Merge remote-tracking branch 'refs/remotes/origin/main'

Philipp von Hartrott · Philipp von Hartrott · commit 20093c96274c · 2026-02-23T12:35:36.000+01:00
diff --git a/docs/navigator.yaml b/docs/navigator.yaml
@@ -63,6 +63,11 @@ sections:
         md: PMDco User Guide.md
         icon: book-open
         
+      - title: Term Obsoletion
+        href: obsolete-ontology-terms.html
+        md: obsolete ontology terms.md
+        icon: delete
+        
       - title: Reused Ontologies
         href: reused-ontologies.html
         md: Reused ontologies.md
@@ -234,6 +239,9 @@ icons:
   settings:
     path: "M12 15a3 3 0 1 0 0-6 3 3 0 0 0 0 6z M19.4 15a1.65 1.65 0 0 0 .33 1.82l.06.06a2 2 0 0 1 0 2.83 2 2 0 0 1-2.83 0l-.06-.06a1.65 1.65 0 0 0-1.82-.33 1.65 1.65 0 0 0-1 1.51V21a2 2 0 0 1-2 2 2 2 0 0 1-2-2v-.09A1.65 1.65 0 0 0 9 19.4a1.65 1.65 0 0 0-1.82.33l-.06.06a2 2 0 0 1-2.83 0 2 2 0 0 1 0-2.83l.06-.06a1.65 1.65 0 0 0 .33-1.82 1.65 1.65 0 0 0-1.51-1H3a2 2 0 0 1-2-2 2 2 0 0 1 2-2h.09A1.65 1.65 0 0 0 4.6 9a1.65 1.65 0 0 0-.33-1.82l-.06-.06a2 2 0 0 1 0-2.83 2 2 0 0 1 2.83 0l.06.06a1.65 1.65 0 0 0 1.82.33H9a1.65 1.65 0 0 0 1-1.51V3a2 2 0 0 1 2-2 2 2 0 0 1 2 2v.09a1.65 1.65 0 0 0 1 1.51 1.65 1.65 0 0 0 1.82-.33l.06-.06a2 2 0 0 1 2.83 0 2 2 0 0 1 0 2.83l-.06.06a1.65 1.65 0 0 0-.33 1.82V9a1.65 1.65 0 0 0 1.51 1H21a2 2 0 0 1 2 2 2 2 0 0 1-2 2h-.09a1.65 1.65 0 0 0-1.51 1z"
     
+  delete:
+    path: "M21 4H8l-7 8 7 8h13a2 2 0 0 0 2-2V6a2 2 0 0 0-2-2z"
+    
   # Search
   search:
     path: "M11 19a8 8 0 1 0 0-16 8 8 0 0 1 0 16z M21 21l-4.35-4.35"
diff --git a/src/ontology/components/materials-listing.owl b/src/ontology/components/materials-listing.owl
@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<https://w3id.org/pmd/co/components/materials-listing.owl>
-<https://w3id.org/pmd/co/releases/2026-02-20/components/materials-listing.owl>
-Annotation(owl:versionInfo "2026-02-20")
+<https://w3id.org/pmd/co/releases/2026-02-23/components/materials-listing.owl>
+Annotation(owl:versionInfo "2026-02-23")
 
