Human Phenotype Ontology Consortium Monarch Initiative Peter Robinson Sebastian Köhler http://www.human-phenotype-ontology.org Peter Robinson, Sebastian Koehler, The Human Phenotype Ontology Consortium, and The Monarch Initiative Phenotypic abnormalities encountered in human disease human_phenotype has_part Peter Robinson, Sebastian Koehler, Sandra Doelken, Chris Mungall, Melissa Haendel, Nicole Vasilevsky, Monarch Initiative, et al. Please see license of HPO at http://www.human-phenotype-ontology.org 2018-05-05T19:01:17Z peter obsolete 2018-07-05T13:18:08Z peter display label HPO:skoehler UK spelling HPO:skoehler abbreviation HPO:skoehler plural form editor preferred term IAO:0000112 uberon example_of_usage true example_of_usage example of usage example of usage has curation status definition definition IAO:0000116 uberon editor_note true editor_note editor note editor note term editor alternative term definition source IAO:0000232 uberon curator_notes true curator_notes curator note curator notes imported from expand expression to expand expression to An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. first order logic expression OBO foundry unique label elucidation term replaced by An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation https://github.com/oborel/obo-relations/wiki/ROAndTime S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg] RO:0002173 uberon ambiguous_for_taxon true true ambiguous_for_taxon ambiguous for taxon ambiguous_for_taxon S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. PHENOSCPAE:asilomar_mtg S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. https://orcid.org/0000-0002-6601-2165 RO:0002174 uberon dubious_for_taxon true true dubious_for_taxon This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost this relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take time to resolve. Example: metencephalon in teleost dubious for taxon dubious_for_taxon S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S https://orcid.org/0000-0002-6601-2165 RO:0002175 applicable for taxon uberon present_in_taxon true true present_in_taxon present in taxon present_in_taxon S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S defined by inverse logical macro assertion on an annotation property relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' Chris Mungall is direct form of 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 cjm 2018-03-14T00:03:16Z is positive form of cjm 2018-03-14T00:03:24Z is negative form of part-of is homeomorphic for independent continuants. R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. cjm 2018-10-21T19:46:34Z R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. is homeomorphic for An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. UBPROP:0000001 uberon external_definition true external_definition This annotation property may be replaced with an annotation property from an external ontology such as IAO external_definition An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. A textual description of an axiom loss in this ontology compared to an external ontology. UBPROP:0000002 uberon axiom_lost_from_external_ontology true axiom_lost_from_external_ontology This annotation property may be replaced with an annotation property from an external ontology such as IAO axiom_lost_from_external_ontology A textual description of an axiom loss in this ontology compared to an external ontology. Notes on the homology status of this class. UBPROP:0000003 uberon homology_notes true homology_notes This annotation property may be replaced with an annotation property from an external ontology such as IAO homology_notes Notes on the homology status of this class. An alternate comment for a class taken unmodified from an external source. Note that obo format only allows a single comment for a class, and does not provide a structured means of adding provenance info. UBPROP:0000005 uberon external_comment true external_comment This annotation property may be replaced with an annotation property from an external ontology such as IAO external_comment An alternate comment for a class taken unmodified from an external source. Note that obo format only allows a single comment for a class, and does not provide a structured means of adding provenance info. UBPROP:0000006 uberon implements_design_pattern true implements_design_pattern implements_design_pattern Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'. UBPROP:0000007 uberon has_relational_adjective true has_relational_adjective Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'. has_relational_adjective Notes on the how instances of this class vary across species. UBPROP:0000008 uberon taxon_notes true taxon_notes taxon_notes Notes on the how instances of this class vary across species. Notes on the evolved function of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000009 uberon function_notes true function_notes function_notes Notes on the evolved function of instances of this class. Notes on the structure, composition or histology of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000010 uberon structure_notes true structure_notes structure_notes Notes on the structure, composition or histology of instances of this class. Notes on the ontogenic development of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000011 uberon development_notes true development_notes development_notes Notes on the ontogenic development of instances of this class. Notes on how similar or equivalent classes are represented in other ontologies. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000012 uberon external_ontology_notes true external_ontology_notes external_ontology_notes Notes on how similar or equivalent classes are represented in other ontologies. Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000013 uberon terminology_notes true terminology_notes terminology_notes Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy. Notes on how instances of this class functon biomechanically. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000014 uberon action_notes true action_notes actions_notes Notes on how instances of this class functon biomechanically. Notes on the location, position or part-parents of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000015 uberon location_notes true location_notes location_notes Notes on the location, position or part-parents of instances of this class. UBPROP:0000100 uberon is_count_of true is_count_of is count of A property used in conjunction with repeated_element_number to indicate an axis and directionality along that axis. If P preceding_element_is R, and P is_count_of S, and X P N, and X' P N+1, then it follows that every X R some X', and the class expression [S and R some X' and inv(R) some X] is empty (i.e. X is followed by X', with no intermediates) UBPROP:0000101 uberon preceding_element_is true preceding_element_is preceding element is A property used in conjunction with repeated_element_number to indicate an axis and directionality along that axis. If P preceding_element_is R, and P is_count_of S, and X P N, and X' P N+1, then it follows that every X R some X', and the class expression [S and R some X' and inv(R) some X] is empty (i.e. X is followed by X', with no intermediates) x pharyngeal_arch_number N if and only if (i) x is a pharyngeal arch, and (ii) x is ancestrally pharyngeal arch number N in a series of pharyngeal arches repeated along a antero-posterior axis, with arch_number 1 being the mandibular arch. gill arch N = PA N-2. the term branchial_arch is ambiguous. UBPROP:0000103 uberon pharyngeal_arch_number true pharyngeal_arch_number pharyngeal arch number x pharyngeal_arch_number N if and only if (i) x is a pharyngeal arch, and (ii) x is ancestrally pharyngeal arch number N in a series of pharyngeal arches repeated along a antero-posterior axis, with arch_number 1 being the mandibular arch. x ray_number N if and only if (i) x is a ray, and (ii) x is ancestrally associated with ray number N in a series of phalanges repeated along a radio-ulnar or equivalent axis, with ray_number 1 being the anteriormost ray. UBPROP:0000104 uberon ray_number true ray_number The correct terminology is yet to be established; in tetrapods 'ray' might mean the mereological sum of the phalanges of a manual digit plus a metatarsal bone (or equivalent for hindlimb) ray number x ray_number N if and only if (i) x is a ray, and (ii) x is ancestrally associated with ray number N in a series of phalanges repeated along a radio-ulnar or equivalent axis, with ray_number 1 being the anteriormost ray. x phalanx_number N if and only if (i) x is a phalanx, and (ii) x is phalanx number N in a series of phalanges repeated along an prixomo-distal axis, with phalanx_number 1 being the proximalmost phalanx. Note that in humans, the distalmost phalanx has phlanax_number 3, except in ray_number 1, where the distalmost has phalanx_number 2 UBPROP:0000105 uberon phalanx_number true phalanx_number Most land mammals including humans have a 2-3-3-3-3 formula in both the hands (or paws) and feet. Primitive reptiles typically had the formula 2-3-4-4-5, and this pattern, with some modification, remained in many later reptiles and in the mammal-like reptiles. The phalangeal formula in the flippers of cetaceans (marine mammals) is 2-12-8-1 phalanx number x phalanx_number N if and only if (i) x is a phalanx, and (ii) x is phalanx number N in a series of phalanges repeated along an prixomo-distal axis, with phalanx_number 1 being the proximalmost phalanx. Note that in humans, the distalmost phalanx has phlanax_number 3, except in ray_number 1, where the distalmost has phalanx_number 2 x rib_number N if and only if (i) x is a rib, and (ii) x is rib number N in a series of ribs repeated along an anterior-posterior axis, with rib_number 1 being the anteriormost rib. Note that this property counts ribs, *not* the adjoining vertebrae. In the early tetrapods, every vertebra bore a pair of ribs, although those on the thoracic vertebrae are typically the longest. In most subsequent forms, many of these early ribs have been lost, and in living amphibians and reptiles, there is great variation in rib structure and number. For example, turtles have only eight pairs of ribs, which are developed into a bony or cartilagenous carapace and plastron, while snakes have numerous ribs running along the full length of their trunk. Frogs typically have no ribs, aside from a sacral pair, which form part of the pelvis. Mammals usually also only have distinct ribs on the thoracic vertebra, although fixed cervical ribs are also present in monotremes. In marsupials and placental mammals, the cervical and lumbar ribs are found only as tiny remnants fused to the vertebrae, where they are referred to as transverse processes. In general, the structure and number of the true ribs in humans is similar to that in other mammals. Unlike reptiles, caudal ribs are never found in mammals. Note that in TAO, ribs are numbered by *vertebrae* UBPROP:0000106 uberon rib_number true rib_number rib number x rib_number N if and only if (i) x is a rib, and (ii) x is rib number N in a series of ribs repeated along