An ontology of phenotypic qualities (properties, attributes or characteristics). PATO - the Phenotype And Trait Ontology quality 1.2 2022-01-12 definition IAO:0000116 uberon editor_note true editor_note editor note 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 'anterior end of organism' is-opposite-of 'posterior end of organism' 'increase in temperature' is-opposite-of 'decrease in temperature' x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). RO:0002604 quality is_opposite_of true true is_opposite_of is opposite of is_opposite_of Abnormal/normal slim Absent/present slim Attribute slim cell_quality Disposition slim Human phenotype slim Pathology slim Relational slim: types of quality that require an additional entity in order to exist Scalar slim Value slim http://purl.org/dc/elements/1.1/creator uberon dc-creator true dc-creator creator subset_property consider has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym in_subset shorthand is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of BFO:0000050 external quality uberon part_of part_of part of part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part BFO:0000051 external quality uberon has_part has_part has part has part has_part preceded by X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X). x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 is preceded by takes place after external uberon preceded_by preceded_by preceded by preceded by preceded_by is preceded by SIO:000249 takes place after Allen:precedes precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 external uberon precedes precedes precedes precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in BFO:0000066 external occurs_in occurs_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in occurs in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t BFO:0000067 uberon contains_process contains_process Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process contains process x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer. cjm 2009-07-31T02:15:46Z BSPO:0000096 uberon anterior_to anterior_to anterior_to x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer. http://orcid.org/0000-0002-6601-2165 x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal). BSPO:0000097 uberon distal_to distal_to distal_to x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal). http://orcid.org/0000-0002-6601-2165 x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000098 uberon dorsal_to dorsal_to dorsal_to x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). http://orcid.org/0000-0002-6601-2165 x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail. BSPO:0000099 caudal_to uberon posterior_to posterior_to posterior_to x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail. http://orcid.org/0000-0002-6601-2165 x proximal_to y iff x is closer to the point of attachment with the body than y. BSPO:0000100 uberon proximal_to proximal_to proximal_to x proximal_to y iff x is closer to the point of attachment with the body than y. http://orcid.org/0000-0002-6601-2165 x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000102 uberon ventral_to ventral_to ventral_to x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). http://orcid.org/0000-0002-6601-2165 BSPO:0000107 uberon deep_to deep_to deep_to BSPO:0000108 uberon superficial_to superficial_to superficial_to X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion. BSPO:0000120 uberon in_left_side_of in_left_side_of in_left_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion. BSPO:PATO_mtg_2009 X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion. BSPO:0000121 uberon in_right_side_of in_right_side_of in_right_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion. BSPO:PATO_mtg_2009 X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion. BSPO:0000122 uberon in_posterior_side_of in_posterior_side_of in_posterior_side_of X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion. BSPO:PATO_mtg_2009 X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion. BSPO:0000123 uberon in_anterior_side_of in_anterior_side_of in_anterior_side_of X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion. BSPO:PATO_mtg_2009 X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. BSPO:0000124 uberon in_proximal_side_of in_proximal_side_of in_proximal_side_of X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. BSPO:PATO_mtg_2009 X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion. BSPO:0000125 uberon in_distal_side_of in_distal_side_of in_distal_side_of X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion. BSPO:PATO_mtg_2009 X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure. BSPO:0000126 uberon in_lateral_side_of in_lateral_side_of in_lateral_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure. https://orcid.org/0000-0002-6601-2165 X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y. BSPO:0001106 uberon proximalmost_part_of proximalmost_part_of proximalmost_part_of X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y. https://orcid.org/0000-0002-6601-2165 This relation holds when both the deep_to and ajdacent_to relationship similarly hold. BSPO:0001107 uberon immediately_deep_to immediately_deep_to immediately_deep_to This relation holds when both the deep_to and ajdacent_to relationship similarly hold. http://orcid.org/0000-0002-6601-2165 GOREL:0002003 external results_in_distribution_of results_in_distribution_of results_in_distribution_of GOREL:0002004 external results_in_fission_of results_in_fission_of results_in_fission_of inheres in this fragility is a characteristic of this vase this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of RO:0000053 external uberon bearer_of bearer_of bearer of has characteristic participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in RO:0000056 external uberon participates_in participates_in participates in participates in participates_in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 external has_participant has_participant has participant has participant this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality RO:0000086 uberon has_quality has_quality has quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ location_of RO:0001015 uberon location_of location_of location of location_of contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): Intended meaning: domain: material entity range: spatial region or site (immaterial continuant) contained_in contained in contains RO:0001019 uberon contains contains contains contains located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ located_in http://www.obofoundry.org/ro/#OBO_REL:located_in RO:0001025 uberon located_in located_in located in located_in This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of RO:0002000 uberon boundary_of boundary_of 2D boundary of boundary of my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. David Osumi-Sutherland has boundary has_2D_boundary RO:0002002 uberon has_boundary has_boundary has 2D boundary has boundary David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 nerve supply uberon innervated_by innervated_by http://code.google.com/p/obo-relations/issues/detail?id=6 innervated_by innervated_by nerve supply FMA:85999 David Osumi-Sutherland has synaptic terminal of X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 David Osumi-Sutherland RO:0002007 external uberon bounding_layer_of bounding_layer_of A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. bounding layer of bounding layer of A relationship that holds between a process that regulates a transport process and the entity transported by that process. David Osumi-Sutherland regulates transport of A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. dos 2017-05-24T09:30:46Z RO:0002013 external has_regulatory_component_activity has_regulatory_component_activity has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. dos 2017-05-24T09:31:01Z RO:0002014 external has_negative_regulatory_component_activity has_negative_regulatory_component_activity By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. dos 2017-05-24T09:49:21Z has component process dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. GOC:dos Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. dos 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. GOC:dos Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. dos 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. GOC:dos A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. GOC:dos David Osumi-Sutherland <= Primitive instance level timing relation between events before or simultaneous with Relation between occurrents, shares start and end boundaries. David Osumi-Sutherland RO:0002082 coincides_with is_equal_to uberon simultaneous_with simultaneous_with t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with simultaneous_with Relation between occurrents, shares start and end boundaries. Allen:is_equal_to https://orcid.org/0000-0002-6601-2165 David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y). David Osumi-Sutherland starts_at_end_of A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. RO:0002087 directly preceded by is directly preceded by is immediately preceded by starts_at_end_of external uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by immediately_preceded_by A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. SIO:000251 is immediately preceded by SIO:000251 David Osumi-Sutherland ends_at_start_of meets RO:0002090 external immediately_precedes immediately_precedes X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes immediately_precedes Relation between a neuron and an anatomical structure that its soma is part of. David Osumi-Sutherland <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) has soma location Relation between a neuron and some structure its axon forms (chemical) synapses in. Chris Mungall David Osumi-Sutherland David Osumi-Sutherland <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) axon synapses in Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. Alexander Diehl Chris Mungall Lindsay Cowell <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) has plasma membrane part Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. Chris Mungall David Osumi-Sutherland synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) has postsynaptic terminal in Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. synapses in <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) has presynaptic terminal in A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. David Osumi-Sutherland has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) has synaptic terminal in x overlaps y if and only if there exists some z such that x has part z and z part of y BFO_0000051 some (BFO_0000050 some ?Y) http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 external uberon overlaps overlaps overlaps overlaps true 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 lactation SubClassOf 'only in taxon' some 'Mammalia' S only_in_taxon T iff: S SubClassOf in_taxon only T. x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria Chris Mungall RO:0002160 uberon only_in_taxon only_in_taxon only in taxon only_in_taxon S only_in_taxon T iff: S SubClassOf in_taxon only T. PMID:20973947 x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. Chris Mungall Jennifer Deegan RO:0002162 uberon in_taxon in_taxon Connects a biological entity to its taxon of origin. in taxon A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. Chris Mungall Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b RO:0002170 uberon connected_to connected_to Connection does not imply overlaps. connected to connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern The M8 connects Glasgow and Edinburgh a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect) RO:0002176 uberon connects connects connects connects https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. attached to part of (anatomical structure to anatomical structure) RO:0002177 uberon attaches_to_part_of attaches_to_part_of attached to part of attaches_to_part_of true true Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. relation between an artery and the structure is supplies with blood. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure RO:0002178 arterial supply of uberon supplies supplies source: FMA supplies supplies arterial supply of FMA:86003 Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure RO:0002179 drains blood from drains from uberon drains drains source: Wikipedia drains drains w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. RO:0002180 external uberon has_component has_component has component has component x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y Chris Mungall David Osumi-Sutherland Melissa Haendel Terry Meehan RO:0002202 uberon develops_from develops_from This is the transitive form of the develops from relation develops from develops_from inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan RO:0002203 uberon develops_into develops_into develops into develops_into Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. Chris Mungall David Osumi-Sutherland has developmental precursor FBbt RO:0002207 uberon directly_develops_from directly_develops_from TODO - add child relations from DOS directly develops from directly_develops_from inverse of directly develops from developmental precursor of directly develops into process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false RO:0002211 external regulates regulates regulates regulates Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall negatively regulates (process to process) RO:0002212 external negatively_regulates negatively_regulates negatively regulates negatively regulates Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall positively regulates (process to process) RO:0002213 external positively_regulates positively_regulates positively regulates positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO:0002215 external uberon capable_of capable_of capable of capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in RO:0002216 external uberon capable_of_part_of capable_of_part_of capable of part of capable of part of true x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y. Chris Mungall RO:0002219 uberon surrounded_by surrounded_by surrounded by surrounded_by x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y. https://orcid.org/0000-0002-6601-2165 A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. x adjacent to y if and only if x and y share a boundary. x adjacent_to y iff: x and y share a boundary. This relation acts as a join point with BSPO Chris Mungall RO:0002220 external uberon adjacent_to adjacent_to adjacent to adjacent to adjacent_to A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. inverse of surrounded by inverse of surrounded_by. Chris Mungall RO:0002221 uberon surrounds surrounds surrounds surrounds inverse of surrounded_by. https://orcid.org/0000-0002-6601-2165 Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to Relation between occurrents, shares a start boundary with. inverse of starts with Chris Mungall Allen RO:0002223 uberon starts starts starts starts Relation between occurrents, shares a start boundary with. Allen:starts https://orcid.org/0000-0002-6601-2165 Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall started by RO:0002224 external uberon starts_with starts_with starts with starts with x develops from part of y if and only if there exists some z such that x develops from z and z is part of y Chris Mungall RO:0002225 uberon develops_from_part_of develops_from_part_of develops from part of develops_from_part_of x develops_in y if x is located in y whilst x is developing Chris Mungall EHDAA2 Jonathan Bard, EHDAA2 RO:0002226 uberon develops_in develops_in This relation take from EHDAA2 - precise semantics yet to be defined develops in develops_in Relation between occurrents, shares an end boundary with. inverse of ends with Chris Mungall RO:0002229 finishes uberon ends ends ends ends Relation between occurrents, shares an end boundary with. Allen:starts ZFS:finishes https://orcid.org/0000-0002-6601-2165 x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall finished by RO:0002230 external uberon ends_with ends_with ends with ends with x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y Chris Mungall starts with process that occurs in RO:0002231 external has_start_location has_start_location has start location has start location x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y Chris Mungall ends with process that occurs in RO:0002232 external has_end_location has_end_location has end location has end location p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes RO:0002233 external has_input has_input has input has input p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. Chris Mungall produces RO:0002234 external has_output has_output has output has output Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y Chris Mungall RO:0002254 uberon has_developmental_contribution_from has_developmental_contribution_from has developmental contribution from has developmental contribution from inverse of has developmental contribution from Chris Mungall RO:0002255 uberon developmentally_contributes_to developmentally_contributes_to developmentally contributes to developmentally_contributes_to t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T. t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T Chris Mungall David Osumi-Sutherland Melissa Haendel induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) GO:0001759 We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] RO:0002256 uberon developmentally_induced_by developmentally_induced_by sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F) developmentally induced by developmentally_induced_by t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T. GO:0001759 Inverse of developmentally induced by Chris Mungall developmentally induces Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false Chris Mungall In general you should not use this relation to make assertions - use one of the more specific relations below this one RO:0002258 uberon developmentally_preceded_by developmentally_preceded_by This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by developmentally preceded by A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage Chris Mungall replaces RO:0002285 uberon developmentally_replaces developmentally_replaces developmentally replaces developmentally_replaces Inverse of developmentally preceded by Chris Mungall developmentally succeeded by 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue Chris Mungall part of developmental precursor of p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. Chris Mungall RO:0002295 external results_in_developmental_progression_of results_in_developmental_progression_of results in developmental progression of results in developmental progression of every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. Chris Mungall http://www.geneontology.org/GO.doc.development.shtml RO:0002296 external results_in_development_of results_in_development_of results in development of results in development of an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) Chris Mungall GOC:mtg_berkeley_2013 RO:0002297 external results_in_formation_of results_in_formation_of results in formation of results in formation of an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. Chris Mungall GOC:mtg_berkeley_2013 RO:0002298 external results_in_morphogenesis_of results_in_morphogenesis_of results in morphogenesis of results in morphogenesis of an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. Chris Mungall GOC:mtg_berkeley_2013 RO:0002299 external results_in_maturation_of results_in_maturation_of results in maturation of results in maturation of cjm RO:0002304 external causally_upstream_of,_positive_effect causally_upstream_of,_positive_effect holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect cjm RO:0002305 external causally_upstream_of,_negative_effect causally_upstream_of,_negative_effect holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. Chris Mungall regulates localization of RO:0002313 external transports_or_maintains_localization_of transports_or_maintains_localization_of transports or maintains localization of transports or maintains localization of q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of Chris Mungall inheres in part of characteristic of part of true an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity Chris Mungall GOC:mtg_berkeley_2013 RO:0002315 external results_in_acquisition_of_features_of results_in_acquisition_of_features_of results in acquisition of features of results in acquisition of features of A relationship that holds via some environmental process Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 uberon functionally_related_to functionally_related_to functionally related to functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false RO:0002329 uberon part_of_structure_that_is_capable_of part_of_structure_that_is_capable_of part of structure that is capable of part of structure that is capable of true 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 uberon output_of output_of output of output of Chris Mungall formed as result of a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a Chris Mungall attached to (anatomical structure to anatomical structure) RO:0002371 uberon attaches_to attaches_to attached to attaches_to m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Chris Mungall Wikipedia:Insertion_(anatomy) RO:0002372 uberon has_muscle_origin has_muscle_origin The origin is the end of a muscle that attaches to the more fixed part of the skeleton, which is the proximal end in limb muscles has muscle origin has_muscle_origin 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 m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Wikipedia:Insertion_(anatomy) A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) in branching relationship with https://github.com/obophenotype/uberon/issues/170 Deschutes River tributary_of Columbia River inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. Chris Mungall drains into drains to tributary channel of http://en.wikipedia.org/wiki/Tributary http://www.medindia.net/glossary/venous_tributary.htm This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) RO:0002376 uberon drains into tributary_of tributary_of tributary of tributary_of http://en.wikipedia.org/wiki/Tributary drains into dbpowl:drainsTo A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location Chris Mungall This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve Chris Mungall RO:0002380 uberon branching_part_of branching_part_of branching part of branching_part_of FMA:85994 x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall has developmental potential involving x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y. Chris Mungall RO:0002385 uberon has_potential_to_developmentally_contribute_to has_potential_to_developmentally_contribute_to has potential to developmentally contribute to has potential to developmentally contribute to x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y Chris Mungall has potential to developmentally induce x has the potential to develop into y iff x develops into y or if x is capable of developing into y x has the potential to develop into y iff x develops into y or if x is capable of developing into y. Chris Mungall RO:0002387 uberon has_potential_to_develop_into has_potential_to_develop_into has potential to develop into has potential to develop into x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y. Chris Mungall RO:0002388 uberon has_potential_to_directly_develop_into has_potential_to_directly_develop_into has potential to directly develop into has potential to directly develop into inverse of upstream of Chris Mungall RO:0002404 external causally_downstream_of causally_downstream_of causally downstream