Alexander Diehl Ceri van Slyke Chris Mungall David Osumi-Sutherland Jim Balhoff Melissa Haendel Nicole Vasilevsky Terry Meehan Yvonne Bradford An ontology of cell types. Cell Ontology See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, University at Buffalo. 2022-01-05 definition IAO:0000116 uberon editor_note true editor_note editor note expand expression to preferred_root term replaced by tooth SubClassOf 'never in taxon' value 'Aves' S never_in_taxon T iff: S SubClassOf in_taxon only not T. x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. Chris Mungall ?X DisjointWith RO_0002162 some ?Y Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y) RO:0002161 uberon never_in_taxon true true never_in_taxon never in taxon never_in_taxon S never_in_taxon T iff: S SubClassOf in_taxon only not T. PMID:20973947 S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S. https://orcid.org/0000-0002-6601-2165 RO:0002175 applicable for taxon uberon present_in_taxon true true present_in_taxon present in taxon present_in_taxon S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S. https://orcid.org/0000-0002-6601-2165 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 preferred term when talking about an instance of this class in Homo sapiens latin term plural term abstract upper-level terms not directly useful for analysis http://purl.org/dc/elements/1.1/contributor uberon dc-contributor true dc-contributor contributor http://purl.org/dc/elements/1.1/creator uberon dc-creator true dc-creator creator http://purl.org/dc/elements/1.1/description uberon dc-description true dc-description description http://purl.org/dc/elements/1.1/title uberon dc-title true dc-title title http://purl.org/dc/terms/license uberon dcterms-license true dcterms-license license subset_property synonym_type_property consider has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_namespace has_related_synonym has_synonym_type in_subset shorthand http://www.w3.org/2000/01/rdf-schema#seeAlso uberon seeAlso true seeAlso see also http://xmlns.com/foaf/0.1/depicted_by uberon depicted_by true depicted_by depicted by 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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 BFO:0000050 external 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) 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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 BFO:0000051 external quality uberon has_part has_part has part has part has_part realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes 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 external uberon preceded_by 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 external 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 BFO:0000066 external 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 x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer. cjm 2009-07-31T02:15:46Z BSPO:0000096 uberon anterior_to anterior_to anterior_to x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer. http://orcid.org/0000-0002-6601-2165 x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal). BSPO:0000097 uberon distal_to distal_to distal_to x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal). http://orcid.org/0000-0002-6601-2165 x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000098 uberon dorsal_to dorsal_to dorsal_to x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). http://orcid.org/0000-0002-6601-2165 x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail. BSPO:0000099 caudal_to uberon posterior_to posterior_to posterior_to x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail. http://orcid.org/0000-0002-6601-2165 x proximal_to y iff x is closer to the point of attachment with the body than y. BSPO:0000100 uberon proximal_to proximal_to proximal_to x proximal_to y iff x is closer to the point of attachment with the body than y. http://orcid.org/0000-0002-6601-2165 x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000102 uberon ventral_to ventral_to ventral_to x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). http://orcid.org/0000-0002-6601-2165 BSPO:0000107 uberon deep_to deep_to deep_to BSPO:0000108 uberon superficial_to superficial_to superficial_to X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion. BSPO:0000120 uberon in_left_side_of in_left_side_of in_left_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion. BSPO:PATO_mtg_2009 X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion. BSPO:0000121 uberon in_right_side_of in_right_side_of in_right_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion. BSPO:PATO_mtg_2009 X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion. BSPO:0000122 uberon in_posterior_side_of in_posterior_side_of in_posterior_side_of X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion. BSPO:PATO_mtg_2009 X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion. BSPO:0000123 uberon in_anterior_side_of in_anterior_side_of in_anterior_side_of X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion. BSPO:PATO_mtg_2009 X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. BSPO:0000124 uberon in_proximal_side_of in_proximal_side_of in_proximal_side_of X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. BSPO:PATO_mtg_2009 X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion. BSPO:0000125 uberon in_distal_side_of in_distal_side_of in_distal_side_of X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion. BSPO:PATO_mtg_2009 X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure. BSPO:0000126 uberon in_lateral_side_of in_lateral_side_of in_lateral_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure. https://orcid.org/0000-0002-6601-2165 X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the superficial portion. BSPO:0001100 uberon in_superficial_part_of in_superficial_part_of in_superficial_part_of X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the superficial portion. http://orcid.org/0000-0002-6601-2165 X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the deep portion. BSPO:0001101 uberon in_deep_part_of in_deep_part_of in_deep_part_of X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the deep portion. http://orcid.org/0000-0002-6601-2165 X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y. BSPO:0001106 uberon proximalmost_part_of proximalmost_part_of proximalmost_part_of X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y. https://orcid.org/0000-0002-6601-2165 This relation holds when both the deep_to and ajdacent_to relationship similarly hold. BSPO:0001107 uberon immediately_deep_to immediately_deep_to immediately_deep_to This relation holds when both the deep_to and ajdacent_to relationship similarly hold. http://orcid.org/0000-0002-6601-2165 X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y. BSPO:0001108 uberon distalmost_part_of distalmost_part_of distalmost_part_of X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y. https://orcid.org/0000-0002-6601-2165 BSPO:0001113 uberon preaxialmost_part_of preaxialmost_part_of preaxialmost_part_of BSPO:0001115 uberon postaxialmost_part_of postaxialmost_part_of postaxialmost_part_of X intersects_median_plane of iff X crosses the midine plane of Y. BSPO:0005001 uberon intersects_midsagittal_plane_of intersects_midsagittal_plane_of intersects_midsagittal_plane_of BSPO:0015014 uberon immediately_superficial_to immediately_superficial_to immediately_superficial_to BSPO:0015101 uberon in_dorsal_side_of in_dorsal_side_of in_dorsal_side_of GOREL:0002003 external results_in_distribution_of results_in_distribution_of results_in_distribution_of GOREL:0002004 external results_in_fission_of results_in_fission_of results_in_fission_of inheres in this fragility is a characteristic of this vase this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of RO:0000053 external uberon bearer_of bearer_of bearer of has characteristic 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 external uberon participates_in participates_in 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 RO:0000057 external has_participant has_participant has participant has participant this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of 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 This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. 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 This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function 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 uberon 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 has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of 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. 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ located_in http://www.obofoundry.org/ro/#OBO_REL:located_in RO:0001025 uberon 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. the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of RO:0002000 uberon boundary_of boundary_of 2D boundary of boundary of my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. David Osumi-Sutherland has boundary has_2D_boundary RO:0002002 uberon has_boundary has_boundary has 2D boundary has boundary David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 nerve supply uberon innervated_by innervated_by http://code.google.com/p/obo-relations/issues/detail?id=6 innervated_by innervated_by nerve supply FMA:85999 David Osumi-Sutherland has synaptic terminal of X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 David Osumi-Sutherland RO:0002007 external uberon bounding_layer_of bounding_layer_of A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. bounding layer of bounding layer of A relationship that holds between a process that regulates a transport process and the entity transported by that process. David Osumi-Sutherland regulates transport of 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 RO:0002013 external has_regulatory_component_activity has_regulatory_component_activity 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 RO:0002014 external has_negative_regulatory_component_activity has_negative_regulatory_component_activity 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 between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. dos 2017-07-20T17:19:37Z occurs across 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 <= Primitive instance level timing relation between events before or simultaneous with Relation between occurrents, shares start and end boundaries. David Osumi-Sutherland RO:0002082 coincides_with is_equal_to uberon simultaneous_with simultaneous_with t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with simultaneous_with Relation between occurrents, shares start and end boundaries. Allen:is_equal_to https://orcid.org/0000-0002-6601-2165 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 external 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 ends_at_start_of meets RO:0002090 external immediately_precedes immediately_precedes X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes immediately_precedes Relation between a neuron and an anatomical structure that its soma is part of. David Osumi-Sutherland <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) has soma location relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. David Osumi-Sutherland fasciculates with (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) (and ("neuron ; CL_0000540" ?x) ("neuron projection bundle ; CARO_0001001" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500' " ?npbs) (part_of ?npbs ?y) (part_of ?nps ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) )))))) fasciculates with Relation between a neuron and some structure its axon forms (chemical) synapses in. Chris Mungall David Osumi-Sutherland David Osumi-Sutherland <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) axon synapses in Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. Chris Mungall David Osumi-Sutherland <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) synapsed by Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. Alexander Diehl Chris Mungall Lindsay Cowell <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) has plasma membrane part Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. Chris Mungall David Osumi-Sutherland synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) has postsynaptic terminal in Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. synapses in <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) has presynaptic terminal in Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. Chris Mungall David Osumi-Sutherland <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) N1 synapsed_to some N2 Expands to: N1 SubclassOf ( has_part some ( ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( ‘synapse ; GO:0045202’ that has_part some ( ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) synapsed to A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. David Osumi-Sutherland has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) has synaptic terminal in 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 external uberon overlaps overlaps overlaps overlaps true The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. David Osumi-Sutherland has fasciculating component (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) (and ("neuron projection bundle ; CARO_0001001" ?x) ("neuron projection ; GO0043005" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500" ?npbs) (part_of ?nps ?y) (part_of ?npbs ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) )))))) has fasciculating neuron projection Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. David Osumi-Sutherland <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) RO:0002134 uberon innervates innervates http://code.google.com/p/obo-relations/issues/detail?id=6 innervates innervates X continuous_with Y if and only if X and Y share a fiat boundary. David Osumi-Sutherland connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) RO:0002150 uberon continuous_with continuous_with continuous with continuous_with FMA:85972 two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. Consider obsoleting and merging with child relation, 'in homology relationship with' RO:0002158 uberon homologous_to homologous_to VBO calls this homologous_to homologous_to shares ancestor with lactation SubClassOf 'only in taxon' some 'Mammalia' S only_in_taxon T iff: S SubClassOf in_taxon only T. x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria Chris Mungall RO:0002160 uberon only_in_taxon only_in_taxon only in taxon only_in_taxon S only_in_taxon T iff: S SubClassOf in_taxon only T. PMID:20973947 x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. Chris Mungall Jennifer Deegan RO:0002162 uberon in_taxon in_taxon Connects a biological entity to its taxon of origin. in taxon A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. Chris Mungall Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b RO:0002170 uberon connected_to connected_to Connection does not imply overlaps. connected to connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern The M8 connects Glasgow and Edinburgh a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect) RO:0002176 uberon connects connects connects connects https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. attached to part of (anatomical structure to anatomical structure) RO:0002177 uberon attaches_to_part_of attaches_to_part_of attached to part of attaches_to_part_of true true Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. relation between an artery and the structure is supplies with blood. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure RO:0002178 arterial supply of uberon supplies supplies source: FMA supplies supplies arterial supply of FMA:86003 Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure RO:0002179 drains blood from drains from uberon drains drains source: Wikipedia drains drains 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 external uberon 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 RO:0002202 uberon develops_from develops_from This is the transitive form of the develops from relation develops from develops_from inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan RO:0002203 uberon develops_into develops_into develops into develops_into 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process Chris Mungall expressed in Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. Chris Mungall David Osumi-Sutherland has developmental precursor FBbt RO:0002207 uberon directly_develops_from directly_develops_from TODO - add child relations from DOS directly develops from directly_develops_from inverse of directly develops from developmental precursor of directly 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:0002215 external 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:0002216 external uberon capable_of_part_of capable_of_part_of capable of part of capable of part of true x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y. Chris Mungall RO:0002219 uberon surrounded_by surrounded_by surrounded by surrounded_by x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y. https://orcid.org/0000-0002-6601-2165 A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. x adjacent to y if and only if x and y share a boundary. x adjacent_to y iff: x and y share a boundary. This relation acts as a join point with BSPO Chris Mungall RO:0002220 external uberon adjacent_to adjacent_to adjacent to adjacent to adjacent_to A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. inverse of surrounded by inverse of surrounded_by. Chris Mungall RO:0002221 uberon surrounds surrounds surrounds surrounds inverse of surrounded_by. https://orcid.org/0000-0002-6601-2165 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 Relation between occurrents, shares a start boundary with. inverse of starts with Chris Mungall Allen RO:0002223 uberon starts starts starts starts Relation between occurrents, shares a start boundary with. Allen:starts https://orcid.org/0000-0002-6601-2165 Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall started by RO:0002224 external uberon starts_with starts_with starts with starts with x develops from part of y if and only if there exists some z such that x develops from z and z is part of y Chris Mungall RO:0002225 uberon develops_from_part_of develops_from_part_of develops from part of develops_from_part_of x develops_in y if x is located in y whilst x is developing Chris Mungall EHDAA2 Jonathan Bard, EHDAA2 RO:0002226 uberon develops_in develops_in This relation take from EHDAA2 - precise semantics yet to be defined develops in develops_in Relation between occurrents, shares an end boundary with. inverse of ends with Chris Mungall RO:0002229 finishes uberon ends ends ends ends Relation between occurrents, shares an end boundary with. Allen:starts ZFS:finishes https://orcid.org/0000-0002-6601-2165 x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall finished by RO:0002230 external uberon ends_with ends_with ends with ends with x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y Chris Mungall starts with process that occurs in RO:0002231 external has_start_location has_start_location has start location has start location x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y Chris Mungall ends with process that occurs in RO:0002232 external has_end_location has_end_location has end location has end location 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 RO:0002233 external has_input has_input has input 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 in the same state at the beginning of p. Chris Mungall produces RO:0002234 external has_output has_output has output 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 RO:0002254 uberon has_developmental_contribution_from has_developmental_contribution_from has developmental contribution from has developmental contribution from inverse of has developmental contribution from Chris Mungall RO:0002255 uberon developmentally_contributes_to developmentally_contributes_to developmentally contributes to developmentally_contributes_to t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T. t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T Chris Mungall David Osumi-Sutherland Melissa Haendel induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) GO:0001759 We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] RO:0002256 uberon developmentally_induced_by developmentally_induced_by sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F) developmentally induced by developmentally_induced_by t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T. GO:0001759 Inverse of developmentally induced by Chris Mungall developmentally induces 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 RO:0002258 uberon developmentally_preceded_by developmentally_preceded_by 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 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 x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage Chris Mungall replaces RO:0002285 uberon developmentally_replaces developmentally_replaces developmentally replaces developmentally_replaces Inverse of developmentally preceded by Chris Mungall developmentally succeeded by 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue Chris Mungall part of developmental precursor of Inverse of 'expressed in' Chris Mungall expresses p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. Chris Mungall RO:0002295 external results_in_developmental_progression_of results_in_developmental_progression_of results in developmental progression of results in developmental progression of every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. Chris Mungall http://www.geneontology.org/GO.doc.development.shtml RO:0002296 external results_in_development_of results_in_development_of results in development of results in development of an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) Chris Mungall GOC:mtg_berkeley_2013 RO:0002297 external results_in_formation_of results_in_formation_of results in formation of results in formation of an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. Chris Mungall GOC:mtg_berkeley_2013 RO:0002298 external results_in_morphogenesis_of results_in_morphogenesis_of results in morphogenesis of results in morphogenesis of an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. Chris Mungall GOC:mtg_berkeley_2013 RO:0002299 external results_in_maturation_of results_in_maturation_of results in maturation of results in maturation of cjm RO:0002304 external causally_upstream_of,_positive_effect causally_upstream_of,_positive_effect 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 RO:0002305 external causally_upstream_of,_negative_effect causally_upstream_of,_negative_effect 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 Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. Chris Mungall regulates localization of RO:0002313 external transports_or_maintains_localization_of transports_or_maintains_localization_of transports or maintains localization of transports or maintains localization of q characteristic of 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 characteristic of part of Chris Mungall inheres in part of characteristic of part of true an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity Chris Mungall GOC:mtg_berkeley_2013 RO:0002315 external results_in_acquisition_of_features_of results_in_acquisition_of_features_of results in acquisition of features of results in acquisition of features of A relationship that holds via some environmental process Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships 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. 