an anterior-posterior axis, with rib_number 1 being the anteriormost rib. Note that this property counts ribs, *not* the adjoining vertebrae. Note that in TAO, ribs are numbered by *vertebrae* TAO x vertebra_number N if and only if (i) x is a vertebra, and (ii) x is vertebra number N in a series of vertebras repeated along an anterior-posterior axis, with vertebra_number 1 being the anteriormost vertebra (also known as the atlas). UBPROP:0000107 uberon vertebra_number true vertebra_number vertebra number x vertebra_number N if and only if (i) x is a vertebra, and (ii) x is vertebra number N in a series of vertebras repeated along an anterior-posterior axis, with vertebra_number 1 being the anteriormost vertebra (also known as the atlas). x rhombomere_number N if and only if (i) x is a rhombomere, and (ii) x is rhombomere number N in a series of rhombomeres repeated along an anterior-posterior axis, with rhombomere_number 1 being the anteriormost rhombomere. UBPROP:0000111 uberon rhombomere_number true rhombomere_number rhombomere number x rhombomere_number N if and only if (i) x is a rhombomere, and (ii) x is rhombomere number N in a series of rhombomeres repeated along an anterior-posterior axis, with rhombomere_number 1 being the anteriormost rhombomere. FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term UBPROP:0000202 uberon fma_set_term true fma_set_term fma_set_term FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term FMA BRAND NAME INN IUPAC NAME Preliminary entries Annotated by 3rd party Manually annotated by ChEBI Team Term not to be used for direct annotation Term not to be used for direct manual annotation AGR slim Aspergillus GO slim Candida GO slim ChEMBL protein targets summary FlyBase Drosophila GO ribbon slim Generic GO slim Metagenomics GO slim Mouse GO slim PIR GO slim Plant GO slim Fission yeast GO slim synapse GO slim Yeast GO slim Systematic synonym Core clinical terminology Consequence of a disorder in another organ system. HPO:skoehler layperson term Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property. human_stages_ontology end_dpf true This is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent. end, days post fertilization Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2 human_stages_ontology end_mpb true This is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent. end, months post birth Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2 human_stages_ontology end_ypb true This is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent. end, years post birth human_stages_ontology has_unit true Used to associate a measurement property (e.g. days post fertilization) with a unit (e.g. days) has unit Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property. human_stages_ontology start_dpf true This is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent. start, days post fertilization Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1. human_stages_ontology start_mpb true This is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent. start, months post birth Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1. human_stages_ontology start_ypb true This is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent. start, years post birth 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 Label appended to organism-specific terms in place of scientific name Synonyms for proteoforms based on use of UniProtKb feature identifier (FTId) and positions and types of modifications or variations Synonyms for proteoforms based on use of UniProtKb accession, subsequence range, and positions and types of modifications or variations Unique short label for PRO terms for display purposes; based on orthology Unique short label curated by PSI-MOD eco subset abbreviation preferred term in the context of comparative anatomy A historic synonym, no longer encouraged dubious or contested synonym a synonym made on the basis of a possibly homologous structure in another species preferred term when talking about an instance of this class in Homo sapiens indicates that a synonym is used in an inconsistent or confusing way, typically between species latin term a mis-spelling that is in common use and thus recorded synonym that is inappropriate for amniotes synonym that is inappropriate for mammals expert consultation and attribution required plural term taxonomic disambiguation a systematic synonym used as the base name for design patterns CUMBO cyclostome structures classes that are defined by relative position counting from first in a series of elements along an axis in an individual organism rather than by strict homology developmental_classification A class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes. EFO slim derived from the union of EHDAA2 and EMAPA - still to be checked subset of classes that have logical defs text defs and synonyms aligned with FEED functional_classification Subset consisting of classes creating for grouping purposes A grouping class that depends on an assumption of homology between subclasses classes that have some inconsistency with FMA somewhat fuzzy grouping for analysis purposes, currently composed of something like: liver, heart, skeletal, kidney, bladder, brain, skin, mouth, esophagus, stomach, small intestine, large intestines, trachea nose, lungs, brain, spinal cord, peripheral nerves, kidneys, ureters, bladder, urethra, gonads abstract class brought in to group ontology classes but not informative organs, excluding individual muscles and skeletal elements Phenotype slim A subset specifically created for the 2012 Phenotype RCN meeting. Includes some human-specific terms that may eventually be removed when they are adequately represented with part of relationships in FMA Uberon slim - subset that excludes obscure terms and deep compositional terms Indicates that the class encompasses classes from other AOs that have not been verified abstract upper-level terms not directly useful for analysis core classes typically found across vertebrates. one purpose is to create a rough set of terms that could be used to start a new vertebrate AO abstract upper-level terms not directly useful for analysis uberon dc-contributor true dc-contributor contributor uberon dc-creator true dc-creator creator uberon dc-description true dc-description description uberon dc-rights true dc-rights rights uberon dc-source true dc-source derived from resource subset_property synonym_type_property consider has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym has_scope has_synonym_type in_subset logical-definition-view-relation shorthand http://www.w3.org/2000/01/rdf-schema#seeAlso uberon true seeAlso see also uberon foaf-page true foaf-page page is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of BFO:0000050 external human_stages_ontology protein quality uberon part_of part_of part of part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part BFO:0000051 chebi_ontology external protein quality uberon has_part false has_part We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. has part has part has_part Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. PATOC:CJM BFO:0000056 uberon participates_in participates_in participates in 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 human_stages_ontology uberon preceded_by preceded_by preceded by preceded_by is preceded by SIO:000249 takes place after Allen:precedes precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 uberon precedes precedes precedes precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in 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 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). 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). 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. 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. 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). Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:0000107 uberon deep_to deep_to deep_to Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:0000108 uberon superficial_to superficial_to superficial_to Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. 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 X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the deep portion. BSPO:0001101 uberon in_deep_part_of in_deep_part_of in_deep_part_of X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the deep portion. 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 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. X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y BSPO:0001108 uberon distalmost_part_of distalmost_part_of distalmost_part_of X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y BSPO:0001113 uberon preaxialmost_part_of preaxialmost_part_of preaxialmost_part_of BSPO:0001115 uberon postaxialmost_part_of postaxialmost_part_of postaxialmost_part_of X intersects_median_plane of iff X crosses the midine plane of Y. BSPO:0005001 uberon intersects_midsagittal_plane_of intersects_midsagittal_plane_of intersects_midsagittal_plane_of BSPO:0015014 uberon immediately_superficial_to immediately_superficial_to immediately_superficial_to BSPO:0015101 uberon in_dorsal_side_of in_dorsal_side_of in_dorsal_side_of BSPO:0015102 uberon in_ventral_side_of in_ventral_side_of in_ventral_side_of x preaxial_to y iff x is further along the preaxial-postaxial axis than y, towards the front. BSPO:1000000 uberon anterior_to (developmentally) lateral (radial) to medial (tibial) to preaxial_to preaxial_to preaxial_to x preaxial_to y iff x is further along the preaxial-postaxial axis than y, towards the front. anterior_to (developmentally) MA:th inheres in this fragility inheres in this vase this red color inheres in this apple a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in RO:0000052 inheres_in inheres_in inheres in inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of RO:0000053 uberon bearer_of bearer_of bearer of bearer of participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in RO:0000056 protein participates_in false participates_in participates in participates_in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant this 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 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 quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of role of this 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 RO:0000085 protein has_function false has_function has function has_function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality RO:0000086 protein uberon has_quality false has_quality has quality has quality has_quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role RO:0000087 chebi_ontology protein has_role false false has_role has role has role has_role A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. David Osumi-Sutherland (forall (?x ?y) (iff (neural_circuit_path ?x ?y) (and ("neuron ; CL_0000540" ?x) ("neuron ; CL_0000540" ?y) (or (synapsed_by ?x ?y) (synapsed_to ?x ?y))))) (forall (...s ?x ?y ?z) (iff (neural_circuit_path ...s ?x ?y ?z) (and (neural_circuit_path ...s ?x ?y) ("neuron ; CL_0000540" ?z) (or (synapsed_by ?y ?z) (synapsed_to ?y ?z))))) (forall (?x ?y) (iff (in_neural_circuit_with ?x ?y) (exists (...s) (neural_circuit_path ?x ...s ?y)))) in neural circuit with A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next. David Osumi-Sutherland (forall (?x ?y) (iff (upstream_neural_circuit_path ?x ?y) (and ("neuron ; CL_0000540" ?x) ("neuron ; CL_0000540" ?y) (synapsed_to ?x ?y)))) (forall (...s ?x ?y ?z) (iff (upstream_neural_circuit_path ...s ?x ?y ?z ) (and (upstream_neural_circuit_path ...s ?x ?y) ("neuron ; CL_0000540" ?z) (synapsed_to ?y ?z)))) (forall (?x ?y) (iff (upstream_in_neural_circuit_with ?x ?y) (exists (...s) (upstream_neural_circuit_path ?x ...s ?y)))) upstream in neural circuit with A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next. David Osumi-Sutherland (forall (?x ?y) (iff (downstream_neural_circuit_path ?x ?y) (and ("neuron ; CL_0000540" ?x) ("neuron ; CL_0000540" ?y) (synapsed_by ?x ?y)))) (forall (...s ?x ?y ?z) (iff (downstream_neural_circuit_path ...s ?x ?y ?z ) (and (downstream_neural_circuit_path ...s ?x ?y) ("neuron ; CL_0000540" ?z) (synapsed_by ?y ?z)))) (forall (?x ?y) (iff (downstream_in_neural_circuit_with ?x ?y) (exists (...s) (downstream_neural_circuit_path ?x ...s ?y)))) downstream in neural circuit with this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. RO:0001000 protein derives_from derives_from derives from derives_from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime location_of RO:0001015 uberon location_of location_of location of location_of contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): Intended meaning: domain: material entity range: spatial region or site (immaterial continuant) contained_in contained in contains RO:0001019 uberon contains contains contains contains located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime located_in http://www.obofoundry.org/ro/#OBO_REL:located_in RO:0001025 protein uberon located_in located_in located in located_in This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of RO:0002000 uberon boundary_of boundary_of 2D boundary of boundary of my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. David Osumi-Sutherland has boundary has_2D_boundary RO:0002002 uberon has_boundary has_boundary has 2D boundary has boundary David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 nerve supply uberon innervated_by innervated_by http://code.google.com/p/obo-relations/issues/detail?id=6 innervated_by innervated_by nerve supply FMA:85999 X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 David Osumi-Sutherland RO:0002007 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 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. dos 2017-05-24T09:30:46Z has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. dos 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. dos 2017-05-24T09:49:21Z has component process A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. dos 2017-07-19T17:30:36Z has ligand dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. GOC:dos Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. dos 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. GOC:dos Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. dos 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. GOC:dos A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. GOC:dos David Osumi-Sutherland Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which ends David Osumi-Sutherland di Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. encompasses David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) David Osumi-Sutherland starts_at_end_of A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. RO:0002087 directly preceded by is directly preceded by is immediately preceded by starts_at_end_of human_stages_ontology uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by immediately_preceded_by A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. SIO:000251 is immediately preceded by SIO:000251 David Osumi-Sutherland Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which starts David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes David Osumi-Sutherland io RO:0002091 external starts_during starts_during X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) starts during starts_during David Osumi-Sutherland d during RO:0002092 external happens_during happens_during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during happens during David Osumi-Sutherland o overlaps RO:0002093 external ends_during ends_during X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). ends during ends_during Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. Chris Mungall David Osumi-Sutherland <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) synapsed by Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. Alexander Diehl Chris Mungall Lindsay Cowell <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) has plasma membrane part Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. Chris Mungall David Osumi-Sutherland <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) N1 synapsed_to some N2 Expands to: N1 SubclassOf ( has_part some ( ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( ‘synapse ; GO:0045202’ that has_part some ( ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) synapsed to A overlaps B if they share some part in common. x overlaps y if and only if there exists some z such that x has part z and z part of y BFO_0000051 some (BFO_0000050 some ?Y) http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 uberon overlaps overlaps overlaps overlaps true Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. David Osumi-Sutherland <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) RO:0002134 uberon innervates innervates http://code.google.com/p/obo-relations/issues/detail?id=6 innervates innervates X continuous_with Y if and only if X and Y share a fiat boundary. David Osumi-Sutherland connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) RO:0002150 uberon continuous_with continuous_with continuous with continuous_with FMA:85972 d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. ancestral_stucture_of evolutionarily_descended_from derived by descent from inverse of derived by descent from has derived by descendant two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. Consider obsoleting and merging with child relation, 'in homology relationship with' RO:0002158 uberon homologous_to homologous_to VBO calls this homologous_to homologous_to shares ancestor with RO:0002159 uberon serially_homologous_to serially_homologous_to serially homologous to serially_homologous_to lactation SubClassOf 'only in taxon' some 'Mammalia' S only_in_taxon T iff: S SubClassOf in_taxon only T U only_in_taxon T: U is a feature found in only in organisms of species of taxon T. The feature cannot be found in an organism of any species outside of (not subsumed by) that taxon. Down-propagates in U hierarchy, up-propagates in T hierarchy (species taxonomy). Implies applicable_to_taxon. x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria Chris Mungall RO:0002160 never_outside_taxon specific_to specific_to_taxon protein uberon only_in_taxon false only_in_taxon Down-propagates. The original name for this in the paper is 'specific_to'. Applicable to genes because some genes are lost in sub-species (strains) of a species. only in taxon only_in_taxon S only_in_taxon T iff: S SubClassOf in_taxon only T U only_in_taxon T: U is a feature found in only in organisms of species of taxon T. The feature cannot be found in an organism of any species outside of (not subsumed by) that taxon. Down-propagates in U hierarchy, up-propagates in T hierarchy (species taxonomy). Implies applicable_to_taxon. ROC:Waclaw x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. Chris Mungall Jennifer Deegan RO:0002162 uberon in_taxon in_taxon Connects a biological entity to its taxon of origin. in taxon A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. Chris Mungall Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b RO:0002170 uberon connected_to connected_to Connection does not imply overlaps. connected to connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. 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. 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 protein uberon has_component false has_component has component has component has_component x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y Chris Mungall David Osumi-Sutherland Melissa Haendel Terry Meehan 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_0000053 some (RO_0000054 only ?Y) RO:0002215 uberon capable_of capable_of capable of capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) RO:0002216 uberon capable_of_part_of capable_of_part_of capable of part of capable of part of true x actively participates in y if and only if x participates in y and x realizes some active role Chris Mungall agent in actively participates in 'heart development' has active participant some Shh protein x has participant y if and only if x realizes some active role that inheres in y This may be obsoleted and replaced by the original 'has agent' relation Chris Mungall has agent obsolete has active participant true 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 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 uberon 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 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 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 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 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 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 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 has end location p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes has input 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 cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of inheres in part of Chris Mungall RO:0002314 inheres_in_part_of inheres_in_part_of inheres in part of inheres in part of true 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. