Human Phenotype Ontology Consortium Monarch Initiative Peter Robinson Sebastian Köhler The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities and clinical features encountered in human disease. Peter Robinson, Sebastian Koehler, The Human Phenotype Ontology Consortium, and The Monarch Initiative Phenotypic abnormalities encountered in human disease Human Phenotype Ontology human_phenotype has_part Peter Robinson, Sebastian Koehler, Sandra Doelken, Chris Mungall, Melissa Haendel, Nicole Vasilevsky, Monarch Initiative, et al. Please see license of HPO at http://www.human-phenotype-ontology.org definition definition IAO:0000116 uberon editor_note true editor_note editor note editor note IAO:0000700 uberon has_ontology_root_term true has_ontology_root_term has ontology root term preferred_root 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 HPO:skoehler abbreviation 2018-07-05T13:18:08Z peter display label Core clinical terminology is_observable_through HPO:skoehler layperson term 2018-05-05T19:01:17Z peter discarded/obsoleted synonym HPO:skoehler plural form Consequence of a disorder in another organ system. HPO:skoehler UK spelling http://purl.org/dc/elements/1.1/contributor uberon dc-contributor true dc-contributor contributor http://purl.org/dc/elements/1.1/description uberon dc-description true dc-description description http://purl.org/dc/elements/1.1/title uberon dc-title true dc-title title http://purl.org/dc/terms/license uberon dcterms-license true dcterms-license license subset_property synonym_type_property consider has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym has_synonym_type in_subset logical-definition-view-relation 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/ 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 human_stages_ontology 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) 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/ 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 protein quality uberon has_part false has_part has part has part has_part preceded by X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X). x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 is preceded by takes place after external human_stages_ontology uberon preceded_by preceded_by preceded by preceded by preceded_by is preceded by SIO:000249 takes place after Allen:precedes precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 external uberon precedes precedes precedes precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in BFO:0000066 external occurs_in occurs_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in occurs in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t BFO:0000067 uberon contains_process contains_process Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process contains process x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that 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. 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. 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 superficial part of Y <=> if Y is subdivided into two superficial and deep portions, X is part of the deep portion. X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the deep portion. BSPO:0001101 uberon in_deep_part_of in_deep_part_of in deep part of in_deep_part_of X superficial part of Y <=> if Y is subdivided into two superficial and deep portions, X is part of the deep portion. BSPO:cjm X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the deep portion. 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 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 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. BSPO:0001113 uberon preaxialmost_part_of preaxialmost_part_of preaxialmost part of preaxialmost_part_of BSPO:0001115 uberon postaxialmost_part_of postaxialmost_part_of postaxialmost part of postaxialmost_part_of 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 X ventral side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the ventral portion. BSPO:0015102 uberon in_ventral_side_of in_ventral_side_of in ventral side of in_ventral_side_of X ventral side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the ventral portion. BSPO:cjm GOREL:0002003 external results_in_distribution_of results_in_distribution_of results_in_distribution_of GOREL:0002004 external results_in_fission_of results_in_fission_of results_in_fission_of inheres in this fragility is a characteristic of this vase this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in RO:0000052 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 bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of RO:0000053 external uberon bearer_of bearer_of bearer of has characteristic participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in RO:0000056 external uberon participates_in participates_in participates in participates in participates_in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 external has_participant has_participant has participant has participant this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality RO:0000086 protein uberon has_quality false has_quality has quality has quality has_quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role RO:0000087 chebi_ontology protein has_role false false has_role has role has role has_role 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 is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ location_of RO:0001015 uberon location_of location_of location of location_of contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): Intended meaning: domain: material entity range: spatial region or site (immaterial continuant) contained_in contained in contains RO:0001019 uberon contains contains contains contains located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ located_in http://www.obofoundry.org/ro/#OBO_REL:located_in RO:0001025 protein uberon located_in located_in located in located_in This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of RO:0002000 uberon boundary_of boundary_of 2D boundary of boundary of my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. David Osumi-Sutherland has boundary has_2D_boundary RO:0002002 uberon has_boundary has_boundary has 2D boundary has boundary David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 nerve supply uberon innervated_by innervated_by http://code.google.com/p/obo-relations/issues/detail?id=6 innervated_by innervated_by nerve supply FMA:85999 X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 David Osumi-Sutherland RO:0002007 external uberon bounding_layer_of bounding_layer_of A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. bounding layer of bounding layer of A relationship that holds between a process that regulates a transport process and the entity transported by that process. David Osumi-Sutherland regulates transport of A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. dos 2017-05-24T09:30:46Z RO:0002013 external has_regulatory_component_activity has_regulatory_component_activity has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. dos 2017-05-24T09:31:01Z RO:0002014 external has_negative_regulatory_component_activity has_negative_regulatory_component_activity By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. dos 2017-05-24T09:49:21Z has component process dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. GOC:dos Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. dos 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. GOC:dos Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. dos 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. GOC:dos A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. GOC:dos David Osumi-Sutherland <= Primitive instance level timing relation between events before or simultaneous with Relation between occurrents, shares start and end boundaries. David Osumi-Sutherland RO:0002082 coincides_with is_equal_to uberon simultaneous_with simultaneous_with t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with simultaneous_with Relation between occurrents, shares start and end boundaries. Allen:is_equal_to Relation between occurrents, shares start and end boundaries. Allen:is_equal_to https://orcid.org/0000-0002-6601-2165 David Osumi-Sutherland RO:0002086 ends_after 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) X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y). David Osumi-Sutherland starts_at_end_of A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. RO:0002087 directly preceded by is directly preceded by is immediately preceded by starts_at_end_of external human_stages_ontology uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by immediately_preceded_by A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. SIO:000251 is immediately preceded by SIO:000251 David Osumi-Sutherland ends_at_start_of meets RO:0002090 external immediately_precedes immediately_precedes X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes immediately_precedes Relation between a neuron and an anatomical structure that its soma is part of. David Osumi-Sutherland <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) has soma location Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. Alexander Diehl Chris Mungall Lindsay Cowell <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) has plasma membrane part x overlaps y if and only if there exists some z such that x has part z and z part of y BFO_0000051 some (BFO_0000050 some ?Y) http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 external uberon overlaps overlaps overlaps overlaps true Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. David Osumi-Sutherland <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) RO:0002134 uberon innervates innervates http://code.google.com/p/obo-relations/issues/detail?id=6 innervates innervates X continuous_with Y if and only if X and Y share a fiat boundary. David Osumi-Sutherland connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) RO:0002150 uberon continuous_with continuous_with continuous with continuous_with FMA:85972 d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. derived by descent from inverse of derived by descent from has derived by descendant two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. RO:0002158 uberon homologous_to homologous_to shares ancestor with RO:0002159 uberon serially_homologous_to serially_homologous_to serially homologous to lactation SubClassOf 'only in taxon' some 'Mammalia' S only_in_taxon T iff: S SubClassOf in_taxon only T. U only_in_taxon T: U is a feature found in only in organisms of species of taxon T. The feature cannot be found in an organism of any species outside of (not subsumed by) that taxon. Down-propagates in U hierarchy, up-propagates in T hierarchy (species taxonomy). Implies applicable_to_taxon. x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria Chris Mungall RO:0002160 never_outside_taxon specific_to specific_to_taxon protein uberon only_in_taxon false only_in_taxon Down-propagates. The original name for this in the paper is 'specific_to'. Applicable to genes because some genes are lost in sub-species (strains) of a species. only in taxon only_in_taxon S only_in_taxon T iff: S SubClassOf in_taxon only T. S only_in_taxon T iff: S SubClassOf in_taxon only T. PMID:20973947 U only_in_taxon T: U is a feature found in only in organisms of species of taxon T. The feature cannot be found in an organism of any species outside of (not subsumed by) that taxon. Down-propagates in U hierarchy, up-propagates in T hierarchy (species taxonomy). Implies applicable_to_taxon. ROC:Waclaw x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. Chris Mungall Jennifer Deegan RO:0002162 uberon in_taxon in_taxon Connects a biological entity to its taxon of origin. in taxon A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. Chris Mungall Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b RO:0002170 uberon connected_to connected_to Connection does not imply overlaps. connected to connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern The M8 connects Glasgow and Edinburgh a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect) RO:0002176 uberon connects connects connects connects https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. attached to part of (anatomical structure to anatomical structure) RO:0002177 uberon attaches_to_part_of attaches_to_part_of attached to part of attaches_to_part_of true true Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. relation between an artery and the structure is supplies with blood. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure RO:0002178 arterial supply of uberon supplies supplies source: FMA supplies supplies arterial supply of FMA:86003 Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure RO:0002179 drains blood from drains from uberon drains drains source: Wikipedia drains drains w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. RO:0002180 external protein uberon has_component false has_component has component has component has_component x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y Chris Mungall 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 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. Chris Mungall David Osumi-Sutherland has developmental precursor FBbt RO:0002207 uberon directly_develops_from directly_develops_from TODO - add child relations from DOS directly develops from directly_develops_from inverse of directly develops from developmental precursor of directly develops into process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false RO:0002211 external regulates regulates regulates regulates Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall negatively regulates (process to process) RO:0002212 external negatively_regulates negatively_regulates negatively regulates negatively regulates Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall positively regulates (process to process) RO:0002213 external positively_regulates positively_regulates positively regulates positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO:0002215 external 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:0002216 external uberon capable_of_part_of capable_of_part_of capable of part of capable of part of true x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y. Chris Mungall RO:0002219 uberon surrounded_by surrounded_by surrounded by surrounded_by x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y. x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y. https://orcid.org/0000-0002-6601-2165 A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. x adjacent to y if and only if x and y share a boundary. x adjacent_to y iff: x and y share a boundary. This relation acts as a join point with BSPO Chris Mungall RO:0002220 external uberon adjacent_to adjacent_to adjacent to adjacent to adjacent_to A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. inverse of surrounded by inverse of surrounded_by. Chris Mungall RO:0002221 uberon surrounds surrounds surrounds surrounds inverse of surrounded_by. 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 RO:0002222 temporally_related_to A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to Relation between occurrents, shares a start boundary with. inverse of starts with Chris Mungall Allen RO:0002223 uberon starts starts starts starts Relation between occurrents, shares a start boundary with. Allen:starts Relation between occurrents, shares a start boundary with. Allen:starts https://orcid.org/0000-0002-6601-2165 Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall started by RO:0002224 external uberon starts_with starts_with starts with starts with x develops from part of y if and only if there exists some z such that x develops from z and z is part of y Chris Mungall RO:0002225 uberon develops_from_part_of develops_from_part_of develops from part of develops_from_part_of x develops_in y if x is located in y whilst x is developing Chris Mungall EHDAA2 Jonathan Bard, EHDAA2 RO:0002226 uberon develops_in develops_in This relation take from EHDAA2 - precise semantics yet to be defined develops in develops_in Relation between occurrents, shares an end boundary with. inverse of ends with Chris Mungall RO:0002229 finishes uberon ends ends ends ends Relation between occurrents, shares an end boundary with. Allen:starts ZFS:finishes Relation between occurrents, shares an end boundary with. Allen:starts ZFS:finishes https://orcid.org/0000-0002-6601-2165 x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall finished by RO:0002230 external uberon ends_with ends_with ends with ends with x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y Chris Mungall starts with process that occurs in RO:0002231 external has_start_location has_start_location has start location has start location x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y Chris Mungall ends with process that occurs in RO:0002232 external has_end_location has_end_location has end location has end location p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes RO:0002233 external has_input has_input has input has input p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. Chris Mungall produces RO:0002234 external has_output has_output has output has output Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y Chris Mungall RO:0002254 uberon has_developmental_contribution_from has_developmental_contribution_from has developmental contribution from has developmental contribution from inverse of has developmental contribution from Chris Mungall RO:0002255 uberon developmentally_contributes_to developmentally_contributes_to developmentally contributes to developmentally_contributes_to t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T. t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T Chris Mungall David Osumi-Sutherland Melissa Haendel induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) GO:0001759 We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] RO:0002256 uberon developmentally_induced_by developmentally_induced_by sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F) developmentally induced by developmentally_induced_by t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T. GO:0001759 Inverse of developmentally induced by Chris Mungall developmentally induces Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false Chris Mungall In general you should not use this relation to make assertions - use one of the more specific relations below this one RO:0002258 uberon developmentally_preceded_by developmentally_preceded_by This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by developmentally preceded by A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage Chris Mungall replaces RO:0002285 uberon developmentally_replaces developmentally_replaces developmentally replaces developmentally_replaces Inverse of developmentally preceded by Chris Mungall RO:0002286 developmentally_succeeded_by developmentally succeeded by 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue Chris Mungall part of developmental precursor of p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. Chris Mungall RO:0002295 external results_in_developmental_progression_of results_in_developmental_progression_of results in developmental progression of results in developmental progression of every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. Chris Mungall http://www.geneontology.org/GO.doc.development.shtml RO:0002296 external results_in_development_of results_in_development_of results in development of results in development of an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) Chris Mungall GOC:mtg_berkeley_2013 RO:0002297 external results_in_formation_of results_in_formation_of results in formation of results in formation of an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. Chris Mungall GOC:mtg_berkeley_2013 RO:0002298 external results_in_morphogenesis_of results_in_morphogenesis_of results in morphogenesis of results in morphogenesis of an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. Chris Mungall GOC:mtg_berkeley_2013 RO:0002299 external results_in_maturation_of results_in_maturation_of results in maturation of results in maturation of cjm RO:0002304 external causally_upstream_of,_positive_effect causally_upstream_of,_positive_effect holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect cjm RO:0002305 external causally_upstream_of,_negative_effect causally_upstream_of,_negative_effect holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. Chris Mungall regulates localization of RO:0002313 external transports_or_maintains_localization_of transports_or_maintains_localization_of transports or maintains localization of transports or maintains localization of q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of Chris Mungall inheres in part of RO:0002314 inheres_in_part_of inheres_in_part_of characteristic of part of inheres in part of true an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity Chris Mungall GOC:mtg_berkeley_2013 RO:0002315 external results_in_acquisition_of_features_of results_in_acquisition_of_features_of results in acquisition of features of results in acquisition of features of A relationship that holds via some environmental process Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) ecologically related to RO:0002322 adapted_for uberon confers_advantage_in confers_advantage_in confers advantage in 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 RO:0002323 mereotopologically_related_to 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 RO:0002324 developmentally_related_to developmentally related to a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 uberon functionally_related_to functionally_related_to functionally related to functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false RO:0002329 uberon part_of_structure_that_is_capable_of part_of_structure_that_is_capable_of part of structure that is capable of part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in enables part of involved in every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c Chris Mungall regulates levels of (process to entity) RO:0002332 external regulates_levels_of regulates_levels_of regulates levels of regulates levels of inverse of enables Chris Mungall enabled by inverse of regulates Chris Mungall regulated by (processual) RO:0002334 external regulated_by regulated_by regulated by regulated by inverse of negatively regulates Chris Mungall RO:0002335 external negatively_regulated_by negatively_regulated_by negatively regulated by negatively regulated by inverse of positively regulates Chris Mungall RO:0002336 external positively_regulated_by positively_regulated_by positively regulated by positively regulated by A relationship that holds via some process of localization Chris Mungall Do not use this relation directly. It is a grouping relation. related via localization to This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. Chris Mungall RO:0002338 external has_target_start_location has_target_start_location has target start location has target start location This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. Chris Mungall RO:0002339 external has_target_end_location has_target_end_location has target end location has target end location Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l Chris Mungall RO:0002341 external results_in_transport_along results_in_transport_along results in transport along results in transport along 'pollen tube growth' results_in growth_of some 'pollen tube' Chris Mungall RO:0002343 external results_in_growth_of results_in_growth_of results in growth of results in growth of 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) Chris Mungall RO:0002344 external results_in_transport_to_from_or_in results_in_transport_to_from_or_in results in transport to from or in results in transport to from or in An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO RO:0002350 uberon member_of member_of member of member of has member is a mereological relation between a collection and an item. SIO RO:0002351 uberon has_member has_member has member has member inverse of has input Chris Mungall RO:0002352 uberon input_of input_of input of input of inverse of has output Chris Mungall RO:0002353 external protein uberon output_of false output_of output of output of output_of Chris Mungall formed as result of a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a Chris Mungall attached to (anatomical structure to anatomical structure) RO:0002371 uberon attaches_to attaches_to attached to attaches_to m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Chris Mungall Wikipedia:Insertion_(anatomy) RO:0002372 uberon has_muscle_origin has_muscle_origin The origin is the end of a muscle that attaches to the more fixed part of the skeleton, which is the proximal end in limb muscles has muscle origin has_muscle_origin We need to import uberon muscle to create a stricter domain constraint m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Wikipedia:Insertion_(anatomy)#Muscles m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Chris Mungall Wikipedia:Insertion_(anatomy) RO:0002373 uberon has_muscle_insertion has_muscle_insertion The insertion is the point of attachment of a muscle that moves the most when the muscle shortens, or the most distal end of limb muscles has muscle insertion has_muscle_insertion We need to import uberon muscle into RO to use as a stricter domain constraint m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. 