A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO. Ontology of Biological Attributes (OBA) TermGenie 1.0 13:11:2015 10:21 oba 1.2 foaf-homepage "http://wiki.geneontology.org/index.php/Extensions/x-attribute" xsd:anyURL cjmungall 2021-12-03 definition IAO:0000116 uberon editor_note true editor_note editor note editor note term replaced by term replaced by If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive http://purl.org/dc/elements/1.1/contributor oba uberon dc-contributor http://purl.org/dc/elements/1.1/contributor true dc-contributor contributor oba http://purl.org/pav/providedBy true has_broad_synonym database_cross_reference has_exact_synonym has_obo_format_version has_obo_namespace has_related_synonym shorthand is part of is part of my brain is part of my body (continuant parthood, two material entities) 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) 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) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole 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. 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/ 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/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. 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 part_of BFO:0000050 external oba protein quality uberon part_of part_of part of part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of has part has part my body has part my brain (continuant parthood, two material entities) 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) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) this year has part this day (occurrent parthood) Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. a core relation that holds between a whole and its part 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. 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/ 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/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. 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 has_part BFO:0000051 chebi_ontology external oba protein quality uberon has_part false has_part We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. has part has part has_part Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. PATOC:CJM preceded by X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 is preceded by takes place after uberon preceded_by preceded_by preceded by preceded by preceded_by is preceded by SIO:000249 takes place after Allen:precedes precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 uberon precedes precedes precedes precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in BFO:0000066 external oba 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 extends through an organism from head end to opposite end of body or tail. 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 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 extends through an organism from head end to opposite end of body or tail. BSPO:cjm 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 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). 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 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). BSPO:cjm 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). 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 extends through an organism from back (e.g. spinal column) to front (e.g. belly). 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 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 extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:cjm 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). 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 extends through an organism from head end to opposite end of body or tail. 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 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 extends through an organism from head end to opposite end of body or tail. BSPO:cjm 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. 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. 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 proximal_to x proximal to y iff x is closer to the point of attachment with the body than y. BSPO:cjm x proximal_to y iff x is closer to the point of attachment with the body than y. 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 extends through an organism from back (e.g. spinal column) to front (e.g. belly). 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 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 extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:cjm 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). 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 Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:0000107 uberon deep_to deep_to deep to deep_to Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:cjm Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:0000108 uberon superficial_to superficial_to superficial to superficial_to Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:cjm X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion. 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 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 two left and right portions, X is part of the left portion. BSPO:PATO_mtg_2009 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 two left and right portions, X is part of the right portion. 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 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 two left and right portions, X is part of the right 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: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. 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 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 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. 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 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 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. x in proximal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the proximal portion. BSPO:0000124 uberon in_proximal_side_of 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 in proximal side of y <=> if y is subdivided into two proximal and distal portions, y 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. x in distal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the distal portion. BSPO:0000125 uberon in_distal_side_of 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 distal side of y <=> if y is subdivided into two proximal and distal portions, y 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 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 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 UBERON:cjm 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 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 proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y 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 proximalmost_part_of X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y https://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 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. x immediately deep to y iff x deep_to y and x is contiguous with y. BSPO:0001107 uberon immediately_deep_to immediately_deep_to immediately deep to immediately_deep_to This relation holds when both the deep_to and ajdacent_to relationship similarly hold. This relation holds when both the deep_to and ajdacent_to relationship similarly hold. http://orcid.org/0000-0002-6601-2165 x immediately deep to y iff x deep_to y and x is contiguous with y. BSPO:curators X distalmost part of Y <=> X is in distal side of Y and X is adjacent to the distal boundary of Y 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 distalmost_part_of X distalmost part of Y <=> X is in distal side of Y and X is adjacent to the distal boundary of Y https://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 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 X intersects median plane of iff X crosses the midine plane of Y. 