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 uberon functionally_related_to functionally_related_to functionally related to functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false RO:0002329 uberon part_of_structure_that_is_capable_of part_of_structure_that_is_capable_of part of structure that is capable of part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in enables part of RO:0002331 protein involved_in false involved_in involved in involved_in inverse of enables Chris Mungall enabled by inverse of regulates Chris Mungall regulated by (processual) regulated by inverse of negatively regulates Chris Mungall negatively regulated by inverse of positively regulates Chris Mungall positively regulated by 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 a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a Chris Mungall attached to (anatomical structure to anatomical structure) RO:0002371 uberon attaches_to attaches_to attached to attaches_to m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Chris Mungall Wikipedia:Insertion_(anatomy) RO:0002372 uberon has_muscle_origin has_muscle_origin The origin is the end of a muscle that attaches to the more fixed part of the skeleton, which is the proximal end in limb muscles has muscle origin has_muscle_origin We need to import uberon muscle to create a stricter domain constraint m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Chris Mungall Wikipedia:Insertion_(anatomy) RO:0002373 uberon has_muscle_insertion has_muscle_insertion The insertion is the point of attachment of a muscle that moves the most when the muscle shortens, or the most distal end of limb muscles has muscle insertion has_muscle_insertion We need to import uberon muscle into RO to use as a stricter domain constraint m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. false x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat Chris Mungall Chris Mungall has fused element RO:0002374 uberon has_fused_element has_fused_element A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. A single bone in one species may correspond to the fusion of two or more bones found as distinct elements in another. For example, tibiofibula has_fused_element tibia. A has_fused_element B does not imply that A has_part some B, rather than A has_part some B', where B' is not a subtype of B (because B is a distinct element but B' is a regional part) but has some evolutionary relationship to B. derived from ancestral fusion of has_fused_element 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 causally downstream of Chris Mungall immediately causally downstream of This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall immediately causally upstream of p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) affects causally upstream of or within inverse of causally upstream of or within Chris Mungall causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p Chris Mungall involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p Chris Mungall involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. Chris Mungall executes activity in enables activity in is active in true c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. GOC:cjm GOC:dos p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. 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/MI_0914 https://github.com/oborel/obo-relations/wiki/InteractionRelations An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. Chris Mungall binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later Chris Mungall An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. Chris Mungall molecularly controls activity directly regulates activity of Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Chris Mungall inhibits molecularly decreases activity of activity directly negatively regulates activity of Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Chris Mungall activates molecularly increases activity of activity 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) Chris Mungall is symbiosis '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 structure and stage Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). Chris Mungall RO:0002488 begins_to_exist_during uberon existence_starts_during existence_starts_during existence starts during Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. Relation between continuant 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. 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 Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). Chris Mungall RO:0002492 ceases_to_exist_during uberon existence_ends_during existence_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. Relation between continuant 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. 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 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 RO:0002503 towards towards towards The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between material entities Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. Chris Mungall has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). RO:0002551 uberon has sekeletal support has supporting framework has_skeleton has_skeleton has skeleton This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. Chris Mungall causally influenced by (material entity to material entity) causally influenced by Chris Mungall interaction relation helper property https://github.com/oborel/obo-relations/wiki/InteractionRelations Chris Mungall molecular interaction relation helper property Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b Chris Mungall causally influences (material entity to material entity) causally influences A relation that holds between elements of a musculoskeletal system or its analogs. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. biomechanically related to m1 has_muscle_antagonist m2 iff m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. Chris Mungall Wikipedia:Antagonist_(muscle) RO:0002568 uberon has_muscle_antagonist has_muscle_antagonist has muscle antagonist has_muscle_antagonist m1 has_muscle_antagonist m2 iff m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. inverse of branching part of Chris Mungall RO:0002569 uberon has_branching_part has_branching_part has branching part x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. Chris Mungall GOC:cjm RO:0002571 uberon lumen_of lumen_of lumen of s is luminal space of x iff s is lumen_of x and s is an immaterial entity Chris Mungall RO:0002572 uberon luminal_space_of luminal_space_of luminal space of A relation that holds between an attribute or a qualifier and another attribute. Chris Mungall This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. RO:0002180 qualifier qualifier placeholder relation to indicate normality/abnormality. has modifier inverse of has skeleton Chris Mungall RO:0002576 uberon skeleton_of skeleton_of skeleton of Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Chris Mungall directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. directly positively regulates (process to process) directly positively regulates Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. directly negatively regulates (process to process) directly negatively regulates a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. Melissa Haendel RO:0003000 uberon produces produces Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces produces a produced_by b iff some process that occurs_in b has_output a. Melissa Haendel RO:0003001 uberon produced_by produced_by produced by produced_by The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition. Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. causes or contributes to condition 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 chebi_ontology has_functional_parent false false has functional parent chebi_ontology has_parent_hydride false false has parent hydride chebi_ontology is_conjugate_acid_of true false is conjugate acid of chebi_ontology is_conjugate_base_of true false is conjugate base of chebi_ontology is_enantiomer_of true false is enantiomer of chebi_ontology is_substituent_group_from false false is substituent group from chebi_ontology is_tautomer_of true is tautomer of has_completed A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). has_high_plasma_membrane_amount A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). PMID:19243617 A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). has_low_plasma_membrane_amount A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). PMID:19243617 has_not_completed http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y lacks_part http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y) lacks_plasma_membrane_part by_means has-input has_participant qualifier quality correlates_with correlates_with q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality decreased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. decreased_in_magnitude_relative_to q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality different_in_magnitude_relative_to different_in_magnitude_relative_to q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. quality has_cross_section Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. has_cross_section s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. PATOC:CJM q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality increased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. increased_in_magnitude_relative_to q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. quality reciprocal_of There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. reciprocal_of q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. PATOC:CJM quality towards Relation binding a relational quality or disposition to the relevant type of entity. towards protein has_gene_template false has_gene_template protein lacks_part false lacks_part 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. 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. uberon existence_starts_and_ends_during existence starts and ends during 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 X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides. uberon in_central_side_of in_central_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides. BSPO:cjm uberon in_innermost_side_of in_innermost_side_of uberon in_outermost_side_of in_outermost_side_of a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s add to RO uberon indirectly_supplies indirectly_supplies uberon layer_part_of layer part of x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. 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. 