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) x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat. RO:0002374 uberon has_fused_element has_fused_element A single bone in one species may correspond to the fusion of two or more bones found as distinct elements in another. For example, tibiofibula has_fused_element tibia. A has_fused_element B does not imply that A has_part some B, rather than A has_part some B', where B' is not a subtype of B (because B is a distinct element but B' is a regional part) but has some evolutionary relationship to B. derived from ancestral fusion of A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) in branching relationship with https://github.com/obophenotype/uberon/issues/170 Deschutes River tributary_of Columbia River inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. Chris Mungall drains into drains to tributary channel of http://en.wikipedia.org/wiki/Tributary http://www.medindia.net/glossary/venous_tributary.htm This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) RO:0002376 uberon drains into tributary_of tributary_of tributary of tributary_of http://en.wikipedia.org/wiki/Tributary drains into dbpowl:drainsTo A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location Chris Mungall This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve Chris Mungall RO:0002380 uberon branching_part_of branching_part_of branching part of branching_part_of FMA:85994 x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall RO:0002384 has_developmental_potential_involving has developmental potential involving x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y. Chris Mungall RO:0002385 uberon has_potential_to_developmentally_contribute_to has_potential_to_developmentally_contribute_to has potential to developmentally contribute to has potential to developmentally contribute to x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y Chris Mungall has potential to developmentally induce x has the potential to develop into y iff x develops into y or if x is capable of developing into y x has the potential to develop into y iff x develops into y or if x is capable of developing into y. Chris Mungall RO:0002387 uberon has_potential_to_develop_into has_potential_to_develop_into has potential to develop into has potential to develop into x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y. Chris Mungall RO:0002388 uberon has_potential_to_directly_develop_into has_potential_to_directly_develop_into has potential to directly develop into has potential to directly develop into inverse of upstream of Chris Mungall RO:0002404 external causally_downstream_of causally_downstream_of causally downstream of causally downstream of Chris Mungall RO:0002405 external immediately_causally_downstream_of immediately_causally_downstream_of immediately causally downstream of immediately causally downstream of This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002410 causally_related_to causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall RO:0002411 external causally_upstream_of causally_upstream_of causally upstream of causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall RO:0002412 external immediately_causally_upstream_of immediately_causally_upstream_of immediately causally upstream of immediately causally upstream of p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) RO:0002418 external affects causally_upstream_of_or_within causally_upstream_of_or_within causally upstream of or within inverse of causally upstream of or within Chris Mungall RO:0002427 external causally_downstream_of_or_within causally_downstream_of_or_within causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p Chris Mungall involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p Chris Mungall involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. Chris Mungall executes activity in enables activity in is active in true c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. GOC:cjm GOC:dos p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. Chris Mungall RO:0002433 uberon contributes_to_morphology_of contributes_to_morphology_of contributes to morphology of A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Chris Mungall Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ http://purl.obolibrary.org/obo/MI_0914 An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. Chris Mungall binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later Chris Mungall An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. Chris Mungall Vasundra Touré molecularly controls directly regulates activity of The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Chris Mungall Vasundra Touré directly inhibits molecularly decreases activity of directly negatively regulates activity of The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Chris Mungall Vasundra Touré directly activates molecularly increases activity of directly positively regulates activity of Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. x composed_primarily_of y iff: more than half of the mass of x is made from parts of y. Chris Mungall RO:0002473 uberon composed_primarily_of composed_primarily_of composed primarily of p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in true Chris Mungall is kinase activity Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. relation between physical entity and a process or stage Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). Chris Mungall RO:0002488 begins_to_exist_during uberon existence_starts_during existence_starts_during existence starts during Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. https://orcid.org/0000-0002-6601-2165 Relation between continuant and occurrent, such that c comes into existence at the start of p. x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). Chris Mungall RO:0002489 uberon existence_starts_with existence_starts_with existence starts with Relation between continuant and occurrent, such that c comes into existence at the start of p. Relation between continuant and occurrent, such that c comes into existence at the start of p. https://orcid.org/0000-0002-6601-2165 x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) Chris Mungall The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) Chris Mungall RO:0002491 exists during uberon existence_starts_and_ends_during existence_starts_and_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts and ends during Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). Chris Mungall RO:0002492 ceases_to_exist_during uberon existence_ends_during existence_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. https://orcid.org/0000-0002-6601-2165 Relation between continuant and occurrent, such that c ceases to exist at the end of p. x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). Chris Mungall RO:0002493 uberon existence_ends_with existence_ends_with The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with Relation between continuant and occurrent, such that c ceases to exist at the end of p. Relation between continuant and occurrent, such that c ceases to exist at the end of p. https://orcid.org/0000-0002-6601-2165 x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships Chris Mungall RO:0002494 transforms from uberon transformation_of transformation_of transformation of transforms from SIO:000657 x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t Chris Mungall RO:0002495 direct_transformation_of immediately transforms from uberon immediate_transformation_of immediate_transformation_of immediate transformation of direct_transformation_of direct_transformation_of https://orcid.org/0000-0002-6601-2165 immediately transforms from SIO:000658 x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). Chris Mungall RO:0002496 uberon existence_starts_during_or_after existence_starts_during_or_after The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. Chris Mungall RO:0002497 uberon existence_ends_during_or_before existence_ends_during_or_before The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before A relationship between a material entity and a process where the material entity has some causal role that influences the process RO:0002500 causal_agent_in_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. RO:0002501 causal_relation_between_processes causal relation between processes Chris Mungall depends on q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. Chris Mungall RO:0002503 towards towards towards The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. Chris Mungall has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). RO:0002551 uberon has sekeletal support has supporting framework has_skeleton has_skeleton has skeleton This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. http://orcid.org/0000-0002-6601-2165 Chris Mungall causally influenced by (entity-centric) causally influenced by Chris Mungall interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ Chris Mungall molecular interaction relation helper property Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall RO:0002565 external results_in_movement_of results_in_movement_of results in movement of The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). Chris Mungall Vasundra Touré causally influences (entity-centric) causally influences A relation that holds between elements of a musculoskeletal system or its analogs. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. biomechanically related to m1 has_muscle_antagonist m2 iff m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. RO:0002568 uberon has_muscle_antagonist has_muscle_antagonist has muscle antagonist m1 has_muscle_antagonist m2 iff m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. inverse of branching part of Chris Mungall RO:0002569 uberon has_branching_part has_branching_part has branching part x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. Chris Mungall GOC:cjm RO:0002571 uberon lumen_of lumen_of lumen of s is luminal space of x iff s is lumen_of x and s is an immaterial entity Chris Mungall RO:0002572 uberon luminal_space_of luminal_space_of luminal space of A relation that holds between an attribute or a qualifier and another attribute. Chris Mungall This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. RO:0002180 qualifier qualifier placeholder relation to indicate normality/abnormality. has modifier inverse of has skeleton Chris Mungall RO:0002576 uberon skeleton_of skeleton_of skeleton of Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Chris Mungall directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall has part structure that is capable of p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p results in breakdown of RO:0002588 external results_in_assembly_of results_in_assembly_of results in assembly of results_in_assembly_of RO:0002590 external results_in_disassembly_of results_in_disassembly_of results in disassembly of results_in_disassembly_of p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 external results_in_organization_of results_in_organization_of results in organization of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall RO:0002595 causal_relation_between_material_entity_and_a_process causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' RO:0002608 external process_has_causal_agent process_has_causal_agent process has causal agent Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. directly positively regulates (process to process) directly positively regulates Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. directly negatively regulates (process to process) directly negatively regulates a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. Melissa Haendel RO:0003000 external uberon produces produces Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces produces a produced_by b iff some process that occurs_in b has_output a. Melissa Haendel RO:0003001 external uberon produced_by produced_by produced by produced by produced_by p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. cjm 2018-12-13T11:26:17Z RO:0004007 external has_primary_input_or_output has_primary_input_or_output has primary input or output p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. cjm 2018-12-13T11:26:32Z RO:0004008 external has_primary_output has_primary_output has primary output p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. GOC:cjm GOC:dph GOC:kva GOC:pt PMID:27812932 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 p acts on population of c iff c' is a collection, has members of type c, and p has participant c pg 2020-06-08T17:21:33Z RO:0012003 external acts_on_population_of acts_on_population_of acts on population of acts on population of pg 2021-02-26T07:28:29Z RO:0012008 external results_in_fusion_of results_in_fusion_of results in fusion of results in fusion of 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. 