of causally downstream of Chris Mungall RO:0002405 external immediately_causally_downstream_of immediately_causally_downstream_of immediately causally downstream of immediately causally downstream of This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall RO:0002411 external causally_upstream_of causally_upstream_of causally upstream of causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall RO:0002412 external immediately_causally_upstream_of immediately_causally_upstream_of immediately causally upstream of immediately causally upstream of p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) RO:0002418 external affects causally_upstream_of_or_within causally_upstream_of_or_within causally upstream of or within inverse of causally upstream of or within Chris Mungall RO:0002427 external causally_downstream_of_or_within causally_downstream_of_or_within causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p Chris Mungall involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p Chris Mungall involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. Chris Mungall executes activity in enables activity in is active in true c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. GOC:cjm GOC:dos p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. Chris Mungall RO:0002433 uberon contributes_to_morphology_of contributes_to_morphology_of contributes to morphology of A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Chris Mungall Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ http://purl.obolibrary.org/obo/MI_0914 An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. Chris Mungall binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later Chris Mungall An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. Chris Mungall Vasundra Touré molecularly controls directly regulates activity of The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Chris Mungall Vasundra Touré directly inhibits molecularly decreases activity of directly negatively regulates activity of The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Chris Mungall Vasundra Touré directly activates molecularly increases activity of directly positively regulates activity of Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. x composed_primarily_of y iff: more than half of the mass of x is made from parts of y. Chris Mungall RO:0002473 uberon composed_primarily_of composed_primarily_of composed primarily of p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in true Chris Mungall is kinase activity Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. relation between physical entity and a process or stage Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). Chris Mungall RO:0002488 begins_to_exist_during uberon existence_starts_during existence_starts_during existence starts during Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. https://orcid.org/0000-0002-6601-2165 Relation between continuant and occurrent, such that c comes into existence at the start of p. x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). Chris Mungall RO:0002489 uberon existence_starts_with existence_starts_with existence starts with Relation between continuant and occurrent, such that c comes into existence at the start of p. https://orcid.org/0000-0002-6601-2165 x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) Chris Mungall The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) Chris Mungall RO:0002491 exists during uberon existence_starts_and_ends_during existence_starts_and_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts and ends during Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). Chris Mungall RO:0002492 ceases_to_exist_during uberon existence_ends_during existence_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. https://orcid.org/0000-0002-6601-2165 Relation between continuant and occurrent, such that c ceases to exist at the end of p. x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). Chris Mungall RO:0002493 uberon existence_ends_with existence_ends_with The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with Relation between continuant and occurrent, such that c ceases to exist at the end of p. https://orcid.org/0000-0002-6601-2165 x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships Chris Mungall RO:0002494 transforms from uberon transformation_of transformation_of transformation of transforms from SIO:000657 x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t Chris Mungall RO:0002495 direct_transformation_of immediately transforms from uberon immediate_transformation_of immediate_transformation_of immediate transformation of direct_transformation_of https://orcid.org/0000-0002-6601-2165 immediately transforms from SIO:000658 x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). Chris Mungall RO:0002496 uberon existence_starts_during_or_after existence_starts_during_or_after The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. Chris Mungall RO:0002497 uberon existence_ends_during_or_before existence_ends_during_or_before The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes Chris Mungall depends on 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 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 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 inverse of branching part of Chris Mungall RO:0002569 uberon has_branching_part has_branching_part has branching part x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. Chris Mungall GOC:cjm RO:0002571 uberon lumen_of lumen_of lumen of s is luminal space of x iff s is lumen_of x and s is an immaterial entity Chris Mungall RO:0002572 uberon luminal_space_of luminal_space_of luminal space of inverse of has skeleton Chris Mungall RO:0002576 uberon skeleton_of skeleton_of skeleton of Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Chris Mungall directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall has part structure that is capable of p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p results in breakdown of RO:0002588 external results_in_assembly_of results_in_assembly_of results in assembly of results_in_assembly_of RO:0002590 external results_in_disassembly_of results_in_disassembly_of results in disassembly of results_in_disassembly_of p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 external results_in_organization_of results_in_organization_of results in organization of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' RO:0002608 external process_has_causal_agent process_has_causal_agent process has causal agent A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Groups both positive and negative correlation correlated with 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 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 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 RO:0002610 quality correlates_with Consider using RO:0002610 instead. See https://github.com/pato-ontology/pato/issues/454 obsolete correlates_with true q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality decreased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. decreased_in_magnitude_relative_to q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality different_in_magnitude_relative_to different_in_magnitude_relative_to q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 directly_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 increases if the magnitude of q2 is increased, or the magnitude of q1 decreases if the magnitude of q2 is decreased. The relationship is not necessarily linear. 2009-08-26T02:50:08Z quality directly_associated_with Example: 'Lewy bodies increased number related to dystrophic neurite increased number' (from annotation of PMID:8740227 in http://ccdb.ucsd.edu/1.0/NDPO.owl#ndpo_404). Here the increase in the number of lewy bodies is directly_associated_with the increase in the number of dystrophic neurites. Association is weaker than correlation or proportionality. These relations may be later added to PATO. directly_associated_with q1 directly_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 increases if the magnitude of q2 is increased, or the magnitude of q1 decreases if the magnitude of q2 is decreased. The relationship is not necessarily linear. PATOC:cjm Wikipedia:Association_(statistics) s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. quality has_cross_section Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. has_cross_section s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. PATOC:CJM quality has_dividend_entity has_dividend_entity quality has_dividend_quality has_dividend_quality quality has_divisor_entity has_divisor_entity quality has_divisor_quality has_divisor_quality quality has_ratio_quality has_ratio_quality quality has_relative_magnitude has_relative_magnitude q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality increased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. increased_in_magnitude_relative_to q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 inversely_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 decreases if the magnitude of q2 is increased, or the magnitude of q1 increases if the magnitude of q2 is decreased. The relationship is not necessarily linear. 2009-08-26T02:50:24Z quality inversely_associated_with Association is weaker than correlation or proportionality. These relations may be later added to PATO. inversely_associated_with q1 inversely_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 decreases if the magnitude of q2 is increased, or the magnitude of q1 increases if the magnitude of q2 is decreased. The relationship is not necessarily linear. PATOC:cjm Wikipedia:Association_(statistics) pato.ontology is_magnitude_of is_magnitude_of pato.ontology is_measurement_of is_measurement_of pato.ontology is_unit_of is_unit_of RO:0009501 quality realized_by Consider using RO:0009501 instead. See https://github.com/pato-ontology/pato/issues/454 realized_by true q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. quality reciprocal_of There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. reciprocal_of q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. PATOC:CJM q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality similar_in_magnitude_relative_to similar_in_magnitude_relative_to q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM monadic_form_of quality singly_occurring_form_of PATO divides qualities between normal (monadic, singly-occurring) qualities and relational qualities. Relational qualities stand in the 'towards' relation with respect to some additional entity. For example, The sensitivity of an eye towards red light. In some cases we want to represent a quality such as 'protruding' in both monadic and relational branches. We use this relation to link them. singly_occurring_form_of RO:0002503 quality towards Consider using RO:0002503 instead. See https://github.com/pato-ontology/pato/issues/454 obsolete towards true A diagnostic testing device utilizes a specimen. X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y. Asiyah Lin Bill Duncan (https://orcid.org/0000-0001-9625-1899) A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08 utilizes x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. uberon anteriorly_connected_to anteriorly connected to x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern carries uberon channel_for channel for uberon channels_from channels_from uberon channels_into channels_into x is a conduit for y iff y passes through the lumen of x. uberon conduit_for conduit for x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to distally connected to x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern uberon extends_fibers_into extends_fibers_into Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity. uberon filtered_through Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed filtered through a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s. add to RO uberon indirectly_supplies indirectly_supplies x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. uberon