Environment Exposure Ontology Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label The user interface label is the label that should be placed on a datum when presented on a form or report Damion Dooley user interface label A user interface feature is a pre-set list of features and their acceptable values that a user interface rendering system should use to display an entity on a form or report Damion Dooley user interface feature editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label example A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> IAO:0000112 uberon example_of_usage true example_of_usage example of usage example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status has curation status definition definition textual definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition textual definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> IAO:0000116 uberon editor_note true editor_note editor note editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition_editor term editor term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term alternative term alternative_term definition source formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source definition source has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg IAO:0000232 uberon curator_notes true curator_notes curator note curator note curator notes imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from imported from expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall expand expression to expand expression to OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI has axiom label term replaced by Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg term replaced by 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 temporal interpretation https://github.com/oborel/obo-relations/wiki/ROAndTime 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 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 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. 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. 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 medically relevant exposure EnvO-Lite-GSC 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 Drosophila GO slim FlyBase Drosophila GO ribbon slim Generic GO slim Metagenomics GO slim Mouse GO slim PIR GO slim Plant GO slim Fission yeast GO slim Yeast GO slim oio:hasRelatedSynonym blast name oio:hasExactSynonym common name oio:hasExactSynonym equivalent name oio:hasExactSynonym genbank common name A metadata relation between a class and its taxonomic rank (eg species, family) ncbi_taxonomy This is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored has_rank oio:hasRelatedSynonym in-part oio:hasRelatedSynonym misspelling oio:hasExactSynonym scientific name oio:hasRelatedSynonym synonym Abnormal/normal slim Absent/present slim Attribute slim cell_quality Disposition slim Pathology slim Relational slim: types of quality that require an additional entity in order to exist Scalar slim Value slim eco subset abbreviation 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 expert consultation and attribution required plural term taxonomic disambiguation CUMBO 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 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 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 uberon dc-contributor true dc-contributor contributor uberon dc-creator true dc-creator creator uberon dc-rights true dc-rights rights uberon dc-source true dc-source derived from resource uberon dc-title true dc-title title subset_property consider has_alternative_id has broad synonym has_broad_synonym database cross reference database_cross_reference has_exact_synonym has narrow synonym has_narrow_synonym has_obo_namespace has_related_synonym has_scope has synonym has_synonym_type in_subset shorthand label label label uberon seeAlso true seeAlso see also uberon depicted_by true depicted_by depicted by 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 experimental_condition_ontology external quality uberon part_of part_of part of part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) 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 JSmith 2014-03-07T11:32:23Z BFO:0000051 chebi_ontology experimental_condition_ontology external quality uberon has_part false has_part We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. has part has part has_part Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. PATOC:CJM preceded by X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 is preceded by takes place after uberon preceded_by preceded_by preceded by preceded_by 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 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 A duck swimming in a pond is partially surrounded by air and partially surrounded by water. x partially_surrounded_by y if and only if (1) x is adjacent to y and for the region r that is adjacent to x, r partially overlaps y (2) the shared boundary between x and y occupies a non-trivial proportion of the outermost boundary of x Definition modified from 'surrounded by'. partially_surrounded_by To be ceded to RO results in proliferation of This document is about information artifacts and their representations is_about is a (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about 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 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 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 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 apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality RO:0000086 uberon has_quality has_quality has quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role RO:0000087 chebi_ontology has_role false false has_role has role has role this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. derives from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See 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 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 X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) David Osumi-Sutherland starts_at_end_of A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. RO:0002087 directly preceded by is directly preceded by is immediately preceded by starts_at_end_of uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by immediately_preceded_by A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. SIO:000251 is immediately preceded by SIO:000251 David Osumi-Sutherland 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 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 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 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 uberon has_component has_component has component has component x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y Chris Mungall David Osumi-Sutherland Melissa Haendel Terry Meehan RO:0002202 uberon develops_from develops_from This is the transitive form of the develops from relation develops from develops_from inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan RO:0002203 uberon develops_into develops_into develops into develops_into Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. 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 participates in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of y comes from x, 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 JSmith 2014-03-07T11:34:22Z RO:0002211 experimental_condition_ontology external has_component regulates has_component regulates has_component regulates regulates regulates (processual) 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 has active participant 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 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 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 direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes has input p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. Chris Mungall produces has output A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor ExO:0000055 has exposure route A broad relationship between an exposure event or process and the course takes from the source to the target. http://purl.obolibrary.org/obo/ExO_0000004 has exposure transport path Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. related via exposure to 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. c involved in regulation of p if c enables 'p' and p' causally upstream of p 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 'p' and p' causally upstream of or within p c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage Chris Mungall replaces RO:0002285 uberon developmentally_replaces developmentally_replaces developmentally replaces developmentally_replaces Inverse of developmentally preceded by Chris Mungall developmentally succeeded by 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue Chris Mungall part of developmental precursor of p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. Chris Mungall results_in_developmental_progression_of results in developmental progression of an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) Chris Mungall GOC:mtg_berkeley_2013 results_in_formation_of results in formation of Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. Pier Buttigieg adapted for living in A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. has habitat has habitat cjm 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 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 A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. Austin Meier Chris Mungall Marie Angelique Laporte cjm 2017-06-05T17:35:04Z has exposure stimulus 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 inheres in part of true A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions ecologically 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 ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. Chris Mungall http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. contributes 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 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 inverse of has output Chris Mungall RO:0002353 uberon output_of output_of output of output of Chris Mungall formed as result of a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a Chris Mungall attached to (anatomical structure to anatomical structure) RO:0002371 uberon attaches_to attaches_to attached to attaches_to m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Chris Mungall Wikipedia:Insertion_(anatomy) RO:0002372 uberon has_muscle_origin has_muscle_origin The origin is the end of a muscle that attaches to the more fixed part of the skeleton, which is the proximal end in limb muscles has muscle origin has_muscle_origin We need to import uberon muscle to create a stricter domain constraint m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. 