-homoserine IUPAC (2S)-2-amino-4-hydroxybutanoic acid IUPAC 2-Amino-4-hydroxybutanoic acid HMDB 2-Amino-4-hydroxybutyric acid KEGG_COMPOUND Homoserine HMDB Any alpha-amino acid having L-configuration at the alpha-carbon. 0 C2H4NO2R 74.05870 74.02420 N[C@@H]([*])C(O)=O CHEBI:13072 CHEBI:13243 CHEBI:13797 CHEBI:21224 CHEBI:6175 KEGG:C00151 L-alpha-amino acid L-alpha-amino acids chebi_ontology L-2-Amino acid L-Amino acid L-alpha-amino acids CHEBI:15705 L-alpha-amino acid L-alpha-amino acid IUPAC L-alpha-amino acids IUPAC L-2-Amino acid KEGG_COMPOUND L-Amino acid KEGG_COMPOUND L-alpha-amino acids ChEBI A ketoheptose phosphate consisting of sedoheptulose having a phosphate group at the 7-position. It is an intermediate metabolite in the pentose phosphate pathway. 0 C7H15O10P InChI=1S/C7H15O10P/c8-1-3(9)5(11)7(13)6(12)4(10)2-17-18(14,15)16/h4-8,10-13H,1-2H2,(H2,14,15,16)/t4-,5-,6-,7+/m1/s1 JDTUMPKOJBQPKX-GBNDHIKLSA-N 290.16180 290.04028 OCC(=O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)COP(O)(O)=O CHEBI:15073 CHEBI:15074 CHEBI:26621 CHEBI:4244 CHEBI:9083 CAS:2646-35-7 HMDB:HMDB0001068 KEGG:C00281 KEGG:C05382 MetaCyc:D-SEDOHEPTULOSE-7-P Wikipedia:Sedoheptulose_7-phosphate D-altro-hept-2-ulose 7-phosphate Sedoheptulose 7-phosphate chebi_ontology D-Sedoheptulose 7-phosphate D-altro-Heptulose 7-phosphate altro-Heptulose 7-phosphate CHEBI:15721 sedoheptulose 7-phosphate CAS:2646-35-7 ChemIDplus D-altro-hept-2-ulose 7-phosphate IUPAC Sedoheptulose 7-phosphate KEGG_COMPOUND D-Sedoheptulose 7-phosphate KEGG_COMPOUND D-altro-Heptulose 7-phosphate KEGG_COMPOUND altro-Heptulose 7-phosphate KEGG_COMPOUND An optically active form of ornithine having L-configuration. 0 C5H12N2O2 InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1 AHLPHDHHMVZTML-BYPYZUCNSA-N 132.16106 132.08988 NCCC[C@H](N)C(O)=O CHEBI:13148 CHEBI:21367 CHEBI:6280 Beilstein:1722298 CAS:70-26-8 DrugBank:DB00129 Drug_Central:3401 Gmelin:327282 HMDB:HMDB0000214 KEGG:C00077 KEGG:D08302 KNApSAcK:C00001384 MetaCyc:ORNITHINE PDBeChem:ORN PMID:15576628 PMID:17190852 PMID:18676473 PMID:19083482 PMID:19173225 PMID:22033378 PMID:22133808 PMID:22387109 PMID:22735334 Reaxys:1722298 Wikipedia:Ornithine (2S)-2,5-diaminopentanoic acid L-Ornithine L-ornithine chebi_ontology (S)-2,5-Diaminopentanoate (S)-2,5-Diaminopentanoic acid (S)-2,5-diaminovaleric acid (S)-alpha,delta-diaminovaleric acid (S)-ornithine CHEBI:15729 L-ornithine Beilstein:1722298 ChemIDplus CAS:70-26-8 ChemIDplus CAS:70-26-8 KEGG COMPOUND Drug_Central:3401 DrugCentral Gmelin:327282 Gmelin PMID:15576628 Europe PMC PMID:17190852 Europe PMC PMID:18676473 Europe PMC PMID:19083482 Europe PMC PMID:19173225 Europe PMC PMID:22033378 Europe PMC PMID:22133808 Europe