 Declaration(Class(<https://w3id.org/pmd/co/PMD_0000000>))
 Declaration(Class(<https://w3id.org/pmd/co/PMD_0000546>))
diff --git a/src/ontology/imports/bfo_import.owl b/src/ontology/imports/bfo_import.owl
@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<https://w3id.org/pmd/co/imports/bfo_import.owl>
-<https://w3id.org/pmd/co/releases/2026-02-20/imports/bfo_import.owl>
+<https://w3id.org/pmd/co/releases/2026-02-23/imports/bfo_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/bfo/2020/notime/bfo.owl>)
-Annotation(owl:versionInfo "2026-02-20")
+Annotation(owl:versionInfo "2026-02-23")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
diff --git a/src/ontology/imports/chebi_import.owl b/src/ontology/imports/chebi_import.owl
@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<https://w3id.org/pmd/co/imports/chebi_import.owl>
-<https://w3id.org/pmd/co/releases/2026-02-20/imports/chebi_import.owl>
-Annotation(owl:versionInfo "2026-02-20")
+<https://w3id.org/pmd/co/releases/2026-02-23/imports/chebi_import.owl>
+Annotation(owl:versionInfo "2026-02-23")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_137980>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_18248>))
diff --git a/src/ontology/imports/cob_import.owl b/src/ontology/imports/cob_import.owl
@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<https://w3id.org/pmd/co/imports/cob_import.owl>
-<https://w3id.org/pmd/co/releases/2026-02-20/imports/cob_import.owl>
+<https://w3id.org/pmd/co/releases/2026-02-23/imports/cob_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/cob/releases/2025-12-12/cob-base.owl>)
-Annotation(owl:versionInfo "2026-02-20")
+Annotation(owl:versionInfo "2026-02-23")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000015>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000040>))
@@ -26,6 +26,7 @@ Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/OBI_0000312>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000057>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000116>))
+Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0100001>))
 Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/source>))
 Declaration(AnnotationProperty(<http://purl.org/dc/terms/contributor>))
 Declaration(AnnotationProperty(<http://purl.org/dc/terms/description>))
diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl
@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<https://w3id.org/pmd/co/imports/iao_import.owl>
-<https://w3id.org/pmd/co/releases/2026-02-20/imports/iao_import.owl>
+<https://w3id.org/pmd/co/releases/2026-02-23/imports/iao_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/iao/2022-11-07/iao.owl>)
-Annotation(owl:versionInfo "2026-02-20")
+Annotation(owl:versionInfo "2026-02-23")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000017>))
diff --git a/src/ontology/imports/nfdicore_import.owl b/src/ontology/imports/nfdicore_import.owl
@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<https://w3id.org/pmd/co/imports/nfdicore_import.owl>
-<https://w3id.org/pmd/co/releases/2026-02-20/imports/nfdicore_import.owl>
+<https://w3id.org/pmd/co/releases/2026-02-23/imports/nfdicore_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <https://nfdi.fiz-karlsruhe.de/ontology/3.0.4>)
-Annotation(owl:versionInfo "2026-02-20")
+Annotation(owl:versionInfo "2026-02-23")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000004>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000015>))
@@ -44,6 +44,7 @@ Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002353>))
 Declaration(DataProperty(<https://nfdi.fiz-karlsruhe.de/ontology/NFDI_0001008>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000112>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000119>))
+Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0100001>))
 Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/source>))
 Declaration(AnnotationProperty(<http://purl.org/dc/terms/bibliographicCitation>))
 Declaration(AnnotationProperty(<http://purl.org/dc/terms/created>))
diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl
@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<https://w3id.org/pmd/co/imports/obi_import.owl>
-<https://w3id.org/pmd/co/releases/2026-02-20/imports/obi_import.owl>
+<https://w3id.org/pmd/co/releases/2026-02-23/imports/obi_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/obi/2025-12-18/obi.owl>)
-Annotation(owl:versionInfo "2026-02-20")
+Annotation(owl:versionInfo "2026-02-23")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000015>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000016>))
@@ -101,6 +101,7 @@ Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000116>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000119>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000232>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000233>))
+Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0100001>))
 Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/source>))
 Declaration(AnnotationProperty(<http://purl.org/dc/terms/contributor>))
 Declaration(AnnotationProperty(<http://purl.org/dc/terms/created>))
@@ -177,6 +178,13 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.ob
 AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/IAO_0000233> "The 'tracker item' can associate a tracker with a specific ontology term."@en)
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000233> "term tracker item"@en)
 
+# Annotation Property: <http://purl.obolibrary.org/obo/IAO_0100001> (term replaced by)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IAO_0100001> "Use on obsolete terms, relating the term to another term that can be used as a substitute"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/IAO_0100001> "Person:Alan Ruttenberg"@en)
+AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/IAO_0100001> "Add as annotation triples in the granting ontology"@en)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0100001> "term replaced by"@en)
+
 # Annotation Property: <http://purl.org/dc/elements/1.1/source> (Source)
 
 AnnotationAssertion(rdfs:comment <http://purl.org/dc/elements/1.1/source> "A reference to a resource from which the present resource
@@ -638,6 +646,7 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.ob
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/OBI_0000011> "branch derived")
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000232> <http://purl.obolibrary.org/obo/OBI_0000011> "6/11/9: Edited at workshop. Used to include: is initiated by an agent")
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000232> <http://purl.obolibrary.org/obo/OBI_0000011> "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0100001> <http://purl.obolibrary.org/obo/OBI_0000011> <http://purl.obolibrary.org/obo/COB_0000035>)
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBI_0000011> "obsolete planned process")
 