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. 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 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 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 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 and are executing molecular processes that are directly causally connected. 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. Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b Chris Mungall molecularly controls activity directly regulates activity of molecularly controls 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) '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 RO:0002473 composed_primarily_of composed_primarily_of composed primarily of p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in true Chris Mungall is kinase activity 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 RO:0002488 existence_starts_during existence_starts_during existence starts during Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. Relation between continuant 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 RO:0002492 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 causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes Chris Mungall depends on The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between material entities A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future Chris Mungall determined by (system to material entity) Chris Mungall Pier Buttigieg Chris Mungall Pier Buttigieg determined by inverse of determined by Chris Mungall determines (material entity to system) determines s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. Chris Mungall determined by part of true 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 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' Inverse of 'causal agent in' has causal agent process has causal agent A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. obsolete related via dependence to related via dependence to true 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 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 part:of chebi_ontology has_functional_parent false false has functional parent chebi_ontology has_parent_hydride false false has parent hydride chebi_ontology is_conjugate_acid_of true false is conjugate acid of chebi_ontology is_conjugate_base_of true false is conjugate base of chebi_ontology is_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 interacts_with interacts_with interacts_with_an_exposure_receptor_via interacts_with_an_exposure_receptor_via interacts_with_an_exposure_stressor_via interacts_with_an_exposure stressor_via q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality decreased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. decreased_in_magnitude_relative_to q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality different_in_magnitude_relative_to different_in_magnitude_relative_to q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 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 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 a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s add to RO uberon indirectly_supplies indirectly_supplies x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. uberon posteriorly_connected_to posteriorly connected to x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. 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 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 . entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] s-region SpatialRegion BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] fiat-object-part FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object fiat object part b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] object aggregate site object gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. 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. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) continuant fiat boundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) immaterial ImmaterialEntity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity anatomical entity anatomical structure connected anatomical structure material anatomical entity immaterial anatomical entity cell part (CARO) cell part multi-cell-part structure neuron projection bundle Material anatomical entity that is a member of an individual species or is a viral or viroid particle. organism or virus or viroid multicellular anatomical structure biological entity A quinolone that is quinolin-4(1H)-one bearing cyclopropyl, carboxylic acid, fluoro and piperazin-1-yl substituents at positions 1, 3, 6 and 7, respectively. 0 C17H18FN3O3 InChI=1S/C17H18FN3O3/c18-13-7-11-14(8-15(13)20-5-3-19-4-6-20)21(10-1-2-10)9-12(16(11)22)17(23)24/h7-10,19H,1-6H2,(H,23,24) MYSWGUAQZAJSOK-UHFFFAOYSA-N 331.34150 331.13322 OC(=O)c1cn(C2CC2)c2cc(N3CCNCC3)c(F)cc2c1=O CHEBI:102718 CHEBI:3717 CHEBI:41638 Beilstein:3568352 CAS:85721-33-1 DrugBank:DB00537 Drug_Central:659 HMDB:HMDB0014677 KEGG:C05349 KEGG:D00186 LINCS:LSM-5226 PDBeChem:CPF PMID:10397494 PMID:10737746 Patent:DE3142854 Patent:US4670444 Reaxys:3568352 VSDB:1763 Wikipedia:Ciprofloxacin 1-cyclopropyl-6-fluoro-4-oxo-7-(piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylic acid Ciprofloxacin ciprofloxacin chebi_ontology 1-CYCLOPROPYL-6-FLUORO-4-OXO-7-PIPERAZIN-1-YL-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC ACID 1-Cyclopropyl-6-fluoro-4-oxo-7-piperazin-1-yl-1,4-dihydro-quinoline-3-carboxylic acid 1-Cyclopropyl-6-fluoro-7-(4-methyl-piperazin-1-yl)-4-oxo-1,4-dihydro-quinoline-3-carboxylic acid 1-cyclopropyl-6-fluoro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid 1-cyclopropyl-6-fluoro-4-oxo-7-(piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylic acid 1-cyclopropyl-6-fluoro-4-oxo-7-piperazin-1-ylquinoline-3-carboxylic acid 1-cyclopropyl-6-fluoro-7-hexahydro-1-pyrazinyl-4-oxo-1,4-dihydro-3-quinolinecarboxylic acid ciprofloxacin ciprofloxacine ciprofloxacino ciprofloxacinum CHEBI:100241 ciprofloxacin Beilstein:3568352 Beilstein CAS:85721-33-1 ChemIDplus CAS:85721-33-1 KEGG COMPOUND Drug_Central:659 DrugCentral PMID:10397494 ChEMBL PMID:10737746 ChEMBL Reaxys:3568352 Reaxys 1-cyclopropyl-6-fluoro-4-oxo-7-(piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylic acid IUPAC Ciprofloxacin KEGG_COMPOUND ciprofloxacin ChEMBL 1-CYCLOPROPYL-6-FLUORO-4-OXO-7-PIPERAZIN-1-YL-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC ACID PDBeChem 1-Cyclopropyl-6-fluoro-4-oxo-7-piperazin-1-yl-1,4-dihydro-quinoline-3-carboxylic acid ChEMBL 1-Cyclopropyl-6-fluoro-7-(4-methyl-piperazin-1-yl)-4-oxo-1,4-dihydro-quinoline-3-carboxylic acid ChEMBL 1-cyclopropyl-6-fluoro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid ChemIDplus 1-cyclopropyl-6-fluoro-4-oxo-7-(piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylic acid ChEMBL 1-cyclopropyl-6-fluoro-4-oxo-7-piperazin-1-ylquinoline-3-carboxylic acid ChEMBL 1-cyclopropyl-6-fluoro-7-hexahydro-1-pyrazinyl-4-oxo-1,4-dihydro-3-quinolinecarboxylic acid ChEMBL ciprofloxacin ChemIDplus ciprofloxacine ChemIDplus ciprofloxacino ChemIDplus ciprofloxacinum ChemIDplus A quinolinemonocarboxylic acid with broad-spectrum antibacterial activity against most gram-negative and gram-positive bacteria. Norfloxacin is bactericidal and its mode of action depends on blocking of bacterial DNA replication by binding itself to an enzyme called DNA gyrase. 0 C16H18FN3O3 InChI=1S/C16H18FN3O3/c1-2-19-9-11(16(22)23)15(21)10-7-12(17)14(8-13(10)19)20-5-3-18-4-6-20/h7-9,18H,2-6H2,1H3,(H,22,23) OGJPXUAPXNRGGI-UHFFFAOYSA-N 319.33080 319.13322 CCn1cc(C(O)=O)c(=O)c2cc(F)c(cc12)N1CCNCC1 CHEBI:7629 Beilstein:567897 CAS:70458-96-7 DrugBank:DB01059 Drug_Central:1967 Gmelin:1576626 HMDB:HMDB0015192 KEGG:C06687 KEGG:D00210 LINCS:LSM-5286 PMID:3317294 PMID:3908074 PMID:6211142 PMID:6224685 PMID:6234465 PMID:6454381 PMID:6461606 Patent:BE863429 Patent:DE2840910 Patent:US4146719 Patent:US4292317 Reaxys:567897 VSDB:1831 Wikipedia:Norfloxacin 1-ethyl-6-fluoro-4-oxo-7-(piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylic acid chebi_ontology 1,4-Dihydro-1-ethyl-6-fluoro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid 1-Ethyl-6-fluor-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-chinolincarbonsaeure 1-Ethyl-6-fluoro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid NFLX norfloxacin norfloxacine norfloxacino norfloxacinum CHEBI:100246 norfloxacin Beilstein:567897 Beilstein CAS:70458-96-7 ChemIDplus CAS:70458-96-7 KEGG COMPOUND Drug_Central:1967 DrugCentral Gmelin:1576626 Gmelin PMID:3317294 Europe PMC PMID:3908074 Europe PMC PMID:6211142 Europe PMC PMID:6224685 Europe PMC PMID:6234465 Europe PMC PMID:6454381 Europe PMC PMID:6461606 Europe PMC Reaxys:567897 Reaxys 1-ethyl-6-fluoro-4-oxo-7-(piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylic acid IUPAC 1,4-Dihydro-1-ethyl-6-fluoro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid ChemIDplus 1-Ethyl-6-fluor-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-chinolincarbonsaeure ChemIDplus 1-Ethyl-6-fluoro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid ChemIDplus NFLX KEGG_DRUG norfloxacin KEGG_DRUG norfloxacine ChemIDplus norfloxacino ChemIDplus norfloxacinum ChemIDplus A piperazine compound having 1,2-benzothiazol-3-yl- and 2-(6-chloro-1,3-dihydro-2-oxindol-5-yl)ethyl substituents attached to the nitrogen atoms. 