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 holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism genomically related to 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 involved in every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c Chris Mungall regulates levels of (process to entity) RO:0002332 external regulates_levels_of regulates_levels_of regulates levels of regulates levels of inverse of enables Chris Mungall enabled by inverse of regulates Chris Mungall regulated by (processual) RO:0002334 external regulated_by regulated_by regulated by regulated by inverse of negatively regulates Chris Mungall RO:0002335 external negatively_regulated_by negatively_regulated_by negatively regulated by negatively regulated by inverse of positively regulates Chris Mungall RO:0002336 external positively_regulated_by positively_regulated_by positively regulated by positively regulated by A relationship that holds via some process of localization Chris Mungall Do not use this relation directly. It is a grouping relation. related via localization to This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. Chris Mungall RO:0002338 external has_target_start_location has_target_start_location has target start location has target start location This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. Chris Mungall RO:0002339 external has_target_end_location has_target_end_location has target end location has target end location Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l Chris Mungall RO:0002341 external results_in_transport_along results_in_transport_along results in transport along results in transport along Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. Chris Mungall RO:0002342 external results_in_transport_across results_in_transport_across results in transport across results in transport across 'pollen tube growth' results_in growth_of some 'pollen tube' Chris Mungall RO:0002343 external results_in_growth_of results_in_growth_of results in growth of results in growth of 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) Chris Mungall RO:0002344 external results_in_transport_to_from_or_in results_in_transport_to_from_or_in results in transport to from or in results in transport to from or in An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO RO:0002350 uberon member_of member_of member of member of has member is a mereological relation between a collection and an item. SIO RO:0002351 uberon has_member has_member has member has member 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 external uberon output_of output_of output of output of Chris Mungall formed as result of a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a Chris Mungall attached to (anatomical structure to anatomical structure) RO:0002371 uberon attaches_to attaches_to attached to attaches_to m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Chris Mungall Wikipedia:Insertion_(anatomy) RO:0002372 uberon has_muscle_origin has_muscle_origin The origin is the end of a muscle that attaches to the more fixed part of the skeleton, which is the proximal end in limb muscles has muscle origin has_muscle_origin We need to import uberon muscle to create a stricter domain constraint m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Wikipedia:Insertion_(anatomy)#Muscles m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Chris Mungall Wikipedia:Insertion_(anatomy) RO:0002373 uberon has_muscle_insertion has_muscle_insertion The insertion is the point of attachment of a muscle that moves the most when the muscle shortens, or the most distal end of limb muscles has muscle insertion has_muscle_insertion We need to import uberon muscle into RO to use as a stricter domain constraint m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Wikipedia:Insertion_(anatomy) A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) in branching relationship with https://github.com/obophenotype/uberon/issues/170 Deschutes River tributary_of Columbia River inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. Chris Mungall drains into drains to tributary channel of http://en.wikipedia.org/wiki/Tributary http://www.medindia.net/glossary/venous_tributary.htm This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) RO:0002376 uberon drains into tributary_of tributary_of tributary of tributary_of http://en.wikipedia.org/wiki/Tributary drains into dbpowl:drainsTo 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 is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve Chris Mungall RO:0002380 uberon branching_part_of branching_part_of branching part of branching_part_of FMA:85994 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 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 RO:0002385 uberon has_potential_to_developmentally_contribute_to has_potential_to_developmentally_contribute_to has potential to developmentally contribute to has potential to developmentally contribute to x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y Chris Mungall has potential to developmentally induce x has the potential to develop into y iff x develops into y or if x is capable of developing into y x has the potential to develop into y iff x develops into y or if x is capable of developing into y. Chris Mungall RO:0002387 uberon has_potential_to_develop_into has_potential_to_develop_into has potential to develop into 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 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 RO:0002388 uberon has_potential_to_directly_develop_into has_potential_to_directly_develop_into has potential to directly develop into has potential to directly develop into inverse of upstream of Chris Mungall RO:0002404 external causally_downstream_of causally_downstream_of causally downstream of causally downstream of Chris Mungall RO:0002405 external immediately_causally_downstream_of immediately_causally_downstream_of immediately causally downstream of 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 RO:0002411 external causally_upstream_of causally_upstream_of causally upstream of 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 RO:0002412 external immediately_causally_upstream_of immediately_causally_upstream_of immediately causally upstream of 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) RO:0002418 external affects causally_upstream_of_or_within causally_upstream_of_or_within causally upstream of or within inverse of causally upstream of or within Chris Mungall RO:0002427 external causally_downstream_of_or_within causally_downstream_of_or_within 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 true 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 p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. Chris Mungall RO:0002433 uberon contributes_to_morphology_of contributes_to_morphology_of contributes to morphology of 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/ro/docs/interaction-relations/ http://purl.obolibrary.org/obo/MI_0914 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 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 directly regulates activity of 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 molecularly decreases activity of directly negatively regulates activity of 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 directly activates molecularly increases 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) 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. x composed_primarily_of y iff: more than half of the mass of x is made from parts of y. Chris Mungall RO:0002473 uberon composed_primarily_of composed_primarily_of composed primarily of 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 See notes for inverse relation Chris Mungall receives input from This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. Chris Mungall sends output to Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. relation between physical entity and a process or stage Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). Chris Mungall RO:0002488 begins_to_exist_during uberon existence_starts_during existence_starts_during existence starts during Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. https://orcid.org/0000-0002-6601-2165 Relation between continuant and occurrent, such that c comes into existence at the start of p. x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). Chris Mungall RO:0002489 uberon existence_starts_with existence_starts_with existence starts with Relation between continuant and occurrent, such that c comes into existence at the start of p. https://orcid.org/0000-0002-6601-2165 x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) Chris Mungall The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) Chris Mungall RO:0002491 exists during uberon existence_starts_and_ends_during existence_starts_and_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts and ends during Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). Chris Mungall RO:0002492 ceases_to_exist_during uberon existence_ends_during existence_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. https://orcid.org/0000-0002-6601-2165 Relation between continuant and occurrent, such that c ceases to exist at the end of p. x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). Chris Mungall RO:0002493 uberon existence_ends_with existence_ends_with The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with Relation between continuant and occurrent, such that c ceases to exist at the end of p. https://orcid.org/0000-0002-6601-2165 x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships Chris Mungall RO:0002494 transforms from uberon transformation_of transformation_of transformation of transforms from SIO:000657 x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t Chris Mungall RO:0002495 direct_transformation_of immediately transforms from uberon immediate_transformation_of immediate_transformation_of immediate transformation of direct_transformation_of https://orcid.org/0000-0002-6601-2165 immediately transforms from SIO:000658 x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). Chris Mungall RO:0002496 uberon existence_starts_during_or_after existence_starts_during_or_after The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. Chris Mungall RO:0002497 uberon existence_ends_during_or_before existence_ends_during_or_before The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before 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 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 Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. Chris Mungall has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). RO:0002551 uberon has sekeletal support has supporting framework has_skeleton has_skeleton has skeleton This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. http://orcid.org/0000-0002-6601-2165 Chris Mungall causally influenced by (entity-centric) causally influenced by Chris Mungall interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ Chris Mungall molecular interaction relation helper property Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall RO:0002565 external results_in_movement_of results_in_movement_of results in movement of 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 A relation that holds between elements of a musculoskeletal system or its analogs. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. biomechanically related to m1 has_muscle_antagonist m2 iff m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. Chris Mungall Wikipedia:Antagonist_(muscle) RO:0002568 uberon has_muscle_antagonist has_muscle_antagonist has muscle antagonist has_muscle_antagonist m1 has_muscle_antagonist m2 iff m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. Wikipedia:Antagonist_(muscle) inverse of branching part of Chris Mungall RO:0002569 uberon has_branching_part has_branching_part has branching part x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. Chris Mungall GOC:cjm RO:0002571 uberon lumen_of lumen_of lumen of s is luminal space of x iff s is lumen_of x and s is an immaterial entity Chris Mungall RO:0002572 uberon luminal_space_of luminal_space_of luminal space of inverse of has skeleton Chris Mungall RO:0002576 uberon skeleton_of skeleton_of skeleton of 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 p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p results in breakdown of RO:0002588 external results_in_assembly_of results_in_assembly_of results in assembly of results_in_assembly_of RO:0002590 external results_in_disassembly_of results_in_disassembly_of results in disassembly of results_in_disassembly_of p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 external results_in_organization_of results_in_organization_of results in organization 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' RO:0002608 external process_has_causal_agent process_has_causal_agent 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 external 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 external uberon produced_by produced_by produced by produced by produced_by p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. cjm 2018-12-13T11:26:17Z RO:0004007 external has_primary_input_or_output has_primary_input_or_output has primary input or output p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. cjm 2018-12-13T11:26:32Z RO:0004008 external has_primary_output has_primary_output has primary output p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. GOC:cjm GOC:dph GOC:kva GOC:pt PMID:27812932 p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. cjm 2018-12-13T11:26:56Z RO:0004009 external has_primary_input has_primary_input has primary input p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. GOC:cjm GOC:dph GOC:kva GOC:pt PMID:27812932 A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. cjm 2017-12-26T19:45:49Z realized in response to stimulus 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 A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. Austin Meier Chris Mungall David Osumi-Sutherland Marie Angelique Laporte triggered by process realized in response to https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit triggered by process RO:cjm 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 p acts on population of c iff c' is a collection, has members of type c, and p has participant c pg 2020-06-08T17:21:33Z RO:0012003 external acts_on_population_of acts_on_population_of acts on population of acts on population of pg 2021-02-26T07:28:29Z RO:0012008 external results_in_fusion_of results_in_fusion_of results in fusion of results in fusion of A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. 2020-07-17T09:26:52Z has synaptic input or output in has synaptic IO in region p has anatomical participant c iff p has participant c, and c is an anatomical entity cjm 2018-09-26T01:08:58Z results in changes to anatomical or cellular structure has_completed A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). has_high_plasma_membrane_amount A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). PMID:19243617 A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). has_low_plasma_membrane_amount A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). PMID:19243617 has_not_completed http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y lacks_part http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y) lacks_plasma_membrane_part 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 quality has_relative_magnitude has_relative_magnitude 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 A diagnostic testing device utilizes a specimen. X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y. Asiyah Lin Bill Duncan (https://orcid.org/0000-0001-9625-1899) A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08 utilizes x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. uberon anteriorly_connected_to anteriorly connected to x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern carries uberon channel_for channel for uberon channels_from channels_from uberon channels_into channels_into x is a conduit for y iff y passes through the lumen of x. uberon conduit_for conduit for x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to distally connected to x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern uberon extends_fibers_into extends_fibers_into Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity. uberon filtered_through Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed filtered through a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s. add to RO uberon indirectly_supplies indirectly_supplies uberon layer_part_of layer part of x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. uberon posteriorly_connected_to posteriorly connected to x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern uberon protects protects x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. uberon proximally_connected_to proximally connected to x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern uberon sexually_homologous_to sexually_homologous_to c site_of p if c is the bearer of a disposition that is realized by a process that has p as part. uberon capable_of_has_part site_of site_of uberon subdivision_of placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B subdivision of Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. uberon synapsed_by synapsed by . uberon transitively_anteriorly_connected_to transitively anteriorly connected to . http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern uberon transitively_connected_to transitively_connected to . uberon transitively_distally_connected_to transitively distally connected to . http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern . uberon transitively_proximally_connected_to transitively proximally connected to . http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern uberon trunk_part_of trunk_part_of http://semanticscience.org/resource/SIO_000658 direct_transformation_of immediately transforms from immediate_transformation_of immediate_transformation_of direct_transformation_of https://orcid.org/0000-0002-6601-2165 immediately transforms from SIO:000658 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. continuant An entity that has temporal parts and that happens, unfolds or develops through time. occurrent A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant spatial region An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process disposition 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 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. specifically dependent continuant 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 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. generically dependent continuant function An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. material entity immaterial entity 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 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 Any steroid substituted by a formyl group. chebi_ontology steroid aldehydes CHEBI:131565 steroid aldehyde steroid aldehydes 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 steroid compound with a structure based on a 19-carbon (androstane) skeleton. chebi_ontology C19-steroids CHEBI:131621 C19-steroid C19-steroids 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 carbohydrate acid derivative anion obtained by deprotonation of the carboxy groups of hyaluronic acid; major species at pH 7.3. -1 (C14H20NO11)n.H2O chebi_ontology hyaluronan hyaluronate polyanion CHEBI:132153 hyaluronate hyaluronan UniProt hyaluronate polyanion ChEBI An organic group derived from any 3-oxo-Delta(4)-steroid. 0 C6H6O 94.111 94.04186 C1=C(C*)*C(CC1=O)* chebi_ontology a 3-oxo-Delta4-steroid group CHEBI:136849 3-oxo-Delta(4)-steroid group a 3-oxo-Delta4-steroid group UniProt Any steroid that has beta-configuration at position 5. chebi_ontology 5beta steroids 5beta-steroid 5beta-steroids CHEBI:136889 5beta steroid 5beta steroids ChEBI 5beta-steroid ChEBI 5beta-steroids ChEBI 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 Any member of a group of hydroxy steroids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine. In mammals bile acids almost invariably have 5beta-configuration, while in lower vertebrates, some bile acids, known as allo-bile acids, have 5alpha-configuration. chebi_ontology CHEBI:138366 bile acids An apoprotein is a protein devoid of its characteristic prosthetic group or metal. KEGG:C16240 apoprotein chebi_ontology apoproteins CHEBI:13850 apoprotein apoprotein IUPAC apoproteins ChEBI 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 -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 Any saturated fatty acid containing 4 carbons. 0 CHO2R 45.017 44.99765 *C(O)=O chebi_ontology CHEBI:140601 fatty acid 4:0 An antigenic epitope recognized by an anti-bilirubin monoclonal antibody designated 24G7. A substructure of bilirubin IXalpha, it is the region containing the oxo group at C-1, the methyl group at C-2, C-(4, 5, 6, 9), and N-21 and -22. 