posteriorly_connected_to posteriorly connected to x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern uberon protects protects x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. uberon proximally_connected_to proximally connected to x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern c site_of p if c is the bearer of a disposition that is realized by a process that has p as part. uberon capable_of_has_part site_of site_of uberon subdivision_of placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B subdivision of Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. uberon synapsed_by synapsed by . uberon transitively_anteriorly_connected_to transitively anteriorly connected to . http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern uberon transitively_connected_to transitively_connected to . uberon transitively_distally_connected_to transitively distally connected to . http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern . uberon transitively_proximally_connected_to transitively proximally connected to . http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. continuant An entity that has temporal parts and that happens, unfolds or develops through time. occurrent A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant spatial region An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process disposition A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. realizable entity quality A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. specifically dependent continuant A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. role function An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. material entity immaterial entity Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV. -1 0.000548579903 0.0 KEGG:C05359 PMID:21614077 Wikipedia:Electron electron chebi_ontology Elektron beta beta(-) beta-particle e e(-) e- negatron CHEBI:10545 electron PMID:21614077 Europe PMC electron ChEBI electron IUPAC electron KEGG_COMPOUND Elektron ChEBI beta IUPAC beta(-) ChEBI beta-particle IUPAC e IUPAC e(-) UniProt e- KEGG_COMPOUND negatron IUPAC A class of carbonyl compound encompassing dicarboxylic acids and any derivatives obtained by substitution of either one or both of the carboxy hydrogens. chebi_ontology dicarboxylic acids and derivatives CHEBI:131927 dicarboxylic acids and O-substituted derivatives dicarboxylic acids and derivatives ChEBI A carbohydrate acid derivative anion obtained by deprotonation of the carboxy groups of hyaluronic acid; major species at pH 7.3. -1 (C14H20NO11)n.H2O chebi_ontology hyaluronan hyaluronate polyanion CHEBI:132153 hyaluronate hyaluronan UniProt hyaluronate polyanion ChEBI 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 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-amino-acid anion that is the conjugate base of glutamic acid, having anionic carboxy groups and a cationic amino group -1 C5H8NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-1 WHUUTDBJXJRKMK-UHFFFAOYSA-M 146.12136 146.04588 [NH3+]C(CCC([O-])=O)C([O-])=O Gmelin:327908 glutamate(1-) hydrogen glutamate chebi_ontology 2-ammoniopentanedioate glutamate glutamic acid monoanion CHEBI:14321 glutamate(1-) Gmelin:327908 Gmelin glutamate(1-) JCBN hydrogen glutamate IUPAC 2-ammoniopentanedioate IUPAC glutamate UniProt glutamic acid monoanion JCBN A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity. CHEBI:13699 CHEBI:2377 KEGG:C00028 KEGG:C16722 Acceptor chebi_ontology A Akzeptor Hydrogen-acceptor Oxidized donor accepteur CHEBI:15339 acceptor Acceptor KEGG_COMPOUND A KEGG_COMPOUND Akzeptor ChEBI Hydrogen-acceptor KEGG_COMPOUND Oxidized donor KEGG_COMPOUND accepteur ChEBI Actylcholine is an ester of acetic acid and choline, which acts as a neurotransmitter. +1 C7H16NO2 InChI=1S/C7H16NO2/c1-7(9)10-6-5-8(2,3)4/h5-6H2,1-4H3/q+1 OIPILFWXSMYKGL-UHFFFAOYSA-N 146.20748 146.11756 CC(=O)OCC[N+](C)(C)C CHEBI:12686 CHEBI:13715 CHEBI:22197 CHEBI:2416 CHEBI:40559 Beilstein:1764436 CAS:51-84-3 DrugBank:DB03128 Drug_Central:65 Gmelin:326108 KEGG:C01996 LINCS:LSM-5888 PDBeChem:ACH PMID:14764638 PMID:15014918 PMID:15231705 PMID:15361288 PMID:18050502 PMID:18407448 PMID:19255787 PMID:20963497 PMID:21130809 PMID:21246223 PMID:21545631 PMID:21601579 Wikipedia:Acetylcholine 2-acetyloxy-N,N,N-trimethylethanaminium ACETYLCHOLINE Acetylcholine acetylcholine chebi_ontology ACh Azetylcholin O-Acetylcholine choline acetate CHEBI:15355 acetylcholine Beilstein:1764436 ChemIDplus CAS:51-84-3 ChemIDplus CAS:51-84-3 KEGG COMPOUND Drug_Central:65 DrugCentral Gmelin:326108 Gmelin PMID:14764638 Europe PMC PMID:15014918 Europe PMC PMID:15231705 Europe PMC PMID:15361288 Europe PMC PMID:18050502 Europe PMC PMID:18407448 Europe PMC PMID:19255787 Europe PMC PMID:20963497 Europe PMC PMID:21130809 Europe PMC PMID:21246223 Europe PMC PMID:21545631 Europe PMC PMID:21601579 Europe PMC 2-acetyloxy-N,N,N-trimethylethanaminium IUPAC ACETYLCHOLINE PDBeChem Acetylcholine KEGG_COMPOUND acetylcholine UniProt ACh ChemIDplus Azetylcholin ChEBI O-Acetylcholine KEGG_COMPOUND choline acetate ChemIDplus A simple monocarboxylic acid containing two carbons. 0 C2H4O2 InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4) QTBSBXVTEAMEQO-UHFFFAOYSA-N 60.05200 60.02113 CC(O)=O CHEBI:22169 CHEBI:2387 CHEBI:40486 Beilstein:506007 CAS:64-19-7 Drug_Central:4211 Gmelin:1380 HMDB:HMDB0000042 KEGG:C00033 KEGG:D00010 KNApSAcK:C00001176 LIPID_MAPS_instance:LMFA01010002 MetaCyc:ACET PDBeChem:ACT PDBeChem:ACY PMID:12005138 PMID:15107950 PMID:16630552 PMID:16774200 PMID:17190852 PMID:19416101 PMID:19469536 PMID:22153255 PMID:22173419 PPDB:1333 Reaxys:506007 Wikipedia:Acetic_acid ACETIC ACID Acetic acid acetic acid chebi_ontology AcOH CH3-COOH CH3CO2H E 260 E-260 E260 Essigsaeure Ethanoic acid Ethylic acid HOAc INS No. 260 MeCO2H MeCOOH Methanecarboxylic acid acide acetique ethoic acid CHEBI:15366 acetic acid Beilstein:506007 Beilstein CAS:64-19-7 ChemIDplus CAS:64-19-7 KEGG COMPOUND CAS:64-19-7 NIST Chemistry WebBook Drug_Central:4211 DrugCentral Gmelin:1380 Gmelin LIPID_MAPS_instance:LMFA01010002 LIPID MAPS PMID:12005138 Europe PMC PMID:15107950 Europe PMC PMID:16630552 Europe PMC PMID:16774200 Europe PMC PMID:17190852 Europe PMC PMID:19416101 Europe PMC PMID:19469536 Europe PMC PMID:22153255 Europe PMC PMID:22173419 Europe PMC Reaxys:506007 Reaxys ACETIC ACID PDBeChem Acetic acid KEGG_COMPOUND acetic acid IUPAC AcOH ChEBI CH3-COOH IUPAC CH3CO2H ChEBI E 260 ChEBI E-260 ChEBI E260 ChEBI Essigsaeure ChEBI Ethanoic acid KEGG_COMPOUND Ethylic acid ChemIDplus HOAc ChEBI INS No. 260 ChEBI MeCO2H ChEBI MeCOOH ChEBI Methanecarboxylic acid ChemIDplus acide acetique ChemIDplus ethoic acid ChEBI 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 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 peptide containing ten or more amino acid residues. C4H6N2O3R2(C2H2NOR)n CHEBI:14860 CHEBI:8314 KEGG:C00403 Polypeptide polypeptides chebi_ontology Polypeptid polipeptido CHEBI:15841 polypeptide Polypeptide KEGG_COMPOUND polypeptides IUPAC Polypeptid ChEBI polipeptido ChEBI A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues. 0 (C5H8O6PR)n.C10H17O10PR2 CHEBI:13672 CHEBI:14859 CHEBI:8312 KEGG:C00419 Polynucleotide chebi_ontology polynucleotides CHEBI:15986 polynucleotide Polynucleotide KEGG_COMPOUND polynucleotides ChEBI An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. 0 H3N InChI=1S/H3N/h1H3 QGZKDVFQNNGYKY-UHFFFAOYSA-N 17.03056 17.02655 [H]N([H])[H] CHEBI:13405 CHEBI:13406 CHEBI:13407 CHEBI:13771 CHEBI:22533 CHEBI:44269 CHEBI:44284 CHEBI:44404 CHEBI:7434 Beilstein:3587154 CAS:7664-41-7 Drug_Central:4625 Gmelin:79 HMDB:HMDB0000051 KEGG:C00014 KEGG:D02916 KNApSAcK:C00007267 MetaCyc:AMMONIA MolBase:930 PDBeChem:NH3 PMID:110589 PMID:11139349 PMID:11540049 PMID:11746427 PMID:11783653 PMID:13753780 PMID:14663195 PMID:15092448 PMID:15094021 PMID:15554424 PMID:15969015 PMID:16008360 PMID:16050680 PMID:16348008 PMID:16349403 PMID:16614889 PMID:16664306 PMID:16842901 PMID:17025297 PMID:17439666 PMID:17569513 PMID:17737668 PMID:18670398 PMID:22002069 PMID:22081570 PMID:22088435 PMID:22100291 PMID:22130175 PMID:22150211 PMID:22240068 PMID:22290316 PMID:22342082 PMID:22385337 PMID:22443779 PMID:22560242 Reaxys:3587154 Wikipedia:Ammonia AMMONIA Ammonia ammonia azane chebi_ontology Ammoniak NH3 R-717 [NH3] ammoniac amoniaco spirit of hartshorn CHEBI:16134 ammonia Beilstein:3587154 Beilstein CAS:7664-41-7 ChemIDplus CAS:7664-41-7 KEGG COMPOUND CAS:7664-41-7 NIST Chemistry WebBook Drug_Central:4625 DrugCentral Gmelin:79 Gmelin PMID:110589 Europe PMC PMID:11139349 Europe PMC PMID:11540049 Europe PMC PMID:11746427 Europe PMC PMID:11783653 Europe PMC PMID:13753780 Europe PMC PMID:14663195 Europe PMC PMID:15092448 Europe PMC PMID:15094021 Europe PMC PMID:15554424 Europe PMC PMID:15969015 Europe PMC PMID:16008360 Europe PMC PMID:16050680 Europe PMC PMID:16348008 Europe PMC PMID:16349403 Europe PMC PMID:16614889 Europe PMC PMID:16664306 Europe PMC PMID:16842901 Europe PMC PMID:17025297 Europe PMC PMID:17439666 Europe PMC PMID:17569513 Europe PMC PMID:17737668 Europe PMC PMID:18670398 Europe PMC PMID:22002069 Europe PMC PMID:22081570 Europe PMC PMID:22088435 Europe PMC PMID:22100291 Europe PMC PMID:22130175 Europe PMC PMID:22150211 Europe PMC PMID:22240068 Europe PMC PMID:22290316 Europe PMC PMID:22342082 Europe PMC PMID:22385337 Europe PMC PMID:22443779 Europe PMC PMID:22560242 Europe PMC Reaxys:3587154 Reaxys AMMONIA PDBeChem Ammonia KEGG_COMPOUND ammonia IUPAC azane IUPAC Ammoniak ChemIDplus NH3 IUPAC NH3 KEGG_COMPOUND NH3 UniProt R-717 ChEBI [NH3] MolBase ammoniac ChEBI amoniaco ChEBI spirit of hartshorn ChemIDplus A sulfur oxoanion obtained by deprotonation of both OH groups of sulfuric acid. -2 O4S InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2 QAOWNCQODCNURD-UHFFFAOYSA-L 96.06360 95.95283 [O-]S([O-])(=O)=O CHEBI:15135 CHEBI:45687 CHEBI:9335 Beilstein:3648446 CAS:14808-79-8 Gmelin:2120 HMDB:HMDB0001448 KEGG:C00059 KEGG:D05963 MetaCyc:SULFATE PDBeChem:SO4 PMID:11200094 PMID:11452993 PMID:11581495 PMID:11798107 PMID:12166931 PMID:12668033 PMID:14597181 PMID:15093386 PMID:15984785 PMID:16186560 PMID:16345535 PMID:16347366 PMID:16348007 PMID:16483812 PMID:16534979 PMID:16656509 PMID:16742508 PMID:16742518 PMID:17120760 PMID:17420092 PMID:17439666 PMID:17709180 PMID:18398178 PMID:18815700 PMID:18846414 PMID:19047345 PMID:19244483 PMID:19544990 PMID:19628332 PMID:19812358 PMID:30398859 Reaxys:3648446 Wikipedia:Sulfate Sulfate sulfate tetraoxidosulfate(2-) tetraoxosulfate(2-) tetraoxosulfate(VI) chebi_ontology SO4(2-) SULFATE ION Sulfate anion(2-) Sulfate dianion Sulfate(2-) Sulfuric acid ion(2-) [SO4](2-) sulphate sulphate ion CHEBI:16189 sulfate Beilstein:3648446 Beilstein CAS:14808-79-8 ChemIDplus CAS:14808-79-8 NIST Chemistry WebBook Gmelin:2120 Gmelin PMID:11200094 Europe PMC PMID:11452993 Europe PMC PMID:11581495 Europe PMC PMID:11798107 Europe PMC PMID:12166931 Europe PMC PMID:12668033 Europe PMC PMID:14597181 Europe PMC PMID:15093386 Europe PMC PMID:15984785 Europe PMC PMID:16186560 Europe PMC PMID:16345535 Europe PMC PMID:16347366 Europe PMC PMID:16348007 Europe PMC PMID:16483812 Europe PMC PMID:16534979 Europe PMC PMID:16656509 Europe PMC PMID:16742508 Europe PMC PMID:16742518 Europe PMC PMID:17120760 Europe PMC PMID:17420092 Europe PMC PMID:17439666 Europe PMC PMID:17709180 Europe PMC PMID:18398178 Europe PMC PMID:18815700 Europe PMC PMID:18846414 Europe PMC PMID:19047345 Europe PMC PMID:19244483 Europe PMC PMID:19544990 Europe PMC PMID:19628332 Europe PMC PMID:19812358 Europe PMC PMID:30398859 Europe PMC Reaxys:3648446 Reaxys Sulfate KEGG_COMPOUND sulfate IUPAC sulfate UniProt tetraoxidosulfate(2-) IUPAC tetraoxosulfate(2-) IUPAC tetraoxosulfate(VI) IUPAC SO4(2-) IUPAC SULFATE ION PDBeChem Sulfate anion(2-) HMDB Sulfate dianion HMDB Sulfate(2-) HMDB Sulfuric acid ion(2-) HMDB [SO4](2-) IUPAC sulphate ChEBI sulphate ion ChEBI A mucopolysaccharide composed of N-acetylglucosamine and glucuronic acid subunits. It is found in the connective tissues of vertebrates. A principal constituent of the extracellular matrix (ECM), it mediates the growth and metastasis of tumour cells. 