0 C21H21ClN4OS InChI=1S/C21H21ClN4OS/c22-17-13-18-15(12-20(27)23-18)11-14(17)5-6-25-7-9-26(10-8-25)21-16-3-1-2-4-19(16)28-24-21/h1-4,11,13H,5-10,12H2,(H,23,27) MVWVFYHBGMAFLY-UHFFFAOYSA-N 412.93600 412.11246 Clc1cc2NC(=O)Cc2cc1CCN1CCN(CC1)c1nsc2ccccc12 Beilstein:6669199 CAS:146939-27-7 DrugBank:DB00246 Drug_Central:2865 KEGG:C07568 KEGG:D08687 LINCS:LSM-5433 Patent:EP281309 Patent:US4831031 Wikipedia:Ziprasidone 5-{2-[4-(1,2-benzothiazol-3-yl)piperazin-1-yl]ethyl}-6-chloro-1,3-dihydro-2H-indol-2-one Ziprasidone chebi_ontology ziprasidona ziprasidone ziprasidonum CHEBI:10119 ziprasidone Beilstein:6669199 Beilstein CAS:146939-27-7 ChemIDplus CAS:146939-27-7 DrugBank CAS:146939-27-7 KEGG DRUG Drug_Central:2865 DrugCentral 5-{2-[4-(1,2-benzothiazol-3-yl)piperazin-1-yl]ethyl}-6-chloro-1,3-dihydro-2H-indol-2-one IUPAC Ziprasidone KEGG_COMPOUND ziprasidona ChEBI ziprasidone ChEBI ziprasidone KEGG_DRUG ziprasidonum ChEBI A 5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydro-1,5-benzothiazepin-3-yl acetate in which both stereocentres have S configuration. A calcium-channel blocker and vasodilator, it is used as the hydrochloride in the management of angina pectoris and hypertension. 0 C22H26N2O4S InChI=1S/C22H26N2O4S/c1-15(25)28-20-21(16-9-11-17(27-4)12-10-16)29-19-8-6-5-7-18(19)24(22(20)26)14-13-23(2)3/h5-12,20-21H,13-14H2,1-4H3/t20-,21+/m1/s1 HSUGRBWQSSZJOP-RTWAWAEBSA-N 414.51800 414.16133 COc1ccc(cc1)[C@@H]1Sc2ccccc2N(CCN(C)C)C(=O)[C@@H]1OC(C)=O CHEBI:4602 Beilstein:3573079 CAS:42399-41-7 DrugBank:DB00343 Drug_Central:897 HMDB:HMDB0014487 KEGG:C06958 KEGG:D07845 LINCS:LSM-2523 PMID:11937779 PMID:16651034 PMID:19167257 PMID:23687551 PMID:24261918 PMID:25122162 PMID:8369596 Patent:DE1805714 Patent:DE3415035 Patent:US3562257 Patent:US4552695 Reaxys:3573079 VSDB:1863 Wikipedia:Diltiazem (2S,3S)-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydro-1,5-benzothiazepin-3-yl acetate chebi_ontology (+)-cis-5-[2-(dimethylamino)ethyl]-2,3-dihydro-3-hydroxy-2-(p-methoxyphenyl)-1,5-benzothiazepin-4(5H)-one acetate ester (2S,3S)-5-(2-(dimethylamino)ethyl)-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydrobenzo[b][1,4]thiazepin-3-yl acetate (2S-cis)-3-(acetyloxy)-5-[2-(dimethylamino)ethyl]-2,3-dihydro-2-(4-methoxyphenyl)-1,5-benzothiazepin-4(5H)-one Acetic acid (2S,3S)-5-(2-dimethylamino-ethyl)-2-(4-methoxy-phenyl)-4-oxo-2,3,4,5-tetrahydro-benzo[b][1,4]thiazepin-3-yl ester D-cis-diltiazem d-cis-diltiazem diltiazem diltiazemum CHEBI:101278 diltiazem Beilstein:3573079 Beilstein CAS:42399-41-7 ChemIDplus CAS:42399-41-7 KEGG COMPOUND CAS:42399-41-7 NIST Chemistry WebBook Drug_Central:897 DrugCentral PMID:11937779 Europe PMC PMID:16651034 Europe PMC PMID:19167257 Europe PMC PMID:23687551 Europe PMC PMID:24261918 Europe PMC PMID:25122162 Europe PMC PMID:8369596 Europe PMC Reaxys:3573079 Reaxys (2S,3S)-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydro-1,5-benzothiazepin-3-yl acetate IUPAC (+)-cis-5-[2-(dimethylamino)ethyl]-2,3-dihydro-3-hydroxy-2-(p-methoxyphenyl)-1,5-benzothiazepin-4(5H)-one acetate ester ChEBI (2S,3S)-5-(2-(dimethylamino)ethyl)-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydrobenzo[b][1,4]thiazepin-3-yl acetate ChEMBL (2S-cis)-3-(acetyloxy)-5-[2-(dimethylamino)ethyl]-2,3-dihydro-2-(4-methoxyphenyl)-1,5-benzothiazepin-4(5H)-one ChEBI Acetic acid (2S,3S)-5-(2-dimethylamino-ethyl)-2-(4-methoxy-phenyl)-4-oxo-2,3,4,5-tetrahydro-benzo[b][1,4]thiazepin-3-yl ester ChEMBL D-cis-diltiazem ChEBI d-cis-diltiazem ChEBI diltiazem ChemIDplus diltiazem WHO_MedNet diltiazemum ChemIDplus A barbiturate, the structure of which is that of 2-thiobarbituric acid substituted at C-5 by ethyl and sec-pentyl groups. 0 C11H18N2O2S InChI=1S/C11H18N2O2S/c1-4-6-7(3)11(5-2)8(14)12-10(16)13-9(11)15/h7H,4-6H2,1-3H3,(H2,12,13,14,15,16) IUJDSEJGGMCXSG-UHFFFAOYSA-N 242.33800 242.10890 CCCC(C)C1(CC)C(=O)NC(=S)NC1=O CHEBI:9560 Beilstein:209361 CAS:76-75-5 DrugBank:DB00599 Drug_Central:2633 KEGG:C07521 PMID:10666006 PMID:10841799 PMID:15857133 PMID:16166909 PMID:16897573 PMID:18484074 PMID:20488867 PMID:2215478 PMID:23305916 PMID:23422796 PMID:23490495 PMID:23542731 PMID:23644730 PMID:23879844 PMID:3654008 PMID:6864729 PMID:9171876 PMID:9699097 Reaxys:209361 5-ethyl-5-(pentan-2-yl)-2-thioxodihydropyrimidine-4,6(1H,5H)-dione Thiopental chebi_ontology (+-)-thiopental 2-Thio-5-ethyl-5-sec-pentylbarbituric acid 5-Ethyl-5-(1-methyl-butyl)-2-thioxo-dihydro-pyrimidine-4,6-dione Penthiobarbital Pentothiobarbital Thiopentobarbital Thiopentobarbitone Thiopentobarbituric acid Thiopentone CHEBI:102166 thiopental Beilstein:209361 Beilstein CAS:76-75-5 ChemIDplus CAS:76-75-5 KEGG COMPOUND Drug_Central:2633 DrugCentral PMID:10666006 Europe PMC PMID:10841799 ChEMBL PMID:15857133 ChEMBL PMID:16166909 Europe PMC PMID:16897573 Europe PMC PMID:18484074 Europe PMC PMID:20488867 Europe PMC PMID:2215478 Europe PMC PMID:23305916 Europe PMC PMID:23422796 Europe PMC PMID:23490495 Europe PMC PMID:23542731 Europe PMC PMID:23644730 Europe PMC PMID:23879844 Europe PMC PMID:3654008 Europe PMC PMID:6864729 ChEMBL PMID:9171876 ChEMBL PMID:9699097 Europe PMC Reaxys:209361 Reaxys 5-ethyl-5-(pentan-2-yl)-2-thioxodihydropyrimidine-4,6(1H,5H)-dione IUPAC Thiopental KEGG_COMPOUND (+-)-thiopental ChemIDplus 2-Thio-5-ethyl-5-sec-pentylbarbituric acid ChemIDplus 5-Ethyl-5-(1-methyl-butyl)-2-thioxo-dihydro-pyrimidine-4,6-dione ChEMBL Penthiobarbital ChemIDplus Pentothiobarbital ChemIDplus Thiopentobarbital ChemIDplus Thiopentobarbitone ChemIDplus Thiopentobarbituric acid ChemIDplus Thiopentone ChemIDplus A sulfonamide consisting of pyrimidine with methyl substituents at the 4- and 6-positions and a 4-aminobenzenesulfonamido group at the 2-position. 0 C12H14N4O2S InChI=1S/C12H14N4O2S/c1-8-7-9(2)15-12(14-8)16-19(17,18)11-5-3-10(13)4-6-11/h3-7H,13H2,1-2H3,(H,14,15,16) ASWVTGNCAZCNNR-UHFFFAOYSA-N 278.33000 278.08375 Cc1cc(C)nc(NS(=O)(=O)c2ccc(N)cc2)n1 Beilstein:261304 CAS:57-68-1 DrugBank:DB01582 Drug_Central:2502 Gmelin:1009759 HMDB:HMDB0015522 KEGG:C19530 KEGG:D02436 LINCS:LSM-5295 PMID:11431418 PMID:14552772 PMID:15603963 PMID:17311370 PMID:17596632 PMID:20028131 PMID:22903812 PMID:23218311 PMID:23384282 PMID:23434485 PMID:23454458 PMID:23562141 PMID:23636590 PMID:23673752 PMID:23673946 PMID:23704574 PMID:6864729 PMID:7021831 PMID:7328159 PMID:8199304 PMID:9886437 Patent:EP1861101 Patent:GB546158 Patent:GB552887 Patent:US2407966 Patent:US3119818 Patent:WO2005016386 Reaxys:261304 VSDB:1829 Wikipedia:Sulfadimidine 4-amino-N-(4,6-dimethylpyrimidin-2-yl)benzenesulfonamide chebi_ontology (p-Aminobenzolsulfonyl)-2-amino-4,6-dimethylpyrimidin 2-(4-Aminobenzenesulfonamido)-4,6-dimethylpyrimidine 2-(p-Aminobenzenesulfonamido)-4,6-dimethylpyrimidine 2-Sulfanilamido-4,6-dimethylpyrimidine 4,6-Dimethyl-2-sulfanilamidopyrimidine 4-Amino-N-(2,6-dimethyl-4-pyrimidinyl)benzenesulfonamide 4-Amino-N-(4,6-dimethyl-pyrimidin-2-yl)-benzenesulfonamide 4-amino-N-(4,6-dimethylpyrimidin-2-yl)benzenesulfonamide 6-(4'-Aminobenzol-sulfonamido)-2,4-dimethylpyrimidin N(1)-(4,6-Dimethyl-2-pyrimidinyl)sulfanilamide N(1)-(4,6-Dimethyl-2-pyrimidyl)sulfanilamide N-(4,6-Dimethyl-2-pyrimidyl)sulfanilamide SMZ Sulfadimethyldiazine Sulfadimethylpyrimidine Sulfametazina Sulfametazyny Sulfamezathine Sulphadimethylpyrimidine Sulphamethazine sulfadimidina sulfadimidine sulfadimidinum sulfamethazone CHEBI:102265 sulfamethazine Beilstein:261304 Beilstein CAS:57-68-1 ChemIDplus CAS:57-68-1 KEGG COMPOUND CAS:57-68-1 NIST Chemistry WebBook Drug_Central:2502 DrugCentral Gmelin:1009759 Gmelin PMID:11431418 Europe PMC PMID:14552772 ChEMBL PMID:15603963 ChEMBL PMID:17311370 ChEMBL PMID:17596632 Europe PMC PMID:20028131 Europe PMC PMID:22903812 Europe PMC PMID:23218311 Europe PMC PMID:23384282 Europe PMC PMID:23434485 Europe PMC PMID:23454458 Europe PMC PMID:23562141 Europe PMC PMID:23636590 Europe PMC PMID:23673752 Europe PMC PMID:23673946 Europe PMC PMID:23704574 Europe PMC PMID:6864729 ChEMBL PMID:7021831 ChEMBL PMID:7328159 Europe PMC PMID:8199304 Europe PMC PMID:9886437 Europe PMC Reaxys:261304 Reaxys 4-amino-N-(4,6-dimethylpyrimidin-2-yl)benzenesulfonamide IUPAC (p-Aminobenzolsulfonyl)-2-amino-4,6-dimethylpyrimidin ChEBI 2-(4-Aminobenzenesulfonamido)-4,6-dimethylpyrimidine NIST_Chemistry_WebBook 2-(p-Aminobenzenesulfonamido)-4,6-dimethylpyrimidine ChemIDplus 2-Sulfanilamido-4,6-dimethylpyrimidine ChemIDplus 4,6-Dimethyl-2-sulfanilamidopyrimidine ChemIDplus 4-Amino-N-(2,6-dimethyl-4-pyrimidinyl)benzenesulfonamide ChemIDplus 4-Amino-N-(4,6-dimethyl-pyrimidin-2-yl)-benzenesulfonamide ChEMBL 4-amino-N-(4,6-dimethylpyrimidin-2-yl)benzenesulfonamide ChEMBL 6-(4'-Aminobenzol-sulfonamido)-2,4-dimethylpyrimidin ChemIDplus N(1)-(4,6-Dimethyl-2-pyrimidinyl)sulfanilamide NIST_Chemistry_WebBook N(1)-(4,6-Dimethyl-2-pyrimidyl)sulfanilamide NIST_Chemistry_WebBook N-(4,6-Dimethyl-2-pyrimidyl)sulfanilamide NIST_Chemistry_WebBook SMZ ChEBI Sulfadimethyldiazine ChemIDplus Sulfadimethylpyrimidine ChemIDplus Sulfametazina ChemIDplus Sulfametazyny ChemIDplus Sulfamezathine ChemIDplus Sulphadimethylpyrimidine ChemIDplus Sulphamethazine ChemIDplus sulfadimidina ChemIDplus sulfadimidine KEGG_DRUG sulfadimidinum ChemIDplus sulfamethazone ChEBI A naphthol carrying a hydroxy group at position 1. 0 C10H8O InChI=1S/C10H8O/c11-10-7-3-5-8-4-1-2-6-9(8)10/h1-7,11H KJCVRFUGPWSIIH-UHFFFAOYSA-N 144.16992 144.05751 Oc1cccc2ccccc12 Beilstein:1817321 CAS:90-15-3 Gmelin:69192 HMDB:HMDB0012138 KEGG:C11714 MetaCyc:NAPHTHOL PDBeChem:1NP PMID:16721410 PMID:18966375 PMID:22740618 Reaxys:1817321 Wikipedia:1-Naphthol 1-Naphthol 1-naphthol naphthalen-1-ol chebi_ontology 1-hydroxynaphthalene 1-naphthalenol alpha-Naphthol alpha-hydroxynaphthalene alpha-naphthol CHEBI:10319 1-naphthol Beilstein:1817321 Beilstein CAS:90-15-3 ChemIDplus CAS:90-15-3 KEGG COMPOUND CAS:90-15-3 NIST Chemistry WebBook Gmelin:69192 Gmelin PMID:16721410 Europe PMC PMID:18966375 Europe PMC PMID:22740618 Europe PMC Reaxys:1817321 Reaxys 1-Naphthol KEGG_COMPOUND 1-naphthol UniProt naphthalen-1-ol IUPAC 1-hydroxynaphthalene HMDB 1-naphthalenol NIST_Chemistry_WebBook alpha-Naphthol KEGG_COMPOUND alpha-hydroxynaphthalene NIST_Chemistry_WebBook alpha-naphthol NIST_Chemistry_WebBook A naphthol carrying a hydroxy group at position 2. 