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. https://orcid.org/0000-0002-6601-2165 q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. increased in magnitude relative to q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. https://orcid.org/0000-0002-6601-2165 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. 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. https://orcid.org/0000-0002-6601-2165 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. 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. https://orcid.org/0000-0002-6601-2165 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. 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. https://orcid.org/0000-0002-6601-2165 A diagnostic testing device utilizes a specimen. X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y. Asiyah Lin https://orcid.org/0000-0001-9625-1899 Bill Duncan A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08 utilizes A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. regulates characteristic A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. positively regulates characteristic A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. negatively regulates characteristic p has anatomical participant c iff p has participant c, and c is an anatomical entity cjm 2018-09-26T01:08:58Z results in changes to anatomical or cellular structure chebi_ontology has_functional_parent false false has functional parent chebi_ontology has_parent_hydride false false has parent hydride chebi_ontology is_conjugate_acid_of true false is conjugate acid of chebi_ontology is_conjugate_base_of true false is conjugate base of chebi_ontology is_enantiomer_of true false is enantiomer of chebi_ontology is_substituent_group_from false false is substituent group from chebi_ontology is_tautomer_of true is tautomer of A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). has_high_plasma_membrane_amount A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). PMID:19243617 A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). has_low_plasma_membrane_amount A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). PMID:19243617 http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y lacks_part http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y) lacks_plasma_membrane_part by_means by_means by_means has-input has_participant has_participant has_participant qualifier protein has_gene_template false has_gene_template 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. anteriorly_connected_to uberon anteriorly_connected_to 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 channel_for uberon channel_for channel_for channel for channels_from uberon channels_from channels_from channels_from channels_into uberon channels_into channels_into channels_into x is a conduit for y iff y passes through the lumen of x. conduit_for uberon conduit_for 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. distally_connected_to uberon distally_connected_to 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. filtered_through uberon filtered_through 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 X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides. uberon in_central_side_of in_central_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides. BSPO:cjm uberon in_innermost_side_of in_innermost_side_of uberon in_outermost_side_of in_outermost_side_of a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s. add to RO uberon indirectly_supplies indirectly_supplies uberon layer_part_of layer part of x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. posteriorly_connected_to uberon posteriorly_connected_to 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 protects uberon protects 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. proximally_connected_to uberon proximally_connected_to 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 uberon sexually_homologous_to sexually_homologous_to c site_of p if c is the bearer of a disposition that is realized by a process that has p as part. uberon capable_of_has_part site_of site_of subdivision_of uberon subdivision_of 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 . transitively_anteriorly_connected_to uberon transitively_anteriorly_connected_to transitively_anteriorly_connected_to transitively anteriorly connected to . http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern transitively_connected_to uberon transitively_connected_to transitively_connected_to transitively_connected to . transitively_distally_connected_to uberon transitively_distally_connected_to transitively_distally_connected_to transitively distally connected to . http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern . transitively_proximally_connected_to uberon transitively_proximally_connected_to transitively_proximally_connected_to transitively proximally connected to . http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern uberon trunk_part_of trunk_part_of entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] An entity that has temporal parts and that happens, unfolds or develops through time. occurrent ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] s-region SpatialRegion BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet 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. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] bfo BFO:0000019 quality quality sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role 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. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] bfo BFO:0000030 object object function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. bfo BFO:0000040 material entity material entity immaterial ImmaterialEntity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity 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 A dicarboxylic acid dianion resulting from the removal of a proton from both of the carboxylic acid groups of 2-hydroxyglutaric acid. -2 C5H6O5 InChI=1S/C5H8O5/c6-3(5(9)10)1-2-4(7)8/h3,6H,1-2H2,(H,7,8)(H,9,10)/p-2 HWXBTNAVRSUOJR-UHFFFAOYSA-L 146.09814 146.02262 OC(CCC([O-])=O)C([O-])=O Beilstein:5736650 MetaCyc:2-HYDROXYGLUTARIC_ACID Reaxys:5736650 2-hydroxypentanedioate chebi_ontology 2-hydroxyglutarate CHEBI:11596 2-hydroxyglutarate(2-) Beilstein:5736650 Beilstein Reaxys:5736650 Reaxys 2-hydroxypentanedioate IUPAC 2-hydroxyglutarate UniProt The conjugate base of gamma-amino-beta-hydroxybutyric acid arising from deprotonation of the carboxy group. -1 C4H8NO3 InChI=1S/C4H9NO3/c5-2-3(6)1-4(7)8/h3,6H,1-2,5H2,(H,7,8)/p-1 YQGDEPYYFWUPGO-UHFFFAOYSA-M 118.11126 118.05097 NCC(O)CC([O-])=O CAS:352-21-6 KEGG:C03678 4-Amino-3-hydroxybutanoate chebi_ontology CHEBI:11955 4-amino-3-hydroxybutanoate CAS:352-21-6 KEGG COMPOUND KEGG:C03678 ChEBI 4-Amino-3-hydroxybutanoate KEGG_COMPOUND -1 C5H8NO3 InChI=1S/C5H9NO3/c6-3-4(7)1-2-5(8)9/h1-3,6H2,(H,8,9)/p-1 ZGXJTSGNIOSYLO-UHFFFAOYSA-M 130.12196 130.05097 NCC(=O)CCC([O-])=O Beilstein:3937762 5-amino-4-oxopentanoate chebi_ontology CHEBI:12109 5-aminolevulinate Beilstein:3937762 Beilstein 5-amino-4-oxopentanoate IUPAC Any member of a group of fat-soluble retinoids produced via metabolism of provitamin A carotenoids that exhibit biological activity against vitamin A deficiency. Vitamin A is involved in immune function, vision, reproduction, and cellular communication. MetaCyc:Vitamin-A Wikipedia:Vitamin_A chebi_ontology vitamin A vitamer vitamin A vitamers vitamin-A vitamins A CHEBI:12777 vitamin A vitamin A vitamer ChEBI vitamin A vitamers ChEBI vitamin-A ChEBI vitamins A ChEBI Any steroid substituted by a formyl group. chebi_ontology steroid aldehydes CHEBI:131565 steroid aldehyde steroid aldehydes ChEBI Any bacterial metabolite produced during a metabolic reaction in Mycoplasma genitalium. chebi_ontology Mycoplasma genitalium metabolites CHEBI:131604 Mycoplasma genitalium metabolite Mycoplasma genitalium metabolites ChEBI A steroid compound with a structure based on a 27-carbon (cholestane) skeleton. chebi_ontology C27-steroids CHEBI:131619 C27-steroid C27-steroids ChEBI A steroid compound with a structure based on a 19-carbon (androstane) skeleton. chebi_ontology C19-steroids CHEBI:131621 C19-steroid C19-steroids ChEBI A class of carbonyl compound encompassing dicarboxylic acids and any derivatives obtained by substitution of either one or both of the carboxy hydrogens. chebi_ontology dicarboxylic acids and derivatives CHEBI:131927 dicarboxylic acids and O-substituted derivatives dicarboxylic acids and derivatives ChEBI A naphthoquinone in which the oxo groups of the quinone moiety are at positions 1 and 4 of the parent naphthalene ring. chebi_ontology CHEBI:132142 1,4-naphthoquinones A carbohydrate acid derivative anion obtained by deprotonation of the carboxy groups of hyaluronic acid; major species at pH 7.3. -1 (C14H20NO11)n.H2O chebi_ontology hyaluronan hyaluronate polyanion CHEBI:132153 hyaluronate hyaluronan UniProt hyaluronate polyanion ChEBI A citrate anion obtained by deprotonation of the three carboxy groups as well as the hydroxy group of citric acid. -4 C6H4O7 InChI=1S/C6H7O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h1-2H2,(H,7,8)(H,9,10)(H,11,12)/q-1/p-3 KSXLKRAZYZIYCZ-UHFFFAOYSA-K 188.092 187.99790 C(=O)([O-])C(CC(=O)[O-])(CC(=O)[O-])[O-] Chemspider:34552020 2-oxidopropane-1,2,3-tricarboxylate chebi_ontology 2-oxido-1,2,3-propanetricarboxylate citric acid tetraanion CHEBI:132362 citrate(4-) 2-oxidopropane-1,2,3-tricarboxylate IUPAC 2-oxido-1,2,3-propanetricarboxylate ChEBI citric acid tetraanion ChEBI A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of ethylmalonic acid. chebi_ontology ethylmalonate anion ethylmalonic acid anion CHEBI:132938 ethylmalonate ethylmalonate anion ChEBI ethylmalonic acid anion ChEBI A dicarboxylic acid dianion resulting from the removal of a proton from both of the carboxylic acid groups of ethylmalonic acid. -2 C5H6O4 InChI=1S/C5H8O4/c1-2-3(4(6)7)5(8)9/h3H,2H2,1H3,(H,6,7)(H,8,9)/p-2 UKFXDFUAPNAMPJ-UHFFFAOYSA-L 130.099 130.02771 [O-]C(C(C(=O)[O-])CC)=O Reaxys:3904851 ethylpropanedioate chebi_ontology CHEBI:132939 ethylmalonate(2-) Reaxys:3904851 Reaxys ethylpropanedioate IUPAC A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of 2-hydroxyglutaric acid. chebi_ontology 2-hydroxyglutarate anion 2-hydroxyglutaric acid anion CHEBI:132941 2-hydroxyglutarate 2-hydroxyglutarate anion ChEBI 2-hydroxyglutaric acid anion ChEBI chebi_ontology CHEBI:132943 aspartate A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of oxalic acid. chebi_ontology ethanedioic acid anion ethanedioic acid anions oxalate anion oxalate anions oxalates oxalic acid anion oxalic acid anions CHEBI:132952 oxalate ethanedioic acid anion ChEBI ethanedioic acid anions ChEBI oxalate anion ChEBI oxalate anions ChEBI oxalates ChEBI oxalic acid anion ChEBI oxalic acid anions ChEBI A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of sebacic acid. chebi_ontology decanedioic acid anion decanedioic acid anions sebacate anion sebacate anions sebacates sebacic acid anion sebacic acid anions CHEBI:132954 sebacate decanedioic acid anion ChEBI decanedioic acid anions ChEBI sebacate anion ChEBI sebacate anions ChEBI sebacates ChEBI sebacic acid anion ChEBI sebacic acid anions ChEBI A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of 3-methylsuccinic acid. chebi_ontology 2-methylbutanedioic acid anion 2-methylbutanedioic acid anions methylsuccinate anion methylsuccinates methylsuccinic acid anion methylsuccinic acid anions CHEBI:132961 methylsuccinate 2-methylbutanedioic acid anion ChEBI 2-methylbutanedioic acid anions ChEBI methylsuccinate anion ChEBI methylsuccinates ChEBI methylsuccinic acid anion ChEBI methylsuccinic acid anions ChEBI An N-acylglycinate obtained by deprotonation of the carboxy group of hippuric acid (N-benzoylglycine) and its derivatives. chebi_ontology N-benzoylglycinate N-benzoylglycinates N-benzoylglycine anion N-benzoylglycine anions hippurates CHEBI:132966 hippurate N-benzoylglycinate ChEBI N-benzoylglycinates ChEBI N-benzoylglycine anion ChEBI N-benzoylglycine anions ChEBI hippurates ChEBI A primary ammonium ion obtained by protonation of the amino group of 5-aminolevulinic acid. +1 C5H10NO3 InChI=1S/C5H9NO3/c6-3-4(7)1-2-5(8)9/h1-3,6H2,(H,8,9)/p+1 ZGXJTSGNIOSYLO-UHFFFAOYSA-O 132.138 132.06552 C(C(=O)C[NH3+])CC(=O)O 4-carboxy-2-oxobutan-1-aminium chebi_ontology 5-aminolevulinic acid cation 5-aminolevulinic acid(1+) CHEBI:132970 5-ammoniolevulinic acid 4-carboxy-2-oxobutan-1-aminium IUPAC 5-aminolevulinic acid cation ChEBI 5-aminolevulinic acid(1+) ChEBI A dicarboxylic acid dianion that results from the removal of a proton from both of the carboxylic acid groups of any 3-hydroxydicarboxylic acid. -2 C4H4O5R 132.072 132.00587 C(*C(CC(=O)[O-])O)([O-])=O chebi_ontology 3-hydroxydicarboxylic acid dianion(2-) a 3-hydroxy dicarboxylic acid CHEBI:133251 3-hydroxydicarboxylate(2-) 3-hydroxydicarboxylic acid dianion(2-) SUBMITTER a 3-hydroxy dicarboxylic acid UniProt A carboxylic acid dianion obtained by deprotonation of both carboxy groups of any dicarboxylic acid that contains no carbon-carbon double bonds. -2 C2O4R 88.019 87.97966 [O-]C(*C([O-])=O)=O chebi_ontology a saturated dicarboxylic acid saturated dicarboxylate(2-) CHEBI:133291 saturated dicarboxylic acid dianion(2-) a saturated dicarboxylic acid UniProt saturated dicarboxylate(2-) SUBMITTER A dicarboxylic acid dianion obtained by deprotonation of both carboxy groups of any oxo dicarboxylic acid. chebi_ontology oxo dicarboxylic acid oxo dicarboxylic acid dianions CHEBI:133294 oxo dicarboxylic acid dianion oxo dicarboxylic acid UniProt oxo dicarboxylic acid dianions ChEBI A monocarboxylic acid anion that is the conjugate base of N-hexanoylglycine, obtained by deprotonation of the carboxy group; major species at pH 7.3. -1 C8H14NO3 InChI=1S/C8H15NO3/c1-2-3-4-5-7(10)9-6-8(11)12/h2-6H2,1H3,(H,9,10)(H,11,12)/p-1 UPCKIPHSXMXJOX-UHFFFAOYSA-M 172.202 172.09792 N(CC([O-])=O)C(CCCCC)=O (hexanoylamino)acetate chebi_ontology N-caproylglycinate N-hexanoylglycine N-hexanoylglycine anion N-hexanoylglycine(1-) CHEBI:133580 N-hexanoylglycinate (hexanoylamino)acetate IUPAC N-caproylglycinate ChEBI N-hexanoylglycine UniProt N-hexanoylglycine anion ChEBI N-hexanoylglycine(1-) ChEBI An alpha-amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of 1-methylhistidine; major species at pH 7.3. 