PMC PMID:22387109 Europe PMC PMID:22735334 Europe PMC Reaxys:1722298 Reaxys (2S)-2,5-diaminopentanoic acid IUPAC L-Ornithine KEGG_COMPOUND L-ornithine ChEBI L-ornithine IUPAC (S)-2,5-Diaminopentanoate KEGG_COMPOUND (S)-2,5-Diaminopentanoic acid KEGG_COMPOUND (S)-2,5-diaminovaleric acid KEGG_COMPOUND (S)-alpha,delta-diaminovaleric acid HMDB (S)-ornithine ChemIDplus A primary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has either three hydrogen atoms attached to it or only one other carbon atom and two hydrogen atoms attached to it. 0 CH3OR 31.034 31.01839 *C(O)([H])[H] CHEBI:13676 CHEBI:14887 CHEBI:26262 CHEBI:57489 CHEBI:8406 KEGG:C00226 Primary alcohol chebi_ontology 1-Alcohol a primary alcohol primary alcohols CHEBI:15734 primary alcohol Primary alcohol KEGG_COMPOUND 1-Alcohol KEGG_COMPOUND a primary alcohol UniProt primary alcohols ChEBI 0 C28H26N4O3 InChI=1S/C28H26N4O3/c1-28-26(34-3)17(29-2)12-20(35-28)31-18-10-6-4-8-14(18)22-23-16(13-30-27(23)33)21-15-9-5-7-11-19(15)32(28)25(21)24(22)31/h4-11,17,20,26,29H,12-13H2,1-3H3,(H,30,33)/t17-,20-,26-,28+/m1/s1 HKSZLNNOFSGOKW-FYTWVXJKSA-N 466.53120 466.20049 CN[C@@H]1C[C@H]2O[C@@](C)([C@@H]1OC)n1c3ccccc3c3c4CNC(=O)c4c4c5ccccc5n2c4c13 CHEBI:15106 CHEBI:45788 CHEBI:9252 CAS:62996-74-1 DrugBank:DB02010 KEGG:C02079 KNApSAcK:C00018127 LINCS:LSM-1103 (5S,6R,7R,9R)-6-methoxy-5-methyl-7-methylamino-6,7,8,9,15,16-hexahydro-5H,14H-5,9-epoxy-4b,9a,15-triazadibenzo[b,h]cyclonona[1,2,3,4-jkl]cyclopenta[e]-as-indacen-14-one Staurosporine chebi_ontology (+)-Staurosporine STS Staurosporin CHEBI:15738 staurosporine CAS:62996-74-1 ChemIDplus CAS:62996-74-1 KEGG COMPOUND (5S,6R,7R,9R)-6-methoxy-5-methyl-7-methylamino-6,7,8,9,15,16-hexahydro-5H,14H-5,9-epoxy-4b,9a,15-triazadibenzo[b,h]cyclonona[1,2,3,4-jkl]cyclopenta[e]-as-indacen-14-one IUPAC Staurosporine KEGG_COMPOUND (+)-Staurosporine ChemIDplus STS KEGG_COMPOUND Staurosporin ChemIDplus A monocarboxylic acid anion that is the conjugate base of formic acid. Induces severe metabolic acidosis and ocular injury in human subjects. -1 CHO2 InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)/p-1 BDAGIHXWWSANSR-UHFFFAOYSA-M 45.01744 44.99820 [H]C([O-])=O CHEBI:14276 CHEBI:24081 Beilstein:1901205 CAS:71-47-6 Gmelin:1006 HMDB:HMDB0000142 KEGG:C00058 MetaCyc:FORMATE PMID:17190852 PMID:3946945 Reaxys:1901205 UM-BBD_compID:c0106 Wikipedia:Formate formate chebi_ontology HCO2 anion aminate formiate formic acid, ion(1-) formylate hydrogen carboxylate methanoate CHEBI:15740 formate Beilstein:1901205 Beilstein CAS:71-47-6 ChemIDplus CAS:71-47-6 NIST Chemistry WebBook Gmelin:1006 Gmelin PMID:17190852 Europe PMC PMID:3946945 Europe PMC Reaxys:1901205 Reaxys UM-BBD_compID:c0106 UM-BBD formate IUPAC formate UniProt HCO2 anion NIST_Chemistry_WebBook aminate ChEBI formiate ChEBI formic acid, ion(1-) ChemIDplus formylate ChEBI hydrogen carboxylate ChEBI methanoate ChEBI An alpha,omega-dicarboxylic acid resulting from the formal oxidation of each of the terminal methyl groups of butane to the corresponding carboxy group. It is an intermediate metabolite in the citric acid cycle. 