0 C10H8O InChI=1S/C10H8O/c11-10-6-5-8-3-1-2-4-9(8)7-10/h1-7,11H JWAZRIHNYRIHIV-UHFFFAOYSA-N 144.16992 144.05751 Oc1ccc2ccccc2c1 Beilstein:742134 CAS:135-19-3 Drug_Central:3370 Gmelin:27395 HMDB:HMDB0012322 KEGG:C11713 PMID:14751800 PMID:18515997 PMID:22740618 Reaxys:742134 Wikipedia:2-Naphthol 2-Naphthol naphthalen-2-ol chebi_ontology 2-hydroxynaphthalene 2-naphthalenol beta-Naphthol beta-hydroxynaphthalene beta-naphthol CHEBI:10432 2-naphthol Beilstein:742134 Beilstein CAS:135-19-3 ChemIDplus CAS:135-19-3 KEGG COMPOUND CAS:135-19-3 NIST Chemistry WebBook Drug_Central:3370 DrugCentral Gmelin:27395 Gmelin PMID:14751800 Europe PMC PMID:18515997 Europe PMC PMID:22740618 Europe PMC Reaxys:742134 Reaxys 2-Naphthol KEGG_COMPOUND naphthalen-2-ol IUPAC 2-hydroxynaphthalene HMDB 2-naphthalenol NIST_Chemistry_WebBook beta-Naphthol KEGG_COMPOUND beta-hydroxynaphthalene NIST_Chemistry_WebBook beta-naphthol NIST_Chemistry_WebBook 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 N-arylpiperazine that is piperazine carrying a 3-chlorophenyl substituent at position 1. It is a metabolite of the antidepressant drug trazodone. 0 C10H13ClN2 InChI=1S/C10H13ClN2/c11-9-2-1-3-10(8-9)13-6-4-12-5-7-13/h1-3,8,12H,4-7H2 VHFVKMTVMIZMIK-UHFFFAOYSA-N 196.67640 196.07673 Clc1cccc(c1)N1CCNCC1 Beilstein:8409 CAS:6640-24-0 HMDB:HMDB0061008 KEGG:C11738 LINCS:LSM-25627 PMID:11311791 PMID:18621591 PMID:23768699 PMID:24062697 PMID:6827905 Reaxys:8409 Wikipedia:Meta-Chlorophenylpiperazine 1-(3-Chlorophenyl)piperazine 1-(3-chlorophenyl)piperazine chebi_ontology (m-CPP) m-Chlorophenylpiperazine CHEBI:10588 1-(3-chlorophenyl)piperazine Beilstein:8409 Beilstein CAS:6640-24-0 ChemIDplus CAS:6640-24-0 KEGG COMPOUND PMID:11311791 Europe PMC PMID:18621591 Europe PMC PMID:23768699 Europe PMC PMID:24062697 Europe PMC PMID:6827905 Europe PMC Reaxys:8409 Reaxys 1-(3-Chlorophenyl)piperazine KEGG_COMPOUND 1-(3-chlorophenyl)piperazine IUPAC (m-CPP) HMDB m-Chlorophenylpiperazine KEGG_COMPOUND A methylbenzoic acid carrying a methyl substituent at position 3. 0 C8H8O2 InChI=1S/C8H8O2/c1-6-3-2-4-7(5-6)8(9)10/h2-5H,1H3,(H,9,10) GPSDUZXPYCFOSQ-UHFFFAOYSA-N 136.14790 136.05243 Cc1cccc(c1)C(O)=O Beilstein:970526 CAS:99-04-7 KEGG:C07211 MetaCyc:CPD-8775 PMID:11339298 PMID:11470206 PMID:22251573 PMID:22451532 PMID:2489427 Reaxys:970526 Wikipedia:M-Toluic_acid 3-methylbenzoic acid m-Toluic Acid chebi_ontology 3-toluic acid beta-Bethylbenzoic acid beta-Methylbenzoic acid m-Toluylic acid meta-Toluic acid CHEBI:10589 m-toluic acid Beilstein:970526 Beilstein CAS:99-04-7 ChemIDplus CAS:99-04-7 KEGG COMPOUND PMID:11339298 Europe PMC PMID:11470206 Europe PMC PMID:22251573 Europe PMC PMID:22451532 Europe PMC PMID:2489427 Europe PMC Reaxys:970526 Reaxys 3-methylbenzoic acid IUPAC m-Toluic Acid KEGG_COMPOUND 3-toluic acid ChemIDplus beta-Bethylbenzoic acid KEGG_COMPOUND beta-Methylbenzoic acid ChemIDplus m-Toluylic acid KEGG_COMPOUND meta-Toluic acid ChemIDplus Any member of the class of naturally-occurring straight-chain fatty acids n carbon atoms long with a carboxyl group at position 1 and a hydroxyl at position n (omega). CH2O3(CH2)n KEGG:C03547 PMID:13771448 PMID:16660004 omega-Hydroxy fatty acid chebi_ontology omega-hydroxy fatty acids CHEBI:10615 omega-hydroxy fatty acid PMID:13771448 Europe PMC PMID:16660004 Europe PMC omega-Hydroxy fatty acid KEGG_COMPOUND omega-hydroxy fatty acids ChEBI 0 C6H12O6 InChI=1S/C6H12O6/c7-1-2(8)4(10)6(12)5(11)3(1)9/h1-12H/t1-,2-,3+,4+,5-,6- CDAISMWEOUEBRE-CDRYSYESSA-N 180.15588 180.06339 O[C@H]1[C@H](O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H]1O CHEBI:26614 Beilstein:2206312 CAS:488-59-5 Gmelin:561300 KEGG:C06153 PMID:24352657 Reaxys:2206312 scyllo-Inositol scyllo-inositol chebi_ontology (1r,2r,3r,4r,5r,6r)-cyclohexane-1,2,3,4,5,6-hexol 1,3,5/2,4,6-cyclohexanehexol Cocositol Quercinitol Scyllitol CHEBI:10642 scyllo-inositol Beilstein:2206312 Beilstein CAS:488-59-5 ChemIDplus CAS:488-59-5 KEGG COMPOUND CAS:488-59-5 NIST Chemistry WebBook Gmelin:561300 Gmelin PMID:24352657 Europe PMC Reaxys:2206312 Reaxys scyllo-Inositol KEGG_COMPOUND scyllo-inositol IUPAC scyllo-inositol UniProt (1r,2r,3r,4r,5r,6r)-cyclohexane-1,2,3,4,5,6-hexol IUPAC 1,3,5/2,4,6-cyclohexanehexol IUPAC Cocositol NIST_Chemistry_WebBook Quercinitol ChemIDplus Scyllitol ChemIDplus A member of the class of benzamides resulting from the formal condensation of 4-amino-5-chloro-2-methoxybenzoic acid with the primary amino group of N,N-diethylethane-1,2-diamine. 0 C14H22ClN3O2 InChI=1S/C14H22ClN3O2/c1-4-18(5-2)7-6-17-14(19)10-8-11(15)12(16)9-13(10)20-3/h8-9H,4-7,16H2,1-3H3,(H,17,19) TTWJBBZEZQICBI-UHFFFAOYSA-N 299.79600 299.14005 CCN(CC)CCNC(=O)c1cc(Cl)c(N)cc1OC CHEBI:6898 CAS:364-62-5 DrugBank:DB01233 Drug_Central:1782 HMDB:HMDB0015363 KEGG:C07868 KEGG:D00726 LINCS:LSM-3689 Patent:BE620543 Patent:US3177252 Reaxys:1884366 VSDB:1821 Wikipedia:Metoclopramide 4-amino-5-chloro-N-[2-(diethylamino)ethyl]-2-methoxybenzamide chebi_ontology 2-methoxy-4-amino-5-chloro-N,N-(dimethylaminoethyl)benzamide 2-methoxy-5-chloroprocainamide 4-amino-5-chloro-2-methoxy-N-(beta-diethylaminoethyl)benzamide 4-amino-5-chloro-N-(2-(diethylamino)ethyl)-2-methoxybenzamide 4-amino-5-chloro-N-(2-(diethylamino)ethyl)-o-anisamide Elieten Reliveran metoclopramida metoclopramide metoclopramidum CHEBI:107736 metoclopramide CAS:364-62-5 ChemIDplus CAS:364-62-5 KEGG DRUG Drug_Central:1782 DrugCentral Reaxys:1884366 Reaxys 4-amino-5-chloro-N-[2-(diethylamino)ethyl]-2-methoxybenzamide IUPAC 2-methoxy-4-amino-5-chloro-N,N-(dimethylaminoethyl)benzamide ChemIDplus 2-methoxy-5-chloroprocainamide ChemIDplus 4-amino-5-chloro-2-methoxy-N-(beta-diethylaminoethyl)benzamide ChemIDplus 4-amino-5-chloro-N-(2-(diethylamino)ethyl)-2-methoxybenzamide ChEMBL 4-amino-5-chloro-N-(2-(diethylamino)ethyl)-o-anisamide ChemIDplus Elieten DrugBank Reliveran DrugBank metoclopramida ChemIDplus metoclopramide ChemIDplus metoclopramidum ChemIDplus Benzothiazole substituted with a hydroxy group at the 2-position. 0 C7H5NOS InChI=1S/C7H5NOS/c9-7-8-5-3-1-2-4-6(5)10-7/h1-4H,(H,8,9) YEDUAINPPJYDJZ-UHFFFAOYSA-N 151.18600 151.00918 Oc1nc2ccccc2s1 Beilstein:742522 CAS:934-34-9 PMID:15750776 PMID:18568896 PMID:23224221 PMID:9544213 Reaxys:742522 1,3-benzothiazol-2-ol chebi_ontology (2-mercatophenyl)carbamothioic acid gamma-lactone 2(3H)-Benzothiazolone 2-Benzothiazolol 2-Benzothiazolone 2-hydroxy-1,3-benzothiazole 3H-Benzothiazol-2-one HBT HOBT CHEBI:115196 2-hydroxybenzothiazole Beilstein:742522 Beilstein CAS:934-34-9 ChemIDplus CAS:934-34-9 NIST Chemistry WebBook PMID:15750776 Europe PMC PMID:18568896 Europe PMC PMID:23224221 Europe PMC PMID:9544213 ChEMBL Reaxys:742522 Reaxys 1,3-benzothiazol-2-ol IUPAC (2-mercatophenyl)carbamothioic acid gamma-lactone NIST_Chemistry_WebBook 2(3H)-Benzothiazolone ChemIDplus 2-Benzothiazolol ChemIDplus 2-Benzothiazolone ChemIDplus 2-hydroxy-1,3-benzothiazole ChEBI 3H-Benzothiazol-2-one ChEMBL HBT ChEBI HOBT ChEBI A member of the class of phenylureas that is urea in which both of the hydrogens attached to one nitrogen are substituted by methyl groups, and one of the hydrogens attached to the other nitrogen is substituted by a 3,4-dichlorophenyl group. 0 C9H10Cl2N2O InChI=1S/C9H10Cl2N2O/c1-13(2)9(14)12-6-3-4-7(10)8(11)5-6/h3-5H,1-2H3,(H,12,14) XMTQQYYKAHVGBJ-UHFFFAOYSA-N 233.09500 232.01702 CN(C)C(=O)Nc1ccc(Cl)c(Cl)c1 CAS:330-54-1 KEGG:C18428 LINCS:LSM-25609 PMID:10866370 PMID:17142046 PMID:17449247 PMID:23081760 PPDB:260 Patent:CN103120180 Patent:CN103125511 Patent:US2768971 Pesticides:diuron Reaxys:2215168 Wikipedia:Diuron 3-(3,4-dichlorophenyl)-1,1-dimethylurea chebi_ontology 1,1-dimethyl-3-(3,4-dichlorophenyl)urea 1-(3,4-dichlorophenyl)-3,3-dimethylurea 1-(3,4-dichlorophenyl)-3,3-dimethyluree 3-(3,4-Dichlor-phenyl)-1,1-dimethyl-harnstoff 3-(3,4-Dichloro-phenyl)-1,1-dimethyl-urea DCMU N'-(3,4-dichlorophenyl)-N,N-dimethylurea N,N,-dimethyl-N'-(3,4-dichlorophenyl)urea N-(3,4-dichlorophenyl)-N',N'-dimethylurea CHEBI:116509 diuron CAS:330-54-1 ChemIDplus CAS:330-54-1 KEGG COMPOUND CAS:330-54-1 NIST Chemistry WebBook PMID:10866370 ChEMBL PMID:17142046 ChEMBL PMID:17449247 ChEMBL PMID:23081760 Europe PMC Pesticides:diuron Alan Wood's Pesticides Reaxys:2215168 Reaxys 3-(3,4-dichlorophenyl)-1,1-dimethylurea IUPAC 1,1-dimethyl-3-(3,4-dichlorophenyl)urea ChemIDplus 1-(3,4-dichlorophenyl)-3,3-dimethylurea ChemIDplus 1-(3,4-dichlorophenyl)-3,3-dimethyluree ChemIDplus 3-(3,4-Dichlor-phenyl)-1,1-dimethyl-harnstoff ChemIDplus 3-(3,4-Dichloro-phenyl)-1,1-dimethyl-urea ChEMBL DCMU ChEBI N'-(3,4-dichlorophenyl)-N,N-dimethylurea ChemIDplus N,N,-dimethyl-N'-(3,4-dichlorophenyl)urea ChemIDplus N-(3,4-dichlorophenyl)-N',N'-dimethylurea ChemIDplus A monocarboxylic acid amide resulting from the formal condensation of the aryl amino group of N-phenyl-1-(2-phenylethyl)piperidin-4-amine with propanoic acid. 0 C22H28N2O InChI=1S/C22H28N2O/c1-2-22(25)24(20-11-7-4-8-12-20)21-14-17-23(18-15-21)16-13-19-9-5-3-6-10-19/h3-12,21H,2,13-18H2,1H3 PJMPHNIQZUBGLI-UHFFFAOYSA-N 336.47050 336.22016 CCC(=O)N(C1CCN(CC1)CCc1ccccc1)c1ccccc1 CHEBI:310077 CHEBI:5012 CAS:437-38-7 DrugBank:DB00813 Drug_Central:1164 KEGG:D00320 PMID:10669565 PMID:10987438 PMID:11585443 PMID:14698188 PMID:16621415 PMID:18462178 PMID:18728103 PMID:30176422 PMID:30305277 Patent:FR1344366 Patent:US3164600 Reaxys:494484 VSDB:1864 Wikipedia:Fentanyl N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide chebi_ontology 1-phenethyl-4-(N-phenylpropionamido)piperidine 1-phenethyl-4-N-propionylanilinopiperidine Duragesic N-(1-phenethyl-4-piperidinyl)-N-phenylpropionamide N-(1-phenethyl-4-piperidyl)propionanilide N-(1-phenethyl-piperidin-4-yl)-N-phenyl-propionamide N-(1-phenethylpiperidin-4-yl)-N-phenylpropionamide N-phenethyl-4-(N-propionylanilino)piperidine N-phenyl-N-(1-(2-phenylethyl)-4-piperidinyl)propanamide fentanilo fentanyl fentanylum phentanyl CHEBI:119915 fentanyl CAS:437-38-7 ChemIDplus CAS:437-38-7 KEGG DRUG Drug_Central:1164 DrugCentral PMID:10669565 ChEMBL PMID:10987438 ChEMBL PMID:11585443 ChEMBL PMID:14698188 ChEMBL PMID:16621415 Europe PMC PMID:18462178 Europe PMC PMID:18728103 Europe PMC PMID:30176422 Europe PMC PMID:30305277 Europe PMC Reaxys:494484 Reaxys N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide IUPAC 1-phenethyl-4-(N-phenylpropionamido)piperidine ChemIDplus 1-phenethyl-4-N-propionylanilinopiperidine ChemIDplus Duragesic ChemIDplus N-(1-phenethyl-4-piperidinyl)-N-phenylpropionamide ChemIDplus N-(1-phenethyl-4-piperidyl)propionanilide ChemIDplus N-(1-phenethyl-piperidin-4-yl)-N-phenyl-propionamide ChEMBL N-(1-phenethylpiperidin-4-yl)-N-phenylpropionamide ChEMBL N-phenethyl-4-(N-propionylanilino)piperidine ChemIDplus N-phenyl-N-(1-(2-phenylethyl)-4-piperidinyl)propanamide ChemIDplus fentanilo WHO_MedNet fentanyl WHO_MedNet fentanylum WHO_MedNet phentanyl DrugBank A secondary amino compound having methyl and 3-(2-methylphenoxy)-3-phenylpropan-1-yl substituents. 