0 C7H11N3O2 InChI=1S/C7H11N3O2/c1-10-3-5(9-4-10)2-6(8)7(11)12/h3-4,6H,2,8H2,1H3,(H,11,12) BRMWTNUJHUMWMS-UHFFFAOYSA-N 169.181 169.08513 [O-]C(=O)C([NH3+])CC=1N=CN(C1)C 2-azaniumyl-3-(1-methyl-1H-imidazol-4-yl)propanoate chebi_ontology CHEBI:133608 1-methylhistidine zwitterion 2-azaniumyl-3-(1-methyl-1H-imidazol-4-yl)propanoate IUPAC An alpha-amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of 3-methylhistidine; major species at pH 7.3. 0 C7H11N3O2 InChI=1S/C7H11N3O2/c1-10-4-9-3-5(10)2-6(8)7(11)12/h3-4,6H,2,8H2,1H3,(H,11,12) JDHILDINMRGULE-UHFFFAOYSA-N 169.181 169.08513 [O-]C(=O)C([NH3+])CC=1N(C=NC1)C 2-azaniumyl-3-(1-methyl-1H-imidazol-5-yl)propanoate chebi_ontology CHEBI:133609 3-methylhistidine zwitterion 2-azaniumyl-3-(1-methyl-1H-imidazol-5-yl)propanoate IUPAC A monocarboxylic acid anion that is the conjugate base of N-isobutyrylglycine, obtained by deprotonation of the carboxy group; major species at pH 7.3. -1 C6H10NO3 InChI=1S/C6H11NO3/c1-4(2)6(10)7-3-5(8)9/h4H,3H2,1-2H3,(H,7,10)(H,8,9)/p-1 DCICDMMXFIELDF-UHFFFAOYSA-M 144.149 144.06662 C(CNC(=O)C(C)C)(=O)[O-] HMDB:HMDB0000730 (2-methylpropanamido)acetate chebi_ontology N-(2-methylpropanoyl)glycinate N-isobutanoylglycinate isobutanoylglycinate isobutyrylglycinate CHEBI:133610 N-isobutyrylglycinate (2-methylpropanamido)acetate IUPAC N-(2-methylpropanoyl)glycinate ChEBI N-isobutanoylglycinate ChEBI isobutanoylglycinate ChEBI isobutyrylglycinate ChEBI A hydroxy monocarboxylic acid anion which is obtained by deprotonation of the carboxy group of homovanillic acid. -1 C9H9O4 InChI=1S/C9H10O4/c1-13-8-4-6(5-9(11)12)2-3-7(8)10/h2-4,10H,5H2,1H3,(H,11,12)/p-1 QRMZSPFSDQBLIX-UHFFFAOYSA-M 181.166 181.05063 C1=C(C(=CC(=C1)CC([O-])=O)OC)O (4-hydroxy-3-methoxyphenyl)acetate chebi_ontology 3-methoxy-4-hydroxyphenylacetate CHEBI:133744 homovanillate (4-hydroxy-3-methoxyphenyl)acetate IUPAC 3-methoxy-4-hydroxyphenylacetate ChEBI A tricarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of citric acid. chebi_ontology citrate citrate anions CHEBI:133748 citrate anion citrate ChEBI citrate anions ChEBI Any organic compound having an initial boiling point less than or equal to 250 degreeC (482 degreeF) measured at a standard atmospheric pressure of 101.3 kPa. Wikipedia:Volatile_organic_compound chebi_ontology VOC VOCs volatile organic compounds CHEBI:134179 volatile organic compound VOC ChEBI VOCs ChEBI volatile organic compounds ChEBI An alkanesulfonate in which the carbon at position 1 is attached to R, which can represent hydrogens, a carbon chain, or other groups. -1 CH2O3SR 94.091 93.97246 C(S([O-])(=O)=O)* CHEBI:22318 MetaCyc:Alkanesulfonates chebi_ontology alkanesulfonate oxoanions alkanesulfonates an alkanesulfonate CHEBI:134249 alkanesulfonate oxoanion alkanesulfonate oxoanions ChEBI alkanesulfonates ChEBI an alkanesulfonate UniProt Any phenol carrying an additional methoxy substituent at the ortho-position. 0 C7H4O2R4 120.106 120.02113 C1(=C(C(=C(C(=C1*)*)*)OC)O)* CHEBI:13645 MetaCyc:Guaiacols chebi_ontology 1-hydroxy-2-methoxybenzenes 2-methoxyphenol 2-methoxyphenol derivative 2-methoxyphenol derivatives 2-methoxyphenols a guaiacol catechol monomethyl ether catechol monomethyl ethers o-methoxyphenol o-methoxyphenols ortho-methoxyphenol ortho-methoxyphenols CHEBI:134251 guaiacols 1-hydroxy-2-methoxybenzenes ChEBI 2-methoxyphenol ChEBI 2-methoxyphenol derivative SUBMITTER 2-methoxyphenol derivatives ChEBI 2-methoxyphenols ChEBI a guaiacol UniProt catechol monomethyl ether ChEBI catechol monomethyl ethers ChEBI o-methoxyphenol ChEBI o-methoxyphenols ChEBI ortho-methoxyphenol ChEBI ortho-methoxyphenols ChEBI A diol in which the two hydroxy groups are on different carbon atoms, usually but not necessarily adjacent. glycols chebi_ontology Glykol CHEBI:13643 glycol glycols IUPAC Glykol ChEBI An organic group derived from any 3-oxo-Delta(4)-steroid. 0 C6H6O 94.111 94.04186 C1=C(C*)*C(CC1=O)* chebi_ontology a 3-oxo-Delta4-steroid group CHEBI:136849 3-oxo-Delta(4)-steroid group a 3-oxo-Delta4-steroid group UniProt A compound that, on administration, undergoes conversion by biochemical (enzymatic), chemical (possibly following an enzymatic step), or physical (e.g. photochemical) activation processes before becoming the active agent for which it is a pro-agent. PMID:26449612 chebi_ontology pro-agents proagent proagents CHEBI:136859 pro-agent PMID:26449612 Europe PMC pro-agents ChEBI proagent ChEBI proagents ChEBI Any steroid that has beta-configuration at position 5. chebi_ontology 5beta steroids 5beta-steroid 5beta-steroids CHEBI:136889 5beta steroid 5beta steroids ChEBI 5beta-steroid ChEBI 5beta-steroids ChEBI chebi_ontology methylhistidines CHEBI:137682 methylhistidine methylhistidines ChEBI An organic cation obtained by protonation of the amino group of any tertiary amino compound. +1 HNR3 15.015 15.01090 [NH+](*)(*)* chebi_ontology a tertiary amine tertiary amine(1+) tertiary ammonium ions CHEBI:137982 tertiary ammonium ion a tertiary amine UniProt tertiary amine(1+) ChEBI tertiary ammonium ions ChEBI A Bronsted acid derived from one or more inorganic compounds. Inorganic acids (also known as mineral acids) form hydrons and conjugate base ions when dissolved in water. Wikipedia:Mineral_acid chebi_ontology inorganic acids mineral acid mineral acids CHEBI:138103 inorganic acid inorganic acids ChEBI mineral acid ChEBI mineral acids ChEBI Any sterol containing two double bonds between positions 5-6 and 7-8. 0 C19H27OR 271.418 271.20619 C12C(C3C(C(CC3)*)(C)CC1)=CC=C4C2(CCC(C4)O)C MetaCyc:Delta5-Delta7-Steroids chebi_ontology a Delta(5),Delta(7)-sterol CHEBI:138131 Delta(5),Delta(7)-sterol a Delta(5),Delta(7)-sterol UniProt Any C21-steroid carrying a hydroxy substituent at the 17alpha-position. Note that individual examples may have ring substituents at other positions and/or contain double bonds, aromatic A-rings, expanded/contracted rings etc., so the formula and mass may vary from that given for the generic structure. 0 C21H36O InChI=1S/C21H36O/c1-4-21(22)14-11-18-16-9-8-15-7-5-6-12-19(15,2)17(16)10-13-20(18,21)3/h15-18,22H,4-14H2,1-3H3/t15?,16?,17?,18?,19?,20?,21-/m1/s1 JSIVWCLRCGAVHN-ILZKQPLKSA-N 304.511 304.27662 C1CCCC2C1(C3C(CC2)C4C(CC3)([C@](CC4)(CC)O)C)C MetaCyc:17a-hydroxy-C21-steroids chebi_ontology a 17alpha-hydroxy-C21-steroid CHEBI:138141 17alpha-hydroxy-C21-steroid MetaCyc:17a-hydroxy-C21-steroids SUBMITTER a 17alpha-hydroxy-C21-steroid UniProt Any member of a group of hydroxy steroids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine. In mammals bile acids almost invariably have 5beta-configuration, while in lower vertebrates, some bile acids, known as allo-bile acids, have 5alpha-configuration. chebi_ontology CHEBI:138366 bile acids An apoprotein is a protein devoid of its characteristic prosthetic group or metal. KEGG:C16240 apoprotein chebi_ontology apoproteins CHEBI:13850 apoprotein apoprotein IUPAC apoproteins ChEBI Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa). Wikipedia:https://en.wikipedia.org/wiki/Gas chebi_ontology gas molecular entities gaseous molecular entities gaseous molecular entity CHEBI:138675 gas molecular entity gas molecular entities ChEBI gaseous molecular entities ChEBI gaseous molecular entity ChEBI -1 CH2NO2 InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4)/p-1 KXDHJXZQYSOELW-UHFFFAOYSA-M 60.03212 60.00910 NC([O-])=O Beilstein:3903503 CAS:302-11-4 Gmelin:239604 carbamate chebi_ontology Carbamat Karbamat carbamate ion carbamic acid, ion(1-) CHEBI:13941 carbamate Beilstein:3903503 Beilstein CAS:302-11-4 ChemIDplus Gmelin:239604 Gmelin carbamate IUPAC carbamate UniProt Carbamat ChEBI Karbamat ChEBI carbamate ion ChemIDplus carbamic acid, ion(1-) ChemIDplus An alpha-oxyketone that has a hydroxy group as the alpha-oxy moiety. PMID:15326516 PMID:19908854 PMID:20382022 PMID:23295224 chebi_ontology alpha-hydroxy ketones alpha-hydroxy-ketone alpha-hydroxy-ketones alpha-hydroxyketone alpha-hydroxyketones CHEBI:139588 alpha-hydroxy ketone PMID:15326516 Europe PMC PMID:19908854 Europe PMC PMID:20382022 Europe PMC PMID:23295224 Europe PMC alpha-hydroxy ketones ChEBI alpha-hydroxy-ketone ChEBI alpha-hydroxy-ketones ChEBI alpha-hydroxyketone ChEBI alpha-hydroxyketones ChEBI An alpha-hydroxy ketone in which the carbonyl group and the hydroxy group are linked by a -CH2 (methylene) group. 0 C2H3O2R 59.044 59.01330 *C(C(O)([H])[H])=O chebi_ontology primary alpha-hydroxy ketones primary alpha-hydroxy-ketone primary alpha-hydroxy-ketones primary alpha-hydroxyketone primary alpha-hydroxyketones CHEBI:139590 primary alpha-hydroxy ketone primary alpha-hydroxy ketones ChEBI primary alpha-hydroxy-ketone ChEBI primary alpha-hydroxy-ketones ChEBI primary alpha-hydroxyketone ChEBI primary alpha-hydroxyketones ChEBI An alpha-hydroxy ketone in which the carbonyl group and the hydroxy group are linked by a carbon bearing two organyl groups. 0 C2HO2R3 57.028 56.99765 C(C(=O)*)(O)(*)* chebi_ontology tertiary alpha-hydroxy ketones tertiary alpha-hydroxy-ketone tertiary alpha-hydroxy-ketones tertiary alpha-hydroxyketone tertiary alpha-hydroxyketones CHEBI:139592 tertiary alpha-hydroxy ketone tertiary alpha-hydroxy ketones ChEBI tertiary alpha-hydroxy-ketone ChEBI tertiary alpha-hydroxy-ketones ChEBI tertiary alpha-hydroxyketone ChEBI tertiary alpha-hydroxyketones ChEBI A carboxamide resulting from the formal condensation of a carboxylic acid with a primary amine; formula RC(=O)NHR(1). 0 CHNOR2 43.025 43.00581 N(C(*)=O)(*)[H] chebi_ontology secondary carboxamides CHEBI:140325 secondary carboxamide secondary carboxamides ChEBI Any saturated fatty acid containing 4 carbons. 0 CHO2R 45.017 44.99765 *C(O)=O chebi_ontology CHEBI:140601 fatty acid 4:0 0 C62H88CoN13O14PR 1329.350 1328.56433 [Co-3]1234(N5C6=C(C7=[N+]4C(=CC8=[N+]3C(=C(C9=[N+]2[C@@]([C@]5([C@@H]([C@@]6(C)CCC(=O)NC[C@H](OP(O[C@@H]%10[C@H](O[C@H](N%11C=[N+]1C%12=CC(=C(C=C%12%11)C)C)[C@@H]%10O)CO)(=O)[O-])C)CC(=O)N)[H])([C@]([C@@H]9CCC(N)=O)(CC(=O)N)C)C)C)[C@](C)([C@@H]8CCC(=O)N)CC(N)=O)C([C@@H]7CCC(=O)N)(C)C)C)* MetaCyc:CPD-20938 chebi_ontology an R-cob(III)alamin CHEBI:140785 R-cob(III)alamin MetaCyc:CPD-20938 SUBMITTER an R-cob(III)alamin UniProt An antigenic epitope recognized by an anti-bilirubin monoclonal antibody designated 24G7. A substructure of bilirubin IXalpha, it is the region containing the oxo group at C-1, the methyl group at C-2, C-(4, 5, 6, 9), and N-21 and -22. 0 C7H6N2O 134.136 134.04801 C(=CC(NC(=*)*)=*)(NC(C(C)=*)=O)* chebi_ontology CHEBI:142163 24G7 epitope An organic group forming part of, and a proposed epitope within, globoside GM1. 