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 intersects_midsagittal_plane_of x immediately superficial to y iff x superficial to y and x is contiguous with y. BSPO:0015014 uberon immediately_superficial_to immediately_superficial_to immediately superficial to immediately_superficial_to x immediately superficial to y iff x superficial to y and x is contiguous with y. BSPO:curators X dorsal side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the dorsal portion. BSPO:0015101 uberon in_dorsal_side_of in_dorsal_side_of in dorsal side of in_dorsal_side_of X dorsal side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the dorsal portion. BSPO:cjm inheres in this fragility inheres in this vase this fragility is a characteristic of this vase this red color inheres in this apple 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. a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in RO:0000052 oba inheres_in 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 inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of RO:0000053 uberon bearer_of bearer_of bearer of bearer of 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 uberon 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 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 this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role RO:0000087 chebi_ontology has_role false false has_role 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 a relation between two independent continuants, the location and the target, in which the target is entirely within the location RO:0001015 uberon location_of location_of location of location_of contained in RO:0001019 uberon contains contains contains contains a relation between two independent continuants, the target and the location, in which the target is entirely within the location 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. a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity RO:0002000 uberon boundary_of boundary_of 2D boundary of a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity RO:0002002 uberon has_boundary has_boundary has 2D boundary has boundary RO:0002005 nerve supply uberon innervated_by innervated_by http://code.google.com/p/obo-relations/issues/detail?id=6 innervated_by nerve supply FMA:85999 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 RO:0002007 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. bounding layer of bounding layer 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 has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. dos 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. dos 2017-05-24T09:49:21Z has component process 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 before or simultaneous with Relation between occurrents, shares start and end boundaries. RO:0002082 coincides_with is_equal_to uberon simultaneous_with 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 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 X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes A overlaps B if they share some part in common. x overlaps y if and only if there exists some z such that x has part z and z part of y x overlaps y iff they have some part in common. BFO_0000051 some (BFO_0000050 some ?Y) http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 uberon overlaps overlaps overlaps overlaps x overlaps y iff they have some part in common. BSPO:cjm true 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. RO:0002134 uberon innervates innervates http://code.google.com/p/obo-relations/issues/detail?id=6 innervates X continuous_with Y if and only if X and Y share a fiat boundary. RO:0002150 uberon continuous_with continuous_with continuous with continuous_with 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. RO:0002160 uberon 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. RO:0002162 uberon in_taxon in_taxon in taxon 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 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. 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 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 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. 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. 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. RO:0002178 arterial supply of uberon supplies supplies source: FMA 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. 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 uberon has_component 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 Chris Mungall David Osumi-Sutherland David Osumi-Sutherland Melissa Haendel Terry Meehan Terry Meehan RO:0002202 uberon develops_from develops_from This is the transitive form of the develops from relation develops from 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 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. RO:0002207 uberon directly_develops_from directly_develops_from directly develops from inverse of directly develops from 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_0000053 some (RO_0000054 only ?Y) RO:0002215 protein uberon capable_of false capable_of capable of capable of capable_of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) RO:0002216 uberon capable_of_part_of capable_of_part_of capable of part of capable of part of true 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 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 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 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 RO:0002220 uberon adjacent_to adjacent_to adjacent to adjacent to adjacent_to inverse of surrounded by inverse of surrounded_by RO:0002221 uberon surrounds surrounds surrounds surrounds inverse of surrounded_by 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 RO:0002223 uberon starts starts starts starts Relation between occurrents, shares a start boundary with. Allen:starts Relation between occurrents, shares a start boundary with. Allen:starts https://orcid.org/0000-0002-6601-2165 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. RO:0002224 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 RO:0002225 uberon 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 RO:0002226 uberon develops_in develops_in This relation take from EHDAA2 - precise semantics yet to be defined develops in Relation between occurrents, shares an end boundary with. inverse of ends with RO:0002229 finishes uberon ends ends ends ends Relation between occurrents, shares an end boundary with. Allen:starts ZFS:finishes 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. RO:0002230 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 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 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 has input p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. 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 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 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 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 RO:0002285 uberon developmentally_replaces developmentally_replaces developmentally replaces developmentally_replaces Inverse of developmentally preceded by Chris Mungall developmentally succeeded by part of developmental precursor of cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of Because part_of is transitive, inheres in is a sub-relation of inheres in part of Chris Mungall inheres in part of RO:0002314 oba inheres_in_part_of inheres_in_part_of characteristic of part of inheres in part of true A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 uberon functionally_related_to functionally_related_to functionally related to 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 true c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in enables part of involved in inverse of enables Chris Mungall enabled by inverse of regulates Chris Mungall regulated by (processual) regulated by inverse of negatively regulates Chris Mungall negatively regulated by inverse of positively regulates Chris Mungall positively regulated by is member of is a mereological relation between a item and a collection. RO:0002350 uberon member_of member_of member of member of has member is a mereological relation between a collection and an item. 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 inverse of has output RO:0002353 uberon output_of output_of output of output 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 RO:0002371 uberon attaches_to attaches_to attached to attaches_to 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. 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 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. in branching relationship with 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. RO:0002376 uberon drains into tributary_of tributary_of tributary of tributary_of drains into dbpowl:drainsTo x spatially_coextensive_with y if and inly if x and y have the same location 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 RO:0002380 uberon branching_part_of branching_part_of branching part of branching_part_of 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 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 inverse of upstream of Chris Mungall causally downstream of Chris Mungall immediately causally downstream of This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall immediately causally upstream of p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) affects causally upstream of or within inverse of causally upstream of or within Chris Mungall causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p Chris Mungall involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p Chris Mungall involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. Chris Mungall executes activity in enables activity in is active in 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. 