0 (C14H21NO12)n CHEBI:14412 CHEBI:24622 CHEBI:24623 CHEBI:5772 Beilstein:8538277 CAS:9004-61-9 HMDB:HMDB0010366 KEGG:C00518 KEGG:D08043 KEGG:G10505 PMID:11122186 PMID:18056362 PMID:18290544 Reaxys:8187837 Wikipedia:Hyaluronan Hyaluronic acid chebi_ontology Hyaluronsaeure [beta-D-glucopyranuronosyl-(1->3)-2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl-(1->4)]n [beta-N-Acetyl-D-glucosaminyl(1,4)beta-D-glucuronosyl(1,3)]n acide hyaluronique acido hialuronico hyaluronan CHEBI:16336 hyaluronic acid Beilstein:8538277 Beilstein CAS:9004-61-9 ChemIDplus CAS:9004-61-9 KEGG COMPOUND PMID:11122186 Europe PMC PMID:18056362 Europe PMC PMID:18290544 Europe PMC Reaxys:8187837 Reaxys Hyaluronic acid KEGG_COMPOUND Hyaluronsaeure ChEBI [beta-D-glucopyranuronosyl-(1->3)-2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl-(1->4)]n ChEBI [beta-N-Acetyl-D-glucosaminyl(1,4)beta-D-glucuronosyl(1,3)]n KEGG_COMPOUND acide hyaluronique ChEBI acido hialuronico ChEBI hyaluronan ChEBI A naturally occurring polypeptide synthesized at the ribosome. CHEBI:8526 KEGG:C00017 chebi_ontology Protein polypeptide chain protein polypeptide chains CHEBI:16541 protein polypeptide chain Protein KEGG_COMPOUND polypeptide chain ChEBI protein polypeptide chains ChEBI Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates. CHEBI:15131 CHEBI:23008 CHEBI:9318 Wikipedia:Carbohydrate carbohydrate carbohydrates chebi_ontology Kohlenhydrat Kohlenhydrate carbohidrato carbohidratos glucide glucides glucido glucidos hydrates de carbone saccharide saccharides saccharidum CHEBI:16646 carbohydrate carbohydrate IUPAC carbohydrates IUPAC Kohlenhydrat ChEBI Kohlenhydrate ChEBI carbohidrato IUPAC carbohidratos IUPAC glucide ChEBI glucides ChEBI glucido ChEBI glucidos ChEBI hydrates de carbone ChEBI saccharide IUPAC saccharides IUPAC saccharidum ChEBI Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. 0 (C2H2NOR)nC2H3NOR CHEBI:14753 CHEBI:25906 CHEBI:7990 KEGG:C00012 Peptide peptides chebi_ontology Peptid peptido peptidos CHEBI:16670 peptide Peptide KEGG_COMPOUND peptides IUPAC Peptid ChEBI peptido ChEBI peptidos ChEBI +1 C8H12NO3 InChI=1S/C8H11NO3/c9-4-8(12)5-1-2-6(10)7(11)3-5/h1-3,8,10-12H,4,9H2/p+1 SFLSHLFXELFNJZ-UHFFFAOYSA-O 170.187 170.08117 C1=CC(=CC(=C1O)O)C(C[NH3+])O chebi_ontology noradrenaline CHEBI:166902 noradrenaline(1+) noradrenaline UniProt Any oligosaccharide, polysaccharide or their derivatives consisting of monosaccharides or monosaccharide derivatives linked by glycosidic bonds. See also http://www.ontobee.org/ontology/GNO?iri=http://purl.obolibrary.org/obo/GNO_00000001. chebi_ontology glycans CHEBI:167559 glycan glycans ChEBI An aminoalkylindole consisting of indole having a 2-aminoethyl group at the 3-position. 0 C10H12N2 InChI=1S/C10H12N2/c11-6-5-8-7-12-10-4-2-1-3-9(8)10/h1-4,7,12H,5-6,11H2 APJYDQYYACXCRM-UHFFFAOYSA-N 160.21570 160.10005 NCCc1c[nH]c2ccccc12 CHEBI:15274 CHEBI:27161 CHEBI:46157 CHEBI:9767 Beilstein:125513 CAS:61-54-1 DrugBank:DB08653 Gmelin:603448 HMDB:HMDB0000303 KEGG:C00398 KNApSAcK:C00001434 MetaCyc:TRYPTAMINE PDBeChem:TSS PMID:16126914 PMID:22770225 PMID:24345948 PMID:24558969 Reaxys:125513 Wikipedia:Tryptamine 2-(1H-indol-3-yl)ethanamine Tryptamine chebi_ontology 1H-indole-3-ethanamine 2-(1H-INDOL-3-YL)ETHANAMINE 2-(3-indolyl)ethylamine 3-(2-Aminoethyl)indole CHEBI:16765 tryptamine Beilstein:125513 Beilstein CAS:61-54-1 ChemIDplus CAS:61-54-1 KEGG COMPOUND CAS:61-54-1 NIST Chemistry WebBook Gmelin:603448 Gmelin PMID:16126914 Europe PMC PMID:22770225 Europe PMC PMID:24345948 Europe PMC PMID:24558969 Europe PMC Reaxys:125513 Reaxys 2-(1H-indol-3-yl)ethanamine IUPAC Tryptamine KEGG_COMPOUND 1H-indole-3-ethanamine NIST_Chemistry_WebBook 2-(1H-INDOL-3-YL)ETHANAMINE PDBeChem 2-(3-indolyl)ethylamine ChemIDplus 3-(2-Aminoethyl)indole KEGG_COMPOUND High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. CHEBI:13302 CHEBI:21123 CHEBI:33698 CHEBI:4291 CAS:9007-49-2 KEGG:C00039 Deoxyribonucleic acid deoxyribonucleic acids chebi_ontology (Deoxyribonucleotide)m (Deoxyribonucleotide)n (Deoxyribonucleotide)n+m DNA DNAn DNAn+1 DNS Desoxyribonukleinsaeure deoxyribonucleic acids desoxyribose nucleic acid thymus nucleic acid CHEBI:16991 deoxyribonucleic acid CAS:9007-49-2 ChemIDplus CAS:9007-49-2 KEGG COMPOUND Deoxyribonucleic acid KEGG_COMPOUND deoxyribonucleic acids IUPAC (Deoxyribonucleotide)m KEGG_COMPOUND (Deoxyribonucleotide)n KEGG_COMPOUND (Deoxyribonucleotide)n+m KEGG_COMPOUND DNA IUPAC DNA KEGG_COMPOUND DNAn KEGG_COMPOUND DNAn+1 KEGG_COMPOUND DNS ChEBI Desoxyribonukleinsaeure ChEBI deoxyribonucleic acids ChEBI desoxyribose nucleic acid ChemIDplus thymus nucleic acid ChEBI A compound in which a carbonyl group is bonded to two carbon atoms: R2C=O (neither R may be H). 0 COR2 28.010 27.99491 [*]C([*])=O CHEBI:13427 CHEBI:13646 CHEBI:24974 CHEBI:6127 CHEBI:8742 KEGG:C01450 Wikipedia:Ketone Ketone ketones chebi_ontology Keton R-CO-R' a ketone cetone ketones CHEBI:17087 ketone Ketone KEGG_COMPOUND ketones IUPAC Keton ChEBI R-CO-R' KEGG_COMPOUND a ketone UniProt cetone ChEBI ketones ChEBI A compound in which a carbohydrate component is covalently bound to a protein component. CHEBI:14349 CHEBI:5481 CHEBI:5493 KEGG:C00326 Glycoprotein glycoproteins chebi_ontology Glykoprotein Glykoproteine glicoproteina glicoproteinas glycoproteine glycoproteines CHEBI:17089 glycoprotein Glycoprotein KEGG_COMPOUND glycoproteins IUPAC Glykoprotein ChEBI Glykoproteine ChEBI glicoproteina ChEBI glicoproteinas ChEBI glycoproteine ChEBI glycoproteines ChEBI A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity. CHEBI:14202 CHEBI:4697 KEGG:C01351 Donor chebi_ontology Donator donneur CHEBI:17891 donor Donor KEGG_COMPOUND Donator ChEBI donneur ChEBI 'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. CHEBI:14517 CHEBI:25054 CHEBI:6486 KEGG:C01356 Lipid lipids chebi_ontology CHEBI:18059 lipid Lipid KEGG_COMPOUND lipids IUPAC Any polysaccharide containing a substantial proportion of aminomonosaccharide residues. CHEBI:14361 CHEBI:24398 CHEBI:5495 KEGG:C02545 Wikipedia:Glycosaminoglycan Glycosaminoglycan glycosaminoglycan chebi_ontology Glykosaminoglykan glicosaminoglicano glycosaminoglycane glycosaminoglycans CHEBI:18085 glycosaminoglycan Glycosaminoglycan KEGG_COMPOUND glycosaminoglycan IUPAC Glykosaminoglykan ChEBI glicosaminoglicano IUPAC glycosaminoglycane IUPAC glycosaminoglycans ChEBI A biomacromolecule consisting of large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues. CHEBI:14864 CHEBI:26205 CHEBI:8322 KEGG:C00420 Polysaccharide polysaccharides chebi_ontology Glycan Glycane Glykan Glykane glycans polisacarido polisacaridos CHEBI:18154 polysaccharide Polysaccharide KEGG_COMPOUND polysaccharides IUPAC Glycan KEGG_COMPOUND Glycane ChEBI Glykan ChEBI Glykane ChEBI glycans IUPAC polisacarido ChEBI polisacaridos IUPAC An alpha-amino acid that is glutaric acid bearing a single amino substituent at position 2. 0 C5H9NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10) WHUUTDBJXJRKMK-UHFFFAOYSA-N 147.12930 147.05316 NC(CCC(O)=O)C(O)=O CHEBI:24314 CHEBI:5431 Beilstein:1723799 CAS:617-65-2 Gmelin:101971 KEGG:C00302 KEGG:D04341 KNApSAcK:C00001358 KNApSAcK:C00019577 PMID:15739367 PMID:17190852 PMID:24616376 PMID:24984001 Reaxys:1723799 Wikipedia:Glutamic_acid 2-aminopentanedioic acid Glutamic acid glutamic acid chebi_ontology 2-Aminoglutaric acid DL-Glutamic acid DL-Glutaminic acid E Glu Glutamate Glutaminic acid Glutaminsaeure CHEBI:18237 glutamic acid Beilstein:1723799 Beilstein CAS:617-65-2 ChemIDplus CAS:617-65-2 KEGG COMPOUND CAS:617-65-2 NIST Chemistry WebBook Gmelin:101971 Gmelin PMID:15739367 Europe PMC PMID:17190852 Europe PMC PMID:24616376 Europe PMC PMID:24984001 Europe PMC Reaxys:1723799 Reaxys 2-aminopentanedioic acid IUPAC Glutamic acid KEGG_COMPOUND glutamic acid IUPAC 2-Aminoglutaric acid KEGG_COMPOUND DL-Glutamic acid KEGG_DRUG DL-Glutaminic acid KEGG_COMPOUND E ChEBI Glu ChEBI Glutamate KEGG_COMPOUND Glutaminic acid KEGG_COMPOUND Glutaminsaeure ChEBI Catechol in which the hydrogen at position 4 is substituted by a 2-aminoethyl group. 0 C8H11NO2 InChI=1S/C8H11NO2/c9-4-3-6-1-2-7(10)8(11)5-6/h1-2,5,10-11H,3-4,9H2 VYFYYTLLBUKUHU-UHFFFAOYSA-N 153.17840 153.07898 NCCc1ccc(O)c(O)c1 CHEBI:11695 CHEBI:11930 CHEBI:14203 CHEBI:1764 CHEBI:23886 CHEBI:43686 CAS:51-61-6 DrugBank:DB00988 Drug_Central:947 HMDB:HMDB0000073 KEGG:C03758 KEGG:D07870 KNApSAcK:C00001408 LINCS:LSM-4630 MetaCyc:DOPAMINE PMID:10629745 PMID:11149432 PMID:9422813 Reaxys:1072822 Wikipedia:Dopamine 4-(2-aminoethyl)benzene-1,2-diol Dopamine chebi_ontology 2-(3,4-Dihydroxyphenyl)ethylamine 2-(3,4-dihydroxyphenyl)ethylamine 3,4-Dihydroxyphenethylamine 3-Hydroxytyramine 4-(2-Aminoethyl)-1,2-benzenediol 4-(2-Aminoethyl)benzene-1,2-diol 4-(2-aminoethyl)-1,2-benzenediol 4-(2-aminoethyl)catechol 4-(2-aminoethyl)pyrocatechol Deoxyepinephrine Hydroxytyramin dopamina dopamine dopaminum CHEBI:18243 dopamine CAS:51-61-6 ChemIDplus Drug_Central:947 DrugCentral PMID:10629745 Europe PMC PMID:11149432 Europe PMC PMID:9422813 Europe PMC Reaxys:1072822 Reaxys 4-(2-aminoethyl)benzene-1,2-diol IUPAC Dopamine KEGG_COMPOUND 2-(3,4-Dihydroxyphenyl)ethylamine KEGG_COMPOUND 2-(3,4-dihydroxyphenyl)ethylamine ChEBI 3,4-Dihydroxyphenethylamine KEGG_COMPOUND 3-Hydroxytyramine ChemIDplus 4-(2-Aminoethyl)-1,2-benzenediol KEGG_COMPOUND 4-(2-Aminoethyl)benzene-1,2-diol KEGG_COMPOUND 4-(2-aminoethyl)-1,2-benzenediol ChEBI 4-(2-aminoethyl)catechol ChemIDplus 4-(2-aminoethyl)pyrocatechol ChemIDplus Deoxyepinephrine DrugBank Hydroxytyramin DrugBank dopamina ChemIDplus dopamine ChEBI dopaminum ChemIDplus An iron group element atom that has atomic number 26. 0 Fe InChI=1S/Fe XEEYBQQBJWHFJM-UHFFFAOYSA-N 55.84500 55.93494 [Fe] CHEBI:13322 CHEBI:24872 CHEBI:5974 CAS:7439-89-6 DrugBank:DB01592 HMDB:HMDB0015531 KEGG:C00023 Reaxys:4122945 WebElements:Fe iron chebi_ontology 26Fe Eisen Fe Iron fer ferrum hierro iron CHEBI:18248 iron atom CAS:7439-89-6 ChemIDplus CAS:7439-89-6 KEGG COMPOUND CAS:7439-89-6 NIST Chemistry WebBook Reaxys:4122945 Reaxys iron IUPAC 26Fe IUPAC Eisen ChEBI Fe IUPAC Iron KEGG_COMPOUND fer ChEBI ferrum IUPAC hierro ChEBI iron ChEBI That part of DNA or RNA that may be involved in pairing. CHEBI:13873 CHEBI:25598 CHEBI:2995 KEGG:C00701 Wikipedia:Nucleobase chebi_ontology Base nucleobases CHEBI:18282 nucleobase Base KEGG_COMPOUND nucleobases ChEBI A phosphate ion that is the conjugate base of hydrogenphosphate. -3 O4P InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3 NBIIXXVUZAFLBC-UHFFFAOYSA-K 94.97136 94.95507 [O-]P([O-])([O-])=O CHEBI:14791 CHEBI:45024 CHEBI:7793 Beilstein:3903772 CAS:14265-44-2 Gmelin:1997 KEGG:C00009 PDBeChem:PO4 Reaxys:3903772 phosphate tetraoxidophosphate(3-) tetraoxophosphate(3-) tetraoxophosphate(V) chebi_ontology Orthophosphate PHOSPHATE ION PO4(3-) Phosphate [PO4](3-) CHEBI:18367 phosphate(3-) Beilstein:3903772 Beilstein CAS:14265-44-2 ChemIDplus CAS:14265-44-2 KEGG COMPOUND Gmelin:1997 Gmelin PDBeChem:PO4 ChEBI Reaxys:3903772 Reaxys phosphate IUPAC tetraoxidophosphate(3-) IUPAC tetraoxophosphate(3-) IUPAC tetraoxophosphate(V) IUPAC Orthophosphate KEGG_COMPOUND PHOSPHATE ION PDBeChem PO4(3-) IUPAC Phosphate KEGG_COMPOUND [PO4](3-) IUPAC An organic group formed by removing one or more hydroxy groups from an oxoacid that has the general structure RkE(=O)l(OH)m (l =/= 0). Although the term is almost always applied to organic compounds, with carboxylic acid as the oxoacid, acyl groups can in principle be derived from other types of acids such as sulfonic acids or phosphonic acids. acyl group alkanoyl chebi_ontology acyl groups alkanoyl group groupe acyle CHEBI:22221 acyl group acyl group IUPAC alkanoyl IUPAC acyl groups ChEBI alkanoyl group ChEBI groupe acyle IUPAC Any of the naturally occurring, basic nitrogen compounds (mostly heterocyclic) occurring mostly in the plant kingdom, but also found in bacteria, fungi, and animals. By extension, certain neutral compounds biogenetically related to basic alkaloids are also