0 C18H30O15 486.423 486.15847 *[C@@H]1O[C@@H]([C@@H](O[C@@H]2O[C@@H]([C@H](O[C@@H]3[C@@H]([C@@H](O)[C@H]([C@@H](CO)O3)O*)O)[C@@H]([C@H]2O)O)CO)[C@@H]([C@H]1O)O)CO PMID:7691279 ->4)-alpha-D-galactopyranosyl-(1->4)-beta-D-galactopyranosylp-(1->4)-beta-D-glucopyranosyl chebi_ontology ->4)-alpha-D-Gal-(1->4)-beta-D-Gal-(1->4)-beta-D-Glc-yl ->4)-alpha-D-Gal-(1->4)-beta-D-Gal-(1->4)-beta-D-Glc-yl group ->4)-alpha-D-galactosyl-(1->4)-beta-D-galactosylp-(1->4)-beta-D-glucosyl CHEBI:142533 ->4)-alpha-D-Galp-(1->4)-beta-D-Galp-(1->4)-beta-D-Glcp-yl group PMID:7691279 Europe PMC ->4)-alpha-D-galactopyranosyl-(1->4)-beta-D-galactopyranosylp-(1->4)-beta-D-glucopyranosyl IUPAC ->4)-alpha-D-Gal-(1->4)-beta-D-Gal-(1->4)-beta-D-Glc-yl ChEBI ->4)-alpha-D-Gal-(1->4)-beta-D-Gal-(1->4)-beta-D-Glc-yl group ChEBI ->4)-alpha-D-galactosyl-(1->4)-beta-D-galactosylp-(1->4)-beta-D-glucosyl ChEBI A trisaccharide beta-D-glucosyl group obtained by removal of the hydroxy group from the hemiacetal function of alpha-D-galactosyl-(1->4)-beta-D-galactosyl-(1->4)-beta-D-glucose. Part of, and the proposed epitope from, alpha-D-galactosyl-(1->4)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1)-ceramide (globoside Gb3Cer; globotriosylceramide; CTH). 0 C18H31O15 487.430 487.16630 [C@@H]1([C@@H]([C@H]([C@@H]([C@H](O1)CO)O[C@H]2[C@@H]([C@H]([C@H]([C@H](O2)CO)O[C@@H]3[C@@H]([C@H]([C@H]([C@H](O3)CO)O)O)O)O)O)O)O)* PMID:33643275 PMID:7691279 alpha-D-galactopyranosyl-(1->4)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranosyl chebi_ontology Gala1-4Galb1-4Glcb-yl Galalpha1-4Galbeta1-4Glcbeta-R Galalpha1-4Galbeta1-4Glcbeta-yl alpha-D-Gal-(1->4)-beta-D-Gal-(1->4)-D-Glc-yl alpha-D-galactosyl-(1->4)-beta-D-galactosyl-(1->4)-beta-D-glucosyl CHEBI:142567 alpha-D-Galp-(1->4)-beta-D-Galp-(1->4)-beta-D-Glcp-yl group PMID:33643275 Europe PMC PMID:7691279 Europe PMC alpha-D-galactopyranosyl-(1->4)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranosyl IUPAC Gala1-4Galb1-4Glcb-yl ChEBI Galalpha1-4Galbeta1-4Glcbeta-R ChEBI Galalpha1-4Galbeta1-4Glcbeta-yl ChEBI alpha-D-Gal-(1->4)-beta-D-Gal-(1->4)-D-Glc-yl ChEBI alpha-D-galactosyl-(1->4)-beta-D-galactosyl-(1->4)-beta-D-glucosyl ChEBI Zwitterionic form of 3-aminoisobutyric acid arising from migration of a proton from the carboxy group to the amino group; major species at pH 7.3. 0 C4H9NO2 InChI=1S/C4H9NO2/c1-3(2-5)4(6)7/h3H,2,5H2,1H3,(H,6,7) QCHPKSFMDHPSNR-UHFFFAOYSA-N 103.120 103.06333 C(C(C)C[NH3+])([O-])=O 3-azaniumyl-2-methylpropanoate chebi_ontology 3-aminoisobutanoate 3-ammonio-2-methylpropanoate CHEBI:142590 3-aminoisobutanoic acid zwitterion 3-azaniumyl-2-methylpropanoate IUPAC 3-aminoisobutanoate UniProt 3-ammonio-2-methylpropanoate ChEBI A beta-D-glucosyl group derived from the trisaccharide N-acetyl-alpha-neuraminyl-(2->3)-beta-D-galactosyl-(1->4)-beta-D-glucose. Implied reactive epitope within ganglioside GM3. 0 C23H38NO18 616.545 616.20889 O([C@@H]1[C@H]([C@H](O[C@@H]2[C@H](O[C@@H](*)[C@@H]([C@H]2O)O)CO)O[C@@H]([C@@H]1O)CO)O)[C@]3(O[C@]([C@@H]([C@H](C3)O)NC(C)=O)([C@@H]([C@@H](CO)O)O)[H])C(O)=O PMID:7534889 5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl-(2->3)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranosyl chebi_ontology 3'-sialyllactosyl Neu5Acalpha2-3Galbeta1-4Glcbeta-yl alpha-N-acetylneuraminyl-(2->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl alpha-Neu5Ac-(2->3)-beta-D-Galp-(1->4)-beta-D-Glcp-yl CHEBI:142767 alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->4)-beta-D-Glc-yl group PMID:7534889 Europe PMC 5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl-(2->3)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranosyl IUPAC 3'-sialyllactosyl ChEBI Neu5Acalpha2-3Galbeta1-4Glcbeta-yl ChEBI alpha-N-acetylneuraminyl-(2->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl ChEBI alpha-Neu5Ac-(2->3)-beta-D-Galp-(1->4)-beta-D-Glcp-yl ChEBI An alpha-amino-acid anion that is the conjugate base of glutamic acid, having anionic carboxy groups and a cationic amino group -1 C5H8NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-1 WHUUTDBJXJRKMK-UHFFFAOYSA-M 146.12136 146.04588 [NH3+]C(CCC([O-])=O)C([O-])=O Gmelin:327908 glutamate(1-) hydrogen glutamate chebi_ontology 2-ammoniopentanedioate glutamate glutamic acid monoanion CHEBI:14321 glutamate(1-) Gmelin:327908 Gmelin glutamate(1-) JCBN hydrogen glutamate IUPAC 2-ammoniopentanedioate IUPAC glutamate UniProt glutamic acid monoanion JCBN The D-stereoisomer of 4-hydroxyproline. 0 C5H9NO3 InChI=1S/C5H9NO3/c7-3-1-4(5(8)9)6-2-3/h3-4,6-7H,1-2H2,(H,8,9)/t3?,4-/m1/s1 PMMYEEVYMWASQN-SRBOSORUSA-N 131.131 131.05824 [C@@H]1(CC(O)CN1)C(O)=O 4-hydroxy-D-proline chebi_ontology (2R)-4-hydroxypyrrolidine-2-carboxylic acid 4-OH-D-Pro 4-hydroxy-D-Pro CHEBI:144637 4-hydroxy-D-proline 4-hydroxy-D-proline IUPAC (2R)-4-hydroxypyrrolidine-2-carboxylic acid ChEBI 4-OH-D-Pro ChEBI 4-hydroxy-D-Pro ChEBI A peptide hormone which consists of two polypeptide chains, A- and B- chains which are linked together by disulfide bonds. The amino acid sequence of insulin varies across species and certain segments of the molecule are highly conserved. In most species, the A chain consists of 21 amino acids and the B chain consists of 30 amino acids. In mammals, insulin is synthesised in the pancreas within the beta cells whereas in certain species of fish, the insulin-producing tissue is uniquely located in separate structures called Brockmann bodies. PMID:12137720 PMID:19251032 PMID:25848166 PMID:5941964 PMID:6069707 Wikipedia:Insulin chebi_ontology CHEBI:145810 insulin PMID:12137720 Europe PMC PMID:19251032 Europe PMC PMID:25848166 Europe PMC PMID:5941964 Europe PMC PMID:6069707 Europe PMC A member of the class of carbohydrates and carbohydrate derivatives that is any oligosaccharide or polysaccharide in which the identity of one or more of the individual monosaccharide units, their connectivity (position of attachment) or the stereochemistry (alpha- or beta-) of one or more of the glycosidic linkages is not known. chebi_ontology partially defined glycan partially defined glycans partially-defined glycans CHEBI:146306 partially-defined glycan partially defined glycan ChEBI partially defined glycans ChEBI partially-defined glycans ChEBI An amino disaccharide that is 2-acetamido-2-deoxy-D-galactopyranose in which the hydroxy group at position 3 has been converted to the corresponding D-galactopyranoside. The stereochemistry at the anomeric position in each of the galactopyranose rings is not stated. 0 C14H25NO11 InChI=1S/C14H25NO11/c1-4(18)15-7-12(9(20)6(3-17)24-13(7)23)26-14-11(22)10(21)8(19)5(2-16)25-14/h5-14,16-17,19-23H,2-3H2,1H3,(H,15,18)/t5-,6-,7-,8+,9+,10+,11-,12-,13?,14?/m1/s1 HMQPEDMEOBLSQB-PVSBWVJQSA-N 383.350 383.14276 O([C@@H]1[C@@H](NC(=O)C)C(O[C@@H]([C@@H]1O)CO)O)C2O[C@@H]([C@H](O)[C@H](O)[C@H]2O)CO GlyGen:G01416HI GlyTouCan:G01416HI KEGG:G10100 2-acetamido-2-deoxy-3-O-D-galactopyranosyl-D-galactopyranose Gal(?1-3)GalNAc chebi_ontology D-galacto-hexopyranosyl-(1->3)-2-acetamido-2-deoxy-D-galacto-hexopyranose N-[(3R,4R,5R,6R)-2,5-dihydroxy-6-(hydroxymethyl)-4-[(3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-3-yl]acetamide WURCS=2.0/2,2,1/[a2112h-1x_1-5_2*NCC/3=O][a2112h-1x_1-5]/1-2/a3-b1 CHEBI:146500 D-Galp-(1->3)-D-GalpNAc 2-acetamido-2-deoxy-3-O-D-galactopyranosyl-D-galactopyranose IUPAC Gal(?1-3)GalNAc IUPAC D-galacto-hexopyranosyl-(1->3)-2-acetamido-2-deoxy-D-galacto-hexopyranose IUPAC N-[(3R,4R,5R,6R)-2,5-dihydroxy-6-(hydroxymethyl)-4-[(3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-3-yl]acetamide IUPAC WURCS=2.0/2,2,1/[a2112h-1x_1-5_2*NCC/3=O][a2112h-1x_1-5]/1-2/a3-b1 SUBMITTER A purine nucleobase found in humans and other organisms. 0 C5H4N4O2 152.111 152.03343 ECMDB:ECMDB00292 KNApSAcK:C00019660 PMID:1557408 PMID:24629268 PMID:9007687 YMDB:YMDB00263 xanthine chebi_ontology 2,6-dioxopurine 2,6-dioxopurines xanthines CHEBI:15318 xanthine PMID:1557408 Europe PMC PMID:24629268 Europe PMC PMID:9007687 Europe PMC xanthine ChEBI 2,6-dioxopurine ChEBI 2,6-dioxopurines ChEBI xanthines ChEBI A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity. CHEBI:13699 CHEBI:2377 KEGG:C00028 KEGG:C16722 Acceptor chebi_ontology A Akzeptor Hydrogen-acceptor Oxidized donor accepteur CHEBI:15339 acceptor Acceptor KEGG_COMPOUND A KEGG_COMPOUND Akzeptor ChEBI Hydrogen-acceptor KEGG_COMPOUND Oxidized donor KEGG_COMPOUND accepteur ChEBI A sulfur-containing amino acid that is propanoic acid with an amino group at position 2 and a sulfanyl group at position 3. 0 C3H7NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6) XUJNEKJLAYXESH-UHFFFAOYSA-N 121.15922 121.01975 NC(CS)C(O)=O CHEBI:14061 CHEBI:23508 CHEBI:4050 Beilstein:1721406 CAS:3374-22-9 Gmelin:2933 KEGG:C00736 KNApSAcK:C00001351 KNApSAcK:C00007323 PMID:17439666 PMID:25181601 Reaxys:1721406 Wikipedia:Cysteine Cysteine cysteine chebi_ontology 2-Amino-3-mercaptopropionic acid 2-amino-3-mercaptopropanoic acid 2-amino-3-sulfanylpropanoic acid C Cys Cystein Hcys Zystein cisteina CHEBI:15356 cysteine Beilstein:1721406 Beilstein CAS:3374-22-9 ChemIDplus CAS:3374-22-9 KEGG COMPOUND CAS:3374-22-9 NIST Chemistry WebBook Gmelin:2933 Gmelin PMID:17439666 Europe PMC PMID:25181601 Europe PMC Reaxys:1721406 Reaxys Cysteine KEGG_COMPOUND cysteine ChEBI cysteine IUPAC 2-Amino-3-mercaptopropionic acid KEGG_COMPOUND 2-amino-3-mercaptopropanoic acid JCBN 2-amino-3-sulfanylpropanoic acid IUPAC C ChEBI Cys ChEBI Cystein ChEBI Hcys IUPAC Zystein ChEBI cisteina ChEBI A 2-oxo monocarboxylic acid anion that is the conjugate base of pyruvic acid, arising from deprotonation of the carboxy group. -1 C3H3O3 InChI=1S/C3H4O3/c1-2(4)3(5)6/h1H3,(H,5,6)/p-1 LCTONWCANYUPML-UHFFFAOYSA-M 87.05412 87.00877 CC(=O)C([O-])=O CHEBI:14987 CHEBI:26462 Beilstein:3587721 CAS:57-60-3 Gmelin:2502 KEGG:C00022 PMID:17190852 PMID:21603897 PMID:21823181 PMID:21854850 PMID:22006570 PMID:22016370 PMID:22215378 PMID:22311625 PMID:22451307 PMID:22458763 Reaxys:3587721 UM-BBD_compID:c0159 2-oxopropanoate pyruvate chebi_ontology 2-oxopropanoate 2-oxopropanoic acid, ion(1-) CHEBI:15361 pyruvate Beilstein:3587721 Beilstein CAS:57-60-3 ChemIDplus Gmelin:2502 Gmelin PMID:17190852 Europe PMC PMID:21603897 Europe PMC PMID:21823181 Europe PMC PMID:21854850 Europe PMC PMID:22006570 Europe PMC PMID:22016370 Europe PMC PMID:22215378 Europe PMC PMID:22311625 Europe PMC PMID:22451307 Europe PMC PMID:22458763 Europe PMC Reaxys:3587721 Reaxys UM-BBD_compID:c0159 UM-BBD 2-oxopropanoate IUPAC pyruvate UniProt 2-oxopropanoate ChEBI 2-oxopropanoic acid, ion(1-) ChemIDplus A simple monocarboxylic acid containing two carbons. 0 C2H4O2 InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4) QTBSBXVTEAMEQO-UHFFFAOYSA-N 60.05200 60.02113 CC(O)=O CHEBI:22169 CHEBI:2387 CHEBI:40486 Beilstein:506007 CAS:64-19-7 Drug_Central:4211 Gmelin:1380 HMDB:HMDB0000042 KEGG:C00033 KEGG:D00010 KNApSAcK:C00001176 LIPID_MAPS_instance:LMFA01010002 MetaCyc:ACET PDBeChem:ACT PDBeChem:ACY PMID:12005138 PMID:15107950 PMID:16630552 PMID:16774200 PMID:17190852 PMID:19416101 PMID:19469536 PMID:22153255 PMID:22173419 PPDB:1333 Reaxys:506007 Wikipedia:Acetic_acid ACETIC ACID Acetic acid acetic acid chebi_ontology AcOH CH3-COOH CH3CO2H E 260 E-260 E260 Essigsaeure Ethanoic acid Ethylic acid HOAc INS No. 260 MeCO2H MeCOOH Methanecarboxylic acid acide acetique ethoic acid CHEBI:15366 acetic acid Beilstein:506007 Beilstein CAS:64-19-7 ChemIDplus CAS:64-19-7 KEGG COMPOUND CAS:64-19-7 NIST Chemistry WebBook Drug_Central:4211 DrugCentral Gmelin:1380 Gmelin LIPID_MAPS_instance:LMFA01010002 LIPID MAPS PMID:12005138 Europe PMC PMID:15107950 Europe PMC PMID:16630552 Europe PMC PMID:16774200 Europe PMC PMID:17190852 Europe PMC PMID:19416101 Europe PMC PMID:19469536 Europe PMC PMID:22153255 Europe PMC PMID:22173419 Europe PMC Reaxys:506007 Reaxys ACETIC ACID PDBeChem Acetic acid KEGG_COMPOUND acetic acid IUPAC AcOH ChEBI CH3-COOH IUPAC CH3CO2H ChEBI E 260 ChEBI E-260 ChEBI E260 ChEBI Essigsaeure ChEBI Ethanoic acid KEGG_COMPOUND Ethylic acid ChemIDplus HOAc ChEBI INS No. 260 ChEBI MeCO2H ChEBI MeCOOH ChEBI Methanecarboxylic acid ChemIDplus acide acetique ChemIDplus ethoic acid ChEBI 0 O2 InChI=1S/O2/c1-2 MYMOFIZGZYHOMD-UHFFFAOYSA-N 31.99880 31.98983 O=O CHEBI:10745 CHEBI:13416 CHEBI:23833 CHEBI:25366 CHEBI:30491 CHEBI:44742 CHEBI:7860 CAS:7782-44-7 Gmelin:485 HMDB:HMDB0001377 KEGG:C00007 KEGG:D00003 MetaCyc:OXYGEN-MOLECULE MolBase:750 PDBeChem:OXY PMID:10906528 PMID:16977326 PMID:18210929 PMID:18638417 PMID:19840863 PMID:7710549 PMID:9463773 Wikipedia:Oxygen dioxygen chebi_ontology Disauerstoff E 948 E-948 E948 O2 OXYGEN MOLECULE Oxygen [OO] dioxygene molecular oxygen CHEBI:15379 dioxygen CAS:7782-44-7 ChemIDplus CAS:7782-44-7 KEGG COMPOUND CAS:7782-44-7 NIST Chemistry WebBook Gmelin:485 Gmelin PMID:10906528 Europe PMC PMID:16977326 Europe PMC PMID:18210929 Europe PMC PMID:18638417 Europe PMC PMID:19840863 Europe PMC PMID:7710549 Europe PMC PMID:9463773 Europe PMC dioxygen IUPAC Disauerstoff ChEBI E 948 ChEBI E-948 ChEBI E948 ChEBI O2 IUPAC O2 KEGG_COMPOUND O2 UniProt OXYGEN MOLECULE PDBeChem Oxygen KEGG_COMPOUND [OO] MolBase dioxygene ChEBI molecular oxygen ChEBI The simplest (and the only achiral) proteinogenic amino acid, with a hydrogen atom as its side chain. 