0 C7H6N2O 134.136 134.04801 C(=CC(NC(=*)*)=*)(NC(C(C)=*)=O)* chebi_ontology CHEBI:142163 24G7 epitope 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 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 Actylcholine is an ester of acetic acid and choline, which acts as a neurotransmitter. +1 C7H16NO2 InChI=1S/C7H16NO2/c1-7(9)10-6-5-8(2,3)4/h5-6H2,1-4H3/q+1 OIPILFWXSMYKGL-UHFFFAOYSA-N 146.20748 146.11756 CC(=O)OCC[N+](C)(C)C CHEBI:12686 CHEBI:13715 CHEBI:22197 CHEBI:2416 CHEBI:40559 Beilstein:1764436 CAS:51-84-3 DrugBank:DB03128 Drug_Central:65 Gmelin:326108 KEGG:C01996 LINCS:LSM-5888 PDBeChem:ACH PMID:14764638 PMID:15014918 PMID:15231705 PMID:15361288 PMID:18050502 PMID:18407448 PMID:19255787 PMID:20963497 PMID:21130809 PMID:21246223 PMID:21545631 PMID:21601579 Wikipedia:Acetylcholine 2-acetyloxy-N,N,N-trimethylethanaminium ACETYLCHOLINE Acetylcholine acetylcholine chebi_ontology ACh Azetylcholin O-Acetylcholine choline acetate CHEBI:15355 acetylcholine Beilstein:1764436 ChemIDplus CAS:51-84-3 ChemIDplus CAS:51-84-3 KEGG COMPOUND Drug_Central:65 DrugCentral Gmelin:326108 Gmelin PMID:14764638 Europe PMC PMID:15014918 Europe PMC PMID:15231705 Europe PMC PMID:15361288 Europe PMC PMID:18050502 Europe PMC PMID:18407448 Europe PMC PMID:19255787 Europe PMC PMID:20963497 Europe PMC PMID:21130809 Europe PMC PMID:21246223 Europe PMC PMID:21545631 Europe PMC PMID:21601579 Europe PMC 2-acetyloxy-N,N,N-trimethylethanaminium IUPAC ACETYLCHOLINE PDBeChem Acetylcholine KEGG_COMPOUND acetylcholine UniProt ACh ChemIDplus Azetylcholin ChEBI O-Acetylcholine KEGG_COMPOUND choline acetate ChemIDplus 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 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 O2 InChI=1S/O2/c1-2 MYMOFIZGZYHOMD-UHFFFAOYSA-N 31.99880 31.98983 O=O CHEBI:10745 CHEBI:13416 CHEBI:23833 CHEBI:25366 CHEBI:30491 CHEBI:44742 CHEBI:7860 CAS:7782-44-7 Gmelin:485 HMDB:HMDB0001377 KEGG:C00007 KEGG:D00003 MetaCyc:OXYGEN-MOLECULE MolBase:750 PDBeChem:OXY PMID:10906528 PMID:16977326 PMID:18210929 PMID:18638417 PMID:19840863 PMID:7710549 PMID:9463773 Wikipedia:Oxygen dioxygen chebi_ontology Disauerstoff E 948 E-948 E948 O2 OXYGEN MOLECULE Oxygen [OO] dioxygene molecular oxygen CHEBI:15379 dioxygen CAS:7782-44-7 ChemIDplus CAS:7782-44-7 KEGG COMPOUND CAS:7782-44-7 NIST Chemistry WebBook Gmelin:485 Gmelin PMID:10906528 Europe PMC PMID:16977326 Europe PMC PMID:18210929 Europe PMC PMID:18638417 Europe PMC PMID:19840863 Europe PMC PMID:7710549 Europe PMC PMID:9463773 Europe PMC dioxygen IUPAC Disauerstoff ChEBI E 948 ChEBI E-948 ChEBI E948 ChEBI O2 IUPAC O2 KEGG_COMPOUND O2 UniProt OXYGEN MOLECULE PDBeChem Oxygen KEGG_COMPOUND [OO] MolBase dioxygene ChEBI molecular oxygen ChEBI 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 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 410.730 410.39125 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 HMDB:HMDB0000256 KEGG:C00751 KNApSAcK:C00003755 LIPID_MAPS_instance:LMPR0106010002 MetaCyc:SQUALENE PDBeChem:SQL PMID:16341241 PMID:23625688 PMID:24362891 PMID:25286851 PMID:25286853 PMID:25987292 Wikipedia:Squalene (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:23625688 Europe PMC PMID:24362891 Europe PMC PMID:25286851 Europe PMC PMID:25286853 Europe PMC PMID:25987292 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 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 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 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 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 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 nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues. 0 (C5H8O6PR)n.C10H17O10PR2 CHEBI:13672 CHEBI:14859 CHEBI:8312 KEGG:C00419 Polynucleotide chebi_ontology polynucleotides CHEBI:15986 polynucleotide Polynucleotide KEGG_COMPOUND polynucleotides ChEBI An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. 0 H3N InChI=1S/H3N/h1H3 QGZKDVFQNNGYKY-UHFFFAOYSA-N 17.03056 17.02655 [H]N([H])[H] CHEBI:13405 CHEBI:13406 CHEBI:13407 CHEBI:13771 CHEBI:22533 CHEBI:44269 CHEBI:44284 CHEBI:44404 CHEBI:7434 Beilstein:3587154 CAS:7664-41-7 Drug_Central:4625 Gmelin:79 HMDB:HMDB0000051 KEGG:C00014 KEGG:D02916 KNApSAcK:C00007267 MetaCyc:AMMONIA MolBase:930 PDBeChem:NH3 PMID:110589 PMID:11139349 PMID:11540049 PMID:11746427 PMID:11783653 PMID:13753780 PMID:14663195 PMID:15092448 PMID:15094021 PMID:15554424 PMID:15969015 PMID:16008360 PMID:16050680 PMID:16348008 PMID:16349403 PMID:16614889 PMID:16664306 PMID:16842901 PMID:17025297 PMID:17439666 PMID:17569513 PMID:17737668 PMID:18670398 PMID:22002069 PMID:22081570 PMID:22088435 PMID:22100291 PMID:22130175 PMID:22150211 PMID:22240068 PMID:22290316 PMID:22342082 PMID:22385337 PMID:22443779 PMID:22560242 Reaxys:3587154 Wikipedia:Ammonia AMMONIA Ammonia ammonia azane chebi_ontology Ammoniak NH3 R-717 [NH3] ammoniac amoniaco spirit of hartshorn CHEBI:16134 ammonia Beilstein:3587154 Beilstein CAS:7664-41-7 ChemIDplus CAS:7664-41-7 KEGG COMPOUND CAS:7664-41-7 NIST Chemistry WebBook Drug_Central:4625 DrugCentral Gmelin:79 Gmelin PMID:110589 Europe PMC PMID:11139349 Europe PMC PMID:11540049 Europe PMC PMID:11746427 Europe PMC PMID:11783653 Europe PMC PMID:13753780 Europe PMC PMID:14663195 Europe PMC PMID:15092448 Europe PMC PMID:15094021 Europe PMC PMID:15554424 Europe PMC PMID:15969015 Europe PMC PMID:16008360 Europe PMC PMID:16050680 Europe PMC PMID:16348008 Europe PMC PMID:16349403 Europe PMC PMID:16614889 Europe PMC PMID:16664306 Europe PMC PMID:16842901 Europe PMC PMID:17025297 Europe PMC PMID:17439666 Europe PMC PMID:17569513 Europe PMC PMID:17737668 Europe PMC PMID:18670398 Europe PMC PMID:22002069 Europe PMC PMID:22081570 Europe PMC PMID:22088435 Europe PMC PMID:22100291 Europe PMC PMID:22130175 Europe PMC PMID:22150211 Europe PMC PMID:22240068 Europe PMC PMID:22290316 Europe PMC PMID:22342082 Europe PMC PMID:22385337 Europe PMC PMID:22443779 Europe PMC PMID:22560242 Europe PMC Reaxys:3587154 Reaxys AMMONIA PDBeChem Ammonia KEGG_COMPOUND ammonia IUPAC azane IUPAC Ammoniak ChemIDplus NH3 IUPAC NH3 KEGG_COMPOUND NH3 UniProt R-717 ChEBI [NH3] MolBase ammoniac ChEBI amoniaco ChEBI spirit of hartshorn ChemIDplus A mucopolysaccharide composed of repeating beta-D-glucopyranuronosyl-(1->3)-beta-D-N-acetylgalactosaminyl units. (C14H21NO11)nH2O CHEBI:13989 CHEBI:13992 CHEBI:23221 CHEBI:3673 KEGG:C00401 KEGG:G11334 chebi_ontology Chondroitin Chondroitin-D-glucuronate CHEBI:16137 chondroitin D-glucuronate Chondroitin KEGG_COMPOUND Chondroitin-D-glucuronate KEGG_COMPOUND A sulfur oxoanion obtained by deprotonation of both OH groups of sulfuric acid. -2 O4S InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2 QAOWNCQODCNURD-UHFFFAOYSA-L 96.06360 95.95283 [O-]S([O-])(=O)=O CHEBI:15135 CHEBI:45687 CHEBI:9335 Beilstein:3648446 CAS:14808-79-8 Gmelin:2120 HMDB:HMDB0001448 KEGG:C00059 KEGG:D05963 MetaCyc:SULFATE PDBeChem:SO4 PMID:11200094 PMID:11452993 PMID:11581495 PMID:11798107 PMID:12166931 PMID:12668033 PMID:14597181 PMID:15093386 PMID:15984785 PMID:16186560 PMID:16345535 PMID:16347366 PMID:16348007 PMID:16483812 PMID:16534979 PMID:16656509 PMID:16742508 PMID:16742518 PMID:17120760 PMID:17420092 PMID:17439666 PMID:17709180 PMID:18398178 PMID:18815700 PMID:18846414 PMID:19047345 PMID:19244483 PMID:19544990 PMID:19628332 PMID:19812358 PMID:30398859 Reaxys:3648446 Wikipedia:Sulfate Sulfate sulfate tetraoxidosulfate(2-) tetraoxosulfate(2-) tetraoxosulfate(VI) chebi_ontology SO4(2-) SULFATE ION Sulfate anion(2-) Sulfate dianion Sulfate(2-) Sulfuric acid ion(2-) [SO4](2-) sulphate sulphate ion CHEBI:16189 sulfate Beilstein:3648446 Beilstein CAS:14808-79-8 ChemIDplus CAS:14808-79-8 NIST Chemistry WebBook Gmelin:2120 Gmelin PMID:11200094 Europe PMC PMID:11452993 Europe PMC PMID:11581495 Europe PMC PMID:11798107 Europe PMC PMID:12166931 Europe PMC PMID:12668033 Europe PMC PMID:14597181 Europe PMC PMID:15093386 Europe PMC PMID:15984785 Europe PMC PMID:16186560 Europe PMC PMID:16345535 Europe PMC PMID:16347366 Europe PMC PMID:16348007 Europe PMC PMID:16483812 Europe PMC PMID:16534979 Europe PMC PMID:16656509 Europe PMC PMID:16742508 Europe PMC PMID:16742518 Europe PMC PMID:17120760 Europe PMC PMID:17420092 Europe PMC PMID:17439666 Europe PMC PMID:17709180 Europe PMC PMID:18398178 Europe PMC PMID:18815700 Europe PMC PMID:18846414 Europe PMC PMID:19047345 Europe PMC PMID:19244483 Europe PMC PMID:19544990 Europe PMC PMID:19628332 Europe PMC PMID:19812358 Europe PMC PMID:30398859 Europe PMC Reaxys:3648446 Reaxys Sulfate KEGG_COMPOUND sulfate IUPAC sulfate UniProt tetraoxidosulfate(2-) IUPAC tetraoxosulfate(2-) IUPAC tetraoxosulfate(VI) IUPAC SO4(2-) IUPAC SULFATE ION PDBeChem Sulfate anion(2-) HMDB Sulfate dianion HMDB Sulfate(2-) HMDB Sulfuric acid ion(2-) HMDB [SO4](2-) IUPAC sulphate ChEBI sulphate ion ChEBI -1 HO InChI=1S/H2O/h1H2/p-1 XLYOFNOQVPJJNP-UHFFFAOYSA-M 17.00734 17.00329 [O-][H] CHEBI:13365 CHEBI:13419 CHEBI:44641 CHEBI:5594 CAS:14280-30-9 Gmelin:24714 KEGG:C01328 PDBeChem:OH hydridooxygenate(1-) hydroxide oxidanide chebi_ontology HO- HYDROXIDE ION Hydroxide ion OH(-) OH- CHEBI:16234 hydroxide CAS:14280-30-9 ChemIDplus CAS:14280-30-9 NIST Chemistry WebBook Gmelin:24714 Gmelin hydridooxygenate(1-) IUPAC hydroxide IUPAC oxidanide IUPAC HO- KEGG_COMPOUND HYDROXIDE ION PDBeChem Hydroxide ion KEGG_COMPOUND OH(-) IUPAC OH- KEGG_COMPOUND A mucopolysaccharide composed of N-acetylglucosamine and glucuronic acid subunits. It is found in the connective tissues of vertebrates. A principal constituent of the extracellular matrix (ECM), it mediates the growth and metastasis of tumour cells. 