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/MI_0914 http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ http://purl.obolibrary.org/obo/MI_0914 https://github.com/oborel/obo-relations/wiki/InteractionRelations An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. Chris Mungall binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 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) 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 RO:0002473 uberon RO:0002473 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 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). RO:0002488 begins_to_exist_during uberon RO:0002488 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. 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). 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. 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)) 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) RO:0002491 uberon existence_starts_and_ends_during existence_starts_and_ends_during 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). RO:0002492 ceases_to_exist_during uberon RO:0002492 existence_ends_during existence_ends_during 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. 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). RO:0002493 uberon existence_ends_with existence_ends_with existence ends with Relation between continuant and occurrent, such that c ceases to exist at the end of p. 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 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 RO:0002495 direct_transformation_of immediately transforms from uberon immediate_transformation_of immediate_transformation_of immediate transformation of direct_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). RO:0002496 uberon existence_starts_during_or_after existence_starts_during_or_after 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. RO:0002497 uberon existence_ends_during_or_before existence_ends_during_or_before 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 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. 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. 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/ https://github.com/oborel/obo-relations/wiki/InteractionRelations Chris Mungall molecular interaction relation helper property 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. biomechanically related to inverse of branching part of 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. 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 RO:0002572 uberon luminal_space_of luminal_space_of luminal space of inverse of has skeleton 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 A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. directly positively regulates (process to process) directly positively regulates Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. directly negatively regulates (process to process) directly negatively regulates a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. RO:0003000 uberon produces produces produces produces a produced_by b iff some process that occurs_in b has_output a. RO:0003001 uberon produced_by produced_by produced by produced by produced_by Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z enables subfunction cjm 2018-01-26T23:49:30Z acts upstream of or within, positive effect cjm 2018-01-26T23:49:51Z acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive cjm 2018-01-26T23:53:14Z acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative cjm 2018-01-26T23:53:22Z acts upstream of, negative effect cjm 2018-03-13T23:55:05Z causally upstream of or within, negative effect cjm 2018-03-13T23:55:19Z causally upstream of or within, positive effect The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. Vasundra Touré regulates activity of chebi_ontology has_functional_parent false false has functional parent chebi_ontology has_parent_hydride false false has parent hydride chebi_ontology is_conjugate_acid_of true false is conjugate acid of chebi_ontology is_conjugate_base_of true false is conjugate base of chebi_ontology is_substituent_group_from false false is substituent group from by_means has_participant in_response_to is_about quality correlates_with correlates_with q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality decreased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. decreased_in_magnitude_relative_to q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality different_in_magnitude_relative_to different_in_magnitude_relative_to q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. quality has_cross_section Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. has_cross_section s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. PATOC:CJM q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. quality reciprocal_of There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. reciprocal_of q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. PATOC:CJM quality towards Relation binding a relational quality or disposition to the relevant type of entity. towards 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. 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. 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 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. 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. 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 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 entity 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 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 object object 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 material entity anatomical entity connected anatomical structure material anatomical entity biological 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 vitamin A 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 Any organic compound having an initial boiling point less than or equal to 250 degreeC (482 degreeF) measured at a standard atmospheric pressure of 101.3 kPa. Wikipedia:Volatile_organic_compound chebi_ontology VOC VOCs volatile organic compounds CHEBI:134179 volatile organic compound VOC ChEBI VOCs ChEBI volatile organic compounds ChEBI apoprotein Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa). Wikipedia:https://en.wikipedia.org/wiki/Gas chebi_ontology gas molecular entities gaseous molecular entities gaseous molecular entity CHEBI:138675 gas molecular entity gas molecular entities ChEBI gaseous molecular entities ChEBI gaseous molecular entity ChEBI A 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 biopterin 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 aldose 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 polypeptide sterol long-chain fatty acid halide anion cholesterol 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 sulfate urea -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 primary alcohol that is ethane in which one of the hydrogens is substituted by a hydroxy group. 0 C2H6O InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 LFQSCWFLJHTTHZ-UHFFFAOYSA-N 46.06844 46.04186 CCO CHEBI:14222 CHEBI:23978 CHEBI:30878 CHEBI:30880 CHEBI:42377 CHEBI:44594 CHEBI:4879 Beilstein:1718733 CAS:64-17-5 DrugBank:DB00898 Drug_Central:1076 Gmelin:787 HMDB:HMDB0000108 KEGG:C00469 KEGG:D00068 KEGG:D06542 KNApSAcK:C00019560 MetaCyc:ETOH MolBase:858 MolBase:859 PDBeChem:EOH PMID:11046114 PMID:11090978 PMID:11198720 PMID:11200745 PMID:11262320 PMID:11303910 PMID:11333032 PMID:11505026 PMID:11590970 PMID:11728426 PMID:11750186 PMID:11754521 PMID:11810019 PMID:11826039 PMID:11981228 PMID:12824058 PMID:12829422 PMID:12888778 PMID:12946583 PMID:14674846 PMID:15019421 PMID:15239123 PMID:15285839 PMID:15464411 PMID:15465973 PMID:15749123 PMID:15900217 PMID:15902919 PMID:16084479 PMID:16133132 PMID:16352430 PMID:16390872 PMID:16737463 PMID:16891664 PMID:16934862 PMID:17043811 PMID:17190852 PMID:17663926 PMID:17687877 PMID:18095657 PMID:18249266 PMID:18320157 PMID:18347649 PMID:18408978 PMID:18411066 PMID:18456322 PMID:18513832 PMID:18922656 PMID:18925476 PMID:19280886 PMID:19359288 PMID:19384566 PMID:19458312 PMID:19851413 PMID:19901811 PMID:21600756 PMID:21762181 PMID:21881875 PMID:21967628 PMID:22019193 PMID:22222864 PMID:22261437 PMID:22286266 PMID:22306018 PMID:22331491 PMID:22336593 PPDB:1373 Reaxys:1718733 UM-BBD_compID:c0038 Wikipedia:Ethanol ETHANOL Ethanol ethanol chebi_ontology 1-hydroxyethane Aethanol Aethylalkohol Alkohol C2H5OH Dehydrated ethanol EtOH Ethyl alcohol Methylcarbinol [CH2Me(OH)] [OEtH] alcohol alcohol etilico alcool ethylique etanol hydroxyethane spiritus vini CHEBI:16236 ethanol Beilstein:1718733 Beilstein CAS:64-17-5 ChemIDplus CAS:64-17-5 KEGG COMPOUND CAS:64-17-5 NIST Chemistry WebBook Drug_Central:1076 DrugCentral Gmelin:787 Gmelin PMID:11046114 Europe PMC PMID:11090978 Europe PMC PMID:11198720 Europe PMC PMID:11200745 Europe PMC PMID:11262320 Europe PMC PMID:11303910 Europe PMC PMID:11333032 Europe PMC PMID:11505026 Europe PMC PMID:11590970 Europe PMC PMID:11728426 Europe PMC PMID:11750186 Europe PMC PMID:11754521 Europe PMC PMID:11810019 Europe PMC PMID:11826039 Europe PMC PMID:11981228 Europe PMC PMID:12824058 