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. uberon sexually_homologous_to sexually_homologous_to 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 . uberon transitively_anteriorly_connected_to transitively anteriorly connected to . uberon transitively_connected_to transitively_connected to . uberon transitively_distally_connected_to transitively distally connected to . . uberon transitively_proximally_connected_to transitively proximally connected to . uberon trunk_part_of trunk_part_of http://semanticscience.org/resource/SIO_000658 direct_transformation_of immediately transforms from immediate_transformation_of immediate_transformation_of direct_transformation_of https://orcid.org/0000-0002-6601-2165 immediately transforms from SIO:000658 An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. continuant An entity that has temporal parts and that happens, unfolds or develops through time. occurrent A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant spatial region An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. bfo BFO:0000015 process 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 bfo BFO:0000019 quality 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 bfo BFO:0000024 fiat object part bfo BFO:0000030 object A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. generically dependent continuant function An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. bfo BFO:0000040 material entity material entity immaterial entity anatomical entity connected anatomical structure material anatomical entity immaterial anatomical entity cell part (CARO) cell part multi-cell-part structure neuron projection bundle organism or virus or viroid multicellular anatomical structure biological entity Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV. -1 0.000548579903 0.0 KEGG:C05359 PMID:21614077 Wikipedia:Electron electron chebi_ontology Elektron beta beta(-) beta-particle e e(-) e- negatron CHEBI:10545 electron PMID:21614077 Europe PMC electron ChEBI electron IUPAC electron KEGG_COMPOUND Elektron ChEBI beta IUPAC beta(-) ChEBI beta-particle IUPAC e IUPAC e(-) UniProt e- KEGG_COMPOUND negatron IUPAC A dicarboxylic acid dianion resulting from the removal of a proton from both of the carboxylic acid groups of 2-hydroxyglutaric acid. -2 C5H6O5 InChI=1S/C5H8O5/c6-3(5(9)10)1-2-4(7)8/h3,6H,1-2H2,(H,7,8)(H,9,10)/p-2 HWXBTNAVRSUOJR-UHFFFAOYSA-L 146.09814 146.02262 OC(CCC([O-])=O)C([O-])=O Beilstein:5736650 MetaCyc:2-HYDROXYGLUTARIC_ACID Reaxys:5736650 2-hydroxypentanedioate chebi_ontology 2-hydroxyglutarate CHEBI:11596 2-hydroxyglutarate(2-) Beilstein:5736650 Beilstein Reaxys:5736650 Reaxys 2-hydroxypentanedioate IUPAC 2-hydroxyglutarate UniProt The conjugate base of gamma-amino-beta-hydroxybutyric acid arising from deprotonation of the carboxy group. -1 C4H8NO3 InChI=1S/C4H9NO3/c5-2-3(6)1-4(7)8/h3,6H,1-2,5H2,(H,7,8)/p-1 YQGDEPYYFWUPGO-UHFFFAOYSA-M 118.11126 118.05097 NCC(O)CC([O-])=O CAS:352-21-6 KEGG:C03678 4-Amino-3-hydroxybutanoate chebi_ontology CHEBI:11955 4-amino-3-hydroxybutanoate CAS:352-21-6 KEGG COMPOUND KEGG:C03678 ChEBI 4-Amino-3-hydroxybutanoate KEGG_COMPOUND -1 C5H8NO3 InChI=1S/C5H9NO3/c6-3-4(7)1-2-5(8)9/h1-3,6H2,(H,8,9)/p-1 ZGXJTSGNIOSYLO-UHFFFAOYSA-M 130.12196 130.05097 NCC(=O)CCC([O-])=O Beilstein:3937762 5-amino-4-oxopentanoate chebi_ontology CHEBI:12109 5-aminolevulinate Beilstein:3937762 Beilstein 5-amino-4-oxopentanoate IUPAC A group of fat-soluble retinoids produced via metabolism of provitamin A carotenoids. Vitamin A is involved in immune function, vision, reproduction, and cellular communication. Wikipedia:Vitamin_A chebi_ontology CHEBI:12777 vitamin A Any steroid substituted by a formyl group. chebi_ontology steroid aldehydes CHEBI:131565 steroid aldehyde steroid aldehydes ChEBI Any bacterial metabolite produced during a metabolic reaction in Mycoplasma genitalium. chebi_ontology Mycoplasma genitalium metabolites CHEBI:131604 Mycoplasma genitalium metabolite Mycoplasma genitalium metabolites ChEBI A steroid compound with a structure based on a 27-carbon (cholestane) skeleton. chebi_ontology C27-steroids CHEBI:131619 C27-steroid C27-steroids ChEBI A steroid compound with a structure based on a 19-carbon (androstane) skeleton. chebi_ontology C19-steroids CHEBI:131621 C19-steroid C19-steroids ChEBI A class of carbonyl compound encompassing dicarboxylic acids and any derivatives obtained by substitution of either one or both of the carboxy hydrogens. chebi_ontology dicarboxylic acids and derivatives CHEBI:131927 dicarboxylic acids and O-substituted derivatives dicarboxylic acids and derivatives ChEBI A naphthoquinone in which the oxo groups of the quinone moiety are at positions 1 and 4 of the parent naphthalene ring. chebi_ontology CHEBI:132142 1,4-naphthoquinones A citrate anion obtained by deprotonation of the three carboxy groups as well as the hydroxy group of citric acid. -4 C6H4O7 InChI=1S/C6H7O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h1-2H2,(H,7,8)(H,9,10)(H,11,12)/q-1/p-3 KSXLKRAZYZIYCZ-UHFFFAOYSA-K 188.092 187.99790 C(=O)([O-])C(CC(=O)[O-])(CC(=O)[O-])[O-] Chemspider:34552020 2-oxidopropane-1,2,3-tricarboxylate chebi_ontology 2-oxido-1,2,3-propanetricarboxylate citric acid tetraanion CHEBI:132362 citrate(4-) 2-oxidopropane-1,2,3-tricarboxylate IUPAC 2-oxido-1,2,3-propanetricarboxylate ChEBI citric acid tetraanion ChEBI A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of ethylmalonic acid. chebi_ontology ethylmalonate anion ethylmalonic acid anion CHEBI:132938 ethylmalonate ethylmalonate anion ChEBI ethylmalonic acid anion ChEBI A dicarboxylic acid dianion resulting from the removal of a proton from both of the carboxylic acid groups of ethylmalonic acid. -2 C5H6O4 InChI=1S/C5H8O4/c1-2-3(4(6)7)5(8)9/h3H,2H2,1H3,(H,6,7)(H,8,9)/p-2 UKFXDFUAPNAMPJ-UHFFFAOYSA-L 130.099 130.02771 [O-]C(C(C(=O)[O-])CC)=O Reaxys:3904851 ethylpropanedioate chebi_ontology CHEBI:132939 ethylmalonate(2-) Reaxys:3904851 Reaxys ethylpropanedioate IUPAC A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of 2-hydroxyglutaric acid. chebi_ontology 2-hydroxyglutarate anion 2-hydroxyglutaric acid anion CHEBI:132941 2-hydroxyglutarate 2-hydroxyglutarate anion ChEBI 2-hydroxyglutaric acid anion ChEBI chebi_ontology CHEBI:132943 aspartate A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of oxalic acid. chebi_ontology ethanedioic acid anion ethanedioic acid anions oxalate anion oxalate anions oxalates oxalic acid anion oxalic acid anions CHEBI:132952 oxalate ethanedioic acid anion ChEBI ethanedioic acid anions ChEBI oxalate anion ChEBI oxalate anions ChEBI oxalates ChEBI oxalic acid anion ChEBI oxalic acid anions ChEBI A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of sebacic acid. chebi_ontology decanedioic acid anion decanedioic acid anions sebacate anion sebacate anions sebacates sebacic acid anion sebacic acid anions CHEBI:132954 sebacate decanedioic acid anion ChEBI decanedioic acid anions ChEBI sebacate anion ChEBI sebacate anions ChEBI sebacates ChEBI sebacic acid anion ChEBI sebacic acid anions ChEBI A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of 3-methylsuccinic acid. chebi_ontology 2-methylbutanedioic acid anion 2-methylbutanedioic acid anions methylsuccinate anion methylsuccinates methylsuccinic acid anion methylsuccinic acid anions CHEBI:132961 methylsuccinate 2-methylbutanedioic acid anion ChEBI 2-methylbutanedioic acid anions ChEBI methylsuccinate anion ChEBI methylsuccinates ChEBI methylsuccinic acid anion ChEBI methylsuccinic acid anions ChEBI An N-acylglycinate obtained by deprotonation of the carboxy group of hippuric acid (N-benzoylglycine) and its derivatives. chebi_ontology N-benzoylglycinate N-benzoylglycinates N-benzoylglycine anion N-benzoylglycine anions hippurates CHEBI:132966 hippurate N-benzoylglycinate ChEBI N-benzoylglycinates ChEBI N-benzoylglycine anion ChEBI N-benzoylglycine anions ChEBI hippurates ChEBI A primary ammonium ion obtained by protonation of the amino group of 5-aminolevulinic acid. +1 C5H10NO3 InChI=1S/C5H9NO3/c6-3-4(7)1-2-5(8)9/h1-3,6H2,(H,8,9)/p+1 ZGXJTSGNIOSYLO-UHFFFAOYSA-O 132.138 132.06552 C(C(=O)C[NH3+])CC(=O)O 4-carboxy-2-oxobutan-1-aminium chebi_ontology 5-aminolevulinic acid cation 5-aminolevulinic acid(1+) CHEBI:132970 5-ammoniolevulinic acid 4-carboxy-2-oxobutan-1-aminium IUPAC 5-aminolevulinic acid cation ChEBI 5-aminolevulinic acid(1+) ChEBI A dicarboxylic acid dianion that results from the removal of a proton from both of the carboxylic acid groups of any 3-hydroxydicarboxylic acid. -2 C4H4O5R 132.072 132.00587 C(*C(CC(=O)[O-])O)([O-])=O chebi_ontology 3-hydroxydicarboxylic acid dianion(2-) a 3-hydroxy dicarboxylic acid CHEBI:133251 3-hydroxydicarboxylate(2-) 3-hydroxydicarboxylic acid dianion(2-) SUBMITTER a 3-hydroxy dicarboxylic acid UniProt A carboxylic acid dianion obtained by deprotonation of both carboxy groups of any dicarboxylic acid that contains no carbon-carbon double bonds. -2 C2O4R 88.019 87.97966 [O-]C(*C([O-])=O)=O chebi_ontology a saturated dicarboxylic acid saturated dicarboxylate(2-) CHEBI:133291 saturated dicarboxylic acid dianion(2-) a saturated dicarboxylic acid UniProt saturated dicarboxylate(2-) SUBMITTER A dicarboxylic acid dianion obtained by deprotonation of both carboxy groups of any oxo dicarboxylic acid. chebi_ontology oxo dicarboxylic acid CHEBI:133294 oxo dicarboxylic acid dianion oxo dicarboxylic acid UniProt A monocarboxylic acid anion that is the conjugate base of N-hexanoylglycine, obtained by deprotonation of the carboxy group; major species at pH 7.3. -1 C8H14NO3 InChI=1S/C8H15NO3/c1-2-3-4-5-7(10)9-6-8(11)12/h2-6H2,1H3,(H,9,10)(H,11,12)/p-1 UPCKIPHSXMXJOX-UHFFFAOYSA-M 172.202 172.09792 N(CC([O-])=O)C(CCCCC)=O (hexanoylamino)acetate chebi_ontology N-caproylglycinate N-hexanoylglycine N-hexanoylglycine anion N-hexanoylglycine(1-) CHEBI:133580 N-hexanoylglycinate (hexanoylamino)acetate IUPAC N-caproylglycinate ChEBI N-hexanoylglycine UniProt N-hexanoylglycine anion ChEBI N-hexanoylglycine(1-) ChEBI An alpha-amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of 1-methylhistidine; major species at pH 7.3. 0 C7H11N3O2 InChI=1S/C7H11N3O2/c1-10-3-5(9-4-10)2-6(8)7(11)12/h3-4,6H,2,8H2,1H3,(H,11,12) BRMWTNUJHUMWMS-UHFFFAOYSA-N 169.181 169.08513 [O-]C(=O)C([NH3+])CC=1N=CN(C1)C 2-azaniumyl-3-(1-methyl-1H-imidazol-4-yl)propanoate chebi_ontology CHEBI:133608 1-methylhistidine zwitterion 2-azaniumyl-3-(1-methyl-1H-imidazol-4-yl)propanoate IUPAC An alpha-amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of 3-methylhistidine; major species at pH 7.3. 0 C7H11N3O2 InChI=1S/C7H11N3O2/c1-10-4-9-3-5(10)2-6(8)7(11)12/h3-4,6H,2,8H2,1H3,(H,11,12) JDHILDINMRGULE-UHFFFAOYSA-N 169.181 169.08513 [O-]C(=O)C([NH3+])CC=1N(C=NC1)C 2-azaniumyl-3-(1-methyl-1H-imidazol-5-yl)propanoate chebi_ontology CHEBI:133609 3-methylhistidine zwitterion 2-azaniumyl-3-(1-methyl-1H-imidazol-5-yl)propanoate IUPAC A monocarboxylic acid anion that is the conjugate base of N-isobutyrylglycine, obtained by deprotonation of the carboxy group; major species at pH 7.3. -1 C6H10NO3 InChI=1S/C6H11NO3/c1-4(2)6(10)7-3-5(8)9/h4H,3H2,1-2H3,(H,7,10)(H,8,9)/p-1 DCICDMMXFIELDF-UHFFFAOYSA-M 144.149 144.06662 C(CNC(=O)C(C)C)(=O)[O-] HMDB:HMDB0000730 (2-methylpropanamido)acetate chebi_ontology N-(2-methylpropanoyl)glycinate N-isobutanoylglycinate isobutanoylglycinate isobutyrylglycinate CHEBI:133610 N-isobutyrylglycinate (2-methylpropanamido)acetate IUPAC N-(2-methylpropanoyl)glycinate ChEBI N-isobutanoylglycinate ChEBI isobutanoylglycinate ChEBI isobutyrylglycinate ChEBI A hydroxy monocarboxylic acid anion which is obtained by deprotonation of the carboxy group of homovanillic acid. -1 C9H9O4 InChI=1S/C9H10O4/c1-13-8-4-6(5-9(11)12)2-3-7(8)10/h2-4,10H,5H2,1H3,(H,11,12)/p-1 QRMZSPFSDQBLIX-UHFFFAOYSA-M 181.166 181.05063 C1=C(C(=CC(=C1)CC([O-])=O)OC)O (4-hydroxy-3-methoxyphenyl)acetate chebi_ontology 3-methoxy-4-hydroxyphenylacetate CHEBI:133744 homovanillate (4-hydroxy-3-methoxyphenyl)acetate IUPAC 3-methoxy-4-hydroxyphenylacetate ChEBI A tricarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of citric acid. chebi_ontology citrate citrate anions CHEBI:133748 citrate anion citrate ChEBI citrate anions ChEBI Any organic compound having an initial boiling point less than or equal to 250 degreeC (482 degreeF) measured at a standard atmospheric pressure of 101.3 kPa. Wikipedia:Volatile_organic_compound chebi_ontology VOC VOCs volatile organic compounds CHEBI:134179 volatile organic compound VOC ChEBI VOCs ChEBI volatile organic compounds ChEBI An alkanesulfonate in which the carbon at position 1 is attached to R, which can represent hydrogens, a carbon chain, or other groups. -1 CH2O3SR 94.091 93.97246 C(S([O-])(=O)=O)* CHEBI:22318 MetaCyc:Alkanesulfonates chebi_ontology alkanesulfonate oxoanions alkanesulfonates an alkanesulfonate CHEBI:134249 alkanesulfonate oxoanion alkanesulfonate oxoanions ChEBI alkanesulfonates ChEBI an alkanesulfonate UniProt Any phenol carrying an additional methoxy substituent at the ortho-position. 