 # Class: <http://purl.obolibrary.org/obo/OBI_0000067> (evaluant role)
diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl
@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<https://w3id.org/pmd/co/imports/ro_import.owl>
-<https://w3id.org/pmd/co/releases/2026-02-20/imports/ro_import.owl>
+<https://w3id.org/pmd/co/releases/2026-02-23/imports/ro_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/ro/releases/2025-12-17/ro.owl>)
-Annotation(owl:versionInfo "2026-02-20")
+Annotation(owl:versionInfo "2026-02-23")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000003>))
diff --git a/src/ontology/imports/stato_import.owl b/src/ontology/imports/stato_import.owl
@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<https://w3id.org/pmd/co/imports/stato_import.owl>
-<https://w3id.org/pmd/co/releases/2026-02-20/imports/stato_import.owl>
+<https://w3id.org/pmd/co/releases/2026-02-23/imports/stato_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/stato/releases/2025-02-23/stato.owl>)
-Annotation(owl:versionInfo "2026-02-20")
+Annotation(owl:versionInfo "2026-02-23")
 
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/STATO_0000102>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
diff --git a/src/ontology/imports/time_import.owl b/src/ontology/imports/time_import.owl
@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<https://w3id.org/pmd/co/imports/time_import.owl>
-<https://w3id.org/pmd/co/releases/2026-02-20/imports/time_import.owl>
+<https://w3id.org/pmd/co/releases/2026-02-23/imports/time_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://www.w3.org/2006/time#2016>)
-Annotation(owl:versionInfo "2026-02-20")
+Annotation(owl:versionInfo "2026-02-23")
 
 Declaration(DataProperty(<http://www.w3.org/2006/time#inXSDDateTime>))
 Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/source>))
diff --git a/src/ontology/imports/uo_import.owl b/src/ontology/imports/uo_import.owl
@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<https://w3id.org/pmd/co/imports/uo_import.owl>
-<https://w3id.org/pmd/co/releases/2026-02-20/imports/uo_import.owl>
-Annotation(owl:versionInfo "2026-02-20")
+<https://w3id.org/pmd/co/releases/2026-02-23/imports/uo_import.owl>
+Annotation(owl:versionInfo "2026-02-23")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/UO_0000000>))
 Declaration(Class(<http://purl.obolibrary.org/obo/UO_0000003>))
diff --git a/src/ontology/pmdco.ttl b/src/ontology/pmdco.ttl
@@ -16,7 +16,7 @@
 @base <https://w3id.org/pmd/pmdco.ttl> .
 
 <https://w3id.org/pmd/pmdco.ttl> rdf:type owl:Ontology ;
-                                  owl:versionIRI <https://w3id.org/pmd/co/releases/2026-02-20/pmdco.ttl> ;
+                                  owl:versionIRI <https://w3id.org/pmd/co/releases/2026-02-23/pmdco.ttl> ;
                                   dcterms:creator <https://orcid.org/0000-0001-6772-1943> ,
                                                   <https://orcid.org/0000-0001-7192-7143> ,
                                                   <https://orcid.org/0000-0002-1058-3102> ,
@@ -43,7 +43,7 @@ Documentation: https://materialdigital.github.io/core-ontology/docs/"""@en ;
                                   dcterms:license <https://creativecommons.org/licenses/by/4.0/> ;
                                   dcterms:title "PMD Core Ontology" ;
                                   doap:repository <https://github.com/materialdigital/core-ontology> ;
-                                  owl:versionInfo "2026-02-20" .
+                                  owl:versionInfo "2026-02-23" .
 
 #################################################################
 #    Annotation properties
@@ -2929,6 +2929,7 @@ obo:OBI_0000011 rdf:type owl:Class ;
                 obo:IAO_0000119 "branch derived" ;
                 obo:IAO_0000232 "6/11/9: Edited at workshop. Used to include: is initiated by an agent" ,
                                 "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)" ;
+                obo:IAO_0100001 obo:COB_0000035 ;
                 rdfs:label "obsolete planned process" ;
                 owl:deprecated "true"^^xsd:boolean .
 