Europe PMC PMID:12829422 Europe PMC PMID:12888778 Europe PMC PMID:12946583 Europe PMC PMID:14674846 Europe PMC PMID:15019421 Europe PMC PMID:15239123 Europe PMC PMID:15285839 Europe PMC PMID:15464411 Europe PMC PMID:15465973 Europe PMC PMID:15749123 Europe PMC PMID:15900217 Europe PMC PMID:15902919 Europe PMC PMID:16084479 Europe PMC PMID:16133132 Europe PMC PMID:16352430 Europe PMC PMID:16390872 Europe PMC PMID:16737463 Europe PMC PMID:16891664 Europe PMC PMID:16934862 Europe PMC PMID:17043811 Europe PMC PMID:17190852 Europe PMC PMID:17663926 Europe PMC PMID:17687877 Europe PMC PMID:18095657 Europe PMC PMID:18249266 Europe PMC PMID:18320157 Europe PMC PMID:18347649 Europe PMC PMID:18408978 Europe PMC PMID:18411066 Europe PMC PMID:18456322 Europe PMC PMID:18513832 Europe PMC PMID:18922656 Europe PMC PMID:18925476 Europe PMC PMID:19280886 Europe PMC PMID:19359288 Europe PMC PMID:19384566 Europe PMC PMID:19458312 Europe PMC PMID:19851413 Europe PMC PMID:19901811 Europe PMC PMID:21600756 Europe PMC PMID:21762181 Europe PMC PMID:21881875 Europe PMC PMID:21967628 Europe PMC PMID:22019193 Europe PMC PMID:22222864 Europe PMC PMID:22261437 Europe PMC PMID:22286266 Europe PMC PMID:22306018 Europe PMC PMID:22331491 Europe PMC PMID:22336593 Europe PMC Reaxys:1718733 Reaxys UM-BBD_compID:c0038 UM-BBD ETHANOL PDBeChem Ethanol KEGG_COMPOUND ethanol ChEBI ethanol IUPAC ethanol UniProt 1-hydroxyethane ChemIDplus Aethanol ChemIDplus Aethylalkohol ChemIDplus Alkohol ChemIDplus C2H5OH ChEBI Dehydrated ethanol KEGG_DRUG EtOH ChemIDplus Ethyl alcohol KEGG_COMPOUND Methylcarbinol KEGG_COMPOUND [CH2Me(OH)] MolBase [OEtH] MolBase alcohol NIST_Chemistry_WebBook alcohol etilico ChEBI alcool ethylique ChemIDplus etanol ChEBI hydroxyethane ChemIDplus spiritus vini ChEBI phospholipid 17beta-hydroxy-5alpha-androstan-3-one hyaluronic acid sphingosine carbon dioxide carbohydrate peptide creatinine glycan corticosterone glutathione creatine bilirubin progesterone ketone carnitine homocysteine glucose testosterone monoglyceride alditol hydrogencarbonate beta-carotene cortisol lactose glycerol ceramide The primary alcohol that is the simplest aliphatic alcohol, comprising a methyl and an alcohol group. 0 CH4O InChI=1S/CH4O/c1-2/h2H,1H3 OKKJLVBELUTLKV-UHFFFAOYSA-N 32.04186 32.02621 CO CHEBI:14588 CHEBI:25227 CHEBI:44080 CHEBI:44553 CHEBI:6816 Beilstein:1098229 CAS:67-56-1 Gmelin:449 HMDB:HMDB0001875 KEGG:C00132 KEGG:D02309 MetaCyc:METOH PDBeChem:MOH PMID:11141607 PMID:11430978 PMID:11489599 PMID:11680737 PMID:11684179 PMID:14012711 PMID:14678513 PMID:14760634 PMID:15172721 PMID:15906011 PMID:16705261 PMID:17451998 PMID:17733096 PMID:19064074 PMID:19850112 PMID:20314698 Reaxys:1098229 UM-BBD_compID:c0132 Wikipedia:Methanol METHANOL Methanol methanol chebi_ontology CH3OH MeOH Methyl alcohol Methylalkohol carbinol spirit of wood wood alcohol wood naphtha wood spirit CHEBI:17790 methanol Beilstein:1098229 Beilstein CAS:67-56-1 ChemIDplus CAS:67-56-1 KEGG COMPOUND CAS:67-56-1 NIST Chemistry WebBook Gmelin:449 Gmelin PMID:11141607 Europe PMC PMID:11430978 Europe PMC PMID:11489599 Europe PMC PMID:11680737 Europe PMC PMID:11684179 Europe PMC PMID:14012711 Europe PMC PMID:14678513 Europe PMC PMID:14760634 Europe PMC PMID:15172721 Europe PMC PMID:15906011 Europe PMC PMID:16705261 Europe PMC PMID:17451998 Europe PMC PMID:17733096 Europe PMC PMID:19064074 Europe PMC PMID:19850112 Europe PMC PMID:20314698 Europe PMC Reaxys:1098229 Reaxys UM-BBD_compID:c0132 UM-BBD METHANOL PDBeChem Methanol KEGG_COMPOUND methanol IUPAC methanol UniProt CH3OH ChEBI MeOH ChEBI Methyl alcohol KEGG_COMPOUND Methylalkohol NIST_Chemistry_WebBook carbinol ChemIDplus spirit of wood HMDB wood alcohol ChemIDplus wood naphtha ChemIDplus wood spirit NIST_Chemistry_WebBook triglyceride 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 chloride dinitrogen diglyceride lipid glycosaminoglycan hexose polysaccharide dopamine iron atom 3,3',5-triiodo-L-thyronine (R)-noradrenaline alkaline earth metal atom alkali metal atom 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 amino alcohol aminodiol aminoglycan 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 ascorbic acid 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 Any benzenoid aromatic compound consisting of the benzene skeleton and its substituted derivatives. chebi_ontology CHEBI:22712 benzenes Any aromatic carboxylic acid that consists of benzene in which at least a single hydrogen has been substituted by a carboxy group. chebi_ontology CHEBI:22723 benzoic acids benzopyran benzopyrrole amino-acid betaine bile salt biopterins calcium atom calcium molecular entity carbon oxide 0 CO 28.01010 27.99491 carbonyl carbonyl group chebi_ontology >C=O CHEBI:23019 carbonyl group carbonyl IUPAC carbonyl group ChEBI carbonyl group UniProt >C=O IUPAC carotene chlorine molecular entity choline ester cholines chromanol chromanes 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 copper molecular entity cyclic amide cyclic peptide cysteine derivative diol diterpenoid dodecenoic acid 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 ChEBI medicine ChEBI icosanoid monoatomic anion monoatomic cation A compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction. enzyme inhibitor chebi_ontology enzyme inhibitors inhibidor enzimatico inhibidores enzimaticos inhibiteur enzymatique inhibiteurs enzymatiques CHEBI:23924 enzyme inhibitor enzyme inhibitor IUPAC enzyme inhibitors ChEBI inhibidor enzimatico ChEBI inhibidores enzimaticos ChEBI inhibiteur enzymatique ChEBI inhibiteurs enzymatiques ChEBI estradiol Any primary alcohol based on an ethanol skeleton. chebi_ontology CHEBI:23982 ethanols fat-soluble vitamin furans glucocorticoid glutamic acid derivative glycerol ether glycine derivative glycogens glycosphingolipid glycosylglucose A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity chebi_ontology CHEBI:24431 chemical entity chemical entity UniProt A role played by the molecular entity or part thereof within a biological context. chebi_ontology biological function CHEBI:24432 biological role biological function ChEBI A defined linked collection of atoms or a single atom within a molecular entity. group chebi_ontology Gruppe Rest groupe grupo grupos CHEBI:24433 group group IUPAC Gruppe ChEBI Rest ChEBI groupe IUPAC grupo IUPAC grupos IUPAC guanidines haloamino acid halogen molecular entity A cyclic compound having as ring members atoms of carbon and at least of one other element. chebi_ontology organic heterocycle organic heterocyclic compounds CHEBI:24532 organic heterocyclic compound organic heterocycle ChEBI organic heterocyclic compounds ChEBI heterodetic cyclic peptide homocysteines hormone hydrocarbon Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)). chebi_ontology CHEBI:24651 hydroxides imide chebi_ontology imides CHEBI:24782 imide imide ChEBI imides ChEBI indoles A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). oxoacid oxoacids chebi_ontology oxacids oxiacids oxo acid oxy-acids oxyacids CHEBI:24833 oxoacid oxoacid IUPAC oxoacids IUPAC oxacids ChEBI oxiacids ChEBI oxo acid ChEBI oxy-acids ChEBI oxyacids ChEBI chebi_ontology inorganic anions CHEBI:24834 inorganic anion inorganic anions ChEBI A molecular entity that contains no carbon. chebi_ontology anorganische Verbindungen inorganic compounds inorganic entity inorganic molecular entities inorganics CHEBI:24835 inorganic molecular entity anorganische Verbindungen ChEBI inorganic compounds ChEBI inorganic entity ChEBI inorganic molecular entities ChEBI inorganics ChEBI inorganic oxide iodine molecular entity iodoamino acid iodophenol iodothyronine salt monoatomic ion organic salt A molecular entity having a net electric charge. Ion ion chebi_ontology Ionen iones ions CHEBI:24870 ion Ion ChEBI ion ChEBI ion IUPAC Ionen ChEBI iones ChEBI ions ChEBI iron molecular entity iron cation isoprenoid ketoaldonic acid lactam lactate leukotriene linear tetrapyrrole magnesium atom Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites. CHEBI:26619 CHEBI:35220 metabolite chebi_ontology metabolites primary metabolites secondary metabolites CHEBI:25212 metabolite metabolite IUPAC metabolites ChEBI primary metabolites ChEBI secondary metabolites ChEBI metal cation Any carboxylic ester resulting from the formal condensation of a carboxy group with methanol. 