0 C4H6O4 InChI=1S/C4H6O4/c5-3(6)1-2-4(7)8/h1-2H2,(H,5,6)(H,7,8) KDYFGRWQOYBRFD-UHFFFAOYSA-N 118.08800 118.02661 OC(=O)CCC(O)=O CHEBI:22943 CHEBI:26807 CHEBI:45639 CHEBI:9304 Beilstein:1754069 CAS:110-15-6 DrugBank:DB00139 Drug_Central:2487 ECMDB:ECMDB00254 Gmelin:2785 HMDB:HMDB0000254 KEGG:C00042 KNApSAcK:C00001205 LIPID_MAPS_instance:LMFA01170043 MetaCyc:SUC PDBeChem:SIN PMID:17439666 Reaxys:1754069 Wikipedia:Succinic_acid YMDB:YMDB00338 SUCCINIC ACID Succinic acid butanedioic acid succinic acid chebi_ontology 1,2-ethanedicarboxylic acid Bernsteinsaeure Butandisaeure Butanedionic acid Dihydrofumaric acid E363 Ethylenesuccinic acid HOOC-CH2-CH2-COOH acide butanedioique acide succinique acidum succinicum amber acid asuccin spirit of amber CHEBI:15741 succinic acid Beilstein:1754069 Beilstein CAS:110-15-6 ChemIDplus CAS:110-15-6 KEGG COMPOUND CAS:110-15-6 NIST Chemistry WebBook Drug_Central:2487 DrugCentral Gmelin:2785 Gmelin LIPID_MAPS_instance:LMFA01170043 LIPID MAPS PMID:17439666 Europe PMC Reaxys:1754069 Reaxys SUCCINIC ACID PDBeChem Succinic acid KEGG_COMPOUND butanedioic acid IUPAC succinic acid IUPAC 1,2-ethanedicarboxylic acid ChemIDplus Bernsteinsaeure ChEBI Butandisaeure ChemIDplus Butanedionic acid KEGG_COMPOUND Dihydrofumaric acid HMDB E363 ChEBI Ethylenesuccinic acid KEGG_COMPOUND HOOC-CH2-CH2-COOH IUPAC acide butanedioique ChEBI acide succinique ChEBI acidum succinicum ChemIDplus amber acid NIST_Chemistry_WebBook asuccin NIST_Chemistry_WebBook spirit of amber ChEBI Any N-acyl-amino acid in which the amino acid moiety has D configuration. 0 C3H3NO3R2 101.06080 101.01129 OC(=O)[C@@H]([*])NC([*])=O CHEBI:12474 CHEBI:21631 CHEBI:7224 chebi_ontology CHEBI:15778 N-acyl-D-amino acid 0 C9H15N3O2 InChI=1S/C9H15N3O2/c1-12(2,3)8(9(13)14)4-7-5-10-6-11-7/h5-6,8H,4H2,1-3H3,(H-,10,11,13,14)/t8-/m0/s1 GPPYTCRVKHULJH-QMMMGPOBSA-N 197.23442 197.11643 C[N+](C)(C)[C@@H](Cc1c[nH]cn1)C([O-])=O CHEBI:12673 CHEBI:21909 CHEBI:7460 CAS:534-30-5 KEGG:C05575 (2S)-3-(1H-imidazol-4-yl)-2-(trimethylammonio)propanoate chebi_ontology (S)-alpha-Carboxy-N,N,N-trimethyl-1H-imidazole-4-ethanaminium hydroxide, inner salt Hercynine Nalpha,Nalpha,Nalpha-Trimethyl-L-histidine hercynine CHEBI:15781 N(alpha),N(alpha),N(alpha)-trimethyl-L-histidine CAS:534-30-5 ChemIDplus CAS:534-30-5 KEGG COMPOUND (2S)-3-(1H-imidazol-4-yl)-2-(trimethylammonio)propanoate IUPAC (S)-alpha-Carboxy-N,N,N-trimethyl-1H-imidazole-4-ethanaminium hydroxide, inner salt ChemIDplus Hercynine KEGG_COMPOUND Nalpha,Nalpha,Nalpha-Trimethyl-L-histidine KEGG_COMPOUND hercynine UniProt A D-alpha-amino acid that is the D-isomer of arginine. 