classed as alkaloids. Amino acids, peptides, proteins, nucleotides, nucleic acids, amino sugars and antibiotics are not normally regarded as alkaloids. Compounds in which the nitrogen is exocyclic (dopamine, mescaline, serotonin, etc.) are usually classed as amines rather than alkaloids. Wikipedia:Alkaloid Alkaloid alkaloids chebi_ontology Alkaloide alcaloide alcaloides CHEBI:22315 alkaloid Alkaloid ChEBI alkaloids IUPAC Alkaloide ChEBI alcaloide ChEBI alcaloides ChEBI chebi_ontology aminoglycans CHEBI:22506 aminoglycan aminoglycans ChEBI A monoatomic or polyatomic species having one or more elementary charges of the electron. Anion anion chebi_ontology Anionen aniones anions CHEBI:22563 anion Anion ChEBI anion ChEBI anion IUPAC Anionen ChEBI aniones ChEBI anions IUPAC A molecular entity having an available pair of electrons capable of forming a covalent bond with a hydron (Bronsted base) or with the vacant orbital of some other molecular entity (Lewis base). KEGG:C00701 Base base chebi_ontology Base1 Base2 Basen Nucleobase bases CHEBI:22695 base Base ChEBI base ChEBI base IUPAC Base1 KEGG_COMPOUND Base2 KEGG_COMPOUND Basen ChEBI Nucleobase KEGG_COMPOUND bases ChEBI chebi_ontology benzopyrroles CHEBI:22728 benzopyrrole benzopyrroles ChEBI The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid. 0 CH2NO 44.03272 44.01364 *C(N)=O PMID:24168430 carbamoyl chebi_ontology -C(O)NH2 -CONH2 aminocarbonyl carbamyl carbamyl group carboxamide CHEBI:23004 carbamoyl group PMID:24168430 Europe PMC carbamoyl IUPAC -C(O)NH2 ChEBI -CONH2 IUPAC aminocarbonyl IUPAC carbamyl ChEBI carbamyl group ChEBI carboxamide IUPAC 0 CO 28.01010 27.99491 O=C(*)* carbonyl carbonyl group chebi_ontology >C=O CHEBI:23019 carbonyl group carbonyl IUPAC carbonyl group ChEBI carbonyl group UniProt >C=O IUPAC An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group). Wikipedia:Cofactor_(biochemistry) cofactor cofactors chebi_ontology CHEBI:23357 cofactor cofactor IUPAC cofactors IUPAC Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity chebi_ontology entidad molecular entidades moleculares entite moleculaire molecular entities molekulare Entitaet CHEBI:23367 molecular entity molecular entity IUPAC entidad molecular IUPAC entidades moleculares IUPAC entite moleculaire IUPAC molecular entities IUPAC molekulare Entitaet ChEBI chebi_ontology Cyclopeptid Zyklopeptid cyclic peptides peptide cyclique peptido ciclico CHEBI:23449 cyclic peptide Cyclopeptid ChEBI Zyklopeptid ChEBI cyclic peptides ChEBI peptide cyclique IUPAC peptido ciclico IUPAC Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances. chebi_ontology drugs medicine CHEBI:23888 drug drugs ChEBI medicine ChEBI chebi_ontology monoatomic cations CHEBI:23906 monoatomic cation monoatomic cations ChEBI A compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction. enzyme inhibitor chebi_ontology enzyme inhibitors inhibidor enzimatico inhibidores enzimaticos inhibiteur enzymatique inhibiteurs enzymatiques CHEBI:23924 enzyme inhibitor enzyme inhibitor IUPAC enzyme inhibitors ChEBI inhibidor enzimatico ChEBI inhibidores enzimaticos ChEBI inhibiteur enzymatique ChEBI inhibiteurs enzymatiques ChEBI An L-alpha-amino acid which is L-glutamic acid or any of the essential amino acids biosynthesised from it (glutamine, proline and arginine). A closed class. PMID:20716061 chebi_ontology glutamine family amino acids CHEBI:24318 glutamine family amino acid PMID:20716061 Europe PMC glutamine family amino acids ChEBI A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity chebi_ontology CHEBI:24431 chemical entity chemical entity UniProt A role played by the molecular entity or part thereof within a biological context. chebi_ontology biological function CHEBI:24432 biological role biological function ChEBI A defined linked collection of atoms or a single atom within a molecular entity. group chebi_ontology Gruppe Rest groupe grupo grupos CHEBI:24433 group group IUPAC Gruppe ChEBI Rest ChEBI groupe IUPAC grupo IUPAC grupos IUPAC A cyclic compound having as ring members atoms of carbon and at least of one other element. chebi_ontology organic heterocycle organic heterocyclic compounds CHEBI:24532 organic heterocyclic compound organic heterocycle ChEBI organic heterocyclic compounds ChEBI A heterodetic cyclic peptide is a peptide consisting only of amino-acid residues, but in which the linkages forming the ring are not solely peptide bonds; one or more is an isopeptide, disulfide, ester, or other bond. heterodetic cyclic peptide chebi_ontology heterodetic cyclic peptides peptide cyclique heterodetique peptido ciclico heterodetico CHEBI:24533 heterodetic cyclic peptide heterodetic cyclic peptide IUPAC heterodetic cyclic peptides ChEBI peptide cyclique heterodetique IUPAC peptido ciclico heterodetico IUPAC Originally referring to an endogenous compound that is formed in specialized organ or group of cells and carried to another organ or group of cells, in the same organism, upon which it has a specific regulatory function, the term is now commonly used to include non-endogenous, semi-synthetic and fully synthetic analogues of such compounds. chebi_ontology endocrine hormones CHEBI:24621 hormone endocrine ChEBI hormones ChEBI Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)). chebi_ontology CHEBI:24651 hydroxides Any compound containing an indole skeleton. chebi_ontology CHEBI:24828 indoles A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). oxoacid oxoacids chebi_ontology oxacids oxiacids oxo acid oxy-acids oxyacids CHEBI:24833 oxoacid oxoacid IUPAC oxoacids IUPAC oxacids ChEBI oxiacids ChEBI oxo acid ChEBI oxy-acids ChEBI oxyacids ChEBI chebi_ontology inorganic anions CHEBI:24834 inorganic anion inorganic anions ChEBI A molecular entity that contains no carbon. chebi_ontology anorganische Verbindungen inorganic compounds inorganic entity inorganic molecular entities inorganics CHEBI:24835 inorganic molecular entity anorganische Verbindungen ChEBI inorganic compounds ChEBI inorganic entity ChEBI inorganic molecular entities ChEBI inorganics ChEBI chebi_ontology inorganic oxides CHEBI:24836 inorganic oxide inorganic oxides ChEBI chebi_ontology monoatomic ions CHEBI:24867 monoatomic ion monoatomic ions ChEBI A molecular entity having a net electric charge. Ion ion chebi_ontology Ionen iones ions CHEBI:24870 ion Ion ChEBI ion ChEBI ion IUPAC Ionen ChEBI iones ChEBI ions ChEBI iron molecular entity chebi_ontology iron compounds iron molecular entities CHEBI:24873 iron molecular entity iron molecular entity ChEBI iron compounds ChEBI iron molecular entities ChEBI Fe 55.845 55.93494 iron cation chebi_ontology Fe cation iron cations CHEBI:24875 iron cation iron cation IUPAC Fe cation UniProt iron cations ChEBI Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites. CHEBI:26619 CHEBI:35220 metabolite chebi_ontology metabolites primary metabolites secondary metabolites CHEBI:25212 metabolite metabolite IUPAC metabolites ChEBI primary metabolites ChEBI secondary metabolites ChEBI chebi_ontology a metal cation metal cations CHEBI:25213 metal cation a metal cation UniProt metal cations ChEBI A molecule all atoms of which have the same atomic number. chebi_ontology homoatomic molecule homoatomic molecules CHEBI:25362 elemental molecule homoatomic molecule ChEBI homoatomic molecules ChEBI Any polyatomic entity that is an electrically neutral entity consisting of more than one atom. molecule chebi_ontology Molekuel molecula molecules neutral molecular compounds CHEBI:25367 molecule molecule IUPAC Molekuel ChEBI molecula IUPAC molecules IUPAC neutral molecular compounds IUPAC A group of neurotransmitters and neuromodulators that contain one amino group that is connected to an aromatic ring by ethylene group (-CH2-CH2-). Monoamines are derived from the aromatic amino acids phenylalanine, tyrosine, histidine and tryptophan. chebi_ontology monamines monoamines CHEBI:25375 monoamine molecular messenger monamines ChEBI monoamines ChEBI An oxoacid containing a single carboxy group. chebi_ontology monocarboxylic acids CHEBI:25384 monocarboxylic acid monocarboxylic acids ChEBI An endogenous compound that is used to transmit information across the synapse between a neuron and another cell. Wikipedia:Neurotransmitter chebi_ontology neurotransmitters CHEBI:25512 neurotransmitter neurotransmitters ChEBI 0 N 14.007 14.00307 WebElements:N nitrogen chebi_ontology 7N N Stickstoff azote nitrogen nitrogeno CHEBI:25555 nitrogen atom nitrogen IUPAC 7N IUPAC N IUPAC Stickstoff ChEBI azote IUPAC nitrogen ChEBI nitrogeno ChEBI nonmetal chebi_ontology Nichtmetall Nichtmetalle no metal no metales non-metal non-metaux nonmetal nonmetals CHEBI:25585 nonmetal atom nonmetal IUPAC Nichtmetall ChEBI Nichtmetalle ChEBI no metal ChEBI no metales ChEBI non-metal ChEBI non-metaux ChEBI nonmetal ChEBI nonmetals ChEBI Any organic ion with a net negative charge. chebi_ontology organic anions CHEBI:25696 organic anion organic anions ChEBI Any organic ion with a net positive charge. chebi_ontology organic cations CHEBI:25697 organic cation organic cations ChEBI chebi_ontology organic ions CHEBI:25699 organic ion organic ions ChEBI Compounds of the general formula SO3HOR where R is an organyl group chebi_ontology organic sulfates CHEBI:25704 organic sulfate organic sulfates ChEBI An oxide is a chemical compound of oxygen with other chemical elements. oxide chebi_ontology oxides CHEBI:25741 oxide oxide ChEBI oxides ChEBI 0 O InChI=1S/O QVGXLLKOCUKJST-UHFFFAOYSA-N 15.99940 15.99491 [O] KEGG:C00007 WebElements:O oxygen chebi_ontology 8O O Sauerstoff oxigeno oxygen oxygene CHEBI:25805 oxygen atom oxygen IUPAC 8O IUPAC O IUPAC Sauerstoff ChEBI oxigeno ChEBI oxygen ChEBI oxygene ChEBI oxygen molecular entity chebi_ontology oxygen molecular entities CHEBI:25806 oxygen molecular entity oxygen molecular entity ChEBI oxygen molecular entities ChEBI Any peptide with hormonal activity in animals, whether endocrine, neuroendocrine, or paracrine. chebi_ontology peptide hormones polypeptide hormone CHEBI:25905 peptide hormone peptide hormones ChEBI polypeptide hormone ChEBI Salts and esters of phosphoric and oligophosphoric acids and their chalcogen analogues. In inorganic chemistry, the term is also used to describe anionic coordination entities with phosphorus as central atom. phosphates chebi_ontology phosphates CHEBI:26020 phosphate phosphates IUPAC phosphates ChEBI A phosphorus oxoacid that consists of one oxo and three hydroxy groups joined covalently to a central phosphorus atom. 0 H3O4P InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N 97.99520 97.97690 [H]OP(=O)(O[H])O[H] Beilstein:1921286 CAS:7664-38-2 Drug_Central:4478 Gmelin:2000 HMDB:HMDB0002142 KEGG:C00009 KEGG:D05467 KNApSAcK:C00007408 PMID:11455380 PMID:15630224 PMID:17439666 PMID:17518491 PMID:22282755 PMID:22333268 PMID:22381614 PMID:22401268 Reaxys:1921286 Wikipedia:Phosphoric_Acid Phosphoric acid phosphoric acid tetraoxophosphoric acid trihydrogen tetraoxophosphate(3-) trihydroxidooxidophosphorus chebi_ontology H3PO4 Orthophosphoric acid Phosphate Phosphorsaeure Phosphorsaeureloesungen [PO(OH)3] acide phosphorique acidum phosphoricum orthophosphoric acid CHEBI:26078 phosphoric acid Drug_Central:4478 DrugCentral Gmelin:2000 Gmelin PMID:11455380 Europe PMC PMID:15630224 Europe PMC PMID:17439666 Europe PMC PMID:17518491 Europe PMC PMID:22282755 Europe PMC PMID:22333268 Europe PMC PMID:22381614 Europe PMC PMID:22401268 Europe PMC Reaxys:1921286 Reaxys Phosphoric acid KEGG_COMPOUND phosphoric acid IUPAC tetraoxophosphoric acid IUPAC trihydrogen tetraoxophosphate(3-) IUPAC trihydroxidooxidophosphorus IUPAC H3PO4 IUPAC Orthophosphoric acid KEGG_COMPOUND Phosphate KEGG_COMPOUND Phosphorsaeure ChEBI Phosphorsaeureloesungen ChEBI [PO(OH)3] IUPAC acide phosphorique ChEBI acidum phosphoricum ChEBI orthophosphoric acid NIST_Chemistry_WebBook Beilstein:1921286 Beilstein CAS:7664-38-2 ChemIDplus CAS:7664-38-2 KEGG COMPOUND CAS:7664-38-2 NIST Chemistry WebBook chebi_ontology CHEBI:26079 phosphoric acid derivative chebi_ontology phosphorus molecular entities CHEBI:26082 phosphorus molecular entity phosphorus molecular entities ChEBI Any amino acid whose side chain is capable of forming one or more hydrogen bonds. 