0 C2H3O2R 59.044 59.01330 COC([*])=O chebi_ontology carboxylic acid methyl ester carboxylic acid methyl esters CHEBI:25248 methyl ester carboxylic acid methyl ester ChEBI carboxylic acid methyl esters ChEBI mineralocorticoid elemental molecule Any polyatomic entity that is an electrically neutral entity consisting of more than one atom. molecule chebi_ontology Molekuel molecula molecules neutral molecular compounds CHEBI:25367 molecule molecule IUPAC Molekuel ChEBI molecula IUPAC molecules IUPAC neutral molecular compounds IUPAC monoamine molecular messenger monocarboxylic acid monounsaturated fatty acid monoatomic monocation neopterins neurotransmitter 0 N 14.007 14.00307 WebElements:N nitrogen chebi_ontology 7N N Stickstoff azote nitrogen nitrogeno CHEBI:25555 nitrogen atom nitrogen IUPAC 7N IUPAC N IUPAC Stickstoff ChEBI azote IUPAC nitrogen ChEBI nitrogeno ChEBI nonmetal chebi_ontology Nichtmetall Nichtmetalle no metal no metales non-metal non-metaux nonmetal nonmetals CHEBI:25585 nonmetal atom nonmetal IUPAC Nichtmetall ChEBI Nichtmetalle ChEBI no metal ChEBI no metales ChEBI non-metal ChEBI non-metaux ChEBI nonmetal ChEBI nonmetals ChEBI octadecadienoic acid oligopeptide omega-3 fatty acid organic heteromonocyclic compound Any organic ion with a net negative charge. chebi_ontology organic anions CHEBI:25696 organic anion organic anions ChEBI ether chebi_ontology organic ions CHEBI:25699 organic ion organic ions ChEBI organic oxide organic phosphate organic sulfate An alcohol derived from an aliphatic compound. 0 HOR 17.007 17.00274 O* KEGG:C02525 Aliphatic alcohol chebi_ontology aliphatic alcohols an aliphatic alcohol CHEBI:2571 aliphatic alcohol Aliphatic alcohol KEGG_COMPOUND aliphatic alcohols ChEBI an aliphatic alcohol UniProt organophosphorus compound An oxide is a chemical compound of oxygen with other chemical elements. oxide chebi_ontology oxides CHEBI:25741 oxide oxide ChEBI oxides ChEBI 0 O InChI=1S/O QVGXLLKOCUKJST-UHFFFAOYSA-N 15.99940 15.99491 [O] KEGG:C00007 WebElements:O oxygen chebi_ontology 8O O Sauerstoff oxigeno oxygen oxygene CHEBI:25805 oxygen atom oxygen IUPAC 8O IUPAC O IUPAC Sauerstoff ChEBI oxigeno ChEBI oxygen ChEBI oxygene ChEBI oxygen molecular entity chebi_ontology oxygen molecular entities CHEBI:25806 oxygen molecular entity oxygen molecular entity ChEBI oxygen molecular entities ChEBI oxopurine peptide hormone phenylalanine derivative phosphate phosphoric acid derivative phosphorus molecular entity phytosteroid phytosterols polyol polyphenol polyunsaturated fatty acid porphyrins potassium atom potassium molecular entity proline prostaglandin prostanoid pteridines pterins purines quaternary nitrogen compound retinoid saturated fatty acid sodium atom sodium molecular entity sodium salt sphingenine sphingolipid sphing-4-enine steroid hormone sulfuric ester sulfates sulfoglycolipid 0 S InChI=1S/S NINIDFKCEFEMDL-UHFFFAOYSA-N 32.06600 31.97207 [S] CAS:7704-34-9 KEGG:C00087 KEGG:D06527 PPDB:605 WebElements:S sulfur chebi_ontology 16S Elemental sulfur S Schwefel azufre soufre sulfur sulphur theion CHEBI:26833 sulfur atom CAS:7704-34-9 ChemIDplus CAS:7704-34-9 NIST Chemistry WebBook sulfur IUPAC 16S IUPAC Elemental sulfur KEGG_COMPOUND S IUPAC S KEGG_COMPOUND Schwefel ChEBI azufre ChEBI soufre ChEBI sulfur ChEBI sulfur UniProt sulphur ChEBI theion IUPAC sulfur-containing amino acid sulfur molecular entity chebi_ontology sulfur molecular entities CHEBI:26835 sulfur molecular entity sulfur molecular entity ChEBI sulfur molecular entities ChEBI terpenoid tetrapyrrole thiamine thromboxane transition element atom triol tryptamines chebi_ontology heterobicyclic compounds organic heterobicyclic compounds CHEBI:27171 organic heterobicyclic compound heterobicyclic compounds ChEBI organic heterobicyclic compounds ChEBI unsaturated fatty acid uric acid vitamin D zwitterion folic acid selenium atom aldosterone 0 C InChI=1S/C OKTJSMMVPCPJKN-UHFFFAOYSA-N 12.01070 12.00000 [C] CHEBI:23009 CHEBI:3399 CAS:7440-44-0 KEGG:C06265 WebElements:C carbon chebi_ontology 6C C Carbon Kohlenstoff carbon carbone carbonium carbono CHEBI:27594 carbon atom CAS:7440-44-0 ChemIDplus CAS:7440-44-0 KEGG COMPOUND carbon IUPAC 6C IUPAC C IUPAC C KEGG_COMPOUND Carbon KEGG_COMPOUND Kohlenstoff ChEBI carbon ChEBI carbone ChEBI carbonium ChEBI carbono ChEBI A tropane alkaloid obtained from leaves of the South American shrub Erythroxylon coca. 0 C17H21NO4 InChI=1S/C17H21NO4/c1-18-12-8-9-13(18)15(17(20)21-2)14(10-12)22-16(19)11-6-4-3-5-7-11/h3-7,12-15H,8-10H2,1-2H3/t12-,13+,14-,15+/m0/s1 ZPUCINDJVBIVPJ-LJISPDSOSA-N 303.35290 303.14706 [H][C@]12CC[C@]([H])([C@H]([C@H](C1)OC(=O)c1ccccc1)C(=O)OC)N2C CHEBI:23346 CHEBI:3801 CHEBI:41642 Beilstein:3621912 Beilstein:5291037 Beilstein:91034 CAS:50-36-2 DrugBank:DB00907 Drug_Central:723 Gmelin:170209 KEGG:C01416 KEGG:D00110 KNApSAcK:C00002285 MetaCyc:CPD-9776 PDBeChem:COC PMID:11416615 PMID:11853120 PMID:14962054 PMID:17551070 PMID:19536276 PMID:21150772 PMID:25303034 Reaxys:5291037 Reaxys:91034 Wikipedia:Cocaine (1R,2R,3S,5S)-2-(methoxycarbonyl)tropan-3-yl benzoate COCAINE Cocaine methyl (1R,2R,3S,5S)-3-(benzoyloxy)-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylate chebi_ontology (-)-cocaine 2-methyl-3beta-hydroxy-1alphaH,5alphaH-tropane-2beta-carboxylate benzoate (ester) Benzoylmethylecgonine Cocain Cocaina Kokain Neurocaine [1R-(exo,exo)]-3-(benzoyloxy)-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylic acid, methyl ester beta-Cocain cocainum l-Cocain l-cocaine methyl [1R-(exo,exo)]-3-(benzoyloxy)-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylate methyl benzoylecgonine CHEBI:27958 cocaine Beilstein:3621912 Beilstein Beilstein:5291037 Beilstein Beilstein:91034 Beilstein CAS:50-36-2 ChemIDplus CAS:50-36-2 KEGG COMPOUND CAS:50-36-2 NIST Chemistry WebBook Drug_Central:723 DrugCentral Gmelin:170209 Gmelin PMID:11416615 Europe PMC PMID:11853120 Europe PMC PMID:14962054 Europe PMC PMID:17551070 Europe PMC PMID:19536276 Europe PMC PMID:21150772 Europe PMC PMID:25303034 Europe PMC Reaxys:5291037 Reaxys Reaxys:91034 Reaxys (1R,2R,3S,5S)-2-(methoxycarbonyl)tropan-3-yl benzoate IUPAC COCAINE PDBeChem Cocaine KEGG_COMPOUND methyl (1R,2R,3S,5S)-3-(benzoyloxy)-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylate IUPAC (-)-cocaine ChEBI 2-methyl-3beta-hydroxy-1alphaH,5alphaH-tropane-2beta-carboxylate benzoate (ester) NIST_Chemistry_WebBook Benzoylmethylecgonine ChemIDplus Cocain DrugBank Cocaina DrugBank Kokain ChEBI Kokain ChemIDplus Neurocaine ChemIDplus [1R-(exo,exo)]-3-(benzoyloxy)-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylic acid, methyl ester NIST_Chemistry_WebBook beta-Cocain KEGG_COMPOUND cocainum ChEBI l-Cocain KEGG_COMPOUND l-cocaine ChemIDplus methyl [1R-(exo,exo)]-3-(benzoyloxy)-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylate ChEBI methyl benzoylecgonine ChemIDplus glycogen phosphorus atom neopterin copper atom serotonin arachidic acid (R)-adrenaline An onium cation obtained by protonation of ammonia. +1 H4N InChI=1S/H3N/h1H3/p+1 QGZKDVFQNNGYKY-UHFFFAOYSA-O 18.03850 18.03383 [H][N+]([H])([H])[H] CHEBI:22534 CHEBI:49783 CHEBI:7435 CAS:14798-03-9 Gmelin:84 KEGG:C01342 MetaCyc:AMMONIUM MolBase:929 PDBeChem:NH4 PMID:11319011 PMID:11341317 PMID:12096804 PMID:14512268 PMID:14879753 PMID:16345391 PMID:16903292 PMID:17392693 PMID:18515490 PMID:19199063 PMID:19596600 PMID:19682559 PMID:19716251 PMID:21993530 PMID:22265469 PMID:22524020 PMID:22562341 PMID:22631217 Reaxys:16093784 Wikipedia:Ammonium ammonium azanium chebi_ontology Ammonium(1+) NH4(+) NH4+ [NH4](+) ammonium ion CHEBI:28938 ammonium CAS:14798-03-9 ChemIDplus CAS:14798-03-9 NIST Chemistry WebBook Gmelin:84 Gmelin PMID:11319011 Europe PMC PMID:11341317 Europe PMC PMID:12096804 Europe PMC PMID:14512268 Europe PMC PMID:14879753 Europe PMC PMID:16345391 Europe PMC PMID:16903292 Europe PMC PMID:17392693 Europe PMC PMID:18515490 Europe PMC PMID:19199063 Europe PMC PMID:19596600 Europe PMC PMID:19682559 Europe PMC PMID:19716251 Europe PMC PMID:21993530 Europe PMC PMID:22265469 Europe PMC PMID:22524020 Europe PMC PMID:22562341 Europe PMC PMID:22631217 Europe PMC Reaxys:16093784 Reaxys ammonium ChEBI ammonium IUPAC azanium IUPAC Ammonium(1+) ChemIDplus NH4(+) IUPAC NH4(+) UniProt NH4+ KEGG_COMPOUND [NH4](+) MolBase ammonium ion PDBeChem dicarboxylic acid dianion The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated. -1 CO2R 44.00950 43.98983 [O-]C([*])=O CHEBI:13626 CHEBI:13945 CHEBI:23026 CHEBI:58657 chebi_ontology a carboxylate carboxylic acid anions carboxylic anions CHEBI:29067 carboxylic acid anion a carboxylate UniProt carboxylic acid anions ChEBI carboxylic anions ChEBI L-ascorbic acid sodium(1+) potassium(1+) thiol -1 H2N InChI=1S/H2N/h1H2/q-1 HYGWNUKOUCZBND-UHFFFAOYSA-N 16.02262 16.01927 [H][N-][H] amide azanide dihydridonitrate(1-) chebi_ontology NH2(-) CHEBI:29337 azanide amide IUPAC azanide IUPAC dihydridonitrate(1-) IUPAC NH2(-) IUPAC A divalent inorganic anion resulting from the removal of two protons from ammonia. -2 HN InChI=1S/HN/h1H/q-2 DZQYTNGKSBCIOE-UHFFFAOYSA-N 15.01468 15.01200 [N--][H] azanediide hydridonitrate(2-) chebi_ontology NH(2-) imide CHEBI:29340 hydridonitrate(2-) azanediide IUPAC hydridonitrate(2-) IUPAC NH(2-) IUPAC imide IUPAC monocarboxylic acid amide +1 H3O InChI=1S/H2O/h1H2/p+1 XLYOFNOQVPJJNP-UHFFFAOYSA-O 19.02322 19.01784 [H][O+]([H])[H] CAS:13968-08-6 Gmelin:141 MolBase:1646 aquahydrogen(1+) oxidanium oxonium trihydridooxygen(1+) chebi_ontology H3O(+) Hydronium cation Hydronium ion [OH3](+) CHEBI:29412 oxonium CAS:13968-08-6 ChemIDplus CAS:13968-08-6 NIST Chemistry WebBook Gmelin:141 Gmelin aquahydrogen(1+) IUPAC oxidanium IUPAC oxonium IUPAC trihydridooxygen(1+) IUPAC H3O(+) IUPAC Hydronium cation NIST_Chemistry_WebBook Hydronium ion ChemIDplus [OH3](+) MolBase copper(0) thyroxine maleate(2-) A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom. 0 HOR 17.007 17.00274 O[*] CHEBI:13804 CHEBI:22288 CHEBI:2553 KEGG:C00069 Alcohol alcohols chebi_ontology an alcohol CHEBI:30879 alcohol Alcohol KEGG_COMPOUND alcohols IUPAC an alcohol UniProt bradykinin A 1,2-benzisothiazole having a keto-group at the 3-position and two oxo substituents at the 1-position. It is used as an artificial sweetening agent. 