0 C2H5NO2 InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) DHMQDGOQFOQNFH-UHFFFAOYSA-N 75.06664 75.03203 NCC(O)=O CHEBI:10792 CHEBI:14344 CHEBI:24368 CHEBI:42964 CHEBI:5460 Beilstein:635782 CAS:56-40-6 DrugBank:DB00145 Drug_Central:1319 ECMDB:ECMDB00123 Gmelin:1808 HMDB:HMDB0000123 KEGG:C00037 KEGG:D00011 KNApSAcK:C00001361 MetaCyc:GLY PDBeChem:GLY PMID:10930630 PMID:11019925 PMID:11174716 PMID:11542461 PMID:11806864 PMID:12631515 PMID:12754315 PMID:12770151 PMID:12921899 PMID:15331688 PMID:15388434 PMID:15710237 PMID:16105183 PMID:16151895 PMID:16214212 PMID:16417482 PMID:16444815 PMID:16664855 PMID:16901953 PMID:16918424 PMID:16986325 PMID:16998855 PMID:17154252 PMID:17383967 PMID:17582620 PMID:17970719 PMID:18079355 PMID:18396796 PMID:18440992 PMID:18593588 PMID:18816054 PMID:18840508 PMID:19028609 PMID:19120667 PMID:19449910 PMID:19526731 PMID:19544666 PMID:19738917 PMID:19916621 PMID:19924257 PMID:21751272 PMID:22044190 PMID:22079563 PMID:22234938 PMID:22264337 PMID:22293292 PMID:22401276 PMID:22434786 Reaxys:635782 Wikipedia:Glycine YMDB:YMDB00016 GLYCINE Glycine aminoacetic acid glycine chebi_ontology Aminoacetic acid Aminoessigsaeure G Gly Glycin Glycocoll Glykokoll Glyzin H2N-CH2-COOH Hgly Leimzucker aminoethanoic acid CHEBI:15428 glycine Beilstein:635782 Beilstein CAS:56-40-6 ChemIDplus CAS:56-40-6 KEGG COMPOUND CAS:56-40-6 NIST Chemistry WebBook Drug_Central:1319 DrugCentral Gmelin:1808 Gmelin PMID:10930630 Europe PMC PMID:11019925 Europe PMC PMID:11174716 Europe PMC PMID:11542461 Europe PMC PMID:11806864 Europe PMC PMID:12631515 Europe PMC PMID:12754315 Europe PMC PMID:12770151 Europe PMC PMID:12921899 Europe PMC PMID:15331688 Europe PMC PMID:15388434 Europe PMC PMID:15710237 Europe PMC PMID:16105183 Europe PMC PMID:16151895 Europe PMC PMID:16214212 Europe PMC PMID:16417482 Europe PMC PMID:16444815 Europe PMC PMID:16664855 Europe PMC PMID:16901953 Europe PMC PMID:16918424 Europe PMC PMID:16986325 Europe PMC PMID:16998855 Europe PMC PMID:17154252 Europe PMC PMID:17383967 Europe PMC PMID:17582620 Europe PMC PMID:17970719 Europe PMC PMID:18079355 Europe PMC PMID:18396796 Europe PMC PMID:18440992 Europe PMC PMID:18593588 Europe PMC PMID:18816054 Europe PMC PMID:18840508 Europe PMC PMID:19028609 Europe PMC PMID:19120667 Europe PMC PMID:19449910 Europe PMC PMID:19526731 Europe PMC PMID:19544666 Europe PMC PMID:19738917 Europe PMC PMID:19916621 Europe PMC PMID:19924257 Europe PMC PMID:21751272 Europe PMC PMID:22044190 Europe PMC PMID:22079563 Europe PMC PMID:22234938 Europe PMC PMID:22264337 Europe PMC PMID:22293292 Europe PMC PMID:22401276 Europe PMC PMID:22434786 Europe PMC Reaxys:635782 Reaxys GLYCINE PDBeChem Glycine KEGG_COMPOUND aminoacetic acid IUPAC glycine IUPAC Aminoacetic acid KEGG_COMPOUND Aminoessigsaeure ChEBI G ChEBI Gly KEGG_COMPOUND Glycin ChemIDplus Glycocoll ChemIDplus Glykokoll ChEBI Glyzin ChEBI H2N-CH2-COOH IUPAC Hgly IUPAC Leimzucker ChemIDplus aminoethanoic acid ChEBI aminoethanoic acid JCBN squalene Prostaglandin F2alpha in which the hydroxy group at position 9 has been oxidised to the corresponding ketone. Prostaglandin E2 is the most common and most biologically potent of mammalian prostaglandins. 0 C20H32O5 InChI=1S/C20H32O5/c1-2-3-6-9-15(21)12-13-17-16(18(22)14-19(17)23)10-7-4-5-8-11-20(24)25/h4,7,12-13,15-17,19,21,23H,2-3,5-6,8-11,14H2,1H3,(H,24,25)/b7-4-,13-12+/t15-,16+,17+,19+/m0/s1 XEYBRNLFEZDVAW-ARSRFYASSA-N 352.471 352.22497 CCCCC[C@H](O)\C=C\[C@H]1[C@H](O)CC(=O)[C@@H]1C\C=C/CCCC(O)=O CHEBI:10910 CHEBI:10911 CHEBI:114125 CHEBI:26323 CHEBI:4625 CHEBI:8512 Beilstein:2224724 CAS:363-24-6 DrugBank:DB00917 Drug_Central:913 FooDB:FDB022498 HMDB:HMDB0001220 KEGG:C00584 KEGG:D00079 LINCS:LSM-42919 LIPID_MAPS_instance:LMFA03010003 PDBeChem:P2E PMID:11279302 PMID:12746806 PMID:12859290 PMID:14499495 PMID:14535055 PMID:14703707 PMID:15542928 PMID:15661432 PMID:16405508 PMID:16787416 PMID:16978535 PMID:20671299 PMID:2403792 PMID:24501112 PMID:32898608 PMID:33271839 PMID:33559528 PMID:33685091 PMID:33715333 PMID:33782420 PMID:33811074 PMID:33958485 PMID:34065827 PMID:34071686 PMID:34102274 PMID:6317292 PMID:7224729 PMID:74611 PMID:7836930 PMID:9276764 Patent:DE2011969 Patent:GB851827 Patent:NL6505799 Patent:US3598858 Reaxys:2224724 Wikipedia:Prostaglandin_E2 (5Z,13E,15S)-11alpha,15-dihydroxy-9-oxoprosta-5,13-dien-1-oic acid Prostaglandin E2 chebi_ontology (15S)-prostaglandin E2 (5Z,11alpha,13E,15S)-11,15-dihydroxy-9-oxoprosta-5,13-dien-1-oic acid (5Z,13E)-(15S)-11alpha,15-Dihydroxy-9-oxoprost-13-enoate (5Z,13E)-(15S)-11alpha,15-Dihydroxy-9-oxoprosta-5,13-dienoate (E,Z)-(1R,2R,3R)-7-(3-Hydroxy-2-((3S)-(3-hydroxy-1-octenyl))-5-oxocyclopentyl)-5-heptenoic acid (Z)-7-((1R,2R,3R)-3-hydroxy-2-((S,E)-3-hydroxyoct-1-enyl)-5-oxocyclopentyl)hept-5-enoic acid Cervidil Cerviprime Cerviprost Dinoproston Enzaprost E Glandin-E2 Minprositin E2 Minprostin E2 PGE2 Prepidil Propess Prostarmon E Prostenone Prostin Prostin E2 U 12062 U-12,062 U-12062 dinoprostona dinoprostone dinoprostonum CHEBI:15551 prostaglandin E2 Beilstein:2224724 Beilstein CAS:363-24-6 ChemIDplus CAS:363-24-6 KEGG COMPOUND Drug_Central:913 DrugCentral LIPID_MAPS_instance:LMFA03010003 LIPID MAPS PMID:11279302 Europe PMC PMID:12746806 Europe PMC PMID:12859290 Europe PMC PMID:14499495 Europe PMC PMID:14535055 Europe PMC PMID:14703707 Europe PMC PMID:15542928 Europe PMC PMID:15661432 Europe PMC PMID:16405508 Europe PMC PMID:16787416 Europe PMC PMID:16978535 Europe PMC PMID:20671299 Europe PMC PMID:2403792 Europe PMC PMID:24501112 Europe PMC PMID:32898608 Europe PMC PMID:33271839 Europe PMC PMID:33559528 Europe PMC PMID:33685091 Europe PMC PMID:33715333 Europe PMC PMID:33782420 Europe PMC PMID:33811074 Europe PMC PMID:33958485 Europe PMC PMID:34065827 Europe PMC PMID:34071686 Europe PMC PMID:34102274 Europe PMC PMID:6317292 Europe PMC PMID:7224729 Europe PMC PMID:74611 Europe PMC PMID:7836930 Europe PMC PMID:9276764 Europe PMC Reaxys:2224724 Reaxys (5Z,13E,15S)-11alpha,15-dihydroxy-9-oxoprosta-5,13-dien-1-oic acid IUPAC Prostaglandin E2 KEGG_COMPOUND (15S)-prostaglandin E2 ChemIDplus (5Z,11alpha,13E,15S)-11,15-dihydroxy-9-oxoprosta-5,13-dien-1-oic acid ChemIDplus (5Z,13E)-(15S)-11alpha,15-Dihydroxy-9-oxoprost-13-enoate KEGG_COMPOUND (5Z,13E)-(15S)-11alpha,15-Dihydroxy-9-oxoprosta-5,13-dienoate KEGG_COMPOUND (E,Z)-(1R,2R,3R)-7-(3-Hydroxy-2-((3S)-(3-hydroxy-1-octenyl))-5-oxocyclopentyl)-5-heptenoic acid ChemIDplus (Z)-7-((1R,2R,3R)-3-hydroxy-2-((S,E)-3-hydroxyoct-1-enyl)-5-oxocyclopentyl)hept-5-enoic acid ChEMBL Cervidil KEGG_DRUG Cerviprime ChemIDplus Cerviprost ChemIDplus Dinoproston ChemIDplus Enzaprost E ChemIDplus Glandin-E2 ChEBI Minprositin E2 ChemIDplus Minprostin E2 ChemIDplus PGE2 ChemIDplus PGE2 KEGG_COMPOUND Prepidil KEGG_DRUG Propess DrugBank Prostarmon E ChemIDplus Prostenone ChemIDplus Prostin ChemIDplus Prostin E2 KEGG_DRUG U 12062 ChemIDplus U-12,062 ChemIDplus U-12062 ChemIDplus dinoprostona WHO_MedNet dinoprostone WHO_MedNet dinoprostonum WHO_MedNet A N-alkylglycine that is the N-methyl derivative of glycine. It is an intermediate in the metabolic pathway of glycine. 0 C3H7NO2 InChI=1S/C3H7NO2/c1-4-2-3(5)6/h4H,2H2,1H3,(H,5,6) FSYKKLYZXJSNPZ-UHFFFAOYSA-N 89.09322 89.04768 CNCC(O)=O CHEBI:10876 CHEBI:12609 CHEBI:15065 CHEBI:21765 CHEBI:45381 CHEBI:45442 CHEBI:45531 CHEBI:45614 CHEBI:9029 Beilstein:1699442 CAS:107-97-1 Gmelin:2018 HMDB:HMDB0000271 KEGG:C00213 MetaCyc:SARCOSINE PDBeChem:SAR PMID:11272730 PMID:11850512 PMID:15023571 PMID:15331688 PMID:16154544 PMID:17095900 PMID:17190852 PMID:17901997 PMID:19433577 PMID:19577367 PMID:19619564 PMID:19944746 Reaxys:1699442 UM-BBD_compID:c0135 Wikipedia:Sarcosine SARCOSINE Sarcosine sarcosine chebi_ontology (methylamino)acetic acid (methylamino)ethanoic acid L-sarcosine MeGly N-Methylglycine N-methylaminoacetic acid Sar methylaminoacetic acid sarcosinic acid CHEBI:15611 sarcosine PMID:11850512 Europe PMC PMID:15023571 Europe PMC PMID:15331688 Europe PMC PMID:16154544 Europe PMC PMID:17095900 Europe PMC PMID:17190852 Europe PMC PMID:17901997 Europe PMC PMID:19433577 Europe PMC PMID:19577367 Europe PMC PMID:19619564 Europe PMC PMID:19944746 Europe PMC Reaxys:1699442 Reaxys UM-BBD_compID:c0135 UM-BBD SARCOSINE PDBeChem Sarcosine KEGG_COMPOUND sarcosine IUPAC (methylamino)acetic acid ChemIDplus (methylamino)ethanoic acid NIST_Chemistry_WebBook L-sarcosine ChEBI MeGly ChEBI N-Methylglycine KEGG_COMPOUND N-methylaminoacetic acid NIST_Chemistry_WebBook Sar IUPAC methylaminoacetic acid NIST_Chemistry_WebBook sarcosinic acid ChemIDplus Beilstein:1699442 ChemIDplus CAS:107-97-1 ChemIDplus CAS:107-97-1 KEGG COMPOUND CAS:107-97-1 NIST Chemistry WebBook Gmelin:2018 Gmelin PMID:11272730 Europe PMC An imidazolidine-2,4-dione that is 5-aminohydantoin in which a carbamoyl group is attached to the exocyclic nitrogen. 0 C4H6N4O3 InChI=1S/C4H6N4O3/c5-3(10)6-1-2(9)8-4(11)7-1/h1H,(H3,5,6,10)(H2,7,8,9,11) POJWUDADGALRAB-UHFFFAOYSA-N 158.11560 158.04399 NC(=O)NC1NC(=O)NC1=O CHEBI:13761 CHEBI:22354 CHEBI:2594 CAS:97-59-6 Drug_Central:4268 HMDB:HMDB0000462 KEGG:C01551 KEGG:D00121 KNApSAcK:C00007468 LINCS:LSM-5190 MetaCyc:ALLANTOIN PMID:11157020 PMID:14619112 PMID:17190852 Patent:US2158098 Reaxys:83514 Wikipedia:Allantoin Allantoin N-(2,5-dioxoimidazolidin-4-yl)urea allantoin chebi_ontology (2,5-Dioxo-4-imidazolidinyl)urea 2,5-Dioxo-4-imidazolidinyl-urea 4-ureido-2,5-imidazolidinedione 5-Ureido-2,4-imidazolidindione 5-Ureidohydantoin Glyoxyldiureide N-(2,5-Dioxo-4-imidazolidinyl)urea CHEBI:15676 allantoin CAS:97-59-6 ChemIDplus CAS:97-59-6 KEGG COMPOUND CAS:97-59-6 NIST Chemistry WebBook Drug_Central:4268 DrugCentral PMID:11157020 Europe PMC PMID:14619112 Europe PMC PMID:17190852 Europe PMC Reaxys:83514 Reaxys Allantoin KEGG_COMPOUND N-(2,5-dioxoimidazolidin-4-yl)urea IUPAC allantoin UniProt (2,5-Dioxo-4-imidazolidinyl)urea ChemIDplus 2,5-Dioxo-4-imidazolidinyl-urea NIST_Chemistry_WebBook 4-ureido-2,5-imidazolidinedione HMDB 5-Ureido-2,4-imidazolidindione ChemIDplus 5-Ureidohydantoin KEGG_COMPOUND Glyoxyldiureide KEGG_COMPOUND N-(2,5-Dioxo-4-imidazolidinyl)urea HMDB A sialodiosylceramide consisting of the trisaccharide alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->4)-beta-D-Glc attached to the primary hydroxy function of ceramide. 0 C42H73N2O21R 942.02980 941.47058 [H][C@]1(O[C@@](C[C@H](O)[C@H]1NC(C)=O)(O[C@H]1[C@@H](O)[C@@H](CO)O[C@@H](O[C@H]2[C@H](O)[C@@H](O)[C@H](OC[C@H](NC([*])=O)[C@H](O)\C=C\CCCCCCCCCCCCC)O[C@@H]2CO)[C@@H]1O)C(O)=O)[C@H](O)[C@H](O)CO CHEBI:10959 CHEBI:12288 CHEBI:12580 CHEBI:15680 CHEBI:21147 CHEBI:21623 CHEBI:5227 KEGG:C04730 KEGG:G00108 LIPID_MAPS_instance:LMSP0601AJ00 PMID:11093705 PMID:11164910 PMID:11534772 PMID:12950986 PMID:1371229 PMID:1379980 PMID:15102521 PMID:15385432 PMID:15546874 PMID:1567198 PMID:15939439 PMID:16212238 PMID:16341241 PMID:16574813 PMID:167132 PMID:1724444 PMID:19364317 PMID:21149694 PMID:2303428 PMID:2448252 PMID:2449247 PMID:2714813 PMID:2775195 PMID:3392043 PMID:3864442 PMID:7534889 PMID:7693874 PMID:8448384 PMID:8496625 PMID:9375803 (2S,3R,4E)-2-(acylamino)-3-hydroxyoctadec-4-en-1-yl 5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl-(2->3)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranoside chebi_ontology (Gal)1 (Glc)1 (Neu5Ac)1 (Cer)1 (N-Acetylneuraminyl)-D-galactosyl-D-glucosylceramide (Neu5Ac)GM3 GM3 GM3 (NeuAc) Hematoside N-Acetylneuraminyl-2,3-alpha-D-galactosyl-1,4-beta-D-glucosylceramide Neu5Ac-alpha2->3Gal-beta1->4Glc-beta1->1'Cer Neu5Acalpha2->3Galbeta1->4Glcbeta-Cer NeuAc-GM3 NeuAcalpha2-3Galbeta1-4Glcbeta1-1'Cer NeuAcalpha2->3Galbeta1->4Glc-Cer alpha-N-Acetylneuraminyl-2,3-beta-D-galactosyl-1,4-beta-D-glucosylceramide alpha-N-acetylneuraminosyl-(2->3)-beta-D-galactosyl-(1->4)-beta-D-glucosylceramide alpha-N-acetylneuraminosyl-(2->3)-beta-D-galactosyl-(1->4)-beta-D-glucosylceramides alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->4)-beta-D-Glc-(1<->1')-Cer alpha-Neu5Ac-(2->3)-beta-D-Galp-(1->4)-beta-D-Glcp-(1<->1')-Cer ganglioside GM3 monosialoganglioside GM3 CHEBI:15681 alpha-N-acetylneuraminyl-(2->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide LIPID_MAPS_instance:LMSP0601AJ00 LIPID MAPS PMID:11093705 Europe PMC PMID:11164910 Europe PMC PMID:11534772 Europe PMC PMID:12950986 Europe PMC PMID:1371229 Europe PMC PMID:1379980 Europe PMC PMID:15102521 Europe PMC PMID:15385432 Europe PMC PMID:15546874 Europe PMC PMID:1567198 Europe PMC PMID:15939439 Europe PMC PMID:16212238 Europe PMC PMID:16341241 Europe PMC PMID:16574813 Europe PMC PMID:167132 Europe PMC PMID:1724444 Europe PMC PMID:19364317 Europe PMC PMID:21149694 Europe PMC PMID:2303428 Europe PMC PMID:2448252 Europe PMC PMID:2449247 Europe PMC PMID:2714813 Europe PMC PMID:2775195 Europe PMC PMID:3392043 Europe PMC PMID:3864442 Europe PMC PMID:7534889 Europe PMC PMID:7693874 Europe PMC PMID:8448384 Europe PMC PMID:8496625 Europe PMC PMID:9375803 Europe PMC (2S,3R,4E)-2-(acylamino)-3-hydroxyoctadec-4-en-1-yl 5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl-(2->3)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranoside IUPAC (Gal)1 (Glc)1 (Neu5Ac)1 (Cer)1 KEGG_GLYCAN (N-Acetylneuraminyl)-D-galactosyl-D-glucosylceramide KEGG_COMPOUND (Neu5Ac)GM3 ChEBI GM3 KEGG_COMPOUND GM3 (NeuAc) ChEBI Hematoside KEGG_GLYCAN N-Acetylneuraminyl-2,3-alpha-D-galactosyl-1,4-beta-D-glucosylceramide KEGG_COMPOUND Neu5Ac-alpha2->3Gal-beta1->4Glc-beta1->1'Cer KEGG_COMPOUND Neu5Acalpha2->3Galbeta1->4Glcbeta-Cer ChEBI NeuAc-GM3 ChEBI NeuAcalpha2-3Galbeta1-4Glcbeta1-1'Cer ChEBI NeuAcalpha2->3Galbeta1->4Glc-Cer ChEBI alpha-N-Acetylneuraminyl-2,3-beta-D-galactosyl-1,4-beta-D-glucosylceramide KEGG_COMPOUND alpha-N-acetylneuraminosyl-(2->3)-beta-D-galactosyl-(1->4)-beta-D-glucosylceramide ChEBI alpha-N-acetylneuraminosyl-(2->3)-beta-D-galactosyl-(1->4)-beta-D-glucosylceramides ChEBI alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->4)-beta-D-Glc-(1<->1')-Cer ChEBI alpha-Neu5Ac-(2->3)-beta-D-Galp-(1->4)-beta-D-Glcp-(1<->1')-Cer ChEBI ganglioside GM3 ChEBI monosialoganglioside GM3 ChEBI Aldehydic parent sugars (polyhydroxy aldehydes H[CH(OH)]nC(=O)H, n >= 2) and their intramolecular hemiacetals. 