Label the deprecation annotation properties IAO:0000231 and IAO:0100001 (closes #519)

turbomam · claude · turbomam · commit 22fddfc4fe53 · 2026-06-05T21:55:54.000-04:00
These were declared but unlabeled, so they showed as bare IRIs in OLS. Add
rdfs:label in metpo-edit.owl following the existing IAO:0000117 pattern; labels
verified against IAO via OLS (has obsolescence reason / term replaced by).
Rebuilt the release artifacts; QC passes (reasoning consistent, 5 SPARQL checks
0 violations, OWL2-DL valid, report 0 ERROR).

Scope note: the obsolescence-reason VALUES (IAO:0000226, OMO:0001000) are
deliberately NOT labeled here pending review of whether they are the correct
codes (filed separately).

Co-Authored-By: Claude Sonnet 4.6 &lt;noreply@anthropic.com&gt;
diff --git a/metpo-base.json b/metpo-base.json
@@ -34,9 +34,9 @@
         "val" : "https://github.com/berkeleybop/metpo"
       }, {
         "pred" : "http://www.w3.org/2002/07/owl#versionInfo",
-        "val" : "2026-06-05"
+        "val" : "2026-06-06"
       } ],
-      "version" : "https://w3id.org/metpo/releases/2026-06-05/metpo-base.json"
+      "version" : "https://w3id.org/metpo/releases/2026-06-06/metpo-base.json"
     },
     "nodes" : [ {
       "id" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass",
diff --git a/metpo-base.obo b/metpo-base.obo
@@ -1,5 +1,5 @@
 format-version: 1.2
-data-version: https://w3id.org/metpo/releases/2026-06-05/metpo-base.owl
+data-version: https://w3id.org/metpo/releases/2026-06-06/metpo-base.owl
 idspace: dc http://purl.org/dc/elements/1.1/ 
 idspace: dcterms http://purl.org/dc/terms/ 
 idspace: metpo https://w3id.org/metpo/ 
@@ -14,7 +14,7 @@ property_value: dcterms:creator https://orcid.org/0000-0001-9076-6066
 property_value: dcterms:description "METPO provides terms for microbial ecophysiological traits and phenotypes: growth preferences (temperature, pH, salinity, oxygen), metabolism, and cell morphology of bacteria and archaea. Its primary purpose is to harmonize terminology across major microbial trait databases (BacDive, BactoTraits, Madin bacteria_archaea_traits, MetaTraits) for use in NMDC and KG-Microbe. METPO uses OBO-style annotation patterns (IAO textual definitions, oboInOwl synonyms) and cites terms from OMP, MicrO, GO, ECOCORE, and PATO as definition sources." xsd:string
 property_value: dcterms:license https://creativecommons.org/licenses/by/4.0/
 property_value: dcterms:title "METPO: Microbial Ecophysiological Trait and Phenotype Ontology" xsd:string
-property_value: owl:versionInfo "2026-06-05" xsd:string
+property_value: owl:versionInfo "2026-06-06" xsd:string
 property_value: seeAlso https://bioportal.bioontology.org/ontologies/METPO
 property_value: seeAlso https://bioregistry.io/registry/metpo
 property_value: seeAlso https://github.com/berkeleybop/metpo
diff --git a/metpo-base.owl b/metpo-base.owl
@@ -15,7 +15,7 @@
      xmlns:dcterms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="https://w3id.org/metpo/metpo-base.owl">
-        <owl:versionIRI rdf:resource="https://w3id.org/metpo/releases/2026-06-05/metpo-base.owl"/>
+        <owl:versionIRI rdf:resource="https://w3id.org/metpo/releases/2026-06-06/metpo-base.owl"/>
         <dc:type rdf:resource="http://purl.obolibrary.org/obo/IAO_8000001"/>
         <dcterms:contributor rdf:resource="https://orcid.org/0000-0001-8175-045X"/>
         <dcterms:contributor rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
@@ -26,7 +26,7 @@
         <rdfs:seeAlso rdf:resource="https://bioportal.bioontology.org/ontologies/METPO"/>
         <rdfs:seeAlso rdf:resource="https://bioregistry.io/registry/metpo"/>
         <rdfs:seeAlso rdf:resource="https://github.com/berkeleybop/metpo"/>
-        <owl:versionInfo>2026-06-05</owl:versionInfo>
+        <owl:versionInfo>2026-06-06</owl:versionInfo>
     </owl:Ontology>
     