0 C7H4O2R4 120.106 120.02113 C1(=C(C(=C(C(=C1*)*)*)OC)O)* CHEBI:13645 MetaCyc:Guaiacols chebi_ontology 1-hydroxy-2-methoxybenzenes 2-methoxyphenol 2-methoxyphenol derivative 2-methoxyphenol derivatives 2-methoxyphenols a guaiacol catechol monomethyl ether catechol monomethyl ethers o-methoxyphenol o-methoxyphenols ortho-methoxyphenol ortho-methoxyphenols CHEBI:134251 guaiacols 1-hydroxy-2-methoxybenzenes ChEBI 2-methoxyphenol ChEBI 2-methoxyphenol derivative SUBMITTER 2-methoxyphenol derivatives ChEBI 2-methoxyphenols ChEBI a guaiacol UniProt catechol monomethyl ether ChEBI catechol monomethyl ethers ChEBI o-methoxyphenol ChEBI o-methoxyphenols ChEBI ortho-methoxyphenol ChEBI ortho-methoxyphenols ChEBI An alcohol where the hydroxy group is attached to a saturated carbon atom adjacent to a double bond (R groups may be H, organyl, etc.). 0 C3HOR5 53.040 53.00274 C(C(=C(*)*)*)(O)(*)* chebi_ontology allylic alcohols CHEBI:134361 allylic alcohol allylic alcohols ChEBI An allylic alcohol in which the carbon atom that links the double bond to the hydroxy group is also attached to two hydrogens. 0 C3H3OR3 55.055 55.01839 C(C(=C(*)*)*)(O)([H])[H] chebi_ontology primary allylic alcohols CHEBI:134394 primary allylic alcohol primary allylic alcohols ChEBI A diol in which the two hydroxy groups are on different carbon atoms, usually but not necessarily adjacent. glycols chebi_ontology Glykol CHEBI:13643 glycol glycols IUPAC Glykol ChEBI An organic group derived from any 3-oxo-Delta(4)-steroid. 0 C6H6O 94.111 94.04186 C1=C(C*)*C(CC1=O)* chebi_ontology a 3-oxo-Delta4-steroid group CHEBI:136849 3-oxo-Delta(4)-steroid group a 3-oxo-Delta4-steroid group UniProt A compound that, on administration, undergoes conversion by biochemical (enzymatic), chemical (possibly following an enzymatic step), or physical (e.g. photochemical) activation processes before becoming the active agent for which it is a pro-agent. PMID:26449612 chebi_ontology pro-agents proagent proagents CHEBI:136859 pro-agent PMID:26449612 Europe PMC pro-agents ChEBI proagent ChEBI proagents ChEBI Any steroid that has beta-configuration at position 5. chebi_ontology 5beta steroids 5beta-steroid 5beta-steroids CHEBI:136889 5beta steroid 5beta steroids ChEBI 5beta-steroid ChEBI 5beta-steroids ChEBI chebi_ontology methylhistidines CHEBI:137682 methylhistidine methylhistidines ChEBI An organic cation obtained by protonation of any tertiary amine. +1 HNR3 15.015 15.01090 [NH+](*)(*)* chebi_ontology a tertiary amine tertiary amine(1+) tertiary ammonium ions CHEBI:137982 tertiary ammonium ion a tertiary amine UniProt tertiary amine(1+) ChEBI tertiary ammonium ions ChEBI A Bronsted acid derived from one or more inorganic compounds. Inorganic acids (also known as mineral acids) form hydrons and conjugate base ions when dissolved in water. Wikipedia:Mineral_acid chebi_ontology inorganic acids mineral acid mineral acids CHEBI:138103 inorganic acid inorganic acids ChEBI mineral acid ChEBI mineral acids ChEBI Any sterol containing two double bonds between positions 5-6 and 7-8. 0 C19H27OR 271.418 271.20619 C12C(C3C(C(CC3)*)(C)CC1)=CC=C4C2(CCC(C4)O)C MetaCyc:Delta5-Delta7-Steroids chebi_ontology a Delta(5),Delta(7)-sterol CHEBI:138131 Delta(5),Delta(7)-sterol a Delta(5),Delta(7)-sterol UniProt Any C21-steroid carrying a hydroxy substituent at the 17alpha-position. Note that individual examples may have ring substituents at other positions and/or contain double bonds, aromatic A-rings, expanded/contracted rings etc., so the formula and mass may vary from that given for the generic structure. 0 C21H36O InChI=1S/C21H36O/c1-4-21(22)14-11-18-16-9-8-15-7-5-6-12-19(15,2)17(16)10-13-20(18,21)3/h15-18,22H,4-14H2,1-3H3/t15?,16?,17?,18?,19?,20?,21-/m1/s1 JSIVWCLRCGAVHN-ILZKQPLKSA-N 304.511 304.27662 C1CCCC2C1(C3C(CC2)C4C(CC3)([C@](CC4)(CC)O)C)C MetaCyc:17a-hydroxy-C21-steroids chebi_ontology a 17alpha-hydroxy-C21-steroid CHEBI:138141 17alpha-hydroxy-C21-steroid MetaCyc:17a-hydroxy-C21-steroids SUBMITTER a 17alpha-hydroxy-C21-steroid UniProt Any member of a group of hydroxy steroids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine. In mammals bile acids almost invariably have 5beta-configuration, while in lower vertebrates, some bile acids, known as allo-bile acids, have 5alpha-configuration. chebi_ontology CHEBI:138366 bile acids An apoprotein is a protein devoid of its characteristic prosthetic group or metal. KEGG:C16240 apoprotein chebi_ontology apoproteins CHEBI:13850 apoprotein apoprotein IUPAC apoproteins ChEBI Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa). Wikipedia:https://en.wikipedia.org/wiki/Gas chebi_ontology gas molecular entities gaseous molecular entities gaseous molecular entity CHEBI:138675 gas molecular entity gas molecular entities ChEBI gaseous molecular entities ChEBI gaseous molecular entity ChEBI -1 CH2NO2 InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4)/p-1 KXDHJXZQYSOELW-UHFFFAOYSA-M 60.03212 60.00910 NC([O-])=O Beilstein:3903503 CAS:302-11-4 Gmelin:239604 carbamate chebi_ontology Carbamat Karbamat carbamate ion carbamic acid, ion(1-) CHEBI:13941 carbamate Beilstein:3903503 Beilstein CAS:302-11-4 ChemIDplus Gmelin:239604 Gmelin carbamate IUPAC carbamate UniProt Carbamat ChEBI Karbamat ChEBI carbamate ion ChemIDplus carbamic acid, ion(1-) ChemIDplus An alpha-oxyketone that has a hydroxy group as the alpha-oxy moiety. PMID:15326516 PMID:19908854 PMID:20382022 PMID:23295224 chebi_ontology alpha-hydroxy ketones alpha-hydroxy-ketone alpha-hydroxy-ketones alpha-hydroxyketone alpha-hydroxyketones CHEBI:139588 alpha-hydroxy ketone PMID:15326516 Europe PMC PMID:19908854 Europe PMC PMID:20382022 Europe PMC PMID:23295224 Europe PMC alpha-hydroxy ketones ChEBI alpha-hydroxy-ketone ChEBI alpha-hydroxy-ketones ChEBI alpha-hydroxyketone ChEBI alpha-hydroxyketones ChEBI A carboxylic acid anion obtained by deprotonation of any retinoid carboxy group. chebi_ontology retinoate retinoates retinoid anions retinoid carboxylate anion retinoid carboxylate anions retinoid carboxylic acid anion retinoid carboxylic acid anions CHEBI:139589 retinoid anion retinoate ChEBI retinoates ChEBI retinoid anions ChEBI retinoid carboxylate anion ChEBI retinoid carboxylate anions ChEBI retinoid carboxylic acid anion ChEBI retinoid carboxylic acid anions ChEBI An alpha-hydroxy ketone in which the carbonyl group and the hydroxy group are linked by a -CH2 (methylene) group. 0 C2H3O2R 59.044 59.01330 *C(C(O)([H])[H])=O chebi_ontology primary alpha-hydroxy ketones primary alpha-hydroxy-ketone primary alpha-hydroxy-ketones primary alpha-hydroxyketone primary alpha-hydroxyketones CHEBI:139590 primary alpha-hydroxy ketone primary alpha-hydroxy ketones ChEBI primary alpha-hydroxy-ketone ChEBI primary alpha-hydroxy-ketones ChEBI primary alpha-hydroxyketone ChEBI primary alpha-hydroxyketones ChEBI An alpha-hydroxy ketone in which the carbonyl group and the hydroxy group are linked by a carbon bearing two organyl groups. 0 C2HO2R3 57.028 56.99765 C(C(=O)*)(O)(*)* chebi_ontology tertiary alpha-hydroxy ketones tertiary alpha-hydroxy-ketone tertiary alpha-hydroxy-ketones tertiary alpha-hydroxyketone tertiary alpha-hydroxyketones CHEBI:139592 tertiary alpha-hydroxy ketone tertiary alpha-hydroxy ketones ChEBI tertiary alpha-hydroxy-ketone ChEBI tertiary alpha-hydroxy-ketones ChEBI tertiary alpha-hydroxyketone ChEBI tertiary alpha-hydroxyketones ChEBI A carboxamide resulting from the formal condensation of a carboxylic acid with a primary amine; formula RC(=O)NHR(1). 0 CHNOR2 43.025 43.00581 N(C(*)=O)(*)[H] chebi_ontology secondary carboxamides CHEBI:140325 secondary carboxamide secondary carboxamides ChEBI Any saturated fatty acid containing 4 carbons. 0 CHO2R 45.017 44.99765 *C(O)=O chebi_ontology CHEBI:140601 fatty acid 4:0 0 C62H88CoN13O14PR 1329.350 1328.56433 [Co-3]1234(N5C6=C(C7=[N+]4C(=CC8=[N+]3C(=C(C9=[N+]2[C@@]([C@]5([C@@H]([C@@]6(C)CCC(=O)NC[C@H](OP(O[C@@H]%10[C@H](O[C@H](N%11C=[N+]1C%12=CC(=C(C=C%12%11)C)C)[C@@H]%10O)CO)(=O)[O-])C)CC(=O)N)[H])([C@]([C@@H]9CCC(N)=O)(CC(=O)N)C)C)C)[C@](C)([C@@H]8CCC(=O)N)CC(N)=O)C([C@@H]7CCC(=O)N)(C)C)C)* MetaCyc:CPD-20938 chebi_ontology an alkylcob(III)alamin CHEBI:140785 alkylcob(III)alamin MetaCyc:CPD-20938 SUBMITTER an alkylcob(III)alamin UniProt An antigenic epitope recognized by an anti-bilirubin monoclonal antibody designated 24G7. A substructure of bilirubin IXalpha, it is the region containing the oxo group at C-1, the methyl group at C-2, C-(4, 5, 6, 9), and N-21 and -22. 0 C7H6N2O 134.136 134.04801 C(=CC(NC(=*)*)=*)(NC(C(C)=*)=O)* chebi_ontology CHEBI:142163 24G7 epitope An organic group forming part of, and a proposed epitope within, globoside GM1. 0 C18H30O15 486.423 486.15847 *[C@@H]1O[C@@H]([C@@H](O[C@@H]2O[C@@H]([C@H](O[C@@H]3[C@@H]([C@@H](O)[C@H]([C@@H](CO)O3)O*)O)[C@@H]([C@H]2O)O)CO)[C@@H]([C@H]1O)O)CO PMID:7691279 ->4)-alpha-D-galactopyranosyl-(1->4)-beta-D-galactopyranosylp-(1->4)-beta-D-glucopyranosyl chebi_ontology ->4)-alpha-D-Gal-(1->4)-beta-D-Gal-(1->4)-beta-D-Glc-yl ->4)-alpha-D-Gal-(1->4)-beta-D-Gal-(1->4)-beta-D-Glc-yl group ->4)-alpha-D-galactosyl-(1->4)-beta-D-galactosylp-(1->4)-beta-D-glucosyl CHEBI:142533 ->4)-alpha-D-Galp-(1->4)-beta-D-Galp-(1->4)-beta-D-Glcp-yl group PMID:7691279 Europe PMC ->4)-alpha-D-galactopyranosyl-(1->4)-beta-D-galactopyranosylp-(1->4)-beta-D-glucopyranosyl IUPAC ->4)-alpha-D-Gal-(1->4)-beta-D-Gal-(1->4)-beta-D-Glc-yl ChEBI ->4)-alpha-D-Gal-(1->4)-beta-D-Gal-(1->4)-beta-D-Glc-yl group ChEBI ->4)-alpha-D-galactosyl-(1->4)-beta-D-galactosylp-(1->4)-beta-D-glucosyl ChEBI A trisaccharide beta-D-glucosyl group obtained by removal of the hydroxy group from the hemiacetal function of alpha-D-galactosyl-(1->4)-beta-D-galactosyl-(1->4)-beta-D-glucose. Part of, and the proposed epitope from, alpha-D-galactosyl-(1->4)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1)-ceramide (globoside Gb3Cer; globotriosylceramide; CTH). 0 C18H31O15 487.430 487.16630 [C@@H]1([C@@H]([C@H]([C@@H]([C@H](O1)CO)O[C@H]2[C@@H]([C@H]([C@H]([C@H](O2)CO)O[C@@H]3[C@@H]([C@H]([C@H]([C@H](O3)CO)O)O)O)O)O)O)O)* PMID:7691279 alpha-D-galactopyranosyl-(1->4)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranosyl chebi_ontology Gala1-4Galb1-4Glcb-yl Galalpha1-4Galbeta1-4Glcbeta-R Galalpha1-4Galbeta1-4Glcbeta-yl alpha-D-Gal-(1->4)-beta-D-Gal-(1->4)-D-Glc-yl alpha-D-galactosyl-(1->4)-beta-D-galactosyl-(1->4)-beta-D-glucosyl CHEBI:142567 alpha-D-Galp-(1->4)-beta-D-Galp-(1->4)-beta-D-Glcp-yl group PMID:7691279 Europe PMC alpha-D-galactopyranosyl-(1->4)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranosyl IUPAC Gala1-4Galb1-4Glcb-yl ChEBI Galalpha1-4Galbeta1-4Glcbeta-R ChEBI Galalpha1-4Galbeta1-4Glcbeta-yl ChEBI alpha-D-Gal-(1->4)-beta-D-Gal-(1->4)-D-Glc-yl ChEBI alpha-D-galactosyl-(1->4)-beta-D-galactosyl-(1->4)-beta-D-glucosyl ChEBI 0 C4H9NO2 InChI=1S/C4H9NO2/c1-3(2-5)4(6)7/h3H,2,5H2,1H3,(H,6,7) QCHPKSFMDHPSNR-UHFFFAOYSA-N 103.120 103.06333 C(C(C)C[NH3+])([O-])=O 3-ammonio-2-methylpropanoate chebi_ontology 3-aminoisobutanoate CHEBI:142590 3-aminoisobutanoic acid zwitterion 3-ammonio-2-methylpropanoate IUPAC 3-aminoisobutanoate UniProt A beta-D-glucosyl group derived from the trisaccharide N-acetyl-alpha-neuraminyl-(2->3)-beta-D-galactosyl-(1->4)-beta-D-glucose. Implied reactive epitope within ganglioside GM3. 