0 (C14H21NO12)n CHEBI:14412 CHEBI:24622 CHEBI:24623 CHEBI:5772 Beilstein:8538277 CAS:9004-61-9 HMDB:HMDB0010366 KEGG:C00518 KEGG:D08043 KEGG:G10505 PMID:11122186 PMID:18056362 PMID:18290544 Reaxys:8187837 Wikipedia:Hyaluronan Hyaluronic acid chebi_ontology Hyaluronsaeure [beta-D-glucopyranuronosyl-(1->3)-2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl-(1->4)]n [beta-N-Acetyl-D-glucosaminyl(1,4)beta-D-glucuronosyl(1,3)]n acide hyaluronique acido hialuronico hyaluronan CHEBI:16336 hyaluronic acid Beilstein:8538277 Beilstein CAS:9004-61-9 ChemIDplus CAS:9004-61-9 KEGG COMPOUND PMID:11122186 Europe PMC PMID:18056362 Europe PMC PMID:18290544 Europe PMC Reaxys:8187837 Reaxys Hyaluronic acid KEGG_COMPOUND Hyaluronsaeure ChEBI [beta-D-glucopyranuronosyl-(1->3)-2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl-(1->4)]n ChEBI [beta-N-Acetyl-D-glucosaminyl(1,4)beta-D-glucuronosyl(1,3)]n KEGG_COMPOUND acide hyaluronique ChEBI acido hialuronico ChEBI hyaluronan ChEBI A nitrogen oxide which is a free radical, each molecule of which consists of one nitrogen and one oxygen atom. 0 NO InChI=1S/NO/c1-2 MWUXSHHQAYIFBG-UHFFFAOYSA-N 30.00614 29.99799 [N]=O CHEBI:14657 CHEBI:25546 CHEBI:44452 CHEBI:7583 CAS:10102-43-9 DrugBank:DB00435 Gmelin:451 KEGG:C00533 KEGG:D00074 MolBase:943 PDBeChem:NO Reaxys:3587257 Wikipedia:Nitric_oxide Nitric oxide nitric oxide oxidonitrogen(.) oxoazanyl chebi_ontology (.)NO (NO)(.) EDRF NO NO(.) Nitrogen monoxide Stickstoff(II)-oxid Stickstoffmonoxid [NO] endothelium-derived relaxing factor mononitrogen monoxide monoxido de nitrogeno monoxyde d'azote nitrogen monooxide nitrogen monoxide nitrosyl oxido de nitrogeno(II) oxido nitrico oxyde azotique oxyde nitrique CHEBI:16480 nitric oxide CAS:10102-43-9 ChemIDplus CAS:10102-43-9 KEGG COMPOUND CAS:10102-43-9 NIST Chemistry WebBook Gmelin:451 Gmelin Reaxys:3587257 Reaxys Nitric oxide KEGG_COMPOUND nitric oxide UniProt oxidonitrogen(.) IUPAC oxoazanyl IUPAC (.)NO ChEBI (NO)(.) IUPAC EDRF ChEBI NO KEGG_COMPOUND NO(.) IUPAC Nitrogen monoxide KEGG_COMPOUND Stickstoff(II)-oxid ChEBI Stickstoffmonoxid ChEBI [NO] MolBase endothelium-derived relaxing factor ChEBI mononitrogen monoxide ChemIDplus monoxido de nitrogeno ChEBI monoxyde d'azote ChEBI nitrogen monooxide IUPAC nitrogen monoxide IUPAC nitrosyl IUPAC oxido de nitrogeno(II) ChEBI oxido nitrico ChEBI oxyde azotique ChEBI oxyde nitrique ChEBI A naturally occurring polypeptide synthesized at the ribosome. CHEBI:8526 KEGG:C00017 chebi_ontology Protein polypeptide chain protein polypeptide chains CHEBI:16541 protein polypeptide chain Protein KEGG_COMPOUND polypeptide chain ChEBI protein polypeptide chains ChEBI Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates. CHEBI:15131 CHEBI:23008 CHEBI:9318 Wikipedia:Carbohydrate carbohydrate carbohydrates chebi_ontology Kohlenhydrat Kohlenhydrate carbohidrato carbohidratos glucide glucides glucido glucidos hydrates de carbone saccharide saccharides saccharidum CHEBI:16646 carbohydrate carbohydrate IUPAC carbohydrates IUPAC Kohlenhydrat ChEBI Kohlenhydrate ChEBI carbohidrato IUPAC carbohidratos IUPAC glucide ChEBI glucides ChEBI glucido ChEBI glucidos ChEBI hydrates de carbone ChEBI saccharide IUPAC saccharides IUPAC saccharidum ChEBI Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. 0 (C2H2NOR)nC2H3NOR CHEBI:14753 CHEBI:25906 CHEBI:7990 KEGG:C00012 Peptide peptides chebi_ontology Peptid peptido peptidos CHEBI:16670 peptide Peptide KEGG_COMPOUND peptides IUPAC Peptid ChEBI peptido ChEBI peptidos ChEBI +1 C8H12NO3 InChI=1S/C8H11NO3/c9-4-8(12)5-1-2-6(10)7(11)3-5/h1-3,8,10-12H,4,9H2/p+1 SFLSHLFXELFNJZ-UHFFFAOYSA-O 170.187 170.08117 C1=CC(=CC(=C1O)O)C(C[NH3+])O chebi_ontology noradrenaline CHEBI:166902 noradrenaline(1+) noradrenaline UniProt Any oligosaccharide, polysaccharide or their derivatives consisting of monosaccharides or monosaccharide derivatives linked by glycosidic bonds. See also http://www.ontobee.org/ontology/GNO?iri=http://purl.obolibrary.org/obo/GNO_00000001. chebi_ontology glycans CHEBI:167559 glycan glycans ChEBI An aminoalkylindole consisting of indole having a 2-aminoethyl group at the 3-position. 0 C10H12N2 InChI=1S/C10H12N2/c11-6-5-8-7-12-10-4-2-1-3-9(8)10/h1-4,7,12H,5-6,11H2 APJYDQYYACXCRM-UHFFFAOYSA-N 160.21570 160.10005 NCCc1c[nH]c2ccccc12 CHEBI:15274 CHEBI:27161 CHEBI:46157 CHEBI:9767 Beilstein:125513 CAS:61-54-1 DrugBank:DB08653 Gmelin:603448 HMDB:HMDB0000303 KEGG:C00398 KNApSAcK:C00001434 MetaCyc:TRYPTAMINE PDBeChem:TSS PMID:16126914 PMID:22770225 PMID:24345948 PMID:24558969 Reaxys:125513 Wikipedia:Tryptamine 2-(1H-indol-3-yl)ethanamine Tryptamine chebi_ontology 1H-indole-3-ethanamine 2-(1H-INDOL-3-YL)ETHANAMINE 2-(3-indolyl)ethylamine 3-(2-Aminoethyl)indole CHEBI:16765 tryptamine Beilstein:125513 Beilstein CAS:61-54-1 ChemIDplus CAS:61-54-1 KEGG COMPOUND CAS:61-54-1 NIST Chemistry WebBook Gmelin:603448 Gmelin PMID:16126914 Europe PMC PMID:22770225 Europe PMC PMID:24345948 Europe PMC PMID:24558969 Europe PMC Reaxys:125513 Reaxys 2-(1H-indol-3-yl)ethanamine IUPAC Tryptamine KEGG_COMPOUND 1H-indole-3-ethanamine NIST_Chemistry_WebBook 2-(1H-INDOL-3-YL)ETHANAMINE PDBeChem 2-(3-indolyl)ethylamine ChemIDplus 3-(2-Aminoethyl)indole KEGG_COMPOUND A member of the class of acetamides that is acetamide in which one of the hydrogens attached to the nitrogen atom is replaced by a 2-(5-methoxy-1H-indol-3-yl)ethyl group. It is a hormone secreted by the pineal gland in humans. 0 C13H16N2O2 InChI=1S/C13H16N2O2/c1-9(16)14-6-5-10-8-15-13-4-3-11(17-2)7-12(10)13/h3-4,7-8,15H,5-6H2,1-2H3,(H,14,16) DRLFMBDRBRZALE-UHFFFAOYSA-N 232.283 232.12118 C=1C=C(C=C2C(=CNC12)CCNC(=O)C)OC CHEBI:14577 CHEBI:25180 CHEBI:6730 Beilstein:205542 CAS:73-31-4 DrugBank:DB01065 Drug_Central:1672 HMDB:HMDB0001389 KEGG:C01598 KEGG:D08170 LINCS:LSM-4779 MetaCyc:N-ACETYL-5-METHOXY-TRYPTAMINE PDBeChem:ML1 PMID:16678784 PMID:18212404 PMID:18485664 PMID:8290600 Reaxys:205542 Wikipedia:Melatonin Melatonin N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide melatonin chebi_ontology 5-methoxy-N-acetyltryptamine N-Acetyl-5-methoxytryptamine N-[2-(5-methoxyindol-3-yl)ethyl]acetamide melatonine CHEBI:16796 melatonin Beilstein:205542 Beilstein CAS:73-31-4 ChemIDplus CAS:73-31-4 KEGG COMPOUND CAS:73-31-4 NIST Chemistry WebBook Drug_Central:1672 DrugCentral PMID:16678784 Europe PMC PMID:18212404 Europe PMC PMID:18485664 Europe PMC PMID:8290600 Europe PMC Reaxys:205542 Reaxys Melatonin KEGG_COMPOUND N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide IUPAC melatonin UniProt 5-methoxy-N-acetyltryptamine ChemIDplus N-Acetyl-5-methoxytryptamine KEGG_COMPOUND N-[2-(5-methoxyindol-3-yl)ethyl]acetamide NIST_Chemistry_WebBook melatonine ChEBI A gamma-amino acid that is butanoic acid with the amino substituent located at C-4. 0 C4H9NO2 InChI=1S/C4H9NO2/c5-3-1-2-4(6)7/h1-3,5H2,(H,6,7) BTCSSZJGUNDROE-UHFFFAOYSA-N 103.11980 103.06333 NCCCC(O)=O CHEBI:1786 CHEBI:193777 CHEBI:20318 CHEBI:40483 BPDB:2298 Beilstein:906818 CAS:56-12-2 DrugBank:DB02530 Drug_Central:1262 Gmelin:49775 HMDB:HMDB0000112 KEGG:C00334 KEGG:D00058 KNApSAcK:C00001337 LIPID_MAPS_instance:LMFA01100039 MetaCyc:4-AMINO-BUTYRATE PDBeChem:ABU PMID:10630630 PMID:10930630 PMID:16276116 PMID:21614609 PMID:22770225 Reaxys:906818 Wikipedia:Gamma-Aminobutyric_acid 4-aminobutanoic acid gamma-Aminobutyric acid gamma-aminobutyric acid chebi_ontology 4-Aminobutanoic acid 4-Aminobutyric acid 4-aminobutanoic acid 4-aminobutyric acid 4Abu GABA GAMMA-AMINO-BUTANOIC ACID gamma-Aminobuttersaeure gamma-amino-n-butyric acid gamma-aminobutanoic acid omega-aminobutyric acid piperidic acid piperidinic acid CHEBI:16865 gamma-aminobutyric acid CAS:56-12-2 NIST Chemistry WebBook Drug_Central:1262 DrugCentral Gmelin:49775 Gmelin LIPID_MAPS_instance:LMFA01100039 LIPID MAPS PMID:10630630 Europe PMC PMID:10930630 Europe PMC PMID:16276116 Europe PMC PMID:21614609 Europe PMC PMID:22770225 Europe PMC Reaxys:906818 Reaxys 4-aminobutanoic acid IUPAC gamma-Aminobutyric acid KEGG_COMPOUND gamma-aminobutyric acid NIST_Chemistry_WebBook 4-Aminobutanoic acid KEGG_COMPOUND 4-Aminobutyric acid KEGG_COMPOUND 4-aminobutanoic acid ChEBI 4-aminobutyric acid ChEBI 4Abu ChEBI GABA IUPHAR GABA KEGG_COMPOUND GAMMA-AMINO-BUTANOIC ACID PDBeChem gamma-Aminobuttersaeure NIST_Chemistry_WebBook gamma-amino-n-butyric acid NIST_Chemistry_WebBook gamma-aminobutanoic acid NIST_Chemistry_WebBook omega-aminobutyric acid NIST_Chemistry_WebBook piperidic acid ChemIDplus piperidinic acid ChemIDplus Beilstein:906818 Beilstein CAS:56-12-2 ChemIDplus CAS:56-12-2 KEGG COMPOUND A member of the class of biladienes that is a linear tetrapyrrole with the dipyrrole units being of both exovinyl and endovinyl type. A product of heme degradation, it is produced in the reticuloendothelial system by the reduction of biliverdin and transported to the liver as a complex with serum albumin. 0 C33H36N4O6 InChI=1S/C33H36N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h7-8,13-14,34-35H,1-2,9-12,15H2,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b26-13-,27-14- BPYKTIZUTYGOLE-IFADSCNNSA-N 584.66230 584.26348 CC1=C(C=C)\C(NC1=O)=C\c1[nH]c(Cc2[nH]c(\C=C3NC(=O)C(C=C)=C/3C)c(C)c2CCC(O)=O)c(CCC(O)=O)c1C CHEBI:13898 CHEBI:22870 CHEBI:3099 Beilstein:74376 CAS:635-65-4 Gmelin:411033 HMDB:HMDB0000054 KEGG:C00486 KNApSAcK:C00029828 MetaCyc:BILIRUBIN PMID:12799017 PMID:18442622 PMID:23763371 PMID:8605219 PMID:9587403 Reaxys:74376 Wikipedia:Bilirubin 3,18-diethenyl-2,7,13,17-tetramethyl-1,19-dioxo-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid bilirubin chebi_ontology 1,10,19,22,23,24-hexahydro-2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinylbiline-8,12-dipropionic acid 2,17-diethenyl-1,10,19,22,23,24-hexahydro-3,7,13,18-tetramethyl-1,19-dioxo-21H-biline-8,12-dipropanoic acid 2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinyl-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid 8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-3,18-divinylbiladiene-ac-1,19(21H,24H)-dione Bilirubin bilirubin(Z,Z) bilirubin-IXalpha CHEBI:16990 bilirubin IXalpha Beilstein:74376 Beilstein CAS:635-65-4 ChemIDplus CAS:635-65-4 KEGG COMPOUND Gmelin:411033 Gmelin PMID:12799017 Europe PMC PMID:18442622 Europe PMC PMID:23763371 Europe PMC PMID:8605219 Europe PMC PMID:9587403 Europe PMC Reaxys:74376 Reaxys 3,18-diethenyl-2,7,13,17-tetramethyl-1,19-dioxo-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid IUPAC bilirubin IUPAC 1,10,19,22,23,24-hexahydro-2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinylbiline-8,12-dipropionic acid ChemIDplus 2,17-diethenyl-1,10,19,22,23,24-hexahydro-3,7,13,18-tetramethyl-1,19-dioxo-21H-biline-8,12-dipropanoic acid ChemIDplus 2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinyl-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid IUPAC 8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-3,18-divinylbiladiene-ac-1,19(21H,24H)-dione JCBN Bilirubin KEGG_COMPOUND bilirubin(Z,Z) ChEBI bilirubin-IXalpha ChEBI High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. CHEBI:13302 CHEBI:21123 CHEBI:33698 CHEBI:4291 CAS:9007-49-2 KEGG:C00039 Deoxyribonucleic acid deoxyribonucleic acids chebi_ontology (Deoxyribonucleotide)m (Deoxyribonucleotide)n (Deoxyribonucleotide)n+m DNA DNAn DNAn+1 DNS Desoxyribonukleinsaeure deoxyribonucleic acids desoxyribose nucleic acid thymus nucleic acid CHEBI:16991 deoxyribonucleic acid CAS:9007-49-2 ChemIDplus CAS:9007-49-2 KEGG COMPOUND Deoxyribonucleic acid KEGG_COMPOUND deoxyribonucleic acids IUPAC (Deoxyribonucleotide)m KEGG_COMPOUND (Deoxyribonucleotide)n KEGG_COMPOUND (Deoxyribonucleotide)n+m KEGG_COMPOUND DNA IUPAC DNA KEGG_COMPOUND DNAn KEGG_COMPOUND DNAn+1 KEGG_COMPOUND DNS ChEBI Desoxyribonukleinsaeure ChEBI deoxyribonucleic acids ChEBI desoxyribose nucleic acid ChemIDplus thymus nucleic acid ChEBI A C21-steroid hormone in which a pregnane skeleton carries oxo substituents at positions 3 and 20 and is unsaturated at C(4)-C(5). As a hormone, it is involved in the female menstrual cycle, pregnancy and embryogenesis of humans and other species. 