 
diff --git a/metpo-full.json b/metpo-full.json
@@ -31,9 +31,9 @@
         "val" : "https://github.com/berkeleybop/metpo"
       }, {
         "pred" : "http://www.w3.org/2002/07/owl#versionInfo",
-        "val" : "2026-06-05"
+        "val" : "2026-06-06"
       } ],
-      "version" : "https://w3id.org/metpo/releases/2026-06-05/metpo-full.json"
+      "version" : "https://w3id.org/metpo/releases/2026-06-06/metpo-full.json"
     },
     "nodes" : [ {
       "id" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass",
@@ -24162,10 +24162,12 @@
       "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://purl.obolibrary.org/obo/IAO_0000231",
+      "lbl" : "has obsolescence reason",
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://purl.obolibrary.org/obo/IAO_0100001",
+      "lbl" : "term replaced by",
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
     }, {
diff --git a/metpo-full.obo b/metpo-full.obo
@@ -1,5 +1,5 @@
 format-version: 1.2
-data-version: https://w3id.org/metpo/releases/2026-06-05/metpo-full.owl
+data-version: https://w3id.org/metpo/releases/2026-06-06/metpo-full.owl
 idspace: dcterms http://purl.org/dc/terms/ 
 idspace: metpo https://w3id.org/metpo/ 
 idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# 
@@ -12,7 +12,7 @@ property_value: dcterms:creator https://orcid.org/0000-0001-9076-6066
 property_value: dcterms:description "METPO provides terms for microbial ecophysiological traits and phenotypes: growth preferences (temperature, pH, salinity, oxygen), metabolism, and cell morphology of bacteria and archaea. Its primary purpose is to harmonize terminology across major microbial trait databases (BacDive, BactoTraits, Madin bacteria_archaea_traits, MetaTraits) for use in NMDC and KG-Microbe. METPO uses OBO-style annotation patterns (IAO textual definitions, oboInOwl synonyms) and cites terms from OMP, MicrO, GO, ECOCORE, and PATO as definition sources." xsd:string
 property_value: dcterms:license https://creativecommons.org/licenses/by/4.0/
 property_value: dcterms:title "METPO: Microbial Ecophysiological Trait and Phenotype Ontology" xsd:string
-property_value: owl:versionInfo "2026-06-05" xsd:string
+property_value: owl:versionInfo "2026-06-06" xsd:string
 property_value: seeAlso https://bioportal.bioontology.org/ontologies/METPO
 property_value: seeAlso https://bioregistry.io/registry/metpo
 property_value: seeAlso https://github.com/berkeleybop/metpo
diff --git a/metpo-full.owl b/metpo-full.owl
@@ -14,7 +14,7 @@
      xmlns:dcterms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="https://w3id.org/metpo/metpo-full.owl">
-        <owl:versionIRI rdf:resource="https://w3id.org/metpo/releases/2026-06-05/metpo-full.owl"/>
+        <owl:versionIRI rdf:resource="https://w3id.org/metpo/releases/2026-06-06/metpo-full.owl"/>
         <dcterms:contributor rdf:resource="https://orcid.org/0000-0001-8175-045X"/>
         <dcterms:contributor rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <dcterms:creator rdf:resource="https://orcid.org/0000-0001-9076-6066"/>
@@ -24,7 +24,7 @@
         <rdfs:seeAlso rdf:resource="https://bioportal.bioontology.org/ontologies/METPO"/>
         <rdfs:seeAlso rdf:resource="https://bioregistry.io/registry/metpo"/>
         <rdfs:seeAlso rdf:resource="https://github.com/berkeleybop/metpo"/>
-        <owl:versionInfo>2026-06-05</owl:versionInfo>
+        <owl:versionInfo>2026-06-06</owl:versionInfo>
     </owl:Ontology>
     
 
@@ -66,13 +66,17 @@
 
     <!-- http://purl.obolibrary.org/obo/IAO_0000231 -->
 
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000231"/>
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000231">
+        <rdfs:label>has obsolescence reason</rdfs:label>
+    </owl:AnnotationProperty>
     
 
 
     <!-- http://purl.obolibrary.org/obo/IAO_0100001 -->
 
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0100001"/>
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0100001">
+        <rdfs:label>term replaced by</rdfs:label>
+    </owl:AnnotationProperty>
     
 
 