0 C17H21NO InChI=1S/C17H21NO/c1-14-8-6-7-11-16(14)19-17(12-13-18-2)15-9-4-3-5-10-15/h3-11,17-18H,12-13H2,1-2H3/t17-/m1/s1 VHGCDTVCOLNTBX-QGZVFWFLSA-N 255.35470 255.16231 CNCC[C@@H](Oc1ccccc1C)c1ccccc1 Beilstein:4318684 CAS:83015-26-3 DrugBank:DB00289 Drug_Central:256 HMDB:HMDB0014434 KEGG:D07473 LINCS:LSM-2452 PMID:15338851 PMID:23048018 Reaxys:4318684 Wikipedia:Atomoxetine (3R)-N-methyl-3-(2-methylphenoxy)-3-phenylpropan-1-amine chebi_ontology (-)-Tomoxetine Tomoxetina Tomoxetinum atomoxetine tomoxetine CHEBI:127342 atomoxetine Beilstein:4318684 Beilstein CAS:83015-26-3 ChemIDplus CAS:83015-26-3 KEGG DRUG Drug_Central:256 DrugCentral PMID:15338851 Europe PMC PMID:23048018 Europe PMC Reaxys:4318684 Reaxys (3R)-N-methyl-3-(2-methylphenoxy)-3-phenylpropan-1-amine IUPAC (-)-Tomoxetine ChEBI Tomoxetina DrugBank Tomoxetinum DrugBank atomoxetine KEGG_DRUG tomoxetine DrugBank 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 A disaccharide formed by a (1<->1)-glycosidic bond between two hexopyranose units. hexopyranosyl hexopyranoside chebi_ontology CHEBI:131401 hexopyranosyl hexopyranoside hexopyranosyl hexopyranoside IUPAC Any steroid substituted by a formyl group. chebi_ontology steroid aldehydes CHEBI:131565 steroid aldehyde steroid aldehydes ChEBI Any bacterial metabolite produced during a metabolic reaction in Mycoplasma genitalium. chebi_ontology Mycoplasma genitalium metabolites CHEBI:131604 Mycoplasma genitalium metabolite Mycoplasma genitalium metabolites ChEBI A steroid compound with a structure based on a 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 DNA polymerase inhibitor that interferes with the action of a DNA-directed DNA polymerase (EC 2.7.7.7). Wikipedia:DNA_polymerase chebi_ontology DNA duplicase inhibitor DNA duplicase inhibitors DNA nucleotidyltransferase (DNA-directed) inhibitor DNA nucleotidyltransferase (DNA-directed) inhibitors DNA nucleotidyltransferase inhibitor DNA nucleotidyltransferase inhibitors DNA polymerase I inhibitor DNA polymerase I inhibitors DNA polymerase II inhibitor DNA polymerase II inhibitors DNA polymerase III inhibitor DNA polymerase III inhibitors DNA polymerase alpha inhibitor DNA polymerase alpha inhibitors DNA polymerase beta inhibitor DNA polymerase beta inhibitors DNA polymerase gamma inhibitor DNA polymerase gamma inhibitors DNA polymerase inhibitor DNA polymerase inhibitors DNA replicase inhibitor DNA replicase inhibitors DNA-dependent DNA polymerase inhibitor DNA-dependent DNA polymerase inhibitors DNA-directed DNA polymerase (EC 2.7.7.7) inhibitor DNA-directed DNA polymerase (EC 2.7.7.7) inhibitors EC 2.7.7.7 (DNA-directed DNA polymerase) inhibitors EC 2.7.7.7 inhibitor EC 2.7.7.7 inhibitors Klenow fragment inhibitor Klenow fragment inhibitors Taq DNA polymerase inhibitor Taq DNA polymerase inhibitors Taq Pol I inhibitor Taq Pol I inhibitors Tca DNA polymerase inhibitor Tca DNA polymerase inhibitors deoxynucleate polymerase inhibitor deoxynucleate polymerase inhibitors deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (DNA-directed) inhibitor deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (DNA-directed) inhibitors deoxyribonucleate nucleotidyltransferase inhibitor deoxyribonucleate nucleotidyltransferase inhibitors deoxyribonucleic acid duplicase inhibitor deoxyribonucleic acid duplicase inhibitors deoxyribonucleic acid polymerase inhibitor deoxyribonucleic acid polymerase inhibitors deoxyribonucleic duplicase inhibitor deoxyribonucleic duplicase inhibitors deoxyribonucleic polymerase I inhibitor deoxyribonucleic polymerase I inhibitors deoxyribonucleic polymerase inhibitor deoxyribonucleic polymerase inhibitors duplicase inhibitor duplicase inhibitors sequenase inhibitor sequenase inhibitors CHEBI:131699 EC 2.7.7.7 (DNA-directed DNA polymerase) inhibitor DNA duplicase inhibitor ChEBI DNA duplicase inhibitors ChEBI DNA nucleotidyltransferase (DNA-directed) inhibitor ChEBI DNA nucleotidyltransferase (DNA-directed) inhibitors ChEBI DNA nucleotidyltransferase inhibitor ChEBI DNA nucleotidyltransferase inhibitors ChEBI DNA polymerase I inhibitor ChEBI DNA polymerase I inhibitors ChEBI DNA polymerase II inhibitor ChEBI DNA polymerase II inhibitors ChEBI DNA polymerase III inhibitor ChEBI DNA polymerase III inhibitors ChEBI DNA polymerase alpha inhibitor ChEBI DNA polymerase alpha inhibitors ChEBI DNA polymerase beta inhibitor ChEBI DNA polymerase beta inhibitors ChEBI DNA polymerase gamma inhibitor ChEBI DNA polymerase gamma inhibitors ChEBI DNA polymerase inhibitor ChEBI DNA polymerase inhibitors ChEBI DNA replicase inhibitor ChEBI DNA replicase inhibitors ChEBI DNA-dependent DNA polymerase inhibitor ChEBI DNA-dependent DNA polymerase inhibitors ChEBI DNA-directed DNA polymerase (EC 2.7.7.7) inhibitor ChEBI DNA-directed DNA polymerase (EC 2.7.7.7) inhibitors ChEBI EC 2.7.7.7 (DNA-directed DNA polymerase) inhibitors ChEBI EC 2.7.7.7 inhibitor ChEBI EC 2.7.7.7 inhibitors ChEBI Klenow fragment inhibitor ChEBI Klenow fragment inhibitors ChEBI Taq DNA polymerase inhibitor ChEBI Taq DNA polymerase inhibitors ChEBI Taq Pol I inhibitor ChEBI Taq Pol I inhibitors ChEBI Tca DNA polymerase inhibitor ChEBI Tca DNA polymerase inhibitors ChEBI deoxynucleate polymerase inhibitor ChEBI deoxynucleate polymerase inhibitors ChEBI deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (DNA-directed) inhibitor ChEBI deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (DNA-directed) inhibitors ChEBI deoxyribonucleate nucleotidyltransferase inhibitor ChEBI deoxyribonucleate nucleotidyltransferase inhibitors ChEBI deoxyribonucleic acid duplicase inhibitor ChEBI deoxyribonucleic acid duplicase inhibitors ChEBI deoxyribonucleic acid polymerase inhibitor ChEBI deoxyribonucleic acid polymerase inhibitors ChEBI deoxyribonucleic duplicase inhibitor ChEBI deoxyribonucleic duplicase inhibitors ChEBI deoxyribonucleic polymerase I inhibitor ChEBI deoxyribonucleic polymerase I inhibitors ChEBI deoxyribonucleic polymerase inhibitor ChEBI deoxyribonucleic polymerase inhibitors ChEBI duplicase inhibitor ChEBI duplicase inhibitors ChEBI sequenase inhibitor ChEBI sequenase inhibitors ChEBI A EC 3.6.3.* (acid anhydride hydrolase catalysing transmembrane movement of substances) inhibitor that interferes with the action of channel-conductance-controlling ATPase (EC 3.6.3.49, also known as cystic fibrosis conductance regulator, CFCR). CHEBI:131771 Wikipedia:Cystic_fibrosis_transmembrane_conductance_regulator chebi_ontology ATP phosphohydrolase (channel-conductance-controlling) inhibitor ATP phosphohydrolase (channel-conductance-controlling) inhibitors CFTR inhibitor CFTR inhibitors EC 3.6.3.49 (channel-conductance-controlling ATPase) inhibitors EC 3.6.3.49 inhibitor EC 3.6.3.49 inhibitors channel-conductance-controlling ATPase (EC 3.6.3.49) inhibitor channel-conductance-controlling ATPase (EC 3.6.3.49) inhibitors channel-conductance-controlling ATPase inhibitor channel-conductance-controlling ATPase inhibitors cystic fibrosis conductance regulator inhibitor cystic fibrosis conductance regulator inhibitors cystic fibrosis transmembrane conductance regulator inhibitor cystic fibrosis transmembrane conductance regulator inhibitors cystic-fibrosis membrane-conductance-regulating protein inhibitor cystic-fibrosis membrane-conductance-regulating protein inhibitors CHEBI:131770 EC 3.6.3.49 (channel-conductance-controlling ATPase) inhibitor ATP phosphohydrolase (channel-conductance-controlling) inhibitor ChEBI ATP phosphohydrolase (channel-conductance-controlling) inhibitors ChEBI CFTR inhibitor ChEBI CFTR inhibitors ChEBI EC 3.6.3.49 (channel-conductance-controlling ATPase) inhibitors ChEBI EC 3.6.3.49 inhibitor ChEBI EC 3.6.3.49 inhibitors ChEBI channel-conductance-controlling ATPase (EC 3.6.3.49) inhibitor ChEBI channel-conductance-controlling ATPase (EC 3.6.3.49) inhibitors ChEBI channel-conductance-controlling ATPase inhibitor ChEBI channel-conductance-controlling ATPase inhibitors ChEBI cystic fibrosis conductance regulator inhibitor ChEBI cystic fibrosis conductance regulator inhibitors ChEBI cystic fibrosis transmembrane conductance regulator inhibitor ChEBI cystic fibrosis transmembrane conductance regulator inhibitors ChEBI cystic-fibrosis membrane-conductance-regulating protein inhibitor ChEBI cystic-fibrosis membrane-conductance-regulating protein inhibitors ChEBI An organosulfonate oxoanion obtained by deprotonation of the N-sulfo group of any sulfamic acid; major species at pH 7.3. -1 HNO3SR 95.079 94.96771 S([O-])(=O)(=O)N* chebi_ontology a sulfamate CHEBI:131822 sulfamate a sulfamate UniProt Any polyunsaturated fatty acid anion carrying one or more hydroxy substituents. -1 CHO3R 61.017 60.99257 O*C([O-])=O chebi_ontology a hydroxy polyunsaturated fatty acid hydroxy PUFA hydroxy polyunsaturated fatty acid anions CHEBI:131871 hydroxy polyunsaturated fatty acid anion a hydroxy polyunsaturated fatty acid UniProt hydroxy PUFA SUBMITTER hydroxy polyunsaturated fatty acid anions ChEBI A monocarboxylic acid anion resulting from the deprotonation of the carboxy group of (R)-imazamox. -1 C15H18N3O4 InChI=1S/C15H19N3O4/c1-8(2)15(3)14(21)17-12(18-15)11-10(13(19)20)5-9(6-16-11)7-22-4/h5-6,8H,7H2,1-4H3,(H,19,20)(H,17,18,21)/p-1/t15-/m1/s1 NUPJIGQFXCQJBK-OAHLLOKOSA-M 304.322 304.13028 C1(=NC=C(C=C1C(=O)[O-])COC)C2=NC([C@@](N2)(C)C(C)C)=O 2-[(4R)-4-isopropyl-4-methyl-5-oxo-4,5-dihydro-1H-imidazol-2-yl]-5-(methoxymethyl)nicotinate chebi_ontology 2-[(4R)-4-isopropyl-4-methyl-5-oxo-2-imidazolin-2-yl]-5-methoxymethylnicotinate 5-(methoxymethyl)-2-[(4R)-4-methyl-5-oxo-4-(propan-2-yl)-4,5-dihydro-1H-imidazol-2-yl]pyridine-3-carboxylate CHEBI:131899 (R)-imazamox(1-) 2-[(4R)-4-isopropyl-4-methyl-5-oxo-4,5-dihydro-1H-imidazol-2-yl]-5-(methoxymethyl)nicotinate IUPAC 2-[(4R)-4-isopropyl-4-methyl-5-oxo-2-imidazolin-2-yl]-5-methoxymethylnicotinate ChEBI 5-(methoxymethyl)-2-[(4R)-4-methyl-5-oxo-4-(propan-2-yl)-4,5-dihydro-1H-imidazol-2-yl]pyridine-3-carboxylate 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 An N-sulfonylurea in which the sulfur atom is attached to a 2-carboxythiophen-3-yl group and in which the non-sulfonated nitrogen is substituted by a 4-methoxy-6-methyl-1,3,5-triazin-2-yl group. The corresponding methyl ester, known as thifensulfuron-methyl, is used as a post-emergence herbicide for the control of grass and broad-leaved weeds. 