From 5fefe5946b0887ac2db908d424ce9dee4ecf61c2 Mon Sep 17 00:00:00 2001 From: XimeAixa Date: Tue, 21 Apr 2026 19:16:13 -0500 Subject: [PATCH 1/2] add material entity to BFO import --- src/ontology/imports/bfo_terms.txt | 1 + src/ontology/imports/merged_import.owl | 23 +++++++++++++++++++++-- 2 files changed, 22 insertions(+), 2 deletions(-) diff --git a/src/ontology/imports/bfo_terms.txt b/src/ontology/imports/bfo_terms.txt index 71fd64c..9d4690e 100644 --- a/src/ontology/imports/bfo_terms.txt +++ b/src/ontology/imports/bfo_terms.txt @@ -1,3 +1,4 @@ BFO:0000015 BFO:0000019 BFO:0000034 +BFO:0000040 \ No newline at end of file diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 6a47fab..2928d32 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 "2026-04-21") + +Annotation(owl:versionInfo "2026-04-22") Declaration(Class()) Declaration(Class()) @@ -22,6 +22,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -623,6 +624,24 @@ AnnotationAssertion( "function"@en) SubClassOf( ) +# Class: (material entity) + +AnnotationAssertion( "a flame"@en) +AnnotationAssertion( "a forest fire"@en) +AnnotationAssertion( "a human being"@en) +AnnotationAssertion( "a hurricane"@en) +AnnotationAssertion( "a photon"@en) +AnnotationAssertion( "a puff of smoke"@en) +AnnotationAssertion( "a sea wave"@en) +AnnotationAssertion( "a tornado"@en) +AnnotationAssertion( "an aggregate of human beings."@en) +AnnotationAssertion( "an energy wave"@en) +AnnotationAssertion( "an epidemic"@en) +AnnotationAssertion( "the undetached arm of a human being"@en) +AnnotationAssertion( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) +AnnotationAssertion(rdfs:label "material entity"@en) +SubClassOf( ) + # Class: (molecular_function) AnnotationAssertion(Annotation( "GOC:pdt") "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.") From e16f55fcef0e88e2f4756979e34ab0202d906531 Mon Sep 17 00:00:00 2001 From: XimeAixa Date: Wed, 22 Apr 2026 07:42:42 -0500 Subject: [PATCH 2/2] create material entity branch --- src/ontology/idpo-edit.owl | 64 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 64 insertions(+) diff --git a/src/ontology/idpo-edit.owl b/src/ontology/idpo-edit.owl index 833aead..7667170 100644 --- a/src/ontology/idpo-edit.owl +++ b/src/ontology/idpo-edit.owl @@ -90,6 +90,14 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -885,6 +893,62 @@ AnnotationAssertion( "state") SubClassOf( ) +# Class: (compound) + +AnnotationAssertion( "A molecule composed of two or more distinct chemical components.") +AnnotationAssertion( "IDPO:0000091") +AnnotationAssertion(rdfs:label "compound") +SubClassOf( ) + +# Class: (condensate) + +AnnotationAssertion( "A compound formed via phase separation or related physicochemical processes.") +AnnotationAssertion( "IDPO:0000092") +AnnotationAssertion(rdfs:label "condensate") +SubClassOf( ) + +# Class: (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( "IDPO:0000093") +AnnotationAssertion(rdfs:label "biomolecular condensate") +SubClassOf( ) + +# Class: (protein) + +AnnotationAssertion( "A molecule composed of one or more polypeptide chains.") +AnnotationAssertion( "IDPO:0000094") +AnnotationAssertion(rdfs:label "protein") +SubClassOf( ) + +# Class: (protein region) + +AnnotationAssertion( "A contiguous segment of a protein that can be distinguished by its structural, functional, or sequence properties.") +AnnotationAssertion( "IDPO:0000095") +AnnotationAssertion(rdfs:label "protein region") +SubClassOf( ) + +# Class: (intrinsically disordered protein) + +AnnotationAssertion( "A protein that wholly lacks a stable, fixed three-dimensional structure under physiological conditions.") +AnnotationAssertion( "IDPO:0000096") +AnnotationAssertion(rdfs:label "intrinsically disordered protein") +SubClassOf( ) + +# Class: (intrinsically disordered region) + +AnnotationAssertion( "A protein region that lacks a stable, fixed three-dimensional structure under physiological conditions.") +AnnotationAssertion( "IDPO:0000097") +AnnotationAssertion(rdfs:label "intrinsically disordered region") +SubClassOf( ) + +# Class: (ordered region) + +AnnotationAssertion( "A protein region that adopts a stable, fixed three-dimensional structure under physiological conditions.") +AnnotationAssertion( "IDPO:0000098") +AnnotationAssertion(rdfs:label "ordered region") +SubClassOf( ) + SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) )