OGMS · dillerm · May 11, 2026
diff --git a/.gitignore b/.gitignore
@@ -4,7 +4,6 @@
 .DS_Store
 semantic.cache
 bin/
-catalog-v001.xml
 
 *.tmp
 *.tmp.obo

diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md
@@ -22,6 +22,7 @@ These are the current imports in OGMS
 | iao | http://purl.obolibrary.org/obo/iao.owl | mirror |
 | ido | http://purl.obolibrary.org/obo/ido.owl | filter |
 | omo | http://purl.obolibrary.org/obo/omo.owl | mirror |
+| cob | http://purl.obolibrary.org/obo/cob.owl | slme |
 ## Components
 Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered _native_ to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases:
 

diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -16,7 +16,7 @@
 # 3. [Update repo to latest ODK](update_repo)
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                04d4c89977807b1ad2521b6386e797df708e1d2805834dc0af9cc669ff68d53d
+CONFIG_HASH=                1fc11db5bb385926b27aa9fa890f57825a32f749e19de3b6ec2c22720f272f95
 
 
 # ----------------------------------------
@@ -194,7 +194,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  ro obi bfo iao ido omo
+IMPORTS =  ro obi bfo iao ido omo cob
 
 IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -571,6 +571,14 @@ mirror-omo: | $(TMPDIR)
 	$(ROBOT) convert -i $(TMPDIR)/omo-download.owl -o $(TMPDIR)/$@.owl
 
 
+## ONTOLOGY: cob
+.PHONY: mirror-cob
+.PRECIOUS: $(MIRRORDIR)/cob.owl
+mirror-cob: | $(TMPDIR)
+	curl -L $(OBOBASE)/cob.owl --create-dirs -o $(TMPDIR)/cob-download.owl --retry 4 --max-time 200 && \
+	$(ROBOT) convert -i $(TMPDIR)/cob-download.owl -o $(TMPDIR)/$@.owl
+
+
 $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
 	if [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\
 		cp $(TMPDIR)/mirror-$*.owl $@; fi; fi

diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml
@@ -7,5 +7,6 @@
     <uri name="http://purl.obolibrary.org/obo/ogms/imports/iao_import.owl" uri="imports/iao_import.owl" />
     <uri name="http://purl.obolibrary.org/obo/ogms/imports/ido_import.owl" uri="imports/ido_import.owl" />
     <uri name="http://purl.obolibrary.org/obo/ogms/imports/omo_import.owl" uri="imports/omo_import.owl" />
+    <uri name="http://purl.obolibrary.org/obo/ogms/imports/cob_import.owl" uri="imports/cob_import.owl" />
   </group>
 </catalog>
diff --git a/src/ontology/imports/cob_import.owl b/src/ontology/imports/cob_import.owl
diff --git a/src/ontology/imports/cob_terms.txt b/src/ontology/imports/cob_terms.txt
diff --git a/src/ontology/ogms-edit.owl b/src/ontology/ogms-edit.owl
@@ -15,6 +15,7 @@ Prefix(oboInOwl:=<http://www.geneontology.org/formats/oboInOwl#>)
 
 Ontology(<http://purl.obolibrary.org/obo/ogms.owl>
 Import(<http://purl.obolibrary.org/obo/ogms/imports/bfo_import.owl>)
+Import(<http://purl.obolibrary.org/obo/ogms/imports/cob_import.owl>)
 Import(<http://purl.obolibrary.org/obo/ogms/imports/iao_import.owl>)
 Import(<http://purl.obolibrary.org/obo/ogms/imports/ido_import.owl>)
 Import(<http://purl.obolibrary.org/obo/ogms/imports/obi_import.owl>)
@@ -604,7 +605,6 @@ SubClassOf(obo:OGMS_0000074 obo:BFO_0000031)
 
 # Class: obo:OGMS_0000077 (pathological formation)
 
-AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000077 "TODO: Define, relate to disorder, and place in the OGMS hierarchy."@en)
 AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000077 "Albert Goldfain")
 AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000077 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf")
 AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000077 "creation date: 2009-07-13T02:14:59Z")
@@ -622,7 +622,6 @@ SubClassOf(obo:OGMS_0000078 obo:BFO_0000040)
 
 # Class: obo:OGMS_0000079 (portion of pathological body substance)
 
-AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000079 "TODO: Define, relate to disorder, and place in the OGMS hierarchy."@en)
 AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000079 "Albert Goldfain")
 AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000079 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf")
 AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000079 "creation date: 2009-07-13T02:15:17Z")
@@ -649,7 +648,6 @@ SubClassOf(obo:OGMS_0000081 obo:OGMS_0000061)
 
 # Class: obo:OGMS_0000082 (pathological invasion)
 
-AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000082 "TODO: Define."@en)
 AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000082 "Albert Goldfain")
 AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000082 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf")
 AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000082 "creation date: 2009-07-13T02:17:47Z")
@@ -658,7 +656,6 @@ SubClassOf(obo:OGMS_0000082 obo:OGMS_0000061)
 
 # Class: obo:OGMS_0000083 (physical examination finding)
 
-AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000083 "TODO: Define."@en)
 AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000083 "Albert Goldfain")
 AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000083 "creation date: 2009-11-24T04:51:11Z")
 AnnotationAssertion(rdfs:label obo:OGMS_0000083 "physical examination finding")
@@ -719,6 +716,7 @@ SubClassOf(obo:OGMS_0000089 obo:BFO_0000040)
 AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000090 "A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process"@en)
 AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000090 "Albert Goldfain")
 AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000090 "creation date: 2010-03-31T04:51:11Z")
+AnnotationAssertion(oboInOwl:hasExactSynonym obo:OGMS_0000090 "medical intervention"@en)
 AnnotationAssertion(rdfs:label obo:OGMS_0000090 "treatment")
 SubClassOf(obo:OGMS_0000090 obo:OGMS_0000096)
 
@@ -804,7 +802,6 @@ SubClassOf(obo:OGMS_0000098 obo:OGMS_0000096)
 
 # Class: obo:OGMS_0000099 (outpatient encounter)
 
-AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000099 "TODO"@en)
 AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000099 "Albert Goldfain")
 AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000099 "creation date: 2011-02-21T09:57:44Z")
 AnnotationAssertion(rdfs:label obo:OGMS_0000099 "outpatient encounter")
@@ -915,6 +912,7 @@ SubClassOf(obo:OGMS_0000110 obo:OGMS_0000096)
 
 AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000111 "A treatment whose completion is hypothesized by a health care provider to prevent the signs and symptoms of a disorder or pathological process.")
 AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000111 "Creation date: 2018-11-27")
+AnnotationAssertion(oboInOwl:hasExactSynonym obo:OGMS_0000111 "preventive intervention"@en)
 AnnotationAssertion(rdfs:label obo:OGMS_0000111 "prophylactic treatment"@en)
 SubClassOf(obo:OGMS_0000111 obo:OGMS_0000090)
 

diff --git a/src/ontology/ogms-odk.yaml b/src/ontology/ogms-odk.yaml
@@ -43,6 +43,9 @@ import_group:
         - http://purl.obolibrary.org/obo/IDO_
     - id: omo
       module_type: mirror
+    - id: cob
+      module_type: slme
+      slme_individuals: exclude
 
 use_custom_import_module: TRUE
 robot_java_args: '-Xmx8G'