diff --git a/src/ontology/components/obsoletes.owl b/src/ontology/components/obsoletes.owl index 6a007ebd..62431f95 100644 --- a/src/ontology/components/obsoletes.owl +++ b/src/ontology/components/obsoletes.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-01-12") + +Annotation(owl:versionInfo "2024-04-26") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/components/synonyms.owl b/src/ontology/components/synonyms.owl index 850f5d95..a7657f7c 100644 --- a/src/ontology/components/synonyms.owl +++ b/src/ontology/components/synonyms.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-01-12") + +Annotation(owl:versionInfo "2024-04-26") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 6f72f6e0..353ac233 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-05-08") + +Annotation(owl:versionInfo "2024-05-09") Declaration(Class()) Declaration(Class()) @@ -882,6 +882,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1544,6 +1545,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1856,6 +1858,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1983,6 +1987,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3177,7 +3182,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -23000,6 +23007,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -23343,6 +23351,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -23399,6 +23408,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -23634,7 +23644,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -52769,7 +52778,7 @@ AnnotationAssertion(rdfs:label "caus SubObjectPropertyOf( ) SubObjectPropertyOf( ) -# Object Property: (disease disrupts) +# Object Property: (disease causes disruption of) AnnotationAssertion( "A relationship between a disease and a process where the disease process disrupts the execution of the process.") AnnotationAssertion(rdfs:label "disease causes disruption of") @@ -60258,6 +60267,13 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (macrolide antibiotic) + +AnnotationAssertion( "A macrocyclic lactone with a ring of twelve or more members which exhibits antibiotic activity.") +AnnotationAssertion(rdfs:label "macrolide antibiotic") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (macrolide) AnnotationAssertion( "A macrocyclic lactone with a ring of twelve or more members derived from a polyketide.") @@ -65345,6 +65361,13 @@ AnnotationAssertion( "aliphatic compound") SubClassOf( ) +# Class: (alicyclic compound) + +AnnotationAssertion( "An aliphatic compound having a carbocyclic ring structure which may be saturated or unsaturated, but may not be a benzenoid or other aromatic system.") +AnnotationAssertion(rdfs:label "alicyclic compound") +SubClassOf( ) +SubClassOf( ) + # Class: (aromatic compound) AnnotationAssertion( "A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character.") @@ -67425,6 +67448,19 @@ EquivalentClasses( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (alicyclic ketone) + +AnnotationAssertion( "A cyclic ketone in which the carbocyclic ring structure which may be saturated or unsaturated, but may not be a benzenoid or other aromatic system.") +AnnotationAssertion(rdfs:label "alicyclic ketone") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cyclopentanones) + +AnnotationAssertion( "Any alicyclic ketone that consists of a cyclopentane skeleton substituted by at least one oxo group.") +AnnotationAssertion(rdfs:label "cyclopentanones") +SubClassOf( ) + # Class: (quinone) AnnotationAssertion( "Compounds having a fully conjugated cyclic dione structure, such as that of benzoquinones, derived from aromatic compounds by conversion of an even number of -CH= groups into -C(=O)- groups with any necessary rearrangement of double bonds (polycyclic and heterocyclic analogues are included).") @@ -68243,6 +68279,16 @@ SubClassOf( "elemental zinc") SubClassOf( ) +# Class: (clarithromycin) + +AnnotationAssertion( "The 6-O-methyl ether of erythromycin A, clarithromycin is a macrolide antibiotic used in the treatment of respiratory-tract, skin and soft-tissue infections. It is also used to eradicate Helicobacter pylori in the treatment of peptic ulcer disease. It prevents bacteria from growing by interfering with their protein synthesis.") +AnnotationAssertion(rdfs:label "clarithromycin") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (tropane alkaloid) AnnotationAssertion(rdfs:label "tropane alkaloid") @@ -76871,6 +76917,20 @@ AnnotationAssertion(rdfs:label "ole SubClassOf( ) SubClassOf( ) +# Class: (loxoprofen) + +AnnotationAssertion( "A monocarboxylic acid that is propionic acid in which one of the hydrogens at position 2 is substituted by a 4-[(2-oxocyclopentyl)methyl]phenyl group. A prodrug that is rapidly converted into its active trans-alcohol metabolite following oral administration.") +AnnotationAssertion(rdfs:label "loxoprofen") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (palmitoyl bioconjugate) AnnotationAssertion( "A