0 C6H14N4O2 InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/t4-/m1/s1 ODKSFYDXXFIFQN-SCSAIBSYSA-N 174.20100 174.11168 N[C@H](CCCNC(N)=N)C(O)=O CHEBI:12917 CHEBI:20917 CHEBI:4106 CHEBI:41855 Beilstein:1725412 CAS:157-06-2 DrugBank:DB04027 Gmelin:364938 HMDB:HMDB0003416 KEGG:C00792 MetaCyc:CPD-220 PDBeChem:DAR PMID:15540275 PMID:15723827 PMID:16912865 PMID:19651461 PMID:22518022 Reaxys:1725412 D-Arginine D-arginine chebi_ontology (2R)-2-amino-5-(carbamimidamido)pentanoic acid (2R)-2-amino-5-guanidinopentanoic acid (R)-2-amino-5-guanidinopentanoic acid D-2-Amino-5-guanidinovaleric acid D-Arginin DAR CHEBI:15816 D-arginine Beilstein:1725412 Beilstein CAS:157-06-2 ChemIDplus CAS:157-06-2 KEGG COMPOUND CAS:157-06-2 NIST Chemistry WebBook Gmelin:364938 Gmelin PMID:15540275 Europe PMC PMID:15723827 Europe PMC PMID:16912865 Europe PMC PMID:19651461 Europe PMC PMID:22518022 Europe PMC Reaxys:1725412 Reaxys D-Arginine KEGG_COMPOUND D-arginine IUPAC (2R)-2-amino-5-(carbamimidamido)pentanoic acid IUPAC (2R)-2-amino-5-guanidinopentanoic acid JCBN (R)-2-amino-5-guanidinopentanoic acid ChEBI D-2-Amino-5-guanidinovaleric acid KEGG_COMPOUND D-Arginin ChEBI DAR PDBeChem Fructose is a levorotatory monosaccharide and an isomer of glucose. Although fructose is a hexose (6 carbon sugar), it generally exists as a 5-member hemiketal ring (a furanose). 0 C6H12O6 180.15588 180.06339 CHEBI:12923 CHEBI:20929 CHEBI:4118 CAS:57-48-7 HMDB:HMDB0000660 KEGG:C00095 MetaCyc:FRU PDBeChem:FRU PMID:22735334 D-arabino-hex-2-ulose D-fructose chebi_ontology D-Fru D-arabino-Hexulose D-laevulose Fruit sugar Laevulose Levulose CHEBI:15824 D-fructose CAS:57-48-7 ChemIDplus CAS:57-48-7 KEGG COMPOUND PMID:22735334 Europe PMC D-arabino-hex-2-ulose IUPAC D-fructose IUPAC D-Fru JCBN D-arabino-Hexulose KEGG_COMPOUND D-laevulose ChEBI Fruit sugar KEGG_COMPOUND Laevulose ChEBI Levulose KEGG_COMPOUND A polyprenol diphosphate having geranylgeranyl as the polyprenyl component. 0 C20H36O7P2 InChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23) OINNEUNVOZHBOX-UHFFFAOYSA-N 450.44316 450.19363 CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCOP(O)(=O)OP(O)(O)=O CHEBI:14300 CHEBI:24230 DrugBank:DB07841 LINCS:LSM-36848 3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl trihydrogen diphosphate chebi_ontology CHEBI:15831 geranylgeranyl diphosphate 3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl trihydrogen diphosphate IUPAC A peptide containing ten or more amino acid residues. C4H6N2O3R2(C2H2NOR)n CHEBI:14860 CHEBI:8314 KEGG:C00403 Polypeptide polypeptides chebi_ontology Polypeptid polipeptido CHEBI:15841 polypeptide Polypeptide KEGG_COMPOUND polypeptides IUPAC Polypeptid ChEBI polipeptido ChEBI A pyrimidine ribonucleoside 5'-monophosphate having 6-carboxyuracil as the nucleobase. 