0 C2H4NO2R 74.059 74.02420 OC(C(*)N)=O CHEBI:8283 MetaCyc:Polar-amino-acids PMID:12016058 polar amino acid chebi_ontology polar amino acids polar amino-acid polar amino-acids CHEBI:26167 polar amino acid PMID:12016058 Europe PMC polar amino acid ChEBI polar amino acids ChEBI polar amino-acid ChEBI polar amino-acids ChEBI Any steroid that acts as hormone. chebi_ontology Steroidhormon Steroidhormone hormona esteroide hormonas esteroideas hormone steroide hormones steroides steroid hormones CHEBI:26764 steroid hormone Steroidhormon ChEBI Steroidhormone ChEBI hormona esteroide ChEBI hormonas esteroideas ChEBI hormone steroide ChEBI hormones steroides ChEBI steroid hormones ChEBI An ester of an alcohol and sulfuric acid. 0 O4SR2 96.06300 95.95173 [*]OS(=O)(=O)O[*] chebi_ontology sulfate ester sulfuric acid ester sulfuric acid esters CHEBI:26819 sulfuric ester sulfate ester ChEBI sulfuric acid ester ChEBI sulfuric acid esters ChEBI Salts and esters of sulfuric acid sulfates chebi_ontology sulfuric acid derivative sulphates CHEBI:26820 sulfates sulfates ChEBI sulfuric acid derivative ChEBI sulphates ChEBI 0 S InChI=1S/S NINIDFKCEFEMDL-UHFFFAOYSA-N 32.06600 31.97207 [S] CAS:7704-34-9 KEGG:C00087 KEGG:D06527 PPDB:605 WebElements:S sulfur chebi_ontology 16S Elemental sulfur S Schwefel azufre soufre sulfur sulphur theion CHEBI:26833 sulfur atom CAS:7704-34-9 ChemIDplus CAS:7704-34-9 NIST Chemistry WebBook sulfur IUPAC 16S IUPAC Elemental sulfur KEGG_COMPOUND S IUPAC S KEGG_COMPOUND Schwefel ChEBI azufre ChEBI soufre ChEBI sulfur ChEBI sulfur UniProt sulphur ChEBI theion IUPAC sulfur molecular entity chebi_ontology sulfur molecular entities CHEBI:26835 sulfur molecular entity sulfur molecular entity ChEBI sulfur molecular entities ChEBI A sulfur oxoacid that consists of two oxo and two hydroxy groups joined covalently to a central sulfur atom. 0 H2O4S InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4) QAOWNCQODCNURD-UHFFFAOYSA-N 98.07948 97.96738 [H]OS(=O)(=O)O[H] CAS:7664-93-9 Gmelin:2122 KEGG:C00059 KEGG:D05963 KNApSAcK:C00007530 MolBase:4 PMID:13568755 PMID:16122922 PMID:19397353 PMID:22047659 PMID:22136045 PMID:22204399 PMID:22267186 PMID:22296037 PMID:22364556 PMID:22435616 PPDB:606 Reaxys:2037554 Wikipedia:Sulfuric_acid Sulfuric acid dihydrogen tetraoxosulfate dihydroxidodioxidosulfur hydrogen tetraoxosulfate(2-) hydrogen tetraoxosulfate(VI) sulfuric acid tetraoxosulfuric acid chebi_ontology Acide sulfurique Acido sulfurico Acidum sulfuricum H2SO4 Schwefelsaeureloesungen [S(OH)2O2] [SO2(OH)2] sulphuric acid CHEBI:26836 sulfuric acid CAS:7664-93-9 ChemIDplus CAS:7664-93-9 KEGG COMPOUND CAS:7664-93-9 NIST Chemistry WebBook Gmelin:2122 Gmelin PMID:13568755 Europe PMC PMID:16122922 Europe PMC PMID:19397353 Europe PMC PMID:22047659 Europe PMC PMID:22136045 Europe PMC PMID:22204399 Europe PMC PMID:22267186 Europe PMC PMID:22296037 Europe PMC PMID:22364556 Europe PMC PMID:22435616 Europe PMC Reaxys:2037554 Reaxys Sulfuric acid KEGG_COMPOUND dihydrogen tetraoxosulfate IUPAC dihydroxidodioxidosulfur IUPAC hydrogen tetraoxosulfate(2-) IUPAC hydrogen tetraoxosulfate(VI) IUPAC sulfuric acid ChEBI sulfuric acid IUPAC tetraoxosulfuric acid IUPAC Acide sulfurique ChemIDplus Acido sulfurico ChemIDplus Acidum sulfuricum ChemIDplus H2SO4 IUPAC Schwefelsaeureloesungen ChemIDplus [S(OH)2O2] MolBase [SO2(OH)2] IUPAC sulphuric acid MolBase Any nutrient required in small quantities by organisms throughout their life in order to orchestrate a range of physiological functions. Wikipedia:Micronutrient chebi_ontology micronutrients trace elements CHEBI:27027 micronutrient micronutrients ChEBI trace elements ChEBI An element whose atom has an incomplete d sub-shell, or which can give rise to cations with an incomplete d sub-shell. transition element chebi_ontology Uebergangselement Uebergangsmetalle metal de transicion metal de transition metales de transicion metaux de transition transition element transition elements transition metal transition metals CHEBI:27081 transition element atom transition element IUPAC Uebergangselement ChEBI Uebergangsmetalle ChEBI metal de transicion ChEBI metal de transition ChEBI metales de transicion ChEBI metaux de transition ChEBI transition element ChEBI transition elements ChEBI transition metal ChEBI transition metals ChEBI Tryptamine and its substitution derivatives. chebi_ontology CHEBI:27162 tryptamines chebi_ontology heterobicyclic compounds organic heterobicyclic compounds CHEBI:27171 organic heterobicyclic compound heterobicyclic compounds ChEBI organic heterobicyclic compounds ChEBI A univalent carboacyl group is a group formed by loss of OH from the carboxy group of a carboxylic acid. chebi_ontology univalent acyl group univalent carboacyl groups univalent carboxylic acyl groups CHEBI:27207 univalent carboacyl group univalent acyl group ChEBI univalent carboacyl groups ChEBI univalent carboxylic acyl groups ChEBI A neutral compound having formal unit electrical charges of opposite sign on non-adjacent atoms. Sometimes referred to as inner salts, dipolar ions (a misnomer). zwitterion zwitterions chebi_ontology compose zwitterionique compuestos zwitterionicos zwitteriones zwitterionic compounds CHEBI:27369 zwitterion zwitterion IUPAC zwitterions IUPAC compose zwitterionique IUPAC compuestos zwitterionicos IUPAC zwitteriones IUPAC zwitterionic compounds IUPAC 0 C InChI=1S/C OKTJSMMVPCPJKN-UHFFFAOYSA-N 12.01070 12.00000 [C] CHEBI:23009 CHEBI:3399 CAS:7440-44-0 KEGG:C06265 WebElements:C carbon chebi_ontology 6C C Carbon Kohlenstoff carbon carbone carbonium carbono CHEBI:27594 carbon atom CAS:7440-44-0 ChemIDplus CAS:7440-44-0 KEGG COMPOUND carbon IUPAC 6C IUPAC C IUPAC C KEGG_COMPOUND Carbon KEGG_COMPOUND Kohlenstoff ChEBI carbon ChEBI carbone ChEBI carbonium ChEBI carbono ChEBI A one-carbon compound that is ammonia in which one of the hydrogens is replaced by a carboxy group. Although carbamic acid derivatives are common, carbamic acid itself has never been synthesised. 0 CH3NO2 InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4) KXDHJXZQYSOELW-UHFFFAOYSA-N 61.04006 61.01638 NC(O)=O CHEBI:22504 CHEBI:23002 CHEBI:3386 CHEBI:44573 Beilstein:1734754 CAS:463-77-4 DrugBank:DB04261 Gmelin:130345 KEGG:C01563 PDBeChem:OUT Wikipedia:Carbamic_acid CARBAMIC ACID Carbamic acid carbamic acid chebi_ontology Aminoameisensaeure Aminoformic acid Carbamate Carbamidsaeure CHEBI:28616 carbamic acid Beilstein:1734754 Beilstein CAS:463-77-4 ChemIDplus CAS:463-77-4 KEGG COMPOUND Gmelin:130345 Gmelin CARBAMIC ACID PDBeChem Carbamic acid KEGG_COMPOUND carbamic acid IUPAC Aminoameisensaeure ChEBI Aminoformic acid KEGG_COMPOUND Carbamate KEGG_COMPOUND Carbamidsaeure ChEBI 0 P InChI=1S/P OAICVXFJPJFONN-UHFFFAOYSA-N 30.97376 30.97376 [P] CHEBI:26080 CHEBI:8168 CAS:7723-14-0 Gmelin:16235 KEGG:C06262 WebElements:P phosphorus chebi_ontology 15P P Phosphor Phosphorus fosforo phosphore phosphorus CHEBI:28659 phosphorus atom CAS:7723-14-0 ChemIDplus CAS:7723-14-0 KEGG COMPOUND Gmelin:16235 Gmelin phosphorus IUPAC 15P IUPAC P IUPAC P KEGG_COMPOUND Phosphor ChEBI Phosphorus KEGG_COMPOUND fosforo ChEBI phosphore ChEBI phosphorus ChEBI A primary amino compound that is the 5-hydroxy derivative of tryptamine. 0 C10H12N2O InChI=1S/C10H12N2O/c11-4-3-7-6-12-10-2-1-8(13)5-9(7)10/h1-2,5-6,12-13H,3-4,11H2 QZAYGJVTTNCVMB-UHFFFAOYSA-N 176.215 176.09496 C1=CC(=CC=2C(=CNC12)CCN)O CHEBI:1420 CHEBI:26652 CHEBI:49894 Beilstein:143524 CAS:50-67-9 Gmelin:1861995 HMDB:HMDB0000259 KEGG:C00780 KNApSAcK:C00001429 LINCS:LSM-6589 MetaCyc:SEROTONIN PDBeChem:SRO PMID:18593914 PMID:22770225 PMID:24136337 Reaxys:143524 Wikipedia:Serotonin 3-(2-aminoethyl)-1H-indol-5-ol SEROTONIN Serotonin chebi_ontology 3-(2-Aminoethyl)-1H-indol-5-ol 5-HT 5-Hydroxytryptamine Enteramine serotonine thrombocytin thrombotonin CHEBI:28790 serotonin Beilstein:143524 Beilstein CAS:50-67-9 ChemIDplus CAS:50-67-9 KEGG COMPOUND Gmelin:1861995 Gmelin PMID:18593914 Europe PMC PMID:22770225 Europe PMC PMID:24136337 Europe PMC Reaxys:143524 Reaxys 3-(2-aminoethyl)-1H-indol-5-ol IUPAC SEROTONIN PDBeChem Serotonin KEGG_COMPOUND 3-(2-Aminoethyl)-1H-indol-5-ol KEGG_COMPOUND 5-HT IUPHAR 5-Hydroxytryptamine KEGG_COMPOUND Enteramine KEGG_COMPOUND serotonine ChEBI thrombocytin ChemIDplus thrombotonin ChemIDplus An onium cation obtained by protonation of ammonia. +1 H4N InChI=1S/H3N/h1H3/p+1 QGZKDVFQNNGYKY-UHFFFAOYSA-O 18.03850 18.03383 [H][N+]([H])([H])[H] CHEBI:22534 CHEBI:49783 CHEBI:7435 CAS:14798-03-9 Gmelin:84 KEGG:C01342 MetaCyc:AMMONIUM MolBase:929 PDBeChem:NH4 PMID:11319011 PMID:11341317 PMID:12096804 PMID:14512268 PMID:14879753 PMID:16345391 PMID:16903292 PMID:17392693 PMID:18515490 PMID:19199063 PMID:19596600 PMID:19682559 PMID:19716251 PMID:21993530 PMID:22265469 PMID:22524020 PMID:22562341 PMID:22631217 Reaxys:16093784 Wikipedia:Ammonium ammonium azanium chebi_ontology Ammonium(1+) NH4(+) NH4+ [NH4](+) ammonium cation ammonium ion CHEBI:28938 ammonium CAS:14798-03-9 ChemIDplus CAS:14798-03-9 NIST Chemistry WebBook Gmelin:84 Gmelin PMID:11319011 Europe PMC PMID:11341317 Europe PMC PMID:12096804 Europe PMC PMID:14512268 Europe PMC PMID:14879753 Europe PMC PMID:16345391 Europe PMC PMID:16903292 Europe PMC PMID:17392693 Europe PMC PMID:18515490 Europe PMC PMID:19199063 Europe PMC PMID:19596600 Europe PMC PMID:19682559 Europe PMC PMID:19716251 Europe PMC PMID:21993530 Europe PMC PMID:22265469 Europe PMC PMID:22524020 Europe PMC PMID:22562341 Europe PMC PMID:22631217 Europe PMC Reaxys:16093784 Reaxys ammonium ChEBI ammonium IUPAC azanium IUPAC Ammonium(1+) ChemIDplus NH4(+) IUPAC NH4(+) UniProt NH4+ KEGG_COMPOUND [NH4](+) MolBase ammonium cation ChemIDplus ammonium ion PDBeChem A carboxylic acid dianion obtained by deprotonation of both carboxy groups of any dicarboxylic acid. -2 C2O4R 88.019 87.97966 [O-]C(=O)[*]C([O-])=O CHEBI:13632 CHEBI:23688 CHEBI:23689 CHEBI:38711 dicarboxylic acid dianion chebi_ontology a dicarboxylate dicarboxylate dicarboxylates dicarboxylic acid dianions CHEBI:28965 dicarboxylic acid dianion dicarboxylic acid dianion ChEBI a dicarboxylate UniProt dicarboxylate ChEBI dicarboxylates ChEBI dicarboxylic acid dianions ChEBI The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated. -1 CO2R 44.00950 43.98983 [O-]C([*])=O CHEBI:13626 CHEBI:13945 CHEBI:23026 CHEBI:58657 chebi_ontology a carboxylate carboxylic acid anions carboxylic anions CHEBI:29067 carboxylic acid anion a carboxylate UniProt carboxylic acid anions ChEBI carboxylic anions ChEBI -1 H2N InChI=1S/H2N/h1H2/q-1 HYGWNUKOUCZBND-UHFFFAOYSA-N 16.02262 16.01927 [H][N-][H] amide azanide dihydridonitrate(1-) chebi_ontology NH2(-) CHEBI:29337 azanide amide IUPAC azanide IUPAC dihydridonitrate(1-) IUPAC NH2(-) IUPAC A divalent inorganic anion resulting from the removal of two protons from ammonia. -2 HN InChI=1S/HN/h1H/q-2 DZQYTNGKSBCIOE-UHFFFAOYSA-N 15.01468 15.01200 [N--][H] azanediide hydridonitrate(2-) chebi_ontology NH(2-) imide CHEBI:29340 hydridonitrate(2-) azanediide IUPAC hydridonitrate(2-) IUPAC NH(2-) IUPAC imide IUPAC +1 HO2 InChI=1S/O2/c1-2/p+1 MYMOFIZGZYHOMD-UHFFFAOYSA-O 33.00674 32.99711 [H][O+]=O Gmelin:508 dioxidenium hydridodioxygen(1+) chebi_ontology HO2(+) HOO(+) [HO2](+) CHEBI:29793 hydridodioxygen(1+) Gmelin:508 Gmelin dioxidenium IUPAC hydridodioxygen(1+) IUPAC HO2(+) IUPAC HOO(+) ChEBI [HO2](+) ChEBI A dicarboxylic acid dianion that is the conjugate base of glutamate(1-). -2 C5H7NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-2 WHUUTDBJXJRKMK-UHFFFAOYSA-L 145.11342 145.03860 NC(CCC([O-])=O)C([O-])=O Beilstein:4134100 Gmelin:327903 Reaxys:4134100 2-aminopentanedioate glutamate glutamate(2-) chebi_ontology glutamic acid dianion CHEBI:29987 glutamate(2-) Beilstein:4134100 Beilstein Gmelin:327903 Gmelin Reaxys:4134100 Reaxys 2-aminopentanedioate IUPAC glutamate IUPAC glutamate(2-) JCBN glutamic acid dianion JCBN A monocarboxylic acid anion resulting from the removal of a proton from the carboxy group of acetic acid. -1 C2H3O2 InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1 QTBSBXVTEAMEQO-UHFFFAOYSA-M 59.04402 59.01385 CC([O-])=O CHEBI:13704 CHEBI:22165 CHEBI:40480 Beilstein:1901470 CAS:71-50-1 DrugBank:DB03166 Gmelin:1379 KEGG:C00033 MetaCyc:ACET PDBeChem:ACT PMID:17190852 PMID:22211106 PMID:22371380 Reaxys:1901470 UM-BBD_compID:c0050 Wikipedia:Acetate acetate chebi_ontology ACETATE ION Azetat CH3-COO(-) Ethanoat MeCO2 anion acetic acid, ion(1-) ethanoate CHEBI:30089 acetate Beilstein:1901470 Beilstein CAS:71-50-1 ChemIDplus CAS:71-50-1 NIST Chemistry WebBook Gmelin:1379 Gmelin PMID:17190852 Europe PMC PMID:22211106 Europe PMC PMID:22371380 Europe PMC Reaxys:1901470 Reaxys UM-BBD_compID:c0050 UM-BBD acetate IUPAC acetate UniProt ACETATE ION PDBeChem Azetat ChEBI CH3-COO(-) IUPAC Ethanoat ChEBI MeCO2 anion NIST_Chemistry_WebBook acetic acid, ion(1-) ChemIDplus ethanoate ChEBI Particle of zero charge, zero rest mass, spin quantum number 1, energy hnu and momentum hnu/c (h is the Planck constant, nu the frequency of radiation and c the speed of light), carrier of electromagnetic force. 