0 C21H30O2 InChI=1S/C21H30O2/c1-13(22)17-6-7-18-16-5-4-14-12-15(23)8-10-20(14,2)19(16)9-11-21(17,18)3/h12,16-19H,4-11H2,1-3H3/t16-,17+,18-,19-,20-,21+/m0/s1 RJKFOVLPORLFTN-LEKSSAKUSA-N 314.46170 314.22458 [H][C@@]12CCC3=CC(=O)CC[C@]3(C)[C@@]1([H])CC[C@]1(C)[C@H](CC[C@@]21[H])C(C)=O CHEBI:14896 CHEBI:18798 CHEBI:26269 CHEBI:439 CHEBI:45786 CHEBI:8453 Beilstein:1915950 CAS:57-83-0 DrugBank:DB00396 Drug_Central:2279 Gmelin:708590 HMDB:HMDB0001830 KEGG:C00410 KEGG:D00066 MetaCyc:PROGESTERONE PDBeChem:STR PMID:10438974 PMID:9506942 Reaxys:1915950 Wikipedia:Progesterone PROGESTERONE Progesterone pregn-4-ene-3,20-dione progesterone chebi_ontology (S)-4-Pregnene-3,20-dione (S)-Pregn-4-en-3,20-dione (S)-Progesterone 17alpha-progesterone 4-Pregnene-3,20-dione Agolutin Akrolutin Crinone Delta(4)-pregnene-3,20-dione Gelbkoerperhormon Progesteron corpus luteum hormone luteohormone CHEBI:17026 progesterone Beilstein:1915950 Beilstein CAS:57-83-0 ChemIDplus CAS:57-83-0 KEGG COMPOUND CAS:57-83-0 NIST Chemistry WebBook Drug_Central:2279 DrugCentral Gmelin:708590 Gmelin PMID:10438974 Europe PMC PMID:9506942 Europe PMC Reaxys:1915950 Reaxys PROGESTERONE PDBeChem Progesterone KEGG_COMPOUND pregn-4-ene-3,20-dione IUPAC progesterone UniProt (S)-4-Pregnene-3,20-dione KEGG_COMPOUND (S)-Pregn-4-en-3,20-dione KEGG_COMPOUND (S)-Progesterone KEGG_COMPOUND 17alpha-progesterone NIST_Chemistry_WebBook 4-Pregnene-3,20-dione KEGG_COMPOUND Agolutin NIST_Chemistry_WebBook Akrolutin ChEBI Crinone ChemIDplus Delta(4)-pregnene-3,20-dione ChEBI Gelbkoerperhormon ChEBI Progesteron ChEBI corpus luteum hormone ChemIDplus luteohormone ChemIDplus A compound in which a carbonyl group is bonded to two carbon atoms: R2C=O (neither R may be H). 0 COR2 28.010 27.99491 [*]C([*])=O CHEBI:13427 CHEBI:13646 CHEBI:24974 CHEBI:6127 CHEBI:8742 KEGG:C01450 Wikipedia:Ketone Ketone ketones chebi_ontology Keton R-CO-R' a ketone cetone ketones CHEBI:17087 ketone Ketone KEGG_COMPOUND ketones IUPAC Keton ChEBI R-CO-R' KEGG_COMPOUND a ketone UniProt cetone ChEBI ketones ChEBI A compound in which a carbohydrate component is covalently bound to a protein component. CHEBI:14349 CHEBI:5481 CHEBI:5493 KEGG:C00326 Glycoprotein glycoproteins chebi_ontology Glykoprotein Glykoproteine glicoproteina glicoproteinas glycoproteine glycoproteines CHEBI:17089 glycoprotein Glycoprotein KEGG_COMPOUND glycoproteins IUPAC Glykoprotein ChEBI Glykoproteine ChEBI glicoproteina ChEBI glicoproteinas ChEBI glycoproteine ChEBI glycoproteines ChEBI An aldohexose used as a source of energy and metabolic intermediate. 0 C6H12O6 180.15588 180.06339 CHEBI:14313 CHEBI:24277 CHEBI:33929 CHEBI:5418 CAS:50-99-7 KEGG:C00293 Wikipedia:Glucose Glucose gluco-hexose glucose chebi_ontology DL-glucose Glc Glukose CHEBI:17234 glucose CAS:50-99-7 KEGG COMPOUND Glucose KEGG_COMPOUND gluco-hexose IUPAC glucose IUPAC DL-glucose ChEBI Glc JCBN Glukose ChEBI An androstanoid having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5.. 0 C19H28O2 InChI=1S/C19H28O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h11,14-17,21H,3-10H2,1-2H3/t14-,15-,16-,17-,18-,19-/m0/s1 MUMGGOZAMZWBJJ-DYKIIFRCSA-N 288.42440 288.20893 [H][C@@]12CCC3=CC(=O)CC[C@]3(C)[C@@]1([H])CC[C@]1(C)[C@@H](O)CC[C@@]21[H] CHEBI:15214 CHEBI:26883 CHEBI:45798 CHEBI:9461 Beilstein:1915399 Beilstein:3653705 CAS:58-22-0 DrugBank:DB00624 Drug_Central:2607 Gmelin:538843 HMDB:HMDB0000234 KEGG:C00535 KEGG:D00075 KNApSAcK:C00003675 LIPID_MAPS_instance:LMST02020002 PDBeChem:TES PMID:10438974 PMID:11786693 PMID:18900503 PMID:24498482 Reaxys:1915399 Wikipedia:Testosterone 17beta-hydroxyandrost-4-en-3-one TESTOSTERONE Testosterone testosterone chebi_ontology 17beta-Hydroxy-4-androsten-3-one 17beta-hydroxy-4-androsten-3-one 4-androsten-17beta-ol-3-one Androderm Testosteron testosterona testosterone testosteronum CHEBI:17347 testosterone Beilstein:1915399 Beilstein Beilstein:3653705 Beilstein CAS:58-22-0 ChemIDplus CAS:58-22-0 KEGG COMPOUND CAS:58-22-0 NIST Chemistry WebBook Drug_Central:2607 DrugCentral Gmelin:538843 Gmelin LIPID_MAPS_instance:LMST02020002 LIPID MAPS PMID:10438974 Europe PMC PMID:11786693 Europe PMC PMID:18900503 Europe PMC PMID:24498482 Europe PMC Reaxys:1915399 Reaxys 17beta-hydroxyandrost-4-en-3-one IUPAC TESTOSTERONE PDBeChem Testosterone KEGG_COMPOUND testosterone UniProt 17beta-Hydroxy-4-androsten-3-one KEGG_COMPOUND 17beta-hydroxy-4-androsten-3-one ChEBI 4-androsten-17beta-ol-3-one NIST_Chemistry_WebBook Androderm ChemIDplus Testosteron ChemIDplus testosterona ChemIDplus testosterone ChemIDplus testosteronum ChemIDplus A compound RC(=O)H, in which a carbonyl group is bonded to one hydrogen atom and to one R group. 0 CHOR 29.01800 29.00274 [H]C([*])=O CHEBI:13432 CHEBI:13753 CHEBI:13805 CHEBI:13806 CHEBI:22291 CHEBI:2554 CHEBI:8750 KEGG:C00071 Aldehyde aldehyde aldehydes chebi_ontology Aldehyd RC(=O)H RCHO aldehido aldehidos aldehydes aldehydum an aldehyde CHEBI:17478 aldehyde Aldehyde KEGG_COMPOUND aldehyde ChEBI aldehyde IUPAC aldehydes IUPAC Aldehyd ChEBI RC(=O)H IUPAC RCHO KEGG_COMPOUND aldehido ChEBI aldehidos ChEBI aldehydes ChEBI aldehydum ChEBI an aldehyde UniProt The carbon oxoanion resulting from the removal of a proton from carbonic acid. -1 CHO3 InChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4)/p-1 BVKZGUZCCUSVTD-UHFFFAOYSA-M 61.01684 60.99312 OC([O-])=O CHEBI:13363 CHEBI:22863 CHEBI:40961 CHEBI:5589 Beilstein:3903504 CAS:71-52-3 Gmelin:49249 HMDB:HMDB0000595 KEGG:C00288 MetaCyc:HCO3 PDBeChem:BCT PMID:17215880 PMID:17505962 PMID:18439416 PMID:28732801 PMID:29150416 PMID:29460248 PMID:29466234 PMID:4208463 Wikipedia:Bicarbonate Hydrogencarbonate hydrogen(trioxidocarbonate)(1-) hydrogencarbonate hydrogencarbonate(1-) hydrogentrioxocarbonate(1-) hydrogentrioxocarbonate(IV) hydroxidodioxidocarbonate(1-) chebi_ontology Acid carbonate BICARBONATE ION Bicarbonate HCO3(-) HCO3- [CO2(OH)](-) hydrogen carbonate CHEBI:17544 hydrogencarbonate Beilstein:3903504 Beilstein CAS:71-52-3 ChemIDplus Gmelin:49249 Gmelin PMID:17215880 Europe PMC PMID:17505962 Europe PMC PMID:18439416 Europe PMC PMID:28732801 Europe PMC PMID:29150416 Europe PMC PMID:29460248 Europe PMC PMID:29466234 Europe PMC PMID:4208463 Europe PMC Hydrogencarbonate KEGG_COMPOUND hydrogen(trioxidocarbonate)(1-) IUPAC hydrogencarbonate IUPAC hydrogencarbonate UniProt hydrogencarbonate(1-) IUPAC hydrogentrioxocarbonate(1-) IUPAC hydrogentrioxocarbonate(IV) IUPAC hydroxidodioxidocarbonate(1-) IUPAC Acid carbonate KEGG_COMPOUND BICARBONATE ION PDBeChem Bicarbonate KEGG_COMPOUND HCO3(-) IUPAC HCO3- KEGG_COMPOUND [CO2(OH)](-) IUPAC hydrogen carbonate PDBeChem Any compound that supports healthy aging, slows the biological aging process, or extends lifespan. PMID:23372317 PMID:28580190 PMID:30885572 PMID:33144142 PMID:33973253 PMID:34606237 Wikipedia:Geroprotector chebi_ontology anti-aging agent anti-aging agents anti-aging drug anti-aging drugs geroprotective agent geroprotective agents geroprotectors CHEBI:176497 geroprotector PMID:23372317 Europe PMC PMID:28580190 Europe PMC PMID:30885572 Europe PMC PMID:33144142 Europe PMC PMID:33973253 Europe PMC PMID:34606237 Europe PMC anti-aging agent ChEBI anti-aging agents ChEBI anti-aging drug ChEBI anti-aging drugs ChEBI geroprotective agent ChEBI geroprotective agents ChEBI geroprotectors ChEBI 0 C18H24O InChI=1S/C18H24O/c1-18-9-2-3-17(18)16-6-4-12-11-13(19)5-7-14(12)15(16)8-10-18/h5,7,11,15-17,19H,2-4,6,8-10H2,1H3 HJKVPZJVBHWFCQ-UHFFFAOYSA-N 256.389 256.18272 C1=C2C(CCC3C4CCCC4(CCC32)C)=CC(=C1)O KEGG:C02453 MetaCyc:PHENOLIC-STEROID chebi_ontology a phenolic steroid CHEBI:177917 phenolic steroid KEGG:C02453 SUBMITTER MetaCyc:PHENOLIC-STEROID SUBMITTER a phenolic steroid UniProt A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity. CHEBI:14202 CHEBI:4697 KEGG:C01351 Donor chebi_ontology Donator donneur CHEBI:17891 donor Donor KEGG_COMPOUND Donator ChEBI donneur ChEBI A short-chain fatty acid anion that is the conjugate base of butyric acid, obtained by deprotonation of the carboxy group. -1 C4H7O2 InChI=1S/C4H8O2/c1-2-3-4(5)6/h2-3H2,1H3,(H,5,6)/p-1 FERIUCNNQQJTOY-UHFFFAOYSA-M 87.09718 87.04515 CCCC([O-])=O CHEBI:13924 CHEBI:22946 Beilstein:3601060 CAS:461-55-2 Gmelin:324289 KEGG:C00246 MetaCyc:BUTYRIC_ACID PMID:17190852 PMID:7496326 Reaxys:3601060 UM-BBD_compID:c0035 butanoate butyrate chebi_ontology 1-butanoate 1-butyrate 1-propanecarboxylate CH3-[CH2]2-COO(-) butanate butanoate butanoic acid, ion(1-) n-butanoate n-butyrate propanecarboxylate propylformate CHEBI:17968 butyrate Beilstein:3601060 Beilstein CAS:461-55-2 ChemIDplus Gmelin:324289 Gmelin PMID:17190852 Europe PMC PMID:7496326 Europe PMC Reaxys:3601060 Reaxys UM-BBD_compID:c0035 UM-BBD butanoate IUPAC butyrate IUPAC 1-butanoate ChEBI 1-butyrate ChEBI 1-propanecarboxylate ChEBI CH3-[CH2]2-COO(-) IUPAC butanate ChEBI butanoate ChEBI butanoate UniProt butanoic acid, ion(1-) ChemIDplus n-butanoate ChEBI n-butyrate ChemIDplus propanecarboxylate ChEBI propylformate ChEBI 'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. CHEBI:14517 CHEBI:25054 CHEBI:6486 KEGG:C01356 Lipid lipids chebi_ontology CHEBI:18059 lipid Lipid KEGG_COMPOUND lipids IUPAC Any polysaccharide containing a substantial proportion of aminomonosaccharide residues. CHEBI:14361 CHEBI:24398 CHEBI:5495 KEGG:C02545 Wikipedia:Glycosaminoglycan Glycosaminoglycan glycosaminoglycan chebi_ontology Glykosaminoglykan glicosaminoglicano glycosaminoglycane glycosaminoglycans CHEBI:18085 glycosaminoglycan Glycosaminoglycan KEGG_COMPOUND glycosaminoglycan IUPAC Glykosaminoglykan ChEBI glicosaminoglicano IUPAC glycosaminoglycane IUPAC glycosaminoglycans ChEBI Any six-carbon monosaccharide which in its linear form contains either an aldehyde group at position 1 (aldohexose) or a ketone group at position 2 (ketohexose). CHEBI:14399 CHEBI:24590 CHEBI:5709 GlyGen:G70994MS GlyTouCan:G70994MS KEGG:C00738 Hexose chebi_ontology WURCS=2.0/1,1,0/[axxxxh-1x_1-5_2*NCC/3=O]/1/ hexoses CHEBI:18133 hexose Hexose KEGG_COMPOUND WURCS=2.0/1,1,0/[axxxxh-1x_1-5_2*NCC/3=O]/1/ GlyTouCan hexoses ChEBI A biomacromolecule consisting of large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues. CHEBI:14864 CHEBI:26205 CHEBI:8322 KEGG:C00420 Polysaccharide polysaccharides chebi_ontology Glycan Glycane Glykan Glykane glycans polisacarido polisacaridos CHEBI:18154 polysaccharide Polysaccharide KEGG_COMPOUND polysaccharides IUPAC Glycan KEGG_COMPOUND Glycane ChEBI Glykan ChEBI Glykane ChEBI glycans IUPAC polisacarido ChEBI polisacaridos IUPAC An alpha-amino acid that is glutaric acid bearing a single amino substituent at position 2. 0 C5H9NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10) WHUUTDBJXJRKMK-UHFFFAOYSA-N 147.12930 147.05316 NC(CCC(O)=O)C(O)=O CHEBI:24314 CHEBI:5431 Beilstein:1723799 CAS:617-65-2 Gmelin:101971 KEGG:C00302 KEGG:D04341 KNApSAcK:C00001358 KNApSAcK:C00019577 PMID:15739367 PMID:17190852 PMID:24616376 PMID:24984001 Reaxys:1723799 Wikipedia:Glutamic_acid 2-aminopentanedioic acid Glutamic acid glutamic acid chebi_ontology 2-Aminoglutaric acid DL-Glutamic acid DL-Glutaminic acid E Glu Glutamate Glutaminic acid Glutaminsaeure CHEBI:18237 glutamic acid Beilstein:1723799 Beilstein CAS:617-65-2 ChemIDplus CAS:617-65-2 KEGG COMPOUND CAS:617-65-2 NIST Chemistry WebBook Gmelin:101971 Gmelin PMID:15739367 Europe PMC PMID:17190852 Europe PMC PMID:24616376 Europe PMC PMID:24984001 Europe PMC Reaxys:1723799 Reaxys 2-aminopentanedioic acid IUPAC Glutamic acid KEGG_COMPOUND glutamic acid IUPAC 2-Aminoglutaric acid KEGG_COMPOUND DL-Glutamic acid KEGG_DRUG DL-Glutaminic acid KEGG_COMPOUND E ChEBI Glu ChEBI Glutamate KEGG_COMPOUND Glutaminic acid KEGG_COMPOUND Glutaminsaeure ChEBI Catechol in which the hydrogen at position 4 is substituted by a 2-aminoethyl group. 