0 C11H11N5O6S2 InChI=1S/C11H11N5O6S2/c1-5-12-9(15-11(13-5)22-2)14-10(19)16-24(20,21)6-3-4-23-7(6)8(17)18/h3-4H,1-2H3,(H,17,18)(H2,12,13,14,15,16,19) LOQQVLXUKHKNIA-UHFFFAOYSA-N 373.368 373.01508 S1C=CC(=C1C(O)=O)S(NC(=O)NC=2N=C(N=C(N2)OC)C)(=O)=O AGR:IND21975725 AGR:IND21983041 AGR:IND21984069 AGR:IND23256565 AGR:IND44616493 AGR:IND88022327 AGR:IND89001613 AGR:IND91008589 CAS:79277-67-1 PPDB:972 Pesticides:thifensulfuron 3-{[(4-methoxy-6-methyl-1,3,5-triazin-2-yl)carbamoyl]sulfamoyl}thiophene-2-carboxylic acid chebi_ontology 3-(4-methoxy-6-methyl-1,3,5-triazin-2-ylcarbamoylsulfamoyl)thiophene-2-carboxylic acid thiameturon thifensulfuron acid CHEBI:132053 thifensulfuron AGR:IND21975725 Europe PMC AGR:IND21983041 Europe PMC AGR:IND21984069 Europe PMC AGR:IND23256565 Europe PMC AGR:IND44616493 Europe PMC AGR:IND88022327 Europe PMC AGR:IND89001613 Europe PMC AGR:IND91008589 Europe PMC CAS:79277-67-1 Alan Wood's Pesticides CAS:79277-67-1 ChemIDplus Pesticides:thifensulfuron Alan Wood's Pesticides 3-{[(4-methoxy-6-methyl-1,3,5-triazin-2-yl)carbamoyl]sulfamoyl}thiophene-2-carboxylic acid IUPAC 3-(4-methoxy-6-methyl-1,3,5-triazin-2-ylcarbamoylsulfamoyl)thiophene-2-carboxylic acid Alan_Wood's_Pesticides thiameturon Alan_Wood's_Pesticides thifensulfuron acid ChEBI Any member of the class of benzoquinones that is 1,4-benzoquinone or its C-substituted derivatives. 0 C6O2R4 104.063 103.98983 O=C1C(*)=C(*)C(=O)C(*)=C1* chebi_ontology a quinone p-benzoquinones para-benzoquinones CHEBI:132124 1,4-benzoquinones a quinone UniProt p-benzoquinones ChEBI para-benzoquinones ChEBI Any quinone in which one or more of the carbons making up the quinone moiety is substituted by a hydroxy group. chebi_ontology hydroxyquinones CHEBI:132130 hydroxyquinone hydroxyquinones 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 Any naphthoquinone in which the naphthaoquinone moiety is substituted by at least one hydroxy group. Wikipedia:Hydroxynaphthoquinone chebi_ontology hydroxynaphthoquinones CHEBI:132155 hydroxynaphthoquinone hydroxynaphthoquinones ChEBI Any member of the class of 1,4-naphthoquinones in which the naphthoquinone moiety is substituted by at least one hydroxy group. chebi_ontology hydroxy-1,4-naphthoquinones CHEBI:132157 hydroxy-1,4-naphthoquinone hydroxy-1,4-naphthoquinones ChEBI A secondary aliphatic ammonium ion resulting from the protonation of the amino group of diethylamine. +1 C4H12N InChI=1S/C4H11N/c1-3-5-4-2/h5H,3-4H2,1-2H3/p+1 HPNMFZURTQLUMO-UHFFFAOYSA-O 74.145 74.09643 CC[NH2+]CC N-ethylethanaminium chebi_ontology CHEBI:132181 diethylammonium N-ethylethanaminium IUPAC A primary amine that is isopropylamine in which a hydrogen attached to one of the methyl grops has been replaced by a phenyl group. 0 C9H13N InChI=1S/C9H13N/c1-8(10)7-9-5-3-2-4-6-9/h2-6,8H,7,10H2,1H3 KWTSXDURSIMDCE-UHFFFAOYSA-N 135.207 135.10480 C=1(C=CC=CC1)CC(C)N 1-phenylpropan-2-amine chebi_ontology CHEBI:132233 1-phenylpropan-2-amine 1-phenylpropan-2-amine IUPAC An organic cation obtained by protonation of the secondary amino function of phenylephrine. +1 C9H14NO2 InChI=1S/C9H13NO2/c1-10-6-9(12)7-3-2-4-8(11)5-7/h2-5,9-12H,6H2,1H3/p+1/t9-/m0/s1 SONNWYBIRXJNDC-VIFPVBQESA-O 168.213 168.10191 C=1C(=CC=CC1[C@H](C[NH2+]C)O)O (2R)-2-hydroxy-2-(3-hydroxyphenyl)-N-methylethan-1-aminium chebi_ontology phenylephrine cation CHEBI:132294 phenylephrine(1+) (2R)-2-hydroxy-2-(3-hydroxyphenyl)-N-methylethan-1-aminium IUPAC phenylephrine cation ChEBI An organic cation obtained by protonation of the secondary amino function of methamphetamine. +1 C10H16N InChI=1S/C10H15N/c1-9(11-2)8-10-6-4-3-5-7-10/h3-7,9,11H,8H2,1-2H3/p+1/t9-/m0/s1 MYWUZJCMWCOHBA-VIFPVBQESA-O 150.241 150.12773 C=1(C[C@@H]([NH2+]C)C)C=CC=CC1 (2S)-N-methyl-1-phenylpropan-2-aminium chebi_ontology methamphetamine cation CHEBI:132297 methamphetamine(1+) (2S)-N-methyl-1-phenylpropan-2-aminium IUPAC methamphetamine cation ChEBI A perfluoroalkanesulfonic acid that is butane-1-sulfonic acid in which all of the hydrogens of the butyl group have been replaced by fluorines. 0 C4HF9O3S InChI=1S/C4HF9O3S/c5-1(6,3(9,10)11)2(7,8)4(12,13)17(14,15)16/h(H,14,15,16) JGTNAGYHADQMCM-UHFFFAOYSA-N 300.101 299.95027 C(C(C(S(O)(=O)=O)(F)F)(F)F)(C(F)(F)F)(F)F CAS:375-73-5 PMID:16433328 PMID:17917760 PMID:19059455 PMID:19429410 PMID:20451658 PMID:23441933 PMID:24238775 PMID:25268321 PMID:26360456 PMID:26610298 PMID:26780052 PMID:26889942 Patent:WO2011093371 Reaxys:1813588 Wikipedia:Perfluorobutanesulfonic_acid nonafluorobutane-1-sulfonic acid chebi_ontology 1,1,2,2,3,3,4,4,4-nonafluoro-1-butanesulfonic acid 1-perfluorobutanesulfonic acid FC-98 PFBS nonafluoro-1-butanesulfonic acid nonafluorobutanesulfonic acid perfluorobutane-1-sulfonic acid CHEBI:132446 perfluorobutanesulfonic acid CAS:375-73-5 ChemIDplus PMID:16433328 Europe PMC PMID:17917760 Europe PMC PMID:19059455 Europe PMC PMID:19429410 Europe PMC PMID:20451658 Europe PMC PMID:23441933 Europe PMC PMID:24238775 Europe PMC PMID:25268321 Europe PMC PMID:26360456 Europe PMC PMID:26610298 Europe PMC PMID:26780052 Europe PMC PMID:26889942 Europe PMC Reaxys:1813588 Reaxys nonafluorobutane-1-sulfonic acid IUPAC 1,1,2,2,3,3,4,4,4-nonafluoro-1-butanesulfonic acid ChemIDplus 1-perfluorobutanesulfonic acid ChemIDplus FC-98 ChEBI PFBS ChEBI nonafluoro-1-butanesulfonic acid ChemIDplus nonafluorobutanesulfonic acid ChemIDplus perfluorobutane-1-sulfonic acid ChEBI An organosulfonic acid in which the sulfo group is directly attached to a perfluoroalkyl group. chebi_ontology perfluoroalkanesulfonic acids perfluoroalkylsulfonic acid perfluoroalkylsulfonic acids CHEBI:132447 perfluoroalkanesulfonic acid perfluoroalkanesulfonic acids ChEBI perfluoroalkylsulfonic acid ChEBI perfluoroalkylsulfonic acids ChEBI A perfluoroalkanesulfonic acid that is hexane-1-sulfonic acid in which all thirteen of the hydrogens that are attached to carbons have been replaced by fluorines. 0 C6HF13O3S InChI=1S/C6HF13O3S/c7-1(8,3(11,12)5(15,16)17)2(9,10)4(13,14)6(18,19)23(20,21)22/h(H,20,21,22) QZHDEAJFRJCDMF-UHFFFAOYSA-N 400.116 399.94388 C(C(C(S(O)(=O)=O)(F)F)(F)F)(C(C(C(F)(F)F)(F)F)(F)F)(F)F CAS:355-46-4 PMID:20471065 PMID:21346631 Reaxys:1813793 tridecafluorohexane-1-sulfonic acid chebi_ontology 1,1,2,2,3,3,4,4,5,5,6,6,6-tridecafluorohexane-1-sulfonic acid perfluorohexane sulfonic acid perfluorohexane-1-sulfonic acid CHEBI:132448 perfluorohexanesulfonic acid CAS:355-46-4 ChemIDplus PMID:20471065 Europe PMC PMID:21346631 Europe PMC Reaxys:1813793 Reaxys tridecafluorohexane-1-sulfonic acid IUPAC 1,1,2,2,3,3,4,4,5,5,6,6,6-tridecafluorohexane-1-sulfonic acid ChemIDplus perfluorohexane sulfonic acid ChemIDplus perfluorohexane-1-sulfonic acid ChemIDplus Any aromatic amide obtained by acylation of aniline. 0 C7H6NOR 120.12860 120.04494 [*]C(=O)Nc1ccccc1 KEGG:C01402 PMID:23535982 PMID:23968552 PMID:24273122 PMID:6205897 chebi_ontology N-phenyl amide N-phenyl amides an anilide CHEBI:13248 anilide PMID:23535982 Europe PMC PMID:23968552 Europe PMC PMID:24273122 Europe PMC PMID:6205897 Europe PMC N-phenyl amide ChEBI N-phenyl amides ChEBI an anilide UniProt Any polyunsaturated fatty acid containing 20 carbons and 4 double bonds. 0 C20H32O2 304.46690 304.24023 C(=O)(O)* chebi_ontology FA 20:4 free fatty acid 20:4 CHEBI:132539 fatty acid 20:4 FA 20:4 ChEBI free fatty acid 20:4 ChEBI A reagent that lightens or whitens a substrate through chemical reaction. Bleaching reactions usually involve oxidative or reductive processes that degrade colour systems. Bleaching can occur by destroying one or more of the double bonds in the conjugated chain, by cleaving the conjugated chain, or by oxidation of one of the other moieties in the conjugated chain. Their reactivity results in many bleaches having strong bactericidal, disinfecting, and sterilising properties. Wikipedia:Bleach chebi_ontology CHEBI:132717 bleaching agent A member of the class of lysophosphatidic acids obtained by hydrolytic removal of one of the two acyl groups of any phosphatidic acid. A 'closed' class. 0 C3H7O6PR2 170.058 169.99802 [C@](CO*)(O*)([H])COP(O)(=O)O chebi_ontology lysophosphatidic acids CHEBI:132742 lysophosphatidic acid lysophosphatidic acids ChEBI A sulfonamide consisting of pyridine with a 4-aminobenzenesulfonamido group at the 2-position. 0 C11H11N3O2S InChI=1S/C11H11N3O2S/c12-9-4-6-10(7-5-9)17(15,16)14-11-3-1-2-8-13-11/h1-8H,12H2,(H,13,14) GECHUMIMRBOMGK-UHFFFAOYSA-N 249.28900 249.05720 Nc1ccc(cc1)S(=O)(=O)Nc1ccccn1 Beilstein:222065 CAS:144-83-2 DrugBank:DB00891 Drug_Central:2524 Gmelin:219135 HMDB:HMDB0015028 KEGG:D02434 LINCS:LSM-5531 PMID:11431418 PMID:17964793 PMID:6136612 PMID:6993682 PMID:7021831 Patent:GB512145 Patent:US2275354 Reaxys:222065 VSDB:1922 Wikipedia:Sulfapyridine 4-amino-N-(pyridin-2-yl)benzenesulfonamide chebi_ontology 2-(p-Aminobenzenesulphonamido)pyridine 2-Sulfanilamidopyridin 2-Sulfanilamidopyridine 2-Sulfanilylaminopyridine 2-Sulfapyridine 4-(2-Pyridinylsulfonyl)aniline 4-Amino-N,2-pyridinylbenzenesulfonamide 4-Amino-N-pyridin-2-yl-benzenesulfonamide 4-[(2-Pyridylamino)sulfonyl]aniline N(1)-2-Pyridylsulfanilamide N(1)-Pyridylsulfanilamide N-2-Pyridylsulfanilamide Solfapiridina Sulphapyridine sulfapiridina sulfapyridine sulfapyridinum CHEBI:132842 sulfapyridine Beilstein:222065 Beilstein CAS:144-83-2 ChemIDplus CAS:144-83-2 DrugBank CAS:144-83-2 KEGG DRUG Drug_Central:2524 DrugCentral Gmelin:219135 Gmelin PMID:11431418 Europe PMC PMID:17964793 ChEMBL PMID:6136612 ChEMBL PMID:6993682 ChEMBL PMID:7021831 ChEMBL Reaxys:222065 Reaxys 4-amino-N-(pyridin-2-yl)benzenesulfonamide IUPAC 2-(p-Aminobenzenesulphonamido)pyridine ChemIDplus 2-Sulfanilamidopyridin ChemIDplus 2-Sulfanilamidopyridine DrugBank 2-Sulfanilylaminopyridine DrugBank 2-Sulfapyridine DrugBank 4-(2-Pyridinylsulfonyl)aniline DrugBank 4-Amino-N,2-pyridinylbenzenesulfonamide NIST_Chemistry_WebBook 4-Amino-N-pyridin-2-yl-benzenesulfonamide ChEMBL 4-[(2-Pyridylamino)sulfonyl]aniline DrugBank N(1)-2-Pyridylsulfanilamide DrugBank N(1)-Pyridylsulfanilamide DrugBank N-2-Pyridylsulfanilamide DrugBank Solfapiridina ChemIDplus Sulphapyridine DrugBank sulfapiridina ChemIDplus sulfapyridine KEGG_DRUG sulfapyridinum ChemIDplus A monocarboxylic acid anion that is the conjugate base of ibuprofen, obtained by deprotonation of the carboxy group; major species at pH 7.3. -1 C13H17O2 InChI=1S/C13H18O2/c1-9(2)8-11-4-6-12(7-5-11)10(3)13(14)15/h4-7,9-10H,8H2,1-3H3,(H,14,15)/p-1 HEFNNWSXXWATRW-UHFFFAOYSA-M 205.273 205.12340 C=1C=C(C=CC1C(C(=O)[O-])C)CC(C)C Reaxys:4784081 2-[4-(2-methylpropyl)phenyl]propanoate chebi_ontology ibuprofen ibuprofen anion CHEBI:132922 ibuprofen(1-) Reaxys:4784081 Reaxys 2-[4-(2-methylpropyl)phenyl]propanoate IUPAC ibuprofen ChEBI ibuprofen anion ChEBI An organic sodium salt that is the disodium salt of GMP. 0 C10H12N5Na2O8P InChI=1S/C10H14N5O8P.2Na/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(23-9)1-22-24(19,20)21;;/h2-3,5-6,9,16-17H,1H2,(H2,19,20,21)(H3,11,13,14,18);;/q;2*+1/p-2/t3-,5-,6-,9-;;/m1../s1 PVBRXXAAPNGWGE-LGVAUZIVSA-L 407.185 407.02189 C1(=O)NC(=NC2=C1N=CN2[C@@H]3O[C@H](COP(=O)([O-])[O-])[C@@H](O)[C@H]3O)N.