0 C2H4O2(CH2O)n CHEBI:13755 CHEBI:22305 CHEBI:2561 KEGG:C01370 Wikipedia:Aldose Aldose chebi_ontology aldoses an aldose CHEBI:15693 aldose Aldose KEGG_COMPOUND aldoses ChEBI an aldose UniProt Any alpha-amino acid having L-configuration at the alpha-carbon. 0 C2H4NO2R 74.05870 74.02420 N[C@@H]([*])C(O)=O CHEBI:13072 CHEBI:13243 CHEBI:13797 CHEBI:21224 CHEBI:6175 KEGG:C00151 L-alpha-amino acid L-alpha-amino acids chebi_ontology L-2-Amino acid L-Amino acid L-alpha-amino acids CHEBI:15705 L-alpha-amino acid L-alpha-amino acid IUPAC L-alpha-amino acids IUPAC L-2-Amino acid KEGG_COMPOUND L-Amino acid KEGG_COMPOUND L-alpha-amino acids ChEBI A dipeptide that is the N-(beta-alanyl) derivative of L-histidine. 0 C9H14N4O3 InChI=1S/C9H14N4O3/c10-2-1-8(14)13-7(9(15)16)3-6-4-11-5-12-6/h4-5,7H,1-3,10H2,(H,11,12)(H,13,14)(H,15,16)/t7-/m0/s1 CQOVPNPJLQNMDC-ZETCQYMHSA-N 226.236 226.10659 NCCC(=O)N[C@@H](CC1=CNC=N1)C(O)=O CHEBI:13948 CHEBI:23040 CHEBI:3428 CAS:305-84-0 Chemspider:388363 DrugBank:DB11695 HMDB:HMDB0000033 KEGG:C00386 KNApSAcK:C00052222 PDBeChem:8V0 PMID:10841274 PMID:10951105 PMID:10951108 PMID:11470131 PMID:11707898 PMID:11911459 PMID:11976203 PMID:12139778 PMID:15853927 PMID:15878720 PMID:15941308 PMID:16162015 PMID:16181134 PMID:16287364 PMID:16406688 PMID:16804013 PMID:17031479 PMID:1735411 PMID:17443912 PMID:18019400 PMID:18076890 PMID:18773880 PMID:19309105 PMID:20017611 PMID:20681748 PMID:24398899 PMID:2674258 PMID:29463897 PMID:31951767 PMID:33586561 PMID:33704575 PMID:34067694 PMID:8689392 PMID:9029640 PMID:9928418 Reaxys:87671 Wikipedia:Carnosine Carnosine N(alpha)-(beta-alanyl)-L-histidine chebi_ontology (2S)-2-(3-aminopropanamido)-3-(1H-imidazol-4-yl)propanoic acid Karnozin Karnozzn L-carnosine N-(3-aminopropanoyl)-L-histidine N-2-M N-beta-alanyl-L-histidine Nalpha-(beta-alanyl)-L-histidine beta-alanyl-L-histidine ignotine CHEBI:15727 carnosine CAS:305-84-0 ChemIDplus CAS:305-84-0 KEGG COMPOUND PMID:10841274 Europe PMC PMID:10951105 Europe PMC PMID:10951108 Europe PMC PMID:11470131 Europe PMC PMID:11707898 Europe PMC PMID:11911459 Europe PMC PMID:11976203 Europe PMC PMID:12139778 Europe PMC PMID:15853927 Europe PMC PMID:15878720 Europe PMC PMID:15941308 Europe PMC PMID:16162015 Europe PMC PMID:16181134 Europe PMC PMID:16287364 Europe PMC PMID:16406688 Europe PMC PMID:16804013 Europe PMC PMID:17031479 Europe PMC PMID:1735411 Europe PMC PMID:17443912 Europe PMC PMID:18019400 Europe PMC PMID:18076890 Europe PMC PMID:18773880 Europe PMC PMID:19309105 Europe PMC PMID:20017611 Europe PMC PMID:20681748 Europe PMC PMID:24398899 Europe PMC PMID:2674258 Europe PMC PMID:29463897 Europe PMC PMID:31951767 Europe PMC PMID:33586561 Europe PMC PMID:33704575 Europe PMC PMID:34067694 Europe PMC PMID:8689392 Europe PMC PMID:9029640 Europe PMC PMID:9928418 Europe PMC Reaxys:87671 Reaxys Carnosine KEGG_COMPOUND N(alpha)-(beta-alanyl)-L-histidine IUPAC (2S)-2-(3-aminopropanamido)-3-(1H-imidazol-4-yl)propanoic acid IUPAC Karnozin ChemIDplus Karnozzn ChemIDplus L-carnosine ChemIDplus N-(3-aminopropanoyl)-L-histidine ChEBI N-2-M ChemIDplus N-beta-alanyl-L-histidine HMDB Nalpha-(beta-alanyl)-L-histidine KEGG_COMPOUND beta-alanyl-L-histidine ChEBI beta-alanyl-L-histidine IUPAC ignotine ChemIDplus A primary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has either three hydrogen atoms attached to it or only one other carbon atom and two hydrogen atoms attached to it. 0 CH3OR 31.034 31.01839 *C(O)([H])[H] CHEBI:13676 CHEBI:14887 CHEBI:26262 CHEBI:57489 CHEBI:8406 KEGG:C00226 Primary alcohol chebi_ontology 1-Alcohol a primary alcohol primary alcohols CHEBI:15734 primary alcohol Primary alcohol KEGG_COMPOUND 1-Alcohol KEGG_COMPOUND a primary alcohol UniProt primary alcohols ChEBI A monocarboxylic acid anion that is the conjugate base of formic acid. Induces severe metabolic acidosis and ocular injury in human subjects. -1 CHO2 InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)/p-1 BDAGIHXWWSANSR-UHFFFAOYSA-M 45.01744 44.99820 [H]C([O-])=O CHEBI:14276 CHEBI:24081 Beilstein:1901205 CAS:71-47-6 Gmelin:1006 HMDB:HMDB0000142 KEGG:C00058 MetaCyc:FORMATE PMID:17190852 PMID:3946945 Reaxys:1901205 UM-BBD_compID:c0106 Wikipedia:Formate formate chebi_ontology HCO2 anion aminate formiate formic acid, ion(1-) formylate hydrogen carboxylate methanoate CHEBI:15740 formate Beilstein:1901205 Beilstein CAS:71-47-6 ChemIDplus CAS:71-47-6 NIST Chemistry WebBook Gmelin:1006 Gmelin PMID:17190852 Europe PMC PMID:3946945 Europe PMC Reaxys:1901205 Reaxys UM-BBD_compID:c0106 UM-BBD formate IUPAC formate UniProt HCO2 anion NIST_Chemistry_WebBook aminate ChEBI formiate ChEBI formic acid, ion(1-) ChemIDplus formylate ChEBI hydrogen carboxylate ChEBI methanoate ChEBI A straight-chain, sixteen-carbon, saturated long-chain fatty acid. 0 C16H32O2 InChI=1S/C16H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16(17)18/h2-15H2,1H3,(H,17,18) IPCSVZSSVZVIGE-UHFFFAOYSA-N 256.42410 256.24023 CCCCCCCCCCCCCCCC(O)=O CHEBI:14730 CHEBI:233028 CHEBI:24540 CHEBI:24541 CHEBI:24542 CHEBI:24550 CHEBI:29889 CHEBI:35978 CHEBI:44952 Beilstein:607489 CAS:57-10-3 DrugBank:DB03796 Gmelin:190200 HMDB:HMDB0000220 KEGG:C00249 KEGG:D05341 KNApSAcK:C00001233 KNApSAcK:C00030479 LIPID_MAPS_instance:LMFA01010001 MetaCyc:PALMITATE PDBeChem:PLM PMID:12492626 PMID:15357969 PMID:1589452 PMID:16509590 PMID:16884313 PMID:17439666 PMID:17502136 PMID:20001317 PMID:22735334 PMID:25584012 PMID:28600633 PPDB:1336 Reaxys:607489 Wikipedia:Palmitic_acid hexadecanoic acid chebi_ontology 1-Pentadecanecarboxylic acid 1-hexyldecanoic acid 16:00 C16 C16 fatty acid C16:0 CH3-[CH2]14-COOH FA 16:0 Hexadecanoate Hexadecylic acid Hexaectylic acid PALMITIC ACID Palmitate Palmitic acid Palmitinic acid Palmitinsaeure Pentadecanecarboxylic acid cetylic acid hexadecoic acid n-hexadecanoic acid n-hexadecoic acid palmitic acid CHEBI:15756 hexadecanoic acid Beilstein:607489 Beilstein CAS:57-10-3 ChemIDplus CAS:57-10-3 KEGG COMPOUND CAS:57-10-3 NIST Chemistry WebBook Gmelin:190200 Gmelin LIPID_MAPS_instance:LMFA01010001 LIPID MAPS PMID:12492626 Europe PMC PMID:15357969 ChEMBL PMID:1589452 Europe PMC PMID:16509590 ChEMBL PMID:16884313 ChEMBL PMID:17439666 Europe PMC PMID:17502136 ChEMBL PMID:20001317 Europe PMC PMID:22735334 Europe PMC PMID:25584012 Europe PMC PMID:28600633 Europe PMC Reaxys:607489 Reaxys hexadecanoic acid IUPAC 1-Pentadecanecarboxylic acid ChemIDplus 1-hexyldecanoic acid HMDB 16:00 ChEBI C16 ChEBI C16 fatty acid HMDB C16:0 LIPID_MAPS CH3-[CH2]14-COOH IUPAC FA 16:0 ChEBI Hexadecanoate KEGG_COMPOUND Hexadecylic acid HMDB Hexadecylic acid KEGG_COMPOUND Hexaectylic acid HMDB PALMITIC ACID PDBeChem Palmitate KEGG_COMPOUND Palmitic acid KEGG_COMPOUND Palmitinic acid HMDB Palmitinsaeure ChEBI Pentadecanecarboxylic acid ChemIDplus cetylic acid KEGG_COMPOUND hexadecoic acid ChEBI n-hexadecanoic acid NIST_Chemistry_WebBook n-hexadecoic acid NIST_Chemistry_WebBook palmitic acid ChEBI Any fatty acid anion containing a ring composed of carbon atoms. Major microspecies at pH 7.3 chebi_ontology carbocyclic fatty acid CHEBI:157668 carbocyclic fatty acid anion carbocyclic fatty acid UniProt A carbohydrate acid derivative anion that is a polyanionic form of heparan sulfate arising from global deprotonation of the carboxy and N-sulfo groups; major species at pH 7.3. -4 (C12H15NO20S3)n 0.0 0.0 chebi_ontology heparan sulfate group CHEBI:157750 heparan sulfate polyanion heparan sulfate group UniProt Any N-acyl-amino acid in which the amino acid moiety has D configuration. 0 C3H3NO3R2 101.06080 101.01129 OC(=O)[C@@H]([*])NC([*])=O CHEBI:12474 CHEBI:21631 CHEBI:7224 chebi_ontology CHEBI:15778 N-acyl-D-amino acid A dicarboxylic acid dianion obtained by the deprotonation of the carboxy groups of malonic acid. -2 C3H2O4 InChI=1S/C3H4O4/c4-2(5)1-3(6)7/h1H2,(H,4,5)(H,6,7)/p-2 OFOBLEOULBTSOW-UHFFFAOYSA-L 102.04558 101.99641 [O-]C(=O)CC([O-])=O CHEBI:14563 CHEBI:25130 CHEBI:44151 Beilstein:3904386 CAS:156-80-9 DrugBank:DB02201 Gmelin:141932 KEGG:C00383 PDBeChem:MLI Reaxys:3904386 propanedioate chebi_ontology (-)OOC-CH2-COO(-) MALONATE ION malo malonate malonic acid, ion(2-) propanedioic acid, ion(2-) CHEBI:15792 malonate(2-) Beilstein:3904386 Beilstein CAS:156-80-9 ChemIDplus Gmelin:141932 Gmelin Reaxys:3904386 Reaxys propanedioate IUPAC (-)OOC-CH2-COO(-) ChEBI MALONATE ION PDBeChem malo IUPAC malonate UniProt malonic acid, ion(2-) ChemIDplus propanedioic acid, ion(2-) ChemIDplus A 2-hydroxyglutarate(2-) that has (2R)-configuration. -2 C5H6O5 InChI=1S/C5H8O5/c6-3(5(9)10)1-2-4(7)8/h3,6H,1-2H2,(H,7,8)(H,9,10)/p-2/t3-/m1/s1 HWXBTNAVRSUOJR-GSVOUGTGSA-L 146.09814 146.02262 O[C@H](CCC([O-])=O)C([O-])=O CHEBI:10974 CHEBI:18650 KEGG:C01087 MetaCyc:R-2-HYDROXYGLUTARATE (2R)-2-hydroxypentanedioate chebi_ontology (R)-2-hydroxyglutarate CHEBI:15801 (R)-2-hydroxyglutarate(2-) (2R)-2-hydroxypentanedioate IUPAC (R)-2-hydroxyglutarate ChEBI (R)-2-hydroxyglutarate UniProt A peptide containing ten or more amino acid residues. C4H6N2O3R2(C2H2NOR)n CHEBI:14860 CHEBI:8314 KEGG:C00403 Polypeptide polypeptides chebi_ontology Polypeptid polipeptido CHEBI:15841 polypeptide Polypeptide KEGG_COMPOUND polypeptides IUPAC Polypeptid ChEBI polipeptido ChEBI Any 3-hydroxy steroid whose skeleton is closely related to cholestan-3-ol (additional carbon atoms may be present in the side chain). 0 C19H31OR 275.450 275.23749 C12C(C3C(C(CC3)*)(C)CC1)CCC4C2(CCC(C4)O)C CHEBI:13688 CHEBI:15114 CHEBI:26771 CHEBI:9266 KEGG:C00370 LIPID_MAPS_class:LMST01 MetaCyc:Sterols Wikipedia:Sterol Sterol sterols chebi_ontology 3-hydroxysteroids a sterol CHEBI:15889 sterol LIPID_MAPS_class:LMST01 LIPID MAPS Sterol KEGG_COMPOUND sterols IUPAC 3-hydroxysteroids ChEBI a sterol UniProt An amino sulfonic acid that is the 2-amino derivative of ethanesulfonic acid. It is a naturally occurring amino acid derived from methionine and cysteine metabolism. An abundant component of fish- and meat-based foods, it has been used as an oral supplement in the treatment of disorders such as cystic fibrosis and hypertension. 0 C2H7NO3S InChI=1S/C2H7NO3S/c3-1-2-7(4,5)6/h1-3H2,(H,4,5,6) XOAAWQZATWQOTB-UHFFFAOYSA-N 125.148 125.01466 C(CS(O)(=O)=O)N CHEBI:15195 CHEBI:26852 CHEBI:45877 CHEBI:9406 Beilstein:1751215 CAS:107-35-7 DrugBank:DB01956 Drug_Central:4486 Gmelin:82121 HMDB:HMDB0000251 KEGG:C00245 KEGG:D00047 KNApSAcK:C00048188 MetaCyc:TAURINE PDBeChem:TAU PMID:10098958 PMID:10325611 PMID:10349454 PMID:10827156 PMID:11162030 PMID:11842876 PMID:11918831 PMID:11931837 PMID:12297216 PMID:12499349 PMID:12834252 PMID:14992292 PMID:15503229 PMID:15780050 PMID:15911239 PMID:16169526 PMID:16444816 PMID:16923232 PMID:17053427 PMID:17081118 PMID:17875433 PMID:17997039 PMID:18060526 PMID:18171928 PMID:19074966 PMID:19212411 PMID:19309105 PMID:19940987 PMID:2122710 PMID:21761941 PMID:22770225 PMID:2370482 PMID:24027187 PMID:2494044 PMID:27291853 PMID:27334436 PMID:27345710 PMID:27380030 PMID:27412799 PMID:27471162 PMID:27535560 PMID:3106924 PMID:3393260 PMID:6198473 PMID:7588651 PMID:8692051 PMID:8818047 PMID:9635063 Reaxys:1751215 Wikipedia:Taurine 2-aminoethanesulfonic acid Taurine chebi_ontology 2-Aminoethanesulfonic acid 2-aminoethyl sulfonate Aminoethylsulfonic acid beta-aminoethylsulfonic acid CHEBI:15891 taurine Beilstein:1751215 Beilstein CAS:107-35-7 ChemIDplus CAS:107-35-7 KEGG COMPOUND CAS:107-35-7 NIST Chemistry WebBook Drug_Central:4486 DrugCentral Gmelin:82121 Gmelin