From ebcbbed6db8db509961d1bdf97b1813ba4808513 Mon Sep 17 00:00:00 2001 From: Ximeaixa Date: Thu, 14 May 2026 10:02:52 +0200 Subject: [PATCH 1/2] fix ontology roots and obo namespace for material entities --- src/ontology/idpo-edit.owl | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/src/ontology/idpo-edit.owl b/src/ontology/idpo-edit.owl index 1535455..dca7176 100644 --- a/src/ontology/idpo-edit.owl +++ b/src/ontology/idpo-edit.owl @@ -13,6 +13,8 @@ Annotation( ) Annotation( ) Annotation( ) +Annotation( ) +Annotation( ) Annotation( ) Annotation( "It describes structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state.") Annotation( ) @@ -932,6 +934,7 @@ AnnotationAssertion(owl:deprecated # Class: (compound) AnnotationAssertion( "A molecule composed of two or more distinct chemical components.") +AnnotationAssertion( "compound") AnnotationAssertion( "IDPO:0000091") AnnotationAssertion(rdfs:label "compound") SubClassOf( ) @@ -939,6 +942,7 @@ SubClassOf( (condensate) AnnotationAssertion( "A compound formed via phase separation or related physicochemical processes.") +AnnotationAssertion( "compound") AnnotationAssertion( "IDPO:0000092") AnnotationAssertion(rdfs:label "condensate") SubClassOf( ) @@ -946,6 +950,7 @@ SubClassOf( (biomolecular condensate) AnnotationAssertion( "A condensate composed of biomolecules such as proteins, protein regions, or nucleic acid strands, typically formed through phase separation driven by weak multivalent interactions.") +AnnotationAssertion( "compound") AnnotationAssertion( "IDPO:0000093") AnnotationAssertion(rdfs:label "biomolecular condensate") SubClassOf( ) @@ -953,6 +958,7 @@ SubClassOf( (protein) AnnotationAssertion( "A molecule composed of one or more polypeptide chains.") +AnnotationAssertion( "protein") AnnotationAssertion( "IDPO:0000094") AnnotationAssertion(rdfs:label "protein") SubClassOf( ) @@ -960,6 +966,7 @@ SubClassOf( (protein region) AnnotationAssertion( "A contiguous segment of a protein that can be distinguished by its structural, functional, or sequence properties.") +AnnotationAssertion( "protein") AnnotationAssertion( "IDPO:0000095") AnnotationAssertion(rdfs:label "protein region") SubClassOf( ) @@ -967,6 +974,8 @@ SubClassOf( (intrinsically disordered protein) AnnotationAssertion( "A protein that wholly lacks a stable, fixed three-dimensional structure under physiological conditions.") +AnnotationAssertion( "IDP") +AnnotationAssertion( "protein") AnnotationAssertion( "IDPO:0000096") AnnotationAssertion(rdfs:label "intrinsically disordered protein") SubClassOf( ) @@ -974,6 +983,8 @@ SubClassOf( (intrinsically disordered region) AnnotationAssertion( "A protein region that lacks a stable, fixed three-dimensional structure under physiological conditions.") +AnnotationAssertion( "IDR") +AnnotationAssertion( "protein") AnnotationAssertion( "IDPO:0000097") AnnotationAssertion(rdfs:label "intrinsically disordered region") SubClassOf( ) @@ -981,6 +992,7 @@ SubClassOf( (ordered region) AnnotationAssertion( "A protein region that adopts a stable, fixed three-dimensional structure under physiological conditions.") +AnnotationAssertion( "protein") AnnotationAssertion( "IDPO:0000098") AnnotationAssertion(rdfs:label "ordered region") SubClassOf( ) From d74bf3287085da1bfe8b3ad117d8d0e3308052fe Mon Sep 17 00:00:00 2001 From: Ximeaixa Date: Thu, 14 May 2026 10:38:02 +0200 Subject: [PATCH 2/2] update imports --- src/ontology/imports/merged_import.owl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 99c3573..e465315 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 "2026-05-05") + +Annotation(owl:versionInfo "2026-05-14") Declaration(Class()) Declaration(Class()) @@ -159,7 +159,7 @@ AnnotationAssertion( "has broad synonym"@en) AnnotationAssertion(rdfs:label "has_broad_synonym") -# Annotation Property: (has cross-reference) +# Annotation Property: (database_cross_reference) AnnotationAssertion( "disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) \"NCIT:C41009\"^^xsd:string") AnnotationAssertion( "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.")