diff --git a/metpo.json b/metpo.json
@@ -31,9 +31,9 @@
         "val" : "https://github.com/berkeleybop/metpo"
       }, {
         "pred" : "http://www.w3.org/2002/07/owl#versionInfo",
-        "val" : "2026-06-05"
+        "val" : "2026-06-06"
       } ],
-      "version" : "https://w3id.org/metpo/releases/2026-06-05/metpo.json"
+      "version" : "https://w3id.org/metpo/releases/2026-06-06/metpo.json"
     },
     "nodes" : [ {
       "id" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass",
@@ -24162,10 +24162,12 @@
       "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://purl.obolibrary.org/obo/IAO_0000231",
+      "lbl" : "has obsolescence reason",
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://purl.obolibrary.org/obo/IAO_0100001",
+      "lbl" : "term replaced by",
       "type" : "PROPERTY",
       "propertyType" : "ANNOTATION"
     }, {
diff --git a/metpo.obo b/metpo.obo
@@ -1,5 +1,5 @@
 format-version: 1.2
-data-version: https://w3id.org/metpo/releases/2026-06-05/metpo.owl
+data-version: https://w3id.org/metpo/releases/2026-06-06/metpo.owl
 idspace: dcterms http://purl.org/dc/terms/ 
 idspace: metpo https://w3id.org/metpo/ 
 idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# 
@@ -12,7 +12,7 @@ property_value: dcterms:creator https://orcid.org/0000-0001-9076-6066
 property_value: dcterms:description "METPO provides terms for microbial ecophysiological traits and phenotypes: growth preferences (temperature, pH, salinity, oxygen), metabolism, and cell morphology of bacteria and archaea. Its primary purpose is to harmonize terminology across major microbial trait databases (BacDive, BactoTraits, Madin bacteria_archaea_traits, MetaTraits) for use in NMDC and KG-Microbe. METPO uses OBO-style annotation patterns (IAO textual definitions, oboInOwl synonyms) and cites terms from OMP, MicrO, GO, ECOCORE, and PATO as definition sources." xsd:string
 property_value: dcterms:license https://creativecommons.org/licenses/by/4.0/
 property_value: dcterms:title "METPO: Microbial Ecophysiological Trait and Phenotype Ontology" xsd:string
-property_value: owl:versionInfo "2026-06-05" xsd:string
+property_value: owl:versionInfo "2026-06-06" xsd:string
 property_value: seeAlso https://bioportal.bioontology.org/ontologies/METPO
 property_value: seeAlso https://bioregistry.io/registry/metpo
 property_value: seeAlso https://github.com/berkeleybop/metpo
diff --git a/metpo.owl b/metpo.owl
@@ -14,7 +14,7 @@
      xmlns:dcterms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="https://w3id.org/metpo/metpo.owl">
-        <owl:versionIRI rdf:resource="https://w3id.org/metpo/releases/2026-06-05/metpo.owl"/>
+        <owl:versionIRI rdf:resource="https://w3id.org/metpo/releases/2026-06-06/metpo.owl"/>
         <dcterms:contributor rdf:resource="https://orcid.org/0000-0001-8175-045X"/>
         <dcterms:contributor rdf:resource="https://orcid.org/0000-0002-6601-2165"/>
         <dcterms:creator rdf:resource="https://orcid.org/0000-0001-9076-6066"/>
@@ -24,7 +24,7 @@
         <rdfs:seeAlso rdf:resource="https://bioportal.bioontology.org/ontologies/METPO"/>
         <rdfs:seeAlso rdf:resource="https://bioregistry.io/registry/metpo"/>
         <rdfs:seeAlso rdf:resource="https://github.com/berkeleybop/metpo"/>
-        <owl:versionInfo>2026-06-05</owl:versionInfo>
+        <owl:versionInfo>2026-06-06</owl:versionInfo>
     </owl:Ontology>
     
 
@@ -66,13 +66,17 @@
 
     <!-- http://purl.obolibrary.org/obo/IAO_0000231 -->
 
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000231"/>
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000231">
+        <rdfs:label>has obsolescence reason</rdfs:label>
+    </owl:AnnotationProperty>
     
 
 
     <!-- http://purl.obolibrary.org/obo/IAO_0100001 -->
 
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0100001"/>
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0100001">
+        <rdfs:label>term replaced by</rdfs:label>
+    </owl:AnnotationProperty>
     
 
 
diff --git a/src/ontology/metpo-edit.owl b/src/ontology/metpo-edit.owl
@@ -27,6 +27,8 @@ Declaration(AnnotationProperty(dcterms:license))
 Declaration(AnnotationProperty(dcterms:title))
 Declaration(AnnotationProperty(<http://qudt.org/schema/qudt/ucumCode>))
 Declaration(AnnotationProperty(IAO:0000117))
+Declaration(AnnotationProperty(IAO:0000231))
+Declaration(AnnotationProperty(IAO:0100001))
 
 
 ############################
@@ -49,6 +51,14 @@ AnnotationAssertion(rdfs:label dcterms:title "title")
 
 AnnotationAssertion(rdfs:label IAO:0000117 "term editor")
 
+# Annotation Property: IAO:0000231 (has obsolescence reason)
+
+AnnotationAssertion(rdfs:label IAO:0000231 "has obsolescence reason")
+
+# Annotation Property: IAO:0100001 (term replaced by)
+
+AnnotationAssertion(rdfs:label IAO:0100001 "term replaced by")
+
 
 ############################
 #   Object Properties
diff --git a/src/ontology/reports/release-diff.md b/src/ontology/reports/release-diff.md