0 C7H5NO3S InChI=1S/C7H5NO3S/c9-7-5-3-1-2-4-6(5)12(10,11)8-7/h1-4H,(H,8,9) CVHZOJJKTDOEJC-UHFFFAOYSA-N 183.18500 182.99901 O=C1NS(=O)(=O)c2ccccc12 CHEBI:49717 Beilstein:6888 CAS:81-07-2 Gmelin:4203 HMDB:HMDB0029723 KEGG:D01085 MetaCyc:CPD-5581 PDBeChem:LSA PMID:24456165 PMID:24549104 PMID:24739358 PMID:24780866 Reaxys:6888 Wikipedia:Saccharin 1,2-benzisothiazol-3(2H)-one 1,1-dioxide Saccharin chebi_ontology 1,1-Dioxo-1,2-benzisothiazol-3(2H)-one 1,1-Dioxo-1,2-dihydro-benzo[d]isothiazol-3-one 1,2-Benzisothiazol-3(2H)-one 1,1-dioxide 1,2-Benzisothiazolin-3-one 1,1-dioxide 1,2-Dihydro-2-ketobenzisosulfonazole 1,2-Dihydro-2-ketobenzisosulphonazole 2,3-Dihydro-3-oxobenzisosulfonazole 2,3-Dihydro-3-oxobenzisosulphonazole 3-Hydroxybenzisothiazole-S,S-dioxide Anhydro-o-sulfaminebenzoic acid Benzo-2-sulphimide Benzoic acid sulfimide Benzoic sulfimide Benzoic sulphimide Benzosulfimide Benzosulphimide Benzoylsulfonic Imide Saccharimide Saccharine o-Benzoic sulfimide o-Benzosulfimide o-Sulfobenzimide o-Sulfobenzoic acid imide CHEBI:32111 saccharin Beilstein:6888 Beilstein CAS:81-07-2 ChemIDplus CAS:81-07-2 KEGG DRUG CAS:81-07-2 NIST Chemistry WebBook Gmelin:4203 Gmelin PMID:24456165 Europe PMC PMID:24549104 Europe PMC PMID:24739358 Europe PMC PMID:24780866 Europe PMC Reaxys:6888 Reaxys 1,2-benzisothiazol-3(2H)-one 1,1-dioxide IUPAC Saccharin KEGG_DRUG 1,1-Dioxo-1,2-benzisothiazol-3(2H)-one NIST_Chemistry_WebBook 1,1-Dioxo-1,2-dihydro-benzo[d]isothiazol-3-one NIST_Chemistry_WebBook 1,2-Benzisothiazol-3(2H)-one 1,1-dioxide ChemIDplus 1,2-Benzisothiazolin-3-one 1,1-dioxide NIST_Chemistry_WebBook 1,2-Dihydro-2-ketobenzisosulfonazole ChemIDplus 1,2-Dihydro-2-ketobenzisosulphonazole ChemIDplus 2,3-Dihydro-3-oxobenzisosulfonazole ChemIDplus 2,3-Dihydro-3-oxobenzisosulphonazole ChemIDplus 3-Hydroxybenzisothiazole-S,S-dioxide ChemIDplus Anhydro-o-sulfaminebenzoic acid ChemIDplus Benzo-2-sulphimide ChemIDplus Benzoic acid sulfimide ChemIDplus Benzoic sulfimide ChemIDplus Benzoic sulphimide ChemIDplus Benzosulfimide ChemIDplus Benzosulphimide ChemIDplus Benzoylsulfonic Imide ChemIDplus Saccharimide ChemIDplus Saccharine ChemIDplus o-Benzoic sulfimide ChemIDplus o-Benzosulfimide ChemIDplus o-Sulfobenzimide ChemIDplus o-Sulfobenzoic acid imide ChemIDplus An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group. CHEBI:22473 CHEBI:2633 KEGG:C00241 Amide amides chebi_ontology CHEBI:32988 amide Amide KEGG_COMPOUND amides IUPAC vitamin Intended use of the molecular entity or part thereof by humans. chebi_ontology CHEBI:33232 application A particle not known to have substructure. elementary particle chebi_ontology elementary particles CHEBI:33233 fundamental particle elementary particle IUPAC elementary particles ChEBI vitamin E monoatomic entity oxoacid derivative chebi_ontology inorganic hydrides CHEBI:33242 inorganic hydride inorganic hydrides ChEBI organic fundamental parent Any substituent group which does not contain carbon. chebi_ontology inorganic groups CHEBI:33246 inorganic group inorganic groups ChEBI Any substituent group or skeleton containing carbon. chebi_ontology organic groups CHEBI:33247 organic group organic groups ChEBI Any organic substituent group, regardless of functional type, having one free valence at a carbon atom. organyl group organyl groups chebi_ontology groupe organyle grupo organilo grupos organilo CHEBI:33249 organyl group organyl group IUPAC organyl groups IUPAC groupe organyle IUPAC grupo organilo IUPAC grupos organilo IUPAC A chemical entity constituting the smallest component of an element having the chemical properties of the element. CHEBI:22671 CHEBI:23907 atom chebi_ontology atome atomo atoms atomus element elements CHEBI:33250 atom atom IUPAC atome IUPAC atomo IUPAC atoms ChEBI atomus ChEBI element ChEBI elements ChEBI A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. nucleus chebi_ontology Atomkern Kern noyau noyau atomique nuclei nucleo nucleo atomico nucleus atomi CHEBI:33252 atomic nucleus nucleus IUPAC Atomkern ChEBI Kern ChEBI noyau IUPAC noyau atomique ChEBI nuclei ChEBI nucleo IUPAC nucleo atomico ChEBI nucleus atomi ChEBI Heavy nuclear particle: proton or neutron. nucleon chebi_ontology Nukleon Nukleonen nucleons CHEBI:33253 nucleon nucleons ChEBI nucleon IUPAC nucleon IUPAC Nukleon ChEBI Nukleonen ChEBI primary amide A derivative of two oxoacids RkE(=O)l(OH)m (l =/= 0) in which two acyl groups are attached to the amino or substituted amino group. secondary amide secondary amides chebi_ontology CHEBI:33257 secondary amide secondary amide IUPAC secondary amides IUPAC elemental molecular entity An organosulfur compound is a compound containing at least one carbon-sulfur bond. CHEBI:23010 CHEBI:25714 Wikipedia:Organosulfur_compounds organosulfur compound chebi_ontology organosulfur compounds CHEBI:33261 organosulfur compound organosulfur compound ChEBI organosulfur compounds ChEBI diatomic nitrogen elemental nitrogen An anion consisting of more than one atom. chebi_ontology polyatomic anions CHEBI:33273 polyatomic anion polyatomic anions ChEBI molecular messenger A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans. CHEBI:22582 PMID:12964249 PMID:22117953 PMID:22439833 PMID:22849268 PMID:22849276 PMID:22958833 chebi_ontology Antibiotika Antibiotikum antibiotic antibiotics antibiotique antimicrobial antimicrobial agents antimicrobials microbicide microbicides CHEBI:33281 antimicrobial agent PMID:12964249 Europe PMC PMID:22117953 Europe PMC PMID:22439833 Europe PMC PMID:22849268 Europe PMC PMID:22849276 Europe PMC PMID:22958833 Europe PMC Antibiotika ChEBI Antibiotikum ChEBI antibiotic ChEBI antibiotics ChEBI antibiotique IUPAC antimicrobial ChEBI antimicrobial agents ChEBI antimicrobials ChEBI microbicide ChEBI microbicides ChEBI A nutrient is a food component that an organism uses to survive and grow. chebi_ontology nutrients CHEBI:33284 nutrient nutrients ChEBI A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms. chebi_ontology heteroorganic entities organoelement compounds CHEBI:33285 heteroorganic entity heteroorganic entities ChEBI organoelement compounds ChEBI Any material that can be ingested by an organism. chebi_ontology food material food materials food role foods foodstuff foodstuffs CHEBI:33290 food food material ChEBI food materials ChEBI food role ChEBI foods ChEBI foodstuff ChEBI foodstuffs ChEBI An energy-rich substance that can be transformed with release of usable energy. chebi_ontology CHEBI:33292 fuel alkali metal molecular entity alkaline earth molecular entity Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth. pnictogens chebi_ontology group 15 elements group V elements nitrogenoideos nitrogenoides pnictogene pnictogenes CHEBI:33300 pnictogen pnictogens IUPAC group 15 elements ChEBI group V elements ChEBI nitrogenoideos ChEBI nitrogenoides ChEBI pnictogene ChEBI pnictogenes ChEBI A p-block molecular entity containing any pnictogen. pnictogen molecular entity chebi_ontology pnictogen molecular entities CHEBI:33302 pnictogen molecular entity pnictogen molecular entity ChEBI pnictogen molecular entities ChEBI Any p-block element belonging to the group 16 family of the periodic table. PMID:17084588 chalcogen chalcogens chebi_ontology Chalkogen Chalkogene anfigeno anfigenos calcogeno calcogenos chalcogene chalcogenes group 16 elements group VI elements CHEBI:33303 chalcogen PMID:17084588 Europe PMC chalcogen IUPAC chalcogens IUPAC Chalkogen ChEBI Chalkogene ChEBI anfigeno ChEBI anfigenos ChEBI calcogeno ChEBI calcogenos ChEBI chalcogene ChEBI chalcogenes ChEBI group 16 elements ChEBI group VI elements ChEBI Any p-block molecular entity containing a chalcogen. chalcogen molecular entity chebi_ontology chalcogen compounds chalcogen molecular entities CHEBI:33304 chalcogen molecular entity chalcogen molecular entity ChEBI chalcogen compounds ChEBI chalcogen molecular entities ChEBI group 14 elements chebi_ontology carbon group element carbon group elements carbonoides cristallogene cristallogenes group IV elements CHEBI:33306 carbon group element atom group 14 elements IUPAC carbon group element ChEBI carbon group elements ChEBI carbonoides ChEBI cristallogene ChEBI cristallogenes ChEBI group IV elements ChEBI An ester of a carboxylic acid, R(1)C(=O)OR(2), where R(1) = H or organyl and R(2) = organyl. 