[Na+].[Na+] CAS:5550-12-9 PMID:1851447 PMID:22391056 PMID:4601956 Wikipedia:Disodium_guanylate disodium 5'-O-phosphonatoguanosine chebi_ontology 5'-gmp disodium salt 5-guanylic acid disodium salt E627 GMP disodium salt disodium 5'-GMP disodium GMP disodium guanosine 5'-monophosphate disodium guanosine-5'-monophosphate disodium guanylate guanosine 5'-monophosphate disodium salt guanosine 5'-phosphate disodium salt sodium guanylate CHEBI:132932 disodium 5'-guanylate GMP disodium salt ChemIDplus disodium 5'-GMP ChemIDplus disodium GMP ChemIDplus disodium guanosine 5'-monophosphate ChemIDplus disodium guanosine-5'-monophosphate ChemIDplus disodium guanylate ChemIDplus guanosine 5'-monophosphate disodium salt ChemIDplus guanosine 5'-phosphate disodium salt ChemIDplus sodium guanylate ChemIDplus CAS:5550-12-9 ChemIDplus PMID:1851447 Europe PMC PMID:22391056 Europe PMC PMID:4601956 Europe PMC disodium 5'-O-phosphonatoguanosine IUPAC 5'-gmp disodium salt ChemIDplus 5-guanylic acid disodium salt ChemIDplus E627 ChEBI chebi_ontology CHEBI:132943 aspartate An octadecenoate in which the double bond is at C-9. -1 C18H33O2 InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1 ZQPPMHVWECSIRJ-UHFFFAOYSA-M 281.454 281.24860 C(=CCCCCCCCC)CCCCCCCC(=O)[O-] octadec-9-enoate chebi_ontology 9-octadecenoate C18:1, n-9(1-) Delta(9)-octadecenoate CHEBI:132944 octadec-9-enoate octadec-9-enoate IUPAC 9-octadecenoate ChEBI C18:1, n-9(1-) ChEBI Delta(9)-octadecenoate ChEBI A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of maleic acid. chebi_ontology maleate anion maleate anions maleates maleic acid anion maleic acid anions CHEBI:132951 maleate maleate anion ChEBI maleate anions ChEBI maleates ChEBI maleic acid anion ChEBI maleic acid anions ChEBI 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 carboxylic ester resulting from the formal condensation of the carboxy group 2-(4-{[5-(trifluoromethyl)pyridin-2-yl]oxy}phenoxy)propanoic acid with the hydroxy group of butan-1-ol. 0 C19H20F3NO4 InChI=1S/C19H20F3NO4/c1-3-4-11-25-18(24)13(2)26-15-6-8-16(9-7-15)27-17-10-5-14(12-23-17)19(20,21)22/h5-10,12-13H,3-4,11H2,1-2H3 VAIZTNZGPYBOGF-UHFFFAOYSA-N 383.362 383.13444 C1(=CC=C(N=C1)OC2=CC=C(C=C2)OC(C(OCCCC)=O)C)C(F)(F)F PPDB:323 butyl 2-(4-{[5-(trifluoromethyl)pyridin-2-yl]oxy}phenoxy)propanoate chebi_ontology CHEBI:132963 butyl 2-(4-{[5-(trifluoromethyl)pyridin-2-yl]oxy}phenoxy)propanoate butyl 2-(4-{[5-(trifluoromethyl)pyridin-2-yl]oxy}phenoxy)propanoate IUPAC A butyl 2-(4-{[5-(trifluoromethyl)pyridin-2-yl]oxy}phenoxy)propanoate that has R configutation. The active enantiomer of the herbicide fluazifop-butyl, it is used as a post-emergence herbicide for the control grass weeds in various broad-leaved crops. 0 C19H20F3NO4 InChI=1S/C19H20F3NO4/c1-3-4-11-25-18(24)13(2)26-15-6-8-16(9-7-15)27-17-10-5-14(12-23-17)19(20,21)22/h5-10,12-13H,3-4,11H2,1-2H3/t13-/m1/s1 VAIZTNZGPYBOGF-CYBMUJFWSA-N 383.362 383.13444 C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F AGR:IND601311742 CAS:79241-46-6 PMID:21487707 PMID:23387923 PMID:25149239 PMID:26147883 PMID:26628016 PMID:26735732 PMID:27157530 PMID:27378613 PPDB:324 Pesticides:fluazifop-p-butyl Reaxys:8346184 butyl (2R)-2-(4-{[5-(trifluoromethyl)pyridin-2-yl]oxy}phenoxy)propanoate chebi_ontology Fusilade II butyl (2R)-2-[4-[[5-(trifluoromethyl)-2-pyridinyl]oxy]phenoxy]propanoate butyl (R)-2-{4-[5-(trifluoromethyl)-2-pyridyloxy]phenoxy}propionate CHEBI:132964 fluazifop-P-butyl AGR:IND601311742 Europe PMC CAS:79241-46-6 Alan Wood's Pesticides CAS:79241-46-6 ChemIDplus PMID:21487707 Europe PMC PMID:23387923 Europe PMC PMID:25149239 Europe PMC PMID:26147883 Europe PMC PMID:26628016 Europe PMC PMID:26735732 Europe PMC PMID:27157530 Europe PMC PMID:27378613 Europe PMC Pesticides:fluazifop-p-butyl Alan Wood's Pesticides Reaxys:8346184 Reaxys butyl (2R)-2-(4-{[5-(trifluoromethyl)pyridin-2-yl]oxy}phenoxy)propanoate IUPAC Fusilade II ChEBI butyl (2R)-2-[4-[[5-(trifluoromethyl)-2-pyridinyl]oxy]phenoxy]propanoate Alan_Wood's_Pesticides butyl (R)-2-{4-[5-(trifluoromethyl)-2-pyridyloxy]phenoxy}propionate Alan_Wood's_Pesticides A butyl 2-(4-{[5-(trifluoromethyl)pyridin-2-yl]oxy}phenoxy)propanoate that has S configuration. It is the inactive enantiomer of the herbicide fluazifop-P-butyl. 0 C19H20F3NO4 InChI=1S/C19H20F3NO4/c1-3-4-11-25-18(24)13(2)26-15-6-8-16(9-7-15)27-17-10-5-14(12-23-17)19(20,21)22/h5-10,12-13H,3-4,11H2,1-2H3/t13-/m0/s1 VAIZTNZGPYBOGF-ZDUSSCGKSA-N 383.362 383.13444 C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@H](C(OCCCC)=O)C)C(F)(F)F PMID:21487707 PMID:26735732 butyl (2S)-2-(4-{[5-(trifluoromethyl)pyridin-2-yl]oxy}phenoxy)propanoate chebi_ontology butyl (2S)-2-[4-[[5-(trifluoromethyl)-2-pyridinyl]oxy]phenoxy]propanoate butyl (S)-2-{4-[5-(trifluoromethyl)-2-pyridyloxy]phenoxy}propionate CHEBI:132965 (S)-fluazifop-butyl PMID:21487707 Europe PMC PMID:26735732 Europe PMC butyl (2S)-2-(4-{[5-(trifluoromethyl)pyridin-2-yl]oxy}phenoxy)propanoate IUPAC butyl (2S)-2-[4-[[5-(trifluoromethyl)-2-pyridinyl]oxy]phenoxy]propanoate ChEBI butyl (S)-2-{4-[5-(trifluoromethyl)-2-pyridyloxy]phenoxy}propionate ChEBI A drug that makes increases the sensitivity of tumour cells to radiation therapy. PMID:12520460 Wikipedia:Radiosensitizer chebi_ontology radiosensitiser radiosensitisers radiosensitising agent radiosensitising agents radiosensitizer radiosensitizers radiosensitizing agents CHEBI:132992 radiosensitizing agent PMID:12520460 Europe PMC radiosensitiser ChEBI radiosensitisers ChEBI radiosensitising agent ChEBI radiosensitising agents ChEBI radiosensitizer ChEBI radiosensitizers ChEBI radiosensitizing agents ChEBI Any organic heteroolycyclic compound whose skeleton two ortho-fused chromene rings, and their derivatives. chebi_ontology chromenochromenes CHEBI:133135 chromenochromene chromenochromenes ChEBI A monocarboxylic acid anion resulting from the deprotonation of the carboxy group of (S)-imazamox. -1 C15H18N3O4 InChI=1S/C15H19N3O4/c1-8(2)15(3)14(21)17-12(18-15)11-10(13(19)20)5-9(6-16-11)7-22-4/h5-6,8H,7H2,1-4H3,(H,19,20)(H,17,18,21)/p-1/t15-/m0/s1 NUPJIGQFXCQJBK-HNNXBMFYSA-M 304.322 304.13028 C1(=NC=C(C=C1C(=O)[O-])COC)C2=NC([C@](N2)(C)C(C)C)=O 2-[(4S)-4-isopropyl-4-methyl-5-oxo-4,5-dihydro-1H-imidazol-2-yl]-5-(methoxymethyl)nicotinate chebi_ontology (S)-imazamox anion 2-[(4S)-4-isopropyl-4-methyl-5-oxo-2-imidazolin-2-yl]-5-methoxymethylnicotinate 5-(methoxymethyl)-2-[(4S)-4-methyl-5-oxo-4-(propan-2-yl)-4,5-dihydro-1H-imidazol-2-yl]pyridine-3-carboxylic acid CHEBI:133193 (S)-imazamox(1-) 2-[(4S)-4-isopropyl-4-methyl-5-oxo-4,5-dihydro-1H-imidazol-2-yl]-5-(methoxymethyl)nicotinate IUPAC (S)-imazamox anion ChEBI 2-[(4S)-4-isopropyl-4-methyl-5-oxo-2-imidazolin-2-yl]-5-methoxymethylnicotinate ChEBI 5-(methoxymethyl)-2-[(4S)-4-methyl-5-oxo-4-(propan-2-yl)-4,5-dihydro-1H-imidazol-2-yl]pyridine-3-carboxylic acid IUPAC A fatty aldehyde in which there is no carbon-carbon unsaturation. 0 CHOR 29.018 29.00274 *C([H])=O PMID:14564727 PMID:17805609 PMID:4531008 chebi_ontology a saturated fatty aldehyde saturated fatty aldehydes CHEBI:133249 saturated fatty aldehyde PMID:14564727 Europe PMC PMID:17805609 Europe PMC PMID:4531008 Europe PMC a saturated fatty aldehyde UniProt saturated fatty aldehydes ChEBI 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 An inorganic oxide that is an oxide of any metal. chebi_ontology metal oxides CHEBI:133331 metal oxide metal oxides ChEBI An L-alpha-amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of L-lysine; major species at pH 7.3. 0 C6H14N2O2 InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/t5-/m0/s1 KDXKERNSBIXSRK-YFKPBYRVSA-N 146.188 146.10553 [O-]C([C@H](CCCCN)[NH3+])=O (2S)-6-amino-2-azaniumylhexanoate chebi_ontology L-lysine Lys lysine zwitterion CHEBI:133538 L-lysine zwitterion (2S)-6-amino-2-azaniumylhexanoate IUPAC L-lysine ChEBI Lys ChEBI lysine zwitterion ChEBI A nitroalkane in which the nitro group is attached to a terminal carbon. Major microspecies at pH 7.3. 0 CH2NO2R 60.032 60.00855 C([N+]([O-])=O)* MetaCyc:Nitroalkanes PMID:1710166 PMID:26506056 PMID:7762004 chebi_ontology a primary nitroalkane CHEBI:133972 primary nitroalkane MetaCyc:Nitroalkanes SUBMITTER PMID:1710166 Europe PMC PMID:26506056 Europe PMC PMID:7762004 Europe PMC a primary nitroalkane UniProt An organochlorine compound derived from methane, ethane or propane that contains atoms of carbon, chlorine, and fluorine only. They are nontoxic, nonflammable chemicals used in aerosol sprays and as refrigerants. Being ozone depletion agents, their manufacture and use is being phased out under the Montreal Protocol. Wikipedia:Chlorofluorocarbon chebi_ontology CFC CFCs chlorofluorocarbons CHEBI:134024 chlorofluorocarbon CFC ChEBI CFCs ChEBI chlorofluorocarbons ChEBI An organochlorine compound derived from methane, ethane or propane that contains atoms of hydrogen, chlorine, fluorine, and carbon only. chebi_ontology HCFC HCFCs hydro-chlorofluorocarbon hydro-chlorofluorocarbons hydrochlorofluorocarbons CHEBI:134040 hydrochlorofluorocarbon HCFC ChEBI HCFCs ChEBI hydro-chlorofluorocarbon ChEBI hydro-chlorofluorocarbons ChEBI hydrochlorofluorocarbons ChEBI Any member of the class of ureas in which at least one of the nitrogens of the urea moiety is substituted by a phenyl or substituted phenyl group. chebi_ontology CHEBI:134043 phenylureas An oxacycle that is 4H-pyran in which the methylene group at position 4 is replaced by an oxygen. Non-aromatic. 