0 C23H38NO18 616.545 616.20889 O([C@@H]1[C@H]([C@H](O[C@@H]2[C@H](O[C@@H](*)[C@@H]([C@H]2O)O)CO)O[C@@H]([C@@H]1O)CO)O)[C@]3(O[C@]([C@@H]([C@H](C3)O)NC(C)=O)([C@@H]([C@@H](CO)O)O)[H])C(O)=O PMID:7534889 5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl-(2->3)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranosyl chebi_ontology 3'-sialyllactosyl Neu5Acalpha2-3Galbeta1-4Glcbeta-yl alpha-N-acetylneuraminyl-(2->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl alpha-Neu5Ac-(2->3)-beta-D-Galp-(1->4)-beta-D-Glcp-yl CHEBI:142767 alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->4)-beta-D-Glc-yl group PMID:7534889 Europe PMC 5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl-(2->3)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranosyl IUPAC 3'-sialyllactosyl ChEBI Neu5Acalpha2-3Galbeta1-4Glcbeta-yl ChEBI alpha-N-acetylneuraminyl-(2->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl ChEBI alpha-Neu5Ac-(2->3)-beta-D-Galp-(1->4)-beta-D-Glcp-yl ChEBI An alpha-amino-acid anion that is the conjugate base of glutamic acid, having anionic carboxy groups and a cationic amino group -1 C5H8NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-1 WHUUTDBJXJRKMK-UHFFFAOYSA-M 146.12136 146.04588 [NH3+]C(CCC([O-])=O)C([O-])=O Gmelin:327908 glutamate(1-) hydrogen glutamate chebi_ontology 2-ammoniopentanedioate glutamate glutamic acid monoanion CHEBI:14321 glutamate(1-) Gmelin:327908 Gmelin glutamate(1-) JCBN hydrogen glutamate IUPAC 2-ammoniopentanedioate IUPAC glutamate UniProt glutamic acid monoanion JCBN An enal that consists of 3,7-dimethyl-9-nona-2,4,6,8-tetraenal (double bond geometry unspecified) carrying a 2,6,6-trimethylcyclohex-1-en-1-yl group at the 9-position. 0 C20H28O InChI=1S/C20H28O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6,8-9,11-13,15H,7,10,14H2,1-5H3 NCYCYZXNIZJOKI-UHFFFAOYSA-N 284.43572 284.21402 [H]C(=O)C=C(C)C=CC=C(C)C=CC1=C(C)CCCC1(C)C MetaCyc:Retinals Reaxys:2055098 3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenal retinal chebi_ontology CHEBI:15035 retinal Reaxys:2055098 Reaxys 3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenal IUPAC retinal UniProt -1 C20H27O2 InChI=1S/C20H28O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22)/p-1 SHGAZHPCJJPHSC-UHFFFAOYSA-M 299.42718 299.20165 CC(C=CC1=C(C)CCCC1(C)C)=CC=CC(C)=CC([O-])=O 3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenoate retinoate chebi_ontology CHEBI:15036 retinoate 3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenoate IUPAC retinoate UniProt A purine nucleobase found in humans and other organisms. 0 C5H4N4O2 152.111 152.03343 ECMDB:ECMDB00292 KNApSAcK:C00019660 PMID:24629268 YMDB:YMDB00263 chebi_ontology CHEBI:15318 xanthine PMID:24629268 Europe PMC A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity. CHEBI:13699 CHEBI:2377 KEGG:C00028 KEGG:C16722 Acceptor chebi_ontology A Akzeptor Hydrogen-acceptor Oxidized donor accepteur CHEBI:15339 acceptor Acceptor KEGG_COMPOUND A KEGG_COMPOUND Akzeptor ChEBI Hydrogen-acceptor KEGG_COMPOUND Oxidized donor KEGG_COMPOUND accepteur ChEBI A sulfur-containing amino acid that is propanoic acid with an amino group at position 2 and a sulfanyl group at position 3. 0 C3H7NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6) XUJNEKJLAYXESH-UHFFFAOYSA-N 121.15922 121.01975 NC(CS)C(O)=O CHEBI:14061 CHEBI:23508 CHEBI:4050 Beilstein:1721406 CAS:3374-22-9 Gmelin:2933 KEGG:C00736 KNApSAcK:C00001351 KNApSAcK:C00007323 PMID:17439666 PMID:25181601 Reaxys:1721406 Wikipedia:Cysteine Cysteine cysteine chebi_ontology 2-Amino-3-mercaptopropionic acid 2-amino-3-mercaptopropanoic acid 2-amino-3-sulfanylpropanoic acid C Cys Cystein Hcys Zystein cisteina CHEBI:15356 cysteine Beilstein:1721406 Beilstein CAS:3374-22-9 ChemIDplus CAS:3374-22-9 KEGG COMPOUND CAS:3374-22-9 NIST Chemistry WebBook Gmelin:2933 Gmelin PMID:17439666 Europe PMC PMID:25181601 Europe PMC Reaxys:1721406 Reaxys Cysteine KEGG_COMPOUND cysteine ChEBI cysteine IUPAC 2-Amino-3-mercaptopropionic acid KEGG_COMPOUND 2-amino-3-mercaptopropanoic acid JCBN 2-amino-3-sulfanylpropanoic acid IUPAC C ChEBI Cys ChEBI Cystein ChEBI Hcys IUPAC Zystein ChEBI cisteina ChEBI A 2-oxo monocarboxylic acid anion that is the conjugate base of pyruvic acid, arising from deprotonation of the carboxy group. -1 C3H3O3 InChI=1S/C3H4O3/c1-2(4)3(5)6/h1H3,(H,5,6)/p-1 LCTONWCANYUPML-UHFFFAOYSA-M 87.05412 87.00877 CC(=O)C([O-])=O CHEBI:14987 CHEBI:26462 Beilstein:3587721 CAS:57-60-3 Gmelin:2502 KEGG:C00022 PMID:17190852 PMID:21603897 PMID:21823181 PMID:21854850 PMID:22006570 PMID:22016370 PMID:22215378 PMID:22311625 PMID:22451307 PMID:22458763 Reaxys:3587721 UM-BBD_compID:c0159 2-oxopropanoate pyruvate chebi_ontology 2-oxopropanoate 2-oxopropanoic acid, ion(1-) CHEBI:15361 pyruvate Beilstein:3587721 Beilstein CAS:57-60-3 ChemIDplus Gmelin:2502 Gmelin PMID:17190852 Europe PMC PMID:21603897 Europe PMC PMID:21823181 Europe PMC PMID:21854850 Europe PMC PMID:22006570 Europe PMC PMID:22016370 Europe PMC PMID:22215378 Europe PMC PMID:22311625 Europe PMC PMID:22451307 Europe PMC PMID:22458763 Europe PMC Reaxys:3587721 Reaxys UM-BBD_compID:c0159 UM-BBD 2-oxopropanoate IUPAC pyruvate UniProt 2-oxopropanoate ChEBI 2-oxopropanoic acid, ion(1-) ChemIDplus A simple monocarboxylic acid containing two carbons. 0 C2H4O2 InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4) QTBSBXVTEAMEQO-UHFFFAOYSA-N 60.05200 60.02113 CC(O)=O CHEBI:22169 CHEBI:2387 CHEBI:40486 Beilstein:506007 CAS:64-19-7 Drug_Central:4211 Gmelin:1380 HMDB:HMDB0000042 KEGG:C00033 KEGG:D00010 KNApSAcK:C00001176 LIPID_MAPS_instance:LMFA01010002 MetaCyc:ACET PDBeChem:ACT PDBeChem:ACY PMID:12005138 PMID:15107950 PMID:16630552 PMID:16774200 PMID:17190852 PMID:19416101 PMID:19469536 PMID:22153255 PMID:22173419 PPDB:1333 Reaxys:506007 Wikipedia:Acetic_acid ACETIC ACID Acetic acid acetic acid chebi_ontology AcOH CH3-COOH CH3CO2H E 260 E-260 E260 Essigsaeure Ethanoic acid Ethylic acid HOAc INS No. 260 MeCO2H MeCOOH Methanecarboxylic acid acide acetique ethoic acid CHEBI:15366 acetic acid Beilstein:506007 Beilstein CAS:64-19-7 ChemIDplus CAS:64-19-7 KEGG COMPOUND CAS:64-19-7 NIST Chemistry WebBook Drug_Central:4211 DrugCentral Gmelin:1380 Gmelin LIPID_MAPS_instance:LMFA01010002 LIPID MAPS PMID:12005138 Europe PMC PMID:15107950 Europe PMC PMID:16630552 Europe PMC PMID:16774200 Europe PMC PMID:17190852 Europe PMC PMID:19416101 Europe PMC PMID:19469536 Europe PMC PMID:22153255 Europe PMC PMID:22173419 Europe PMC Reaxys:506007 Reaxys ACETIC ACID PDBeChem Acetic acid KEGG_COMPOUND acetic acid IUPAC AcOH ChEBI CH3-COOH IUPAC CH3CO2H ChEBI E 260 ChEBI E-260 ChEBI E260 ChEBI Essigsaeure ChEBI Ethanoic acid KEGG_COMPOUND Ethylic acid ChemIDplus HOAc ChEBI INS No. 260 ChEBI MeCO2H ChEBI MeCOOH ChEBI Methanecarboxylic acid ChemIDplus acide acetique ChemIDplus ethoic acid ChEBI A retinoic acid in which all four exocyclic double bonds have E- (trans-) geometry. 0 C20H28O2 InChI=1S/C20H28O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22)/b9-6+,12-11+,15-8+,16-14+ SHGAZHPCJJPHSC-YCNIQYBTSA-N 300.43512 300.20893 CC(\C=C\C1=C(C)CCCC1(C)C)=C/C=C/C(C)=C/C(O)=O CHEBI:45376 CHEBI:8815 Beilstein:2057223 CAS:302-79-4 DrugBank:DB00755 Drug_Central:2722 HMDB:HMDB0001852 KEGG:C00777 KEGG:D00094 LIPID_MAPS_instance:LMPR01090019 PDBeChem:REA PMID:11073974 PMID:11214352 PMID:11332619 PMID:11343416 PMID:11437362 PMID:11556813 PMID:11722649 PMID:11896294 PMID:11904404 PMID:14581379 PMID:14605492 PMID:14627725 PMID:14704332 PMID:14705145 PMID:14978018 PMID:15194426 PMID:15318809 PMID:15327395 PMID:15359008 PMID:15376324 PMID:15476854 PMID:15537748 PMID:15539337 PMID:15675886 PMID:15839997 PMID:16569247 PMID:16685080 PMID:16688769 PMID:16720557 PMID:16819260 PMID:16847436 PMID:16920920 PMID:17073551 PMID:17166212 PMID:17204142 PMID:18052213 PMID:18085670 PMID:18162363 PMID:18183617 PMID:18318655 PMID:18322276 PMID:18400206 PMID:18404486 PMID:18440196 PMID:18678272 PMID:18819820 PMID:18977311 PMID:19112091 PMID:19144697 PMID:19427305 PMID:19587328 PMID:19597529 PMID:19814868 PMID:19841174 PMID:21898109 PMID:21924320 PMID:21993673 PMID:22134377 PMID:22177959 PMID:22180426 PMID:22244299 PMID:22261335 PMID:22428994 PMID:22514600 PMID:22532966 PMID:22534100 PMID:22538278 PMID:22741806 Reaxys:2057223 Wikipedia:Tretinoin (2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenoic acid all-trans-Retinoic acid chebi_ontology (all-E)-3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoic acid 3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexene-1-yl)-2,4,6,8-nonatetraenoic acid (ECL) AGN 100335 Acide retinoique (French) (DSL) RETINOIC ACID Renova Retin-A Retinoic acid Retisol-A Ro 1-5488 Stieva-A Tretin M Tretinoine (French) (EINECS) Vesanoid Vitamin A acid all-(E)-Retinoic acid all-trans-Tretinoin all-trans-Vitamin A acid all-trans-Vitamin A1 acid all-trans-beta-Retinoic acid beta-Retinoic acid trans-Retinoic acid tretinoin CHEBI:15367 all-trans-retinoic acid Beilstein:2057223 Beilstein CAS:302-79-4 ChemIDplus CAS:302-79-4 KEGG COMPOUND Drug_Central:2722 DrugCentral LIPID_MAPS_instance:LMPR01090019 LIPID MAPS PMID:11073974 Europe PMC PMID:11214352 Europe PMC PMID:11332619 Europe PMC PMID:11343416 Europe PMC PMID:11437362 Europe PMC PMID:11556813 Europe PMC PMID:11722649 Europe PMC PMID:11896294 Europe PMC PMID:11904404 Europe PMC PMID:14581379 Europe PMC PMID:14605492 Europe PMC PMID:14627725 Europe PMC PMID:14704332 Europe PMC PMID:14705145 Europe PMC PMID:14978018 Europe PMC PMID:15194426 Europe PMC PMID:15318809 Europe PMC PMID:15327395 Europe PMC PMID:15359008 Europe PMC PMID:15376324 Europe PMC PMID:15476854 Europe PMC PMID:15537748 Europe PMC PMID:15539337 Europe PMC PMID:15675886 Europe PMC PMID:15839997 Europe PMC PMID:16569247 Europe PMC PMID:16685080 Europe PMC PMID:16688769 Europe PMC PMID:16720557 Europe PMC PMID:16819260 Europe PMC PMID:16847436 Europe PMC PMID:16920920 Europe PMC PMID:17073551 Europe PMC PMID:17166212 Europe PMC PMID:17204142 Europe PMC PMID:18052213 Europe PMC PMID:18085670 Europe PMC PMID:18162363 Europe PMC PMID:18183617 Europe PMC PMID:18318655 Europe PMC PMID:18322276 Europe PMC PMID:18400206 Europe PMC PMID:18404486 Europe PMC PMID:18440196 Europe PMC PMID:18678272 Europe PMC PMID:18819820 Europe PMC PMID:18977311 Europe PMC PMID:19112091 Europe PMC PMID:19144697 Europe PMC PMID:19427305 Europe PMC PMID:19587328 Europe PMC PMID:19597529 Europe PMC PMID:19814868 Europe PMC PMID:19841174 Europe PMC PMID:21898109 Europe PMC PMID:21924320 Europe PMC PMID:21993673 Europe PMC PMID:22134377 Europe PMC PMID:22177959 Europe PMC PMID:22180426 Europe PMC PMID:22244299 Europe PMC PMID:22261335 Europe PMC PMID:22428994 Europe PMC PMID:22514600 Europe PMC PMID:22532966 Europe PMC PMID:22534100 Europe PMC PMID:22538278 Europe PMC PMID:22741806 Europe PMC Reaxys:2057223 Reaxys (2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenoic acid IUPAC all-trans-Retinoic acid KEGG_COMPOUND (all-E)-3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoic acid KEGG_COMPOUND 3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexene-1-yl)-2,4,6,8-nonatetraenoic acid (ECL) KEGG_COMPOUND AGN 100335 KEGG_COMPOUND Acide retinoique (French) (DSL) KEGG_COMPOUND RETINOIC ACID PDBeChem Renova DrugBank Retin-A DrugBank Retinoic acid KEGG_COMPOUND Retisol-A DrugBank Ro 1-5488 KEGG_COMPOUND Stieva-A DrugBank Tretin M KEGG_COMPOUND Tretinoine (French) (EINECS) KEGG_COMPOUND Vesanoid DrugBank Vitamin A acid KEGG_COMPOUND all-(E)-Retinoic acid KEGG_COMPOUND all-trans-Tretinoin KEGG_COMPOUND all-trans-Vitamin A acid KEGG_COMPOUND all-trans-Vitamin A1 acid KEGG_COMPOUND all-trans-beta-Retinoic acid KEGG_COMPOUND beta-Retinoic acid KEGG_COMPOUND trans-Retinoic acid KEGG_COMPOUND tretinoin ChemIDplus 0 O2 InChI=1S/O2/c1-2 MYMOFIZGZYHOMD-UHFFFAOYSA-N 31.99880 31.98983 O=O CHEBI:10745 CHEBI:13416 CHEBI:23833 CHEBI:25366 CHEBI:30491 CHEBI:44742 CHEBI:7860 CAS:7782-44-7 Gmelin:485 HMDB:HMDB0001377 KEGG:C00007 KEGG:D00003 MetaCyc:OXYGEN-MOLECULE MolBase:750 PDBeChem:OXY PMID:10906528 PMID:16977326 PMID:18210929 PMID:18638417 PMID:19840863 PMID:7710549 PMID:9463773 Wikipedia:Oxygen dioxygen chebi_ontology Disauerstoff E 948 E-948 E948 O2 OXYGEN MOLECULE Oxygen [OO] dioxygene molecular oxygen CHEBI:15379 dioxygen CAS:7782-44-7 ChemIDplus CAS:7782-44-7 KEGG COMPOUND CAS:7782-44-7 NIST Chemistry WebBook Gmelin:485 Gmelin PMID:10906528 Europe PMC PMID:16977326 Europe PMC PMID:18210929 Europe PMC PMID:18638417 Europe PMC PMID:19840863 Europe PMC PMID:7710549 Europe PMC PMID:9463773 Europe PMC dioxygen IUPAC Disauerstoff ChEBI E 948 ChEBI E-948 ChEBI E948 ChEBI O2 IUPAC O2 KEGG_COMPOUND O2 UniProt OXYGEN MOLECULE PDBeChem Oxygen KEGG_COMPOUND [OO] MolBase dioxygene ChEBI molecular oxygen ChEBI The simplest (and the only achiral) proteinogenic amino acid, with a hydrogen atom as its side chain. 0 C2H5NO2 InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) DHMQDGOQFOQNFH-UHFFFAOYSA-N 75.06664 75.03203 NCC(O)=O CHEBI:10792 CHEBI:14344 CHEBI:24368 CHEBI:42964 CHEBI:5460 Beilstein:635782 CAS:56-40-6 DrugBank:DB00145 Drug_Central:1319 ECMDB:ECMDB00123 Gmelin:1808 HMDB:HMDB0000123 KEGG:C00037 KEGG:D00011 KNApSAcK:C00001361 MetaCyc:GLY PDBeChem:GLY PMID:10930630 PMID:11019925 PMID:11174716 PMID:11542461 PMID:11806864 PMID:12631515 PMID:12754315 PMID:12770151 PMID:12921899 PMID:15331688 PMID:15388434 PMID:15710237 PMID:16105183 PMID:16151895 PMID:16214212 PMID:16417482 PMID:16444815 PMID:16664855 PMID:16901953 PMID:16918424 PMID:16986325 PMID:16998855 PMID:17154252 PMID:17383967 PMID:17582620 PMID:17970719 PMID:18079355 PMID:18396796 PMID:18440992 PMID:18593588 PMID:18816054 PMID:18840508 PMID:19028609 PMID:19120667 PMID:19449910 PMID:19526731 PMID:19544666 PMID:19738917 PMID:19916621 PMID:19924257 PMID:21751272 PMID:22044190 PMID:22079563 PMID:22234938 PMID:22264337 PMID:22293292 PMID:22401276 PMID:22434786 Reaxys:635782 Wikipedia:Glycine YMDB:YMDB00016 GLYCINE Glycine aminoacetic acid glycine chebi_ontology Aminoacetic acid Aminoessigsaeure G Gly Glycin Glycocoll Glykokoll Glyzin H2N-CH2-COOH Hgly Leimzucker aminoethanoic acid CHEBI:15428 glycine Beilstein:635782 Beilstein CAS:56-40-6 ChemIDplus CAS:56-40-6 KEGG COMPOUND CAS:56-40-6 NIST Chemistry WebBook Drug_Central:1319 DrugCentral Gmelin:1808 Gmelin PMID:10930630 Europe PMC PMID:11019925 Europe PMC PMID:11174716 Europe PMC PMID:11542461 Europe PMC PMID:11806864 Europe PMC PMID:12631515 Europe PMC PMID:12754315 Europe PMC PMID:12770151 Europe PMC PMID:12921899 Europe PMC PMID:15331688 Europe PMC PMID:15388434 Europe PMC PMID:15710237 Europe PMC PMID:16105183 Europe PMC PMID:16151895 Europe PMC PMID:16214212 Europe PMC PMID:16417482 Europe PMC PMID:16444815 Europe PMC PMID:16664855 Europe PMC PMID:16901953 Europe PMC PMID:16918424 Europe PMC PMID:16986325 Europe PMC PMID:16998855 Europe PMC PMID:17154252 Europe PMC PMID:17383967 Europe PMC PMID:17582620 Europe PMC PMID:17970719 Europe PMC PMID:18079355 Europe PMC PMID:18396796 Europe PMC PMID:18440992 Europe PMC PMID:18593588 Europe PMC PMID:18816054 Europe PMC PMID:18840508 Europe PMC PMID:19028609 Europe PMC PMID:19120667 Europe PMC PMID:19449910 Europe PMC PMID:19526731 Europe PMC PMID:19544666 Europe PMC PMID:19738917 Europe PMC PMID:19916621 Europe PMC PMID:19924257 Europe PMC PMID:21751272 Europe PMC PMID:22044190 Europe PMC PMID:22079563 Europe PMC PMID:22234938 Europe PMC PMID:22264337 Europe PMC PMID:22293292 Europe PMC PMID:22401276 Europe PMC PMID:22434786 Europe PMC Reaxys:635782 Reaxys GLYCINE PDBeChem Glycine KEGG_COMPOUND aminoacetic acid IUPAC glycine IUPAC Aminoacetic acid KEGG_COMPOUND Aminoessigsaeure ChEBI G ChEBI Gly KEGG_COMPOUND Glycin ChemIDplus Glycocoll ChemIDplus Glykokoll ChEBI Glyzin ChEBI H2N-CH2-COOH IUPAC Hgly IUPAC Leimzucker ChemIDplus aminoethanoic acid ChEBI aminoethanoic acid JCBN Prostaglandin F2alpha in which the hydroxy group at position 9 has been oxidised to the corresponding ketone. Prostaglandin E2 is the most common and most biologically potent of mammalian prostaglandins. 0 C20H32O5 InChI=1S/C20H32O5/c1-2-3-6-9-15(21)12-13-17-16(18(22)14-19(17)23)10-7-4-5-8-11-20(24)25/h4,7,12-13,15-17,19,21,23H,2-3,5-6,8-11,14H2,1H3,(H,24,25)/b7-4-,13-12+/t15-,16+,17+,19+/m0/s1 XEYBRNLFEZDVAW-ARSRFYASSA-N 352.46510 352.22497 CCCCC[C@H](O)\C=C\[C@H]1[C@H](O)CC(=O)[C@@H]1C\C=C/CCCC(O)=O CHEBI:10910 CHEBI:10911 CHEBI:114125 CHEBI:26323 CHEBI:4625 CHEBI:8512 Beilstein:2224724 CAS:363-24-6 DrugBank:DB00917 Drug_Central:913 HMDB:HMDB0001220 KEGG:C00584 KEGG:D00079 LIPID_MAPS_instance:LMFA03010003 MetaCyc:5Z13E-15S-1115-DIHYDROXY-9-OXOPROS PMID:24501112 PMID:7224729 PMID:7836930 Patent:DE2011969 Patent:GB851827 Patent:NL6505799 Patent:US3598858 Reaxys:2224724 Wikipedia:Prostaglandin_E2 (5Z,13E,15S)-11alpha,15-dihydroxy-9-oxoprosta-5,13-dien-1-oic acid Prostaglandin E2 chebi_ontology (15S)-prostaglandin E2 (5Z,11alpha,13E,15S)-11,15-dihydroxy-9-oxoprosta-5,13-dien-1-oic acid (5Z,13E)-(15S)-11alpha,15-Dihydroxy-9-oxoprost-13-enoate (5Z,13E)-(15S)-11alpha,15-Dihydroxy-9-oxoprosta-5,13-dienoate (E,Z)-(1R,2R,3R)-7-(3-Hydroxy-2-((3S)-(3-hydroxy-1-octenyl))-5-oxocyclopentyl)-5-heptenoic acid (Z)-7-((1R,2R,3R)-3-hydroxy-2-((S,E)-3-hydroxyoct-1-enyl)-5-oxocyclopentyl)hept-5-enoic acid Dinoproston Dinoprostone PGE2 Prepidil Propess Prostin E2 dinoprostona dinoprostone dinoprostonum CHEBI:15551 prostaglandin E2 Beilstein:2224724 Beilstein CAS:363-24-6 ChemIDplus CAS:363-24-6 KEGG COMPOUND Drug_Central:913 DrugCentral LIPID_MAPS_instance:LMFA03010003 LIPID MAPS PMID:24501112 Europe PMC PMID:7224729 Europe PMC PMID:7836930 Europe PMC Reaxys:2224724 Reaxys (5Z,13E,15S)-11alpha,15-dihydroxy-9-oxoprosta-5,13-dien-1-oic acid IUPAC Prostaglandin E2 KEGG_COMPOUND (15S)-prostaglandin E2 ChemIDplus (5Z,11alpha,13E,15S)-11,15-dihydroxy-9-oxoprosta-5,13-dien-1-oic acid ChemIDplus (5Z,13E)-(15S)-11alpha,15-Dihydroxy-9-oxoprost-13-enoate KEGG_COMPOUND (5Z,13E)-(15S)-11alpha,15-Dihydroxy-9-oxoprosta-5,13-dienoate KEGG_COMPOUND (E,Z)-(1R,2R,3R)-7-(3-Hydroxy-2-((3S)-(3-hydroxy-1-octenyl))-5-oxocyclopentyl)-5-heptenoic acid ChemIDplus (Z)-7-((1R,2R,3R)-3-hydroxy-2-((S,E)-3-hydroxyoct-1-enyl)-5-oxocyclopentyl)hept-5-enoic acid ChEMBL Dinoproston ChemIDplus Dinoprostone KEGG_COMPOUND PGE2 ChemIDplus PGE2 KEGG_COMPOUND Prepidil KEGG_DRUG Propess DrugBank Prostin E2 KEGG_DRUG dinoprostona ChemIDplus dinoprostone KEGG_DRUG dinoprostonum ChemIDplus A N-alkylglycine that is the N-methyl derivative of glycine. It is an intermediate in the metabolic pathway of glycine. 0 C3H7NO2 InChI=1S/C3H7NO2/c1-4-2-3(5)6/h4H,2H2,1H3,(H,5,6) FSYKKLYZXJSNPZ-UHFFFAOYSA-N 89.09322 89.04768 CNCC(O)=O CHEBI:10876 CHEBI:12609 CHEBI:15065 CHEBI:21765 CHEBI:45381 CHEBI:45442 CHEBI:45531 CHEBI:45614 CHEBI:9029 Beilstein:1699442 CAS:107-97-1 Gmelin:2018 HMDB:HMDB0000271 KEGG:C00213 MetaCyc:SARCOSINE PDBeChem:SAR PMID:11272730 PMID:11850512 PMID:15023571 PMID:15331688 PMID:16154544 PMID:17095900 PMID:17190852 PMID:17901997 PMID:19433577 PMID:19577367 PMID:19619564 PMID:19944746 Reaxys:1699442 UM-BBD_compID:c0135 Wikipedia:Sarcosine SARCOSINE Sarcosine sarcosine chebi_ontology (methylamino)acetic acid (methylamino)ethanoic acid L-sarcosine MeGly N-Methylglycine N-methylaminoacetic acid Sar methylaminoacetic acid sarcosinic acid CHEBI:15611 sarcosine SARCOSINE PDBeChem Sarcosine KEGG_COMPOUND sarcosine IUPAC (methylamino)acetic acid ChemIDplus (methylamino)ethanoic acid NIST_Chemistry_WebBook L-sarcosine ChEBI MeGly ChEBI N-Methylglycine KEGG_COMPOUND N-methylaminoacetic acid NIST_Chemistry_WebBook Sar IUPAC methylaminoacetic acid NIST_Chemistry_WebBook sarcosinic acid ChemIDplus Beilstein:1699442 ChemIDplus CAS:107-97-1 ChemIDplus CAS:107-97-1 KEGG COMPOUND CAS:107-97-1 NIST Chemistry WebBook Gmelin:2018 Gmelin PMID:11272730 Europe PMC PMID:11850512 Europe PMC PMID:15023571 Europe PMC PMID:15331688 Europe PMC PMID:16154544 Europe PMC PMID:17095900 Europe PMC PMID:17190852 Europe PMC PMID:17901997 Europe PMC PMID:19433577 Europe PMC PMID:19577367 Europe PMC PMID:19619564 Europe PMC PMID:19944746 Europe PMC Reaxys:1699442 Reaxys UM-BBD_compID:c0135 UM-BBD 0 C20H25N7O6 InChI=1S/C20H25N7O6/c1-27-12(9-23-16-15(27)18(31)26-20(21)25-16)8-22-11-4-2-10(3-5-11)17(30)24-13(19(32)33)6-7-14(28)29/h2-5,12-13,22H,6-9H2,1H3,(H,24,30)(H,28,29)(H,32,33)(H4,21,23,25,26,31)/t12-,13-/m0/s1 ZNOVTXRBGFNYRX-STQMWFEESA-N 459.45580 459.18663 CN1[C@@H](CNc2ccc(cc2)C(=O)N[C@@H](CCC(O)=O)C(O)=O)CNc2nc(N)[nH]c(=O)c12 CHEBI:12146 CHEBI:2097 CAS:134-35-0 DrugBank:DB04789 KEGG:C00440 KNApSAcK:C00007252 N-[4-({[(6S)-2-amino-5-methyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid chebi_ontology 5-Methyltetrahydrofolate N-(5-methyl-5,6,7,8-tetrahydropteroyl)-L-glutamic acid [(6S)-5-methyl-5,6,7,8-tetrahydropteroyl]glutamate CHEBI:15641 5-methyltetrahydrofolic acid CAS:134-35-0 KEGG COMPOUND N-[4-({[(6S)-2-amino-5-methyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid IUPAC 5-Methyltetrahydrofolate KEGG_COMPOUND N-(5-methyl-5,6,7,8-tetrahydropteroyl)-L-glutamic acid ChEBI [(6S)-5-methyl-5,6,7,8-tetrahydropteroyl]glutamate ChEBI An imidazolidine-2,4-dione that is 5-aminohydantoin in which a carbamoyl group is attached to the exocyclic nitrogen. 0 C4H6N4O3 InChI=1S/C4H6N4O3/c5-3(10)6-1-2(9)8-4(11)7-1/h1H,(H3,5,6,10)(H2,7,8,9,11) POJWUDADGALRAB-UHFFFAOYSA-N 158.11560 158.04399 NC(=O)NC1NC(=O)NC1=O CHEBI:13761 CHEBI:22354 CHEBI:2594 CAS:97-59-6 Drug_Central:4268 HMDB:HMDB0000462 KEGG:C01551 KEGG:D00121 KNApSAcK:C00007468 LINCS:LSM-5190 MetaCyc:ALLANTOIN PMID:11157020 PMID:14619112 PMID:17190852 Patent:US2158098 Reaxys:83514 Wikipedia:Allantoin Allantoin N-(2,5-dioxoimidazolidin-4-yl)urea allantoin chebi_ontology (2,5-Dioxo-4-imidazolidinyl)urea 2,5-Dioxo-4-imidazolidinyl-urea 4-ureido-2,5-imidazolidinedione 5-Ureido-2,4-imidazolidindione 5-Ureidohydantoin Glyoxyldiureide N-(2,5-Dioxo-4-imidazolidinyl)urea CHEBI:15676 allantoin CAS:97-59-6 ChemIDplus CAS:97-59-6 KEGG COMPOUND CAS:97-59-6 NIST Chemistry WebBook Drug_Central:4268 DrugCentral PMID:11157020 Europe PMC PMID:14619112 Europe PMC PMID:17190852 Europe PMC Reaxys:83514 Reaxys Allantoin KEGG_COMPOUND N-(2,5-dioxoimidazolidin-4-yl)urea IUPAC allantoin