0 0.0 0.0 * CHEBI:10581 CHEBI:14383 KEGG:C00205 photon chebi_ontology Lichtquant Light foton gamma hnu light quantum CHEBI:30212 photon photon IUPAC Lichtquant ChEBI Light KEGG_COMPOUND foton ChEBI gamma IUPAC hnu IUPAC hnu UniProt light quantum ChEBI A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups. CHEBI:13814 CHEBI:22474 CHEBI:2641 KEGG:C00706 Amine amines chebi_ontology Amin Substituted amine CHEBI:32952 amine Amine KEGG_COMPOUND amines IUPAC Amin ChEBI Substituted amine KEGG_COMPOUND An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group. CHEBI:22473 CHEBI:2633 KEGG:C00241 Amide amides chebi_ontology CHEBI:32988 amide Amide KEGG_COMPOUND amides IUPAC Intended use of the molecular entity or part thereof by humans. chebi_ontology CHEBI:33232 application A particle not known to have substructure. elementary particle chebi_ontology elementary particles CHEBI:33233 fundamental particle elementary particle IUPAC elementary particles ChEBI A monoatomic entity is a molecular entity consisting of a single atom. chebi_ontology atomic entity monoatomic entities CHEBI:33238 monoatomic entity atomic entity ChEBI monoatomic entities ChEBI chebi_ontology oxoacid derivatives CHEBI:33241 oxoacid derivative oxoacid derivatives ChEBI chebi_ontology inorganic hydrides CHEBI:33242 inorganic hydride inorganic hydrides ChEBI Any substituent group which does not contain carbon. chebi_ontology inorganic groups CHEBI:33246 inorganic group inorganic groups ChEBI Any substituent group or skeleton containing carbon. chebi_ontology organic groups CHEBI:33247 organic group organic groups ChEBI Any organic substituent group, regardless of functional type, having one free valence at a carbon atom. organyl group organyl groups chebi_ontology groupe organyle grupo organilo grupos organilo CHEBI:33249 organyl group organyl group IUPAC organyl groups IUPAC groupe organyle IUPAC grupo organilo IUPAC grupos organilo IUPAC A chemical entity constituting the smallest component of an element having the chemical properties of the element. CHEBI:22671 CHEBI:23907 atom chebi_ontology atome atomo atoms atomus element elements CHEBI:33250 atom atom IUPAC atome IUPAC atomo IUPAC atoms ChEBI atomus ChEBI element ChEBI elements ChEBI A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. nucleus chebi_ontology Atomkern Kern noyau noyau atomique nuclei nucleo nucleo atomico nucleus atomi CHEBI:33252 atomic nucleus nucleus IUPAC Atomkern ChEBI Kern ChEBI noyau IUPAC noyau atomique ChEBI nuclei ChEBI nucleo IUPAC nucleo atomico ChEBI nucleus atomi ChEBI Heavy nuclear particle: proton or neutron. nucleon chebi_ontology Nukleon Nukleonen nucleons CHEBI:33253 nucleon nucleon IUPAC nucleon IUPAC Nukleon ChEBI Nukleonen ChEBI nucleons ChEBI A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group. primary amide primary amides chebi_ontology CHEBI:33256 primary amide primary amide IUPAC primary amides IUPAC A molecular entity all atoms of which have the same atomic number. chebi_ontology homoatomic entity homoatomic molecular entities homoatomic molecular entity CHEBI:33259 elemental molecular entity homoatomic entity ChEBI homoatomic molecular entities ChEBI homoatomic molecular entity ChEBI chebi_ontology CHEBI:33262 elemental oxygen 0 O2 31.999 31.98983 chebi_ontology CHEBI:33263 diatomic oxygen An anion consisting of more than one atom. chebi_ontology polyatomic anions CHEBI:33273 polyatomic anion polyatomic anions ChEBI chebi_ontology chemical messenger CHEBI:33280 molecular messenger chemical messenger ChEBI A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans. CHEBI:22582 PMID:12964249 PMID:22117953 PMID:22439833 PMID:22849268 PMID:22849276 PMID:22958833 chebi_ontology Antibiotika Antibiotikum antibiotic antibiotics antibiotique antimicrobial antimicrobial agents antimicrobials microbicide microbicides CHEBI:33281 antimicrobial agent PMID:12964249 Europe PMC PMID:22117953 Europe PMC PMID:22439833 Europe PMC PMID:22849268 Europe PMC PMID:22849276 Europe PMC PMID:22958833 Europe PMC Antibiotika ChEBI Antibiotikum ChEBI antibiotic ChEBI antibiotics ChEBI antibiotique IUPAC antimicrobial ChEBI antimicrobial agents ChEBI antimicrobials ChEBI microbicide ChEBI microbicides ChEBI A nutrient is a food component that an organism uses to survive and grow. chebi_ontology nutrients CHEBI:33284 nutrient nutrients ChEBI A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms. chebi_ontology heteroorganic entities organoelement compounds CHEBI:33285 heteroorganic entity heteroorganic entities ChEBI organoelement compounds ChEBI An agrochemical is a substance that is used in agriculture or horticulture. Wikipedia:Agrochemical chebi_ontology agrichemical agrichemicals agricultural chemicals agrochemicals CHEBI:33286 agrochemical agrichemical ChEBI agrichemicals ChEBI agricultural chemicals ChEBI agrochemicals ChEBI A fertilizer is any substance that is added to soil or water to assist the growth of plants. chebi_ontology fertiliser fertilizers CHEBI:33287 fertilizer fertiliser ChEBI fertilizers ChEBI Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth. pnictogens chebi_ontology group 15 elements group V elements nitrogenoideos nitrogenoides pnictogene pnictogenes CHEBI:33300 pnictogen pnictogens IUPAC group 15 elements ChEBI group V elements ChEBI nitrogenoideos ChEBI nitrogenoides ChEBI pnictogene ChEBI pnictogenes ChEBI A p-block molecular entity containing any pnictogen. pnictogen molecular entity chebi_ontology pnictogen molecular entities CHEBI:33302 pnictogen molecular entity pnictogen molecular entity ChEBI pnictogen molecular entities ChEBI Any p-block element belonging to the group 16 family of the periodic table. PMID:17084588 chalcogen chalcogens chebi_ontology Chalkogen Chalkogene anfigeno anfigenos calcogeno calcogenos chalcogene chalcogenes group 16 elements group VI elements CHEBI:33303 chalcogen PMID:17084588 Europe PMC chalcogen IUPAC chalcogens IUPAC Chalkogen ChEBI Chalkogene ChEBI anfigeno ChEBI anfigenos ChEBI calcogeno ChEBI calcogenos ChEBI chalcogene ChEBI chalcogenes ChEBI group 16 elements ChEBI group VI elements ChEBI Any p-block molecular entity containing a chalcogen. chalcogen molecular entity chebi_ontology chalcogen compounds chalcogen molecular entities CHEBI:33304 chalcogen molecular entity chalcogen molecular entity ChEBI chalcogen compounds ChEBI chalcogen molecular entities ChEBI group 14 elements chebi_ontology carbon group element carbon group elements carbonoides cristallogene cristallogenes group IV elements CHEBI:33306 carbon group element atom group 14 elements IUPAC carbon group element ChEBI carbon group elements ChEBI carbonoides ChEBI cristallogene ChEBI cristallogenes ChEBI group IV elements ChEBI An ester of a carboxylic acid, R(1)C(=O)OR(2), where R(1) = H or organyl and R(2) = organyl. 0 CO2R2 44.010 43.98983 [*]C(=O)O[*] CHEBI:13204 CHEBI:23028 CHEBI:3408 KEGG:C02391 Wikipedia:Ester Carboxylic ester carboxylic esters chebi_ontology a carboxylic ester carboxylic acid esters CHEBI:33308 carboxylic ester Carboxylic ester KEGG_COMPOUND carboxylic esters IUPAC a carboxylic ester UniProt carboxylic acid esters ChEBI An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table. main group elements chebi_ontology Hauptgruppenelement Hauptgruppenelemente main group element CHEBI:33318 main group element atom main group elements IUPAC Hauptgruppenelement ChEBI Hauptgruppenelemente ChEBI main group element ChEBI group 8 elements chebi_ontology iron group element iron group elements CHEBI:33356 iron group element atom group 8 elements IUPAC iron group element ChEBI iron group elements ChEBI chebi_ontology oxoacids of sulfur sulfur oxoacids CHEBI:33402 sulfur oxoacid oxoacids of sulfur ChEBI sulfur oxoacids ChEBI chebi_ontology pnictogen oxoacids CHEBI:33408 pnictogen oxoacid pnictogen oxoacids ChEBI sulfur oxoacid derivative chebi_ontology sulfur oxoacid derivatives CHEBI:33424 sulfur oxoacid derivative sulfur oxoacid derivative ChEBI sulfur oxoacid derivatives ChEBI A pnictogen oxoacid which contains phosphorus and oxygen, at least one hydrogen atom bound to oxygen, and forms an ion by the loss of one or more protons. phosphorus oxoacid chebi_ontology Oxosaeure des Phosphors oxoacids of phosphorus phosphorus oxoacids CHEBI:33457 phosphorus oxoacid phosphorus oxoacid ChEBI Oxosaeure des Phosphors ChEBI oxoacids of phosphorus ChEBI phosphorus oxoacids ChEBI pnictogen oxoanion chebi_ontology pnictogen oxoanions CHEBI:33459 pnictogen oxoanion pnictogen oxoanion ChEBI pnictogen oxoanions ChEBI phosphorus oxoanion chebi_ontology oxoanions of phosphorus phosphorus oxoanions CHEBI:33461 phosphorus oxoanion phosphorus oxoanion ChEBI oxoanions of phosphorus ChEBI phosphorus oxoanions ChEBI sulfur oxoanion chebi_ontology oxoanions of sulfur sulfur oxoanions CHEBI:33482 sulfur oxoanion sulfur oxoanion ChEBI oxoanions of sulfur ChEBI sulfur oxoanions ChEBI chalcogen oxoacid chebi_ontology chalcogen oxoacids CHEBI:33484 chalcogen oxoacid chalcogen oxoacid ChEBI chalcogen oxoacids ChEBI chalcogen oxoanion chebi_ontology chalcogen oxoanions CHEBI:33485 chalcogen oxoanion chalcogen oxoanion ChEBI chalcogen oxoanions ChEBI A molecular entity containing one or more atoms of a transition element. chebi_ontology transition element molecular entities transition metal molecular entity CHEBI:33497 transition element molecular entity transition element molecular entities ChEBI transition metal molecular entity ChEBI chebi_ontology transition element cations transition metal cation CHEBI:33515 transition element cation transition element cations ChEBI transition metal cation ChEBI An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity. CHEBI:25217 CHEBI:6788 KEGG:C00050 PMID:21784043 Wikipedia:Metal chebi_ontology elemental metal elemental metals metal element metal elements metals CHEBI:33521 metal atom PMID:21784043 Europe PMC elemental metal ChEBI elemental metals ChEBI metal element ChEBI metal elements ChEBI metals ChEBI An amino-acid anion obtained by deprotonation of any alpha-amino acid. alpha-amino-acid anion chebi_ontology alpha-amino acid anions alpha-amino-acid anions CHEBI:33558 alpha-amino-acid anion alpha-amino-acid anion ChEBI alpha-amino acid anions ChEBI alpha-amino-acid anions ChEBI chebi_ontology s-block element s-block elements CHEBI:33559 s-block element atom s-block element ChEBI s-block elements ChEBI Any main group element atom belonging to the p-block of the periodic table. chebi_ontology p-block element p-block elements CHEBI:33560 p-block element atom p-block element ChEBI p-block elements ChEBI chebi_ontology d-block element d-block elements CHEBI:33561 d-block element atom d-block element ChEBI d-block elements ChEBI Any compound containing an o-diphenol component. 0 C6H2O2R4 106.079 106.00548 OC1=C(O)C(*)=C(*)C(*)=C1* CHEBI:134187 CHEBI:13628 CHEBI:18862 KEGG:C15571 chebi_ontology 1,2-benzenediols a catechol benzene-1,2-diols CHEBI:33566 catechols