0 CO2R2 44.010 43.98983 [*]C(=O)O[*] CHEBI:13204 CHEBI:23028 CHEBI:3408 KEGG:C02391 Wikipedia:Ester Carboxylic ester carboxylic esters chebi_ontology a carboxylic ester carboxylic acid esters CHEBI:33308 carboxylic ester Carboxylic ester KEGG_COMPOUND carboxylic esters IUPAC a carboxylic ester UniProt carboxylic acid esters ChEBI An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table. main group elements chebi_ontology Hauptgruppenelement Hauptgruppenelemente main group element CHEBI:33318 main group element atom main group elements IUPAC Hauptgruppenelement ChEBI Hauptgruppenelemente ChEBI main group element ChEBI iron group element atom copper group element atom sulfur oxoacid derivative monoatomic monoanion elemental chlorine monoatomic chlorine monoatomic halogen elemental halogen elemental pnictogen sulfur oxoanion chalcogen oxoanion transition element molecular entity alkali metal cation transition element cation metal atom chebi_ontology s-block element s-block elements CHEBI:33559 s-block element atom s-block element ChEBI s-block elements ChEBI Any main group element atom belonging to the p-block of the periodic table. chebi_ontology p-block element p-block elements CHEBI:33560 p-block element atom p-block element ChEBI p-block elements ChEBI d-block element atom glycolipid catechols catecholamine adrenaline noradrenaline benzenediols A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid. 0 CHO2R 45.01740 44.99765 OC([*])=O CHEBI:13428 CHEBI:13627 CHEBI:23027 PMID:17147560 PMID:18433345 Wikipedia:Carboxylic_acid carboxylic acid carboxylic acids chebi_ontology Carbonsaeure Carbonsaeuren Karbonsaeure RC(=O)OH acide carboxylique acides carboxyliques acido carboxilico acidos carboxilicos CHEBI:33575 carboxylic acid PMID:17147560 Europe PMC PMID:18433345 Europe PMC carboxylic acid IUPAC carboxylic acids IUPAC Carbonsaeure ChEBI Carbonsaeuren ChEBI Karbonsaeure ChEBI RC(=O)OH IUPAC acide carboxylique IUPAC acides carboxyliques IUPAC acido carboxilico IUPAC acidos carboxilicos IUPAC sulfur-containing carboxylic acid A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table. chebi_ontology main group compounds main group molecular entities CHEBI:33579 main group molecular entity main group compounds ChEBI main group molecular entities ChEBI carbon group molecular entity chebi_ontology carbon group molecular entities CHEBI:33582 carbon group molecular entity carbon group molecular entity ChEBI carbon group molecular entities ChEBI Any molecule that consists of a series of atoms joined together to form a ring. Wikipedia:Cyclic_compound chebi_ontology cyclic compounds CHEBI:33595 cyclic compound cyclic compounds ChEBI A cyclic compound having as ring members atoms of the same element only. homocyclic compound homocyclic compounds chebi_ontology isocyclic compounds CHEBI:33597 homocyclic compound homocyclic compound IUPAC homocyclic compounds IUPAC isocyclic compounds IUPAC A homocyclic compound in which all of the ring members are carbon atoms. carbocyclic compound carbocyclic compounds chebi_ontology carbocycle CHEBI:33598 carbocyclic compound carbocyclic compound IUPAC carbocyclic compounds IUPAC carbocycle ChEBI chebi_ontology hydrogen compounds hydrogen molecular entities CHEBI:33608 hydrogen molecular entity hydrogen compounds ChEBI hydrogen molecular entities ChEBI chebi_ontology polycyclic compounds CHEBI:33635 polycyclic compound polycyclic compounds ChEBI A molecule that features two fused rings. chebi_ontology bicyclic compounds CHEBI:33636 bicyclic compound bicyclic compounds ChEBI ortho-fused compound A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character. aromatic compounds aromatic molecular entity chebi_ontology aromatics aromatische Verbindungen CHEBI:33655 aromatic compound aromatic compounds IUPAC aromatic molecular entity IUPAC aromatics ChEBI aromatische Verbindungen ChEBI chebi_ontology organic aromatic compounds CHEBI:33659 organic aromatic compound organic aromatic compounds ChEBI monocyclic compound heteromonocyclic compound A polycyclic compound in which at least one of the rings contains at least one non-carbon atom. heteropolycyclic compounds chebi_ontology polyheterocyclic compounds CHEBI:33671 heteropolycyclic compound heteropolycyclic compounds IUPAC polyheterocyclic compounds ChEBI A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom. heterobicyclic compounds chebi_ontology CHEBI:33672 heterobicyclic compound heterobicyclic compounds IUPAC An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element. s-block molecular entity chebi_ontology s-block compounds s-block molecular entities CHEBI:33674 s-block molecular entity s-block molecular entity ChEBI s-block compounds ChEBI s-block molecular entities ChEBI A main group molecular entity that contains one or more atoms of a p-block element. chebi_ontology p-block compounds p-block molecular entities p-block molecular entitiy CHEBI:33675 p-block molecular entity p-block compounds ChEBI p-block molecular entities ChEBI p-block molecular entitiy ChEBI d-block molecular entity Hydrides are chemical compounds of hydrogen with other chemical elements. chebi_ontology CHEBI:33692 hydrides oxygen hydride chebi_ontology hydrides of oxygen oxygen hydrides CHEBI:33693 oxygen hydride oxygen hydride ChEBI hydrides of oxygen ChEBI oxygen hydrides ChEBI biomacromolecule information biomacromolecule A cation consisting of more than one atom. chebi_ontology polyatomic cations CHEBI:33702 polyatomic cation polyatomic cations ChEBI alpha-amino acid amino acid carbohydrate acid iron group molecular entity copper group molecular entity An organic compound having at least one hydroxy group attached to a carbon atom. CHEBI:64710 hydroxy compounds chebi_ontology organic alcohol organic hydroxy compounds CHEBI:33822 organic hydroxy compound hydroxy compounds IUPAC organic alcohol ChEBI organic hydroxy compounds ChEBI Any organic molecule that consists of atoms connected in the form of a ring. chebi_ontology organic cyclic compounds CHEBI:33832 organic cyclic compound organic cyclic compounds ChEBI heteroarene chebi_ontology benzenoid aromatic compounds benzenoid compound CHEBI:33836 benzenoid aromatic compound benzenoid aromatic compounds ChEBI benzenoid compound ChEBI conjugated protein macromolecule phenols Any carboxylic acid in which the carboxy group is directly bonded to an aromatic ring. CHEBI:13817 CHEBI:13821 CHEBI:2830 chebi_ontology aromatic carboxylic acids CHEBI:33859 aromatic carboxylic acid aromatic carboxylic acids ChEBI aromatic amine A substance used in a chemical reaction to detect, measure, examine, or produce other substances. reagent chebi_ontology reactif reactivo reagents CHEBI:33893 reagent reagent IUPAC reactif IUPAC reactivo IUPAC reagents ChEBI aldohexose chebi_ontology CHEBI:33937 macronutrient chebi_ontology nitrogen hydrides CHEBI:35106 nitrogen hydride nitrogen hydrides ChEBI Saturated acyclic nitrogen hydrides having the general formula NnHn+2. chebi_ontology azanes CHEBI:35107 azane azanes ChEBI metalloprotein iron protein hemoprotein hemoglobin elemental calcium cyclic carotene terpene tetraterpene A substance that diminishes the rate of a chemical reaction. inhibitor chebi_ontology inhibidor inhibiteur inhibitors CHEBI:35222 inhibitor inhibitor IUPAC inhibidor ChEBI inhibiteur ChEBI inhibitors ChEBI quaternary ammonium ion A derivative of ammonium, NH4(+), in which one (or more) of the hydrogens bonded to the nitrogen have been replaced with univalent organyl groups. The substituting carbon of the organyl group must not itself be directly attached to a heteroatom (thereby excluding protonated amides, hemiaminals, etc). chebi_ontology ammonium ion derivatives ammonium ions azanium ion derivative azanium ion derivatives azanium ions CHEBI:35274 ammonium ion ammonium ion derivative ammonium ion derivatives ChEBI ammonium ions ChEBI azanium ion derivative ChEBI azanium ion derivatives ChEBI azanium ions ChEBI onium betaine ammonium betaine fused compound Any drug that enhances the activity of the central nervous system. Wikipedia:Central_nervous_system_stimulants central nervous system stimulant chebi_ontology CNS stimulant analeptic analeptic agent analeptic drug analeptics central stimulant CHEBI:35337 central nervous system stimulant central nervous system stimulant ChEBI CNS stimulant ChEBI analeptic ChEBI analeptic agent ChEBI analeptic drug ChEBI analeptics ChEBI central stimulant ChEBI steroid 17alpha-hydroxy steroid 17beta-hydroxy steroid 21-hydroxy steroid 11beta-hydroxy steroid 3beta-sterol hydroxy steroid Any heteroorganic entity containing at least one carbon-nitrogen bond. organonitrogen compounds chebi_ontology organonitrogens CHEBI:35352 organonitrogen compound organonitrogen compounds IUPAC organonitrogens ChEBI fatty acid monosaccharide An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen. CHEBI:33274 CHEBI:33436 oxoanion chebi_ontology oxoacid anions oxoanions CHEBI:35406 oxoanion oxoanion ChEBI oxoacid anions ChEBI oxoanions ChEBI A substance used in the prophylaxis or therapy of infectious diseases. chebi_ontology anti-infective agents anti-infective drugs antiinfective agents antiinfective drug CHEBI:35441 antiinfective agent anti-infective agents ChEBI anti-infective drugs ChEBI antiinfective agents ChEBI antiinfective drug ChEBI A class of drugs producing both physiological and psychological effects through a variety of mechanisms