0 C8H11NO2 InChI=1S/C8H11NO2/c9-4-3-6-1-2-7(10)8(11)5-6/h1-2,5,10-11H,3-4,9H2 VYFYYTLLBUKUHU-UHFFFAOYSA-N 153.17840 153.07898 NCCc1ccc(O)c(O)c1 CHEBI:11695 CHEBI:11930 CHEBI:14203 CHEBI:1764 CHEBI:23886 CHEBI:43686 CAS:51-61-6 DrugBank:DB00988 Drug_Central:947 HMDB:HMDB0000073 KEGG:C03758 KEGG:D07870 KNApSAcK:C00001408 LINCS:LSM-4630 MetaCyc:DOPAMINE PMID:10629745 PMID:11149432 PMID:9422813 Reaxys:1072822 Wikipedia:Dopamine 4-(2-aminoethyl)benzene-1,2-diol Dopamine chebi_ontology 2-(3,4-Dihydroxyphenyl)ethylamine 2-(3,4-dihydroxyphenyl)ethylamine 3,4-Dihydroxyphenethylamine 3-Hydroxytyramine 4-(2-Aminoethyl)-1,2-benzenediol 4-(2-Aminoethyl)benzene-1,2-diol 4-(2-aminoethyl)-1,2-benzenediol 4-(2-aminoethyl)catechol 4-(2-aminoethyl)pyrocatechol Deoxyepinephrine Hydroxytyramin dopamina dopamine dopaminum CHEBI:18243 dopamine CAS:51-61-6 ChemIDplus Drug_Central:947 DrugCentral PMID:10629745 Europe PMC PMID:11149432 Europe PMC PMID:9422813 Europe PMC Reaxys:1072822 Reaxys 4-(2-aminoethyl)benzene-1,2-diol IUPAC Dopamine KEGG_COMPOUND 2-(3,4-Dihydroxyphenyl)ethylamine KEGG_COMPOUND 2-(3,4-dihydroxyphenyl)ethylamine ChEBI 3,4-Dihydroxyphenethylamine KEGG_COMPOUND 3-Hydroxytyramine ChemIDplus 4-(2-Aminoethyl)-1,2-benzenediol KEGG_COMPOUND 4-(2-Aminoethyl)benzene-1,2-diol KEGG_COMPOUND 4-(2-aminoethyl)-1,2-benzenediol ChEBI 4-(2-aminoethyl)catechol ChemIDplus 4-(2-aminoethyl)pyrocatechol ChemIDplus Deoxyepinephrine DrugBank Hydroxytyramin DrugBank dopamina ChemIDplus dopamine ChEBI dopaminum ChemIDplus An iron group element atom that has atomic number 26. 0 Fe InChI=1S/Fe XEEYBQQBJWHFJM-UHFFFAOYSA-N 55.84500 55.93494 [Fe] CHEBI:13322 CHEBI:24872 CHEBI:5974 CAS:7439-89-6 DrugBank:DB01592 HMDB:HMDB0015531 KEGG:C00023 Reaxys:4122945 WebElements:Fe iron chebi_ontology 26Fe Eisen Fe Iron fer ferrum hierro iron CHEBI:18248 iron atom CAS:7439-89-6 ChemIDplus CAS:7439-89-6 KEGG COMPOUND CAS:7439-89-6 NIST Chemistry WebBook Reaxys:4122945 Reaxys iron IUPAC 26Fe IUPAC Eisen ChEBI Fe IUPAC Iron KEGG_COMPOUND fer ChEBI ferrum IUPAC hierro ChEBI iron ChEBI That part of DNA or RNA that may be involved in pairing. CHEBI:13873 CHEBI:25598 CHEBI:2995 KEGG:C00701 Wikipedia:Nucleobase chebi_ontology Base nucleobases CHEBI:18282 nucleobase Base KEGG_COMPOUND nucleobases ChEBI A member of the class of imidazoles that is 1H-imidazole substituted at position C-4 by a 2-aminoethyl group. 0 C5H9N3 InChI=1S/C5H9N3/c6-2-1-5-3-7-4-8-5/h3-4H,1-2,6H2,(H,7,8) NTYJJOPFIAHURM-UHFFFAOYSA-N 111.14518 111.07965 NCCc1c[nH]cn1 CHEBI:14401 CHEBI:24596 CHEBI:43187 CHEBI:817 Beilstein:2012 CAS:51-45-6 Drug_Central:1375 Gmelin:2968 HMDB:HMDB0000870 KEGG:C00388 KEGG:D08040 KNApSAcK:C00001414 MetaCyc:HISTAMINE PDBeChem:HSM PMID:16399866 PMID:19547708 PMID:19843401 PMID:22770225 PMID:24101735 Reaxys:2012 Wikipedia:Histamine 2-(1H-imidazol-4-yl)ethanamine HISTAMINE Histamine chebi_ontology 1H-Imidazole-4-ethanamine 2-(4-Imidazolyl)ethylamine CHEBI:18295 histamine Beilstein:2012 Beilstein CAS:51-45-6 ChemIDplus CAS:51-45-6 KEGG COMPOUND CAS:51-45-6 NIST Chemistry WebBook Drug_Central:1375 DrugCentral Gmelin:2968 Gmelin PMID:16399866 Europe PMC PMID:19547708 Europe PMC PMID:19843401 Europe PMC PMID:22770225 Europe PMC PMID:24101735 Europe PMC Reaxys:2012 Reaxys 2-(1H-imidazol-4-yl)ethanamine IUPAC HISTAMINE PDBeChem Histamine KEGG_COMPOUND 1H-Imidazole-4-ethanamine KEGG_COMPOUND 2-(4-Imidazolyl)ethylamine KEGG_COMPOUND An acyclic branched or unbranched hydrocarbon having the general formula CnH2n+2, and therefore consisting entirely of hydrogen atoms and saturated carbon atoms. 0 CH3R 15.035 15.02348 C[*] CHEBI:13435 CHEBI:22317 CHEBI:2576 KEGG:C01371 Alkane alkane alkanes chebi_ontology Alkan RH alcane alcanes alcano alcanos an alkane CHEBI:18310 alkane Alkane KEGG_COMPOUND alkane IUPAC alkanes IUPAC Alkan ChEBI RH KEGG_COMPOUND alcane IUPAC alcanes IUPAC alcano IUPAC alcanos IUPAC an alkane UniProt A phosphate ion that is the conjugate base of hydrogenphosphate. -3 O4P InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3 NBIIXXVUZAFLBC-UHFFFAOYSA-K 94.97136 94.95507 [O-]P([O-])([O-])=O CHEBI:14791 CHEBI:45024 CHEBI:7793 Beilstein:3903772 CAS:14265-44-2 Gmelin:1997 KEGG:C00009 PDBeChem:PO4 Reaxys:3903772 phosphate tetraoxidophosphate(3-) tetraoxophosphate(3-) tetraoxophosphate(V) chebi_ontology Orthophosphate PHOSPHATE ION PO4(3-) Phosphate [PO4](3-) CHEBI:18367 phosphate(3-) Beilstein:3903772 Beilstein CAS:14265-44-2 ChemIDplus CAS:14265-44-2 KEGG COMPOUND Gmelin:1997 Gmelin PDBeChem:PO4 ChEBI Reaxys:3903772 Reaxys phosphate IUPAC tetraoxidophosphate(3-) IUPAC tetraoxophosphate(3-) IUPAC tetraoxophosphate(V) IUPAC Orthophosphate KEGG_COMPOUND PHOSPHATE ION PDBeChem PO4(3-) IUPAC Phosphate KEGG_COMPOUND [PO4](3-) IUPAC -1 O2 InChI=1S/HO2/c1-2/h1H/p-1 OUUQCZGPVNCOIJ-UHFFFAOYSA-M 31.99880 31.98983 [O][O-] CHEBI:15143 CHEBI:26839 CHEBI:7710 CAS:11062-77-4 Gmelin:487 KEGG:C00704 dioxidanidyl dioxide(.1-) superoxide chebi_ontology (O2)(.-) Hyperoxid O2(-) O2(.-) O2- O2.- Superoxide anion dioxide(1-) hyperoxide superoxide anion radical superoxide radical superoxide radical anion superoxyde CHEBI:18421 superoxide CAS:11062-77-4 ChemIDplus CAS:11062-77-4 NIST Chemistry WebBook Gmelin:487 Gmelin dioxidanidyl IUPAC dioxide(.1-) IUPAC superoxide IUPAC superoxide UniProt (O2)(.-) IUPAC Hyperoxid ChEBI O2(-) IUPAC O2(.-) IUPAC O2- KEGG_COMPOUND O2.- KEGG_COMPOUND Superoxide anion KEGG_COMPOUND dioxide(1-) IUPAC hyperoxide IUPAC superoxide anion radical ChemIDplus superoxide radical ChEBI superoxide radical anion ChEBI superoxyde ChEBI 0 C24H42 InChI=1S/C24H42/c1-5-8-17(2)20-12-13-21-19-11-10-18-9-6-7-15-23(18,3)22(19)14-16-24(20,21)4/h17-22H,5-16H2,1-4H3/t17-,18+,19+,20-,21+,22+,23+,24-/m1/s1 QSHQKIURKJITMZ-OBUPQJQESA-N 330.59028 330.32865 [H][C@@]12CCCC[C@]1(C)[C@@]1([H])CC[C@]3(C)[C@]([H])(CC[C@@]3([H])[C@]1([H])CC2)[C@H](C)CCC Beilstein:2048472 5beta-cholane chebi_ontology CHEBI:20664 5beta-cholane Beilstein:2048472 Beilstein 5beta-cholane IUPAC Compounds with the general formula RNHC(=O)CH3. chebi_ontology CHEBI:22160 acetamides An organic group formed by removing one or more hydroxy groups from an oxoacid that has the general structure RkE(=O)l(OH)m (l =/= 0). Although the term is almost always applied to organic compounds, with carboxylic acid as the oxoacid, acyl groups can in principle be derived from other types of acids such as sulfonic acids or phosphonic acids. acyl group alkanoyl chebi_ontology acyl groups alkanoyl group groupe acyle CHEBI:22221 acyl group acyl group IUPAC alkanoyl IUPAC acyl groups ChEBI alkanoyl group ChEBI groupe acyle IUPAC alkaline earth metals chebi_ontology Erdalkalimetall Erdalkalimetalle alkaline earth metal alkaline-earth metal alkaline-earth metals metal alcalino-terreux metal alcalinoterreo metales alcalinoterreos metaux alcalino-terreux CHEBI:22313 alkaline earth metal atom alkaline earth metals IUPAC Erdalkalimetall ChEBI Erdalkalimetalle ChEBI alkaline earth metal ChEBI alkaline-earth metal ChEBI alkaline-earth metals ChEBI metal alcalino-terreux ChEBI metal alcalinoterreo ChEBI metales alcalinoterreos ChEBI metaux alcalino-terreux ChEBI alkali metals chebi_ontology Alkalimetall Alkalimetalle alkali metal metal alcalin metal alcalino metales alcalinos metaux alcalins CHEBI:22314 alkali metal atom alkali metals IUPAC Alkalimetall ChEBI Alkalimetalle ChEBI alkali metal ChEBI metal alcalin ChEBI metal alcalino ChEBI metales alcalinos ChEBI metaux alcalins ChEBI Any of the naturally occurring, basic nitrogen compounds (mostly heterocyclic) occurring mostly in the plant kingdom, but also found in bacteria, fungi, and animals. By extension, certain neutral compounds biogenetically related to basic alkaloids are also classed as alkaloids. Amino acids, peptides, proteins, nucleotides, nucleic acids, amino sugars and antibiotics are not normally regarded as alkaloids. Compounds in which the nitrogen is exocyclic (dopamine, mescaline, serotonin, etc.) are usually classed as amines rather than alkaloids. Wikipedia:Alkaloid Alkaloid alkaloids chebi_ontology Alkaloide alcaloide alcaloides CHEBI:22315 alkaloid Alkaloid ChEBI alkaloids IUPAC Alkaloide ChEBI alcaloide ChEBI alcaloides ChEBI chebi_ontology aminoglycans CHEBI:22506 aminoglycan aminoglycans ChEBI A monoatomic or polyatomic species having one or more elementary charges of the electron. Anion anion chebi_ontology Anionen aniones anions CHEBI:22563 anion Anion ChEBI anion ChEBI anion IUPAC Anionen ChEBI aniones ChEBI anions IUPAC A substance that opposes oxidation or inhibits reactions brought about by dioxygen or peroxides. chebi_ontology antioxidants antioxydant antoxidant CHEBI:22586 antioxidant antioxidants ChEBI antioxydant ChEBI antoxidant ChEBI A molecular entity having an available pair of electrons capable of forming a covalent bond with a hydron (Bronsted base) or with the vacant orbital of some other molecular entity (Lewis base). KEGG:C00701 Base base chebi_ontology Base1 Base2 Basen Nucleobase bases CHEBI:22695 base Base ChEBI base ChEBI base IUPAC Base1 KEGG_COMPOUND Base2 KEGG_COMPOUND Basen ChEBI Nucleobase KEGG_COMPOUND bases ChEBI chebi_ontology benzopyrroles CHEBI:22728 benzopyrrole benzopyrroles ChEBI A sodium salt of the conjugate of any bile acid with either glycine or taurine. KEGG:C01558 chebi_ontology Bile acid bile salts CHEBI:22868 bile salt Bile acid KEGG_COMPOUND bile salts ChEBI 0 Ca InChI=1S/Ca OYPRJOBELJOOCE-UHFFFAOYSA-N 40.07800 39.96259 [Ca] CAS:7440-70-2 DrugBank:DB01373 KEGG:C00076 WebElements:Ca calcium chebi_ontology 20Ca Ca Calcium Kalzium calcio calcium CHEBI:22984 calcium atom CAS:7440-70-2 ChemIDplus calcium IUPAC 20Ca IUPAC Ca IUPAC Calcium KEGG_COMPOUND Kalzium ChEBI calcio ChEBI calcium ChEBI calcium molecular entity chebi_ontology calcium compounds calcium molecular entities CHEBI:22985 calcium molecular entity calcium molecular entity ChEBI calcium compounds ChEBI calcium molecular entities ChEBI The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid. 0 CH2NO 44.03272 44.01364 *C(N)=O PMID:24168430 carbamoyl chebi_ontology -C(O)NH2 -CONH2 aminocarbonyl carbamyl carbamyl group carboxamide CHEBI:23004 carbamoyl group PMID:24168430 Europe PMC carbamoyl IUPAC -C(O)NH2 ChEBI -CONH2 IUPAC aminocarbonyl IUPAC carbamyl ChEBI carbamyl group ChEBI carboxamide IUPAC 0 CO 28.01010 27.99491 O=C(*)* carbonyl carbonyl group chebi_ontology >C=O CHEBI:23019 carbonyl group carbonyl IUPAC carbonyl group ChEBI carbonyl group UniProt >C=O IUPAC An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group). Wikipedia:Cofactor_(biochemistry) cofactor cofactors chebi_ontology CHEBI:23357 cofactor cofactor IUPAC cofactors IUPAC Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity chebi_ontology entidad molecular entidades moleculares entite moleculaire molecular entities molekulare Entitaet CHEBI:23367 molecular entity molecular entity IUPAC entidad molecular IUPAC entidades moleculares IUPAC entite moleculaire IUPAC molecular entities IUPAC molekulare Entitaet ChEBI chebi_ontology Cyclopeptid Zyklopeptid cyclic peptides peptide cyclique peptido ciclico CHEBI:23449 cyclic peptide Cyclopeptid ChEBI Zyklopeptid ChEBI cyclic peptides ChEBI peptide cyclique IUPAC peptido ciclico IUPAC An azole that is either one of a pair of heterocyclic organic compounds comprising three carbon atoms and two nitrogen atoms arranged in a ring. chebi_ontology diazoles CHEBI:23677 diazole diazoles ChEBI Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances. chebi_ontology drugs medicine CHEBI:23888 drug drugs ChEB