bioconjugate obtained by coupling of palmitic acid to another biomolecule (e.g. coenzyme A, an acyl-carrier protein, a phospholipid, an oligosaccharide, a nucleic acid etc.), which for the sake of convenience, is represented by an R group.") @@ -76878,6 +76938,13 @@ AnnotationAssertion(rdfs:label "pal SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (loxoprofen(1-)) + +AnnotationAssertion( "An oxo monocarboxylic acid anion that is the conjugate base of loxoprofen, obtained by deprotonation of the carboxy group.") +AnnotationAssertion(rdfs:label "loxoprofen(1-)") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (xenobiotic metabolite) AnnotationAssertion( "Any metabolite produced by metabolism of a xenobiotic compound.") @@ -226788,6 +226855,13 @@ EquivalentClasses( ObjectIntersect SubClassOf( ) SubClassOf( ) +# Class: (invasive tubular breast carcinoma) + +AnnotationAssertion(rdfs:label "invasive tubular breast carcinoma") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + # Class: (spondylitis) AnnotationAssertion(rdfs:label "spondylitis") @@ -228521,7 +228595,8 @@ SubClassOf( (pancreatic ductal adenocarcinoma) AnnotationAssertion(rdfs:label "pancreatic ductal adenocarcinoma") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -229294,6 +229369,11 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (tubular adenocarcinoma) + +AnnotationAssertion(rdfs:label "tubular adenocarcinoma") +SubClassOf( ) + # Class: (chronic bronchitis) AnnotationAssertion(rdfs:label "chronic bronchitis") @@ -229725,6 +229805,13 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (gastric tubular adenocarcinoma) + +AnnotationAssertion(rdfs:label "gastric tubular adenocarcinoma") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + # Class: (granulosa cell tumor) AnnotationAssertion(rdfs:label "granulosa cell tumor") @@ -231466,14 +231553,6 @@ EquivalentClasses( ObjectIntersect SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (hereditary predisposition to infections) - -AnnotationAssertion(rdfs:comment "Reason: out of scope. MONDO:excludeGrouping. Term to consider:MONDO:0020573 inherited disease susceptibility") -AnnotationAssertion(rdfs:label "hereditary predisposition to infections") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (endophthalmitis) AnnotationAssertion(rdfs:label "endophthalmitis") @@ -232411,8 +232490,8 @@ SubClassOf( (inherited susceptibility to mycobacterial diseases) AnnotationAssertion(rdfs:label "inherited susceptibility to mycobacterial diseases") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (inherited obesity) diff --git a/src/patterns/data/default/response_to_chemical_stimulus_trait.tsv b/src/patterns/data/default/response_to_chemical_stimulus_trait.tsv index 36073eef..81071fad 100644 --- a/src/patterns/data/default/response_to_chemical_stimulus_trait.tsv +++ b/src/patterns/data/default/response_to_chemical_stimulus_trait.tsv @@ -117,3 +117,5 @@ OBA:2050330 CHEBI:135983 teriparatide https://orcid.org/0000-0001-6757-4744 OBA:2050333 CHEBI:31941 oxaliplatin https://orcid.org/0000-0001-6757-4744 OBA:2045298 CHEBI:145810 insulin https://orcid.org/0000-0001-8314-2140 OBA:2045299 CHEBI:17234 glucose https://orcid.org/0000-0001-8314-2140 +OBA:2050420 CHEBI:76172 loxoprofen https://orcid.org/0000-0001-6757-4744 +OBA:2050421 CHEBI:3732 clarithromycin https://orcid.org/0000-0001-6757-4744 diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index 0ee7da40..79ce14e8 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-05-08") + +Annotation(owl:versionInfo "2024-05-09") Declaration(Class()) Declaration(Class()) @@ -286,6 +286,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -434,6 +435,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -12641,6 +12643,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -105194,6 +105198,22 @@ AnnotationAssertion(Annotation( "level of endocrine disruptor in urine") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ))))) +# Class: (trait in response to loxoprofen) + +AnnotationAssertion( "A trait that affects the response to a stimulus with loxoprofen.") +AnnotationAssertion( "https://orcid.org/0000-0001-6757-4744") +AnnotationAssertion( "response to loxoprofen trait") +AnnotationAssertion(rdfs:label "trait in response to loxoprofen") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + +# Class: (trait in response to clarithromycin) + +AnnotationAssertion( "A trait that affects the response to a stimulus with clarithromycin.") +AnnotationAssertion( "https://orcid.org/0000-0001-6757-4744") +AnnotationAssertion( "response to clarithromycin trait") +AnnotationAssertion(rdfs:label "trait in response to clarithromycin") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + # Class: (aggressive behavior towards inanimate objects rate) AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "The rate of a aggressive behavior towards inanimate objects.")