involving the central nervous system. chebi_ontology CNS agent CNS drugs central nervous system agents CHEBI:35470 central nervous system drug CNS agent ChEBI CNS drugs ChEBI central nervous system agents ChEBI alkali metal salt A loosely defined group of drugs that tend to reduce the activity of the central nervous system. chebi_ontology CNS depressants central nervous system depressants CHEBI:35488 central nervous system depressant CNS depressants ChEBI central nervous system depressants ChEBI natural product fundamental parent A drug that mimics the effects of stimulating postganglionic adrenergic sympathetic nerves. Included in this class are drugs that directly stimulate adrenergic receptors and drugs that act indirectly by provoking the release of adrenergic transmitters. chebi_ontology sympathomimetic sympathomimetics CHEBI:35524 sympathomimetic agent sympathomimetic ChEBI sympathomimetics ChEBI heterocyclic organic fundamental parent A drug that affects the rate or intensity of cardiac contraction, blood vessel diameter or blood volume. chebi_ontology cardiovascular agent cardiovascular drugs CHEBI:35554 cardiovascular drug cardiovascular agent ChEBI cardiovascular drugs ChEBI mancude ring mancude organic heterobicyclic parent mancude organic heterocyclic parent organic mancude parent indole carbon oxoanion chebi_ontology carbon oxoacids oxoacids of carbon CHEBI:35605 carbon oxoacid carbon oxoacids ChEBI oxoacids of carbon ChEBI A food additive that is used to added improve the taste or odour of a food. chebi_ontology flavoring agent flavoring agents flavour enhancer flavour enhancers flavouring agents CHEBI:35617 flavouring agent flavoring agent ChEBI flavoring agents ChEBI flavour enhancer ChEBI flavour enhancers ChEBI flavouring agents ChEBI Adrenergic uptake inhibitors are drugs that block the transport of adrenergic transmitters into axon terminals or into storage vesicles within terminals. The tricyclic antidepressants and amphetamines are among the therapeutically important drugs that may act via inhibition of adrenergic transport. Many of these drugs also block transport of serotonin. chebi_ontology ARI NERI NRI adrenergic reuptake inhibitor adrenergic reuptake inhibitors adrenergic uptake inhibitors norepinephrine reuptake inhibitor norepinephrine reuptake inhibitors CHEBI:35640 adrenergic uptake inhibitor ARI ChEBI NERI ChEBI NRI ChEBI adrenergic reuptake inhibitor ChEBI adrenergic reuptake inhibitors ChEBI adrenergic uptake inhibitors ChEBI norepinephrine reuptake inhibitor ChEBI norepinephrine reuptake inhibitors ChEBI secondary alcohol dicarboxylic acid dicarboxylic acid anion A compound formally derived from an oxoacid RkE(=O)l(OH)m (l > 0) and an alcohol, phenol, heteroarenol, or enol by linking with formal loss of water from an acidic hydroxy group of the former and a hydroxy group of the latter. CHEBI:23960 CHEBI:4859 KEGG:C00287 Wikipedia:Ester Ester chebi_ontology esters CHEBI:35701 ester Ester KEGG_COMPOUND esters ChEBI A xenobiotic (Greek, xenos "foreign"; bios "life") is a compound that is foreign to a living organism. Principal xenobiotics include: drugs, carcinogens and various compounds that have been introduced into the environment by artificial means. CHEBI:10074 CHEBI:27333 KEGG:C06708 Wikipedia:Xenobiotic Xenobiotic xenobiotic xenobiotics chebi_ontology xenobiotic compounds CHEBI:35703 xenobiotic Xenobiotic KEGG_COMPOUND xenobiotic IUPAC xenobiotics IUPAC xenobiotic compounds ChEBI sulfated glycosaminoglycan carbohydrate sulfate liposaccharide glycerolipid monocarboxylic acid anion sphingoid phosphosphingolipid seco-steroid oxo steroid tetrapyrrole fundamental parent imidazopyrimidine pnictogen hydride chebi_ontology pnictogen hydrides CHEBI:35881 pnictogen hydride pnictogen hydride ChEBI pnictogen hydrides ChEBI A substance used for its pharmacological action on any aspect of neurotransmitter systems. Neurotransmitter agents include agonists, antagonists, degradation inhibitors, uptake inhibitors, depleters, precursors, and modulators of receptor function. chebi_ontology neurotransmitter agents CHEBI:35942 neurotransmitter agent neurotransmitter agents ChEBI omega-6 fatty acid Esters of benzoic acid or substituted benzoic acids. benzoate ester chebi_ontology benzoate esters benzoic acid esters CHEBI:36054 benzoate ester benzoate ester ChEBI benzoate esters ChEBI benzoic acid esters ChEBI hydroxy monocarboxylic acid anion cholanoid protein butenedioate disaccharide cyclic tetrapyrrole Any member of a group of drugs that reversibly inhibit the propagation of signals along nerves. Wide variations in potency, stability, toxicity, water-solubility and duration of action determine the route used for administration, e.g. topical, intravenous, epidural or spinal block. local anaesthetic chebi_ontology Lokalanaesthetikum anesthesique local local anaesthetics local anesthetics CHEBI:36333 local anaesthetic local anaesthetic IUPAC Lokalanaesthetikum ChEBI anesthesique local ChEBI local anaesthetics ChEBI local anesthetics ChEBI Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin). chebi_ontology leptons CHEBI:36338 lepton leptons ChEBI Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy). chebi_ontology baryons CHEBI:36339 baryon baryons ChEBI Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi. fermion chebi_ontology fermions CHEBI:36340 fermion fermion IUPAC fermions ChEBI A particle smaller than an atom. chebi_ontology subatomic particles CHEBI:36342 subatomic particle subatomic particles ChEBI A subatomic particle known to have substructure (i.e. consisting of smaller particles). chebi_ontology composite particles CHEBI:36343 composite particle composite particles ChEBI Hadron is a subatomic particle which experiences the strong force. chebi_ontology hadrons CHEBI:36344 hadron hadrons ChEBI A nucleus or any of its constituents in any of their energy states. nuclear particle chebi_ontology CHEBI:36347 nuclear particle nuclear particle IUPAC Any molecular entity consisting of more than one atom. chebi_ontology polyatomic entities CHEBI:36357 polyatomic entity polyatomic entities ChEBI An ion consisting of more than one atom. chebi_ontology polyatomic ions CHEBI:36358 polyatomic ion polyatomic ions ChEBI phosphorus oxoacid derivative phosphorus oxoacids and derivatives sulfoglycosphingolipid acidic glycosphingolipid Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives. carbonyl compounds chebi_ontology CHEBI:36586 carbonyl compound carbonyl compounds IUPAC Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element. oxo compounds chebi_ontology organic oxo compounds CHEBI:36587 organic oxo compound oxo compounds IUPAC organic oxo compounds ChEBI organohalogen compound corticosteroid hormone phosphocholines biladienes ring assembly monoanion 3-hydroxy steroid 3beta-hydroxy steroid 17-hydroxy steroid 11-hydroxy steroid hydroxy seco-steroid 20-oxo steroid 18-oxo steroid chalcogen hydride chebi_ontology chalcogen hydrides CHEBI:36902 chalcogen hydride chalcogen hydride ChEBI chalcogen hydrides ChEBI chebi_ontology inorganic ions CHEBI:36914 inorganic ion inorganic ions ChEBI chebi_ontology inorganic cations CHEBI:36915 inorganic cation inorganic cations ChEBI A monoatomic or polyatomic species having one or more elementary charges of the proton. CHEBI:23058 CHEBI:3473 KEGG:C01373 Cation cation chebi_ontology Kation Kationen cationes cations CHEBI:36916 cation Cation KEGG_COMPOUND cation ChEBI cation IUPAC Kation ChEBI Kationen ChEBI cationes ChEBI cations ChEBI An organochalcogen compound is a compound containing at least one carbon-chalcogen bond. organochalcogen compound chebi_ontology organochalcogen compounds CHEBI:36962 organochalcogen compound organochalcogen compound ChEBI organochalcogen compounds ChEBI An organochalcogen compound containing at least one carbon-oxygen bond. PMID:17586126 organooxygen compound chebi_ontology organooxygen compounds CHEBI:36963 organooxygen compound PMID:17586126 Europe PMC organooxygen compound ChEBI organooxygen compounds ChEBI organoiodine compound glucan homopolysaccharide organic hydride mononuclear parent hydrides chebi_ontology mononuclear hydride mononuclear hydrides CHEBI:37176 mononuclear parent hydride mononuclear parent hydrides IUPAC mononuclear hydride ChEBI mononuclear hydrides IUPAC elemental sodium elemental potassium CHEBI:27154 CHEBI:27155 chebi_ontology tropane alkaloids CHEBI:37332 tropane alkaloid tropane alkaloids ChEBI mucopolysaccharide elemental copper folic acids An acid is a molecular entity capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid). CHEBI:13800 CHEBI:13801 CHEBI:22209 CHEBI:2426 KEGG:C00174 Acid acid chebi_ontology Saeure Saeuren acide acido acids CHEBI:37527 acid Acid KEGG_COMPOUND acid IUPAC Saeure ChEBI Saeuren ChEBI acide IUPAC acido ChEBI acids ChEBI A molecular entity consisting of two or more chemical elements. chebi_ontology chemical compound heteroatomic molecular entities CHEBI:37577 heteroatomic molecular entity chemical compound ChEBI heteroatomic molecular entities ChEBI halide carboxamide