prepare release

pfabry · Apr 20, 2023 · 5ccd03d · 5ccd03d
1 parent 96f1a03
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diff --git a/ODKRepo-base.owl b/ODKRepo-base.owl
@@ -2,19 +2,20 @@
 <rdf:RDF xmlns="http://purl.obolibrary.org/obo/ODKRepo/ODKRepo-base.owl#"
      xml:base="http://purl.obolibrary.org/obo/ODKRepo/ODKRepo-base.owl"
      xmlns:dc="http://purl.org/dc/elements/1.1/"
+     xmlns:obo="http://purl.obolibrary.org/obo/"
      xmlns:owl="http://www.w3.org/2002/07/owl#"
      xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
      xmlns:xml="http://www.w3.org/XML/1998/namespace"
      xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      xmlns:terms="http://purl.org/dc/terms/">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/ODKRepo/ODKRepo-base.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ODKRepo/releases/2023-04-18/ODKRepo-base.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ODKRepo/releases/2023-04-20/ODKRepo-base.owl"/>
         <dc:type rdf:resource="http://purl.obolibrary.org/obo/IAO_8000001"/>
         <terms:description>None</terms:description>
         <terms:license rdf:resource="https://creativecommons.org/licenses/unspecified"/>
         <terms:title>ODK test repository</terms:title>
-        <owl:versionInfo>2023-04-18</owl:versionInfo>
+        <owl:versionInfo>2023-04-20</owl:versionInfo>
     </owl:Ontology>
 
 
@@ -30,6 +31,12 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/IAO_0000115 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115"/>
+
+
+
     <!-- http://purl.org/dc/elements/1.1/type -->
 
     <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/type"/>
@@ -71,10 +78,18 @@
 
 
 
-    <!-- http://purl.obolibrary.org/obo/ODKREPO_0000000 -->
+    <!-- http://purl.obolibrary.org/obo/OBI_0000011 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000011"/>
+
+
+
+    <!-- http:/purl.obolibrary.org/obo/ODKREPO_0000001 -->
 
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/ODKREPO_0000000">
-        <rdfs:label xml:lang="en">root node</rdfs:label>
+    <owl:Class rdf:about="http:/purl.obolibrary.org/obo/ODKREPO_0000001">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
+        <obo:IAO_0000115 xml:lang="en">A planned process that is an intervention.</obo:IAO_0000115>
+        <rdfs:label xml:lang="en">health intervention</rdfs:label>
     </owl:Class>
 </rdf:RDF>
 

diff --git a/ODKRepo-full.owl b/ODKRepo-full.owl
diff --git a/ODKRepo.owl b/ODKRepo.owl
diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md
@@ -16,10 +16,9 @@ These are the current imports in ODKREPO
 
 | Import | URL | Type |
 | ------ | --- | ---- |
-| bfo | http://purl.obolibrary.org/obo/bfo.owl | None |
-| omo | http://purl.obolibrary.org/obo/omo.owl | None |
+| bfo-2020 | https://raw.githubusercontent.com/BFO-ontology/BFO-2020/master/21838-2/owl/bfo-2020.owl | mirror |
+| omo | http://purl.obolibrary.org/obo/omo.owl | mirror |
 | obi | http://purl.obolibrary.org/obo/obi.owl | None |
-| omrse | http://purl.obolibrary.org/obo/omrse.owl | None |
 
 ## 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
@@ -54,7 +54,7 @@ OTHER_SRC =
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 EDIT_PREPROCESSED =         $(TMPDIR)/$(ONT)-preprocess.owl
 
-FORMATS = $(sort  owl json owl)
+FORMATS = $(sort  owl owl)
 FORMATS_INCL_TSV = $(sort $(FORMATS) tsv)
 RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full )
 
@@ -108,7 +108,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  bfo omo obi omrse
+IMPORTS =  bfo-2020 omo obi
 
 IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -309,6 