0 C4H4O2 InChI=1S/C4H4O2/c1-2-6-4-3-5-1/h1-4H KVGZZAHHUNAVKZ-UHFFFAOYSA-N 84.074 84.02113 C1=COC=CO1 CAS:290-67-5 Wikipedia:1,4-Dioxin 1,4-dioxine chebi_ontology 1,4-dioxin dioxin p-dioxin CHEBI:134044 1,4-dioxine CAS:290-67-5 ChemIDplus CAS:290-67-5 NIST Chemistry WebBook 1,4-dioxine IUPAC 1,4-dioxin ChemIDplus dioxin ChEBI p-dioxin ChemIDplus Organochlorine compounds that are polychlorinated dibenzodioxines and structurally related entities that are persistant organic pollutants. These include polychlorinated dibenzofurans as well as polychlorinated and polybrominated biphenyls They vary widely in their toxicity, but their toxic mode of action is through the aryl hydrocarbon receptor. Wikipedia:Dioxins_and_dioxin-like_compounds chebi_ontology DLCs PCDDs and related compounds dioxins and dioxin-like compounds polychlorinated dibenzodioxins and related compounds CHEBI:134045 polychlorinated dibenzodioxines and related compounds DLCs ChEBI PCDDs and related compounds ChEBI dioxins and dioxin-like compounds ChEBI polychlorinated dibenzodioxins and related compounds ChEBI A member of the class of benzofurans that is benzofuran in which two or more of the hydrogens have reen replaced by chlorines. PMID:24279584 PMID:25754105 PMID:27043380 PMID:27555483 PMID:27776226 PMID:27776233 Wikipedia:Polychlorinated_dibenzofurans chebi_ontology PCDF PCDFs polychlorinated dibenzofurans CHEBI:134046 polychlorinated dibenzofuran PMID:24279584 Europe PMC PMID:25754105 Europe PMC PMID:27043380 Europe PMC PMID:27555483 Europe PMC PMID:27776226 Europe PMC PMID:27776233 Europe PMC PCDF ChEBI PCDFs ChEBI polychlorinated dibenzofurans ChEBI A bromoarene that consists of a biphenyl skeleton substituted by one or more bromo groups. chebi_ontology bromobiphenyls CHEBI:134047 bromobiphenyl bromobiphenyls ChEBI A biphenyl compound containing between 2 and 10 bromine atoms attached to the two benzene rings. Wikipedia:Polybrominated_biphenyl chebi_ontology PBB PBBs polybrominated biphenyl polybrominated biphenyls polybromobiphenyls CHEBI:134049 polybromobiphenyl PBB ChEBI PBBs ChEBI polybrominated biphenyl ChEBI polybrominated biphenyls ChEBI polybromobiphenyls ChEBI A polybromobiphenyl that is biphenyl in which the hydrogens at positions 2, 2', 4, 4', 5, and 5' have been replace by bromines. 0 C12H4Br6 InChI=1S/C12H4Br6/c13-7-3-11(17)9(15)1-5(7)6-2-10(16)12(18)4-8(6)14/h1-4H HMBBJSKXDBUNNT-UHFFFAOYSA-N 627.582 621.54133 C1(C2=C(C=C(C(=C2)Br)Br)Br)=C(C=C(C(=C1)Br)Br)Br CAS:59080-40-9 PMID:15099731 PMID:18255122 PMID:19034893 PMID:23721586 PMID:27474862 PMID:27521000 Reaxys:1991358 2,2',4,4',5,5'-hexabromo[biphenyl] chebi_ontology 2,2'4,4',5,5'-hexabromo-1,1'-biphenyl 2,4,5,2',4',5'-hexabromobiphenyl PBB 153 PBB-153 PBB153 CHEBI:134050 2,2',4,4',5,5'-hexabromobiphenyl CAS:59080-40-9 ChemIDplus CAS:59080-40-9 NIST Chemistry WebBook PMID:15099731 Europe PMC PMID:18255122 Europe PMC PMID:19034893 Europe PMC PMID:23721586 Europe PMC PMID:27474862 Europe PMC PMID:27521000 Europe PMC Reaxys:1991358 Reaxys 2,2',4,4',5,5'-hexabromo[biphenyl] IUPAC 2,2'4,4',5,5'-hexabromo-1,1'-biphenyl ChemIDplus 2,4,5,2',4',5'-hexabromobiphenyl ChemIDplus PBB 153 ChemIDplus PBB-153 ChEBI PBB153 ChEBI Any metal oxide in which the metallic component is copper. chebi_ontology copper oxides CHEBI:134069 copper oxide copper oxides ChEBI An organofluorine compound containing only C-F bonds (no C-H bonds) and C-C bonds but also other heteroatoms (particularly other halogens, oxygen, and sulfur). Their properties represent a blend of fluorocarbons (containing only C-F and C-C bonds) and the parent functionalised organic species. Wikipedia:Perfluorinated_compound chebi_ontology PFC PFCs perfluorinated compounds CHEBI:134091 perfluorinated compound PFC ChEBI PFCs ChEBI perfluorinated compounds ChEBI An arsonium ion that is choline in which the central nitrogen has been replaced by arsenic. +1 C5H14AsO InChI=1S/C5H14AsO/c1-6(2,3)4-5-7/h7H,4-5H2,1-3H3/q+1 ORLOBEXOFQEWFQ-UHFFFAOYSA-N 165.086 165.02551 [As+](CCO)(C)(C)C AGR:IND86035749 AGR:IND92025878 CAS:39895-81-3 HMDB:HMDB0032683 PMID:1580419 PMID:16746711 PMID:2363511 PMID:27277209 PMID:2953397 PMID:3288685 PMID:3349210 PMID:3435795 PMID:6642710 PMID:6719099 Reaxys:1736750 (2-hydroxyethyl)(trimethyl)arsanium chebi_ontology (2-Hydroxyethyl)trimethylarsonium CHEBI:134092 arsenocholine AGR:IND86035749 Europe PMC AGR:IND92025878 Europe PMC CAS:39895-81-3 ChemIDplus PMID:1580419 Europe PMC PMID:16746711 Europe PMC PMID:2363511 Europe PMC PMID:27277209 Europe PMC PMID:2953397 Europe PMC PMID:3288685 Europe PMC PMID:3349210 Europe PMC PMID:3435795 Europe PMC PMID:6642710 Europe PMC PMID:6719099 Europe PMC Reaxys:1736750 Reaxys (2-hydroxyethyl)(trimethyl)arsanium IUPAC (2-Hydroxyethyl)trimethylarsonium ChemIDplus An aromatic ether that is diphenyl ether carrying between 2 and 10 bromo substituents attached to the two benzene rings. PMID:11482396 PMID:12850095 PMID:15568467 PMID:17638602 PMID:17904639 PMID:19100622 PMID:19260376 PMID:20100501 PMID:20557935 PMID:24270005 Wikipedia:Polybrominated_diphenyl_ethers chebi_ontology PBDE polybrominated diphenyl ether polybrominated diphenyl ethers polybromodiphenyl ethers CHEBI:134094 polybromodiphenyl ether PMID:11482396 Europe PMC PMID:12850095 Europe PMC PMID:15568467 Europe PMC PMID:17638602 Europe PMC PMID:17904639 Europe PMC PMID:19100622 Europe PMC PMID:19260376 Europe PMC PMID:20100501 Europe PMC PMID:20557935 Europe PMC PMID:24270005 Europe PMC PBDE ChEBI polybrominated diphenyl ether ChEBI polybrominated diphenyl ethers ChEBI polybromodiphenyl ethers 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 aliphatic alcohol where the hydroxy carbon is beta to a double bond. 0 C4HOR7 65.050 65.00274 C(=C(*)*)(C(C(O)(*)*)(*)*)* chebi_ontology homoallylic alcohols CHEBI:134362 homoallylic alcohol homoallylic alcohols ChEBI An N-oxide where there are three organic groups bonded to the nitrogen atom. 0 NOR3 30.006 29.99799 *[N+](*)([O-])* Patent:EP0545208 Patent:EP0757983 Patent:EP0866058 Patent:EP1068179 Patent:US4206204 Patent:WO9950236 chebi_ontology tertiary amine oxides CHEBI:134363 tertiary amine oxide tertiary amine oxides 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 An allylic alcohol in which the carbon atom that links the double bond to the hydroxy group is also attached to one other carbon and one hydrogen. 0 C3H2OR4 54.047 54.01056 C(C(=C(*)*)*)(O)([H])* chebi_ontology secondary allylic alcohols CHEBI:134396 secondary allylic alcohol secondary 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 other carbons (R4,R5 =/= H). 0 C3HOR5 53.040 53.00274 C(C(=C(*)*)*)(O)(*)* chebi_ontology tertiary allylic alcohols CHEBI:134397 tertiary allylic alcohol tertiary allylic alcohols ChEBI A class containing any titanium molecular entity that is an oxide of titanium. chebi_ontology titanium oxide CHEBI:134438 titanium oxides titanium oxide ChEBI A nanoparticle composed of any titanium oxide. chebi_ontology CHEBI:134441 titanium oxide nanoparticle chebi_ontology CHEBI:134688 naltrexone(1+) A 5-oxo monocarboxylic acid anion obtained by deprotonation of the carboxy group of any diastereomer of jasmonic acid; major species at pH 7.3. -1 C12H17O3 InChI=1S/C12H18O3/c1-2-3-4-5-10-9(8-12(14)15)6-7-11(10)13/h3-4,9-10H,2,5-8H2,1H3,(H,14,15)/p-1/b4-3- ZNJFBWYDHIGLCU-ARJAWSKDSA-M 209.262 209.11832 C1(C(CCC1=O)CC([O-])=O)C/C=C\CC MetaCyc:Jasmonic-Acids {3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetate chebi_ontology a jasmonate jasmonate anion CHEBI:136184 jasmonic acid anion {3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetate IUPAC a jasmonate UniProt jasmonate anion 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 Organonitrogen compounds that have the general structure R(1)(R(2))C=N(O)OH (R(1),R(2) = H, organyl). They are tautomers of C-nitro compounds. 0 CHNO2R2 59.024 59.00073 C(*)(=[N+](O)[O-])* chebi_ontology aci-nitro compounds oxime N-oxide oxime N-oxides CHEBI:136622 aci-nitro compound aci-nitro compounds ChEBI oxime N-oxide ChEBI oxime N-oxides ChEBI A prodrug that, on administration, undergoes chemical conversion by biochemical (enzymatic), chemical (possibly following an enzymatic step), or physical (e.g. photochemical) activation processes before becoming the pharmacologically active pesticide for which it is a propesticide. AGR:IND84086009 PMID:26449612 chebi_ontology pro-pesticide pro-pesticides propesticides CHEBI:136643 propesticide AGR:IND84086009 Europe PMC PMID:26449612 Europe PMC pro-pesticide ChEBI pro-pesticides ChEBI propesticides ChEBI A compound that, on administration, must undergo chemical conversion by metabolic processes before becoming the pharmacologically active insecticide for which it is a proinsecticide. AGR:IND20386178 AGR:IND84086011 AGR:IND89021681 AGR:IND92003154 PMID:16172027 PMID:26449612 PMID:27414472 PMID:27976502 chebi_ontology pro-insecticide pro-insecticides proinsecticides CHEBI:136644 proinsecticide AGR:IND20386178 Europe PMC AGR:IND84086011 Europe PMC AGR:IND89021681 Europe PMC AGR:IND92003154 Europe PMC PMID:16172027 Europe PMC PMID:26449612 Europe PMC PMID:27414472 Europe PMC PMID:27976502 Europe PMC pro-insecticide ChEBI pro-insecticides ChEBI proinsecticides ChEBI A compound that, on administration, must undergo chemical conversion by biochemical (enzymatic), chemical (possibly following an enzymatic step), or physical (e.g. photochemical) activation processes before becoming the pharmacologically active herbicide for which it is a proherbicide. AGR:IND43789627 PMID:12232216 PMID:26449612 PMID:27280658 chebi_ontology pro-herbicide pro-herbicides proherbicides CHEBI:136646 proherbicide AGR:IND43789627 Europe PMC PMID:12232216 Europe PMC PMID:26449612 Europe PMC PMID:27280658 Europe PMC pro-herbicide ChEBI pro-herbicides ChEBI proherbicides ChEBI An organic heterobicyclic compound whose skeleton consists of a pyrazole ring ortho-fused to a diazepine ring. chebi_ontology pyrazolooxadiazepin pyrazolooxadiazepines pyrazolooxadiazepins CHEBI:136684 pyrazolooxadiazepine pyrazolooxadiazepin ChEBI pyrazolooxadiazepines ChEBI pyrazolooxadiazepins ChEBI