0 C10H13N2O11P InChI=1S/C10H13N2O11P/c13-5-1-3(9(16)17)12(10(18)11-5)8-7(15)6(14)4(23-8)2-22-24(19,20)21/h1,4,6-8,14-15H,2H2,(H,16,17)(H,11,13,18)(H2,19,20,21)/t4-,6-,7-,8-/m1/s1 KYOBSHFOBAOFBF-XVFCMESISA-N 368.19080 368.02570 O[C@@H]1[C@@H](COP(O)(O)=O)O[C@H]([C@@H]1O)n1c(cc(=O)[nH]c1=O)C(O)=O CHEBI:14699 CHEBI:25723 CHEBI:7788 CAS:2149-82-8 KEGG:C01103 KNApSAcK:C00007583 PDBeChem:OMP 2,6-dioxo-3-(5-O-phosphono-beta-D-ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid Orotidine 5'-phosphate chebi_ontology 6-carboxy-5'-uridylic acid Orotidylic acid orotidine 5'-(dihydrogen phosphate) CHEBI:15842 orotidine 5'-phosphate CAS:2149-82-8 KEGG COMPOUND 2,6-dioxo-3-(5-O-phosphono-beta-D-ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid IUPAC Orotidine 5'-phosphate KEGG_COMPOUND 6-carboxy-5'-uridylic acid ChEBI Orotidylic acid KEGG_COMPOUND orotidine 5'-(dihydrogen phosphate) ChEBI -1 Br InChI=1S/BrH/h1H/p-1 CPELXLSAUQHCOX-UHFFFAOYSA-M 79.90400 78.91889 [Br-] CHEBI:13918 CHEBI:3178 CHEBI:49515 Beilstein:3587179 CAS:24959-67-9 Gmelin:14908 KEGG:C00720 KEGG:C01324 PDBeChem:BR Bromide bromide bromide(1-) chebi_ontology BROMIDE ION Br(-) Br- bromine anion CHEBI:15858 bromide Beilstein:3587179 Beilstein CAS:24959-67-9 ChemIDplus CAS:24959-67-9 KEGG COMPOUND CAS:24959-67-9 NIST Chemistry WebBook Gmelin:14908 Gmelin Bromide KEGG_COMPOUND bromide IUPAC bromide UniProt bromide(1-) IUPAC BROMIDE ION PDBeChem Br(-) IUPAC Br- KEGG_COMPOUND bromine anion NIST_Chemistry_WebBook A deoxyglucose that is D-glucose in which the hydroxy group at position 2 has been replaced by a hydrogen. It is an antimetabolite of glucose with antiviral activity, which acts by inhibiting the glycosylation of glycoproteins and glycolipids. Used as an antiherpes agent. 0 C6H12O5 164.15650 164.06847 CHEBI:1078 CHEBI:11565 CHEBI:11569 CHEBI:19553 CHEBI:57546 CAS:154-17-6 KEGG:C00586 MetaCyc:2-DEOXY-D-GLUCOSE Wikipedia:2-Deoxy-D-glucose 2-Deoxy-D-glucose 2-deoxy-D-arabino-hexose chebi_ontology 2-Deoxy-D-arabino-hexose 2-Deoxy-D-mannose D-2dGlc D-arabino-2-Deoxyhexose Deoxyglucose CHEBI:15866 2-deoxy-D-glucose CAS:154-17-6 KEGG COMPOUND 2-Deoxy-D-glucose KEGG_COMPOUND 2-deoxy-D-arabino-hexose IUPAC 2-Deoxy-D-arabino-hexose KEGG_COMPOUND 2-Deoxy-D-mannose ChemIDplus D-2dGlc JCBN D-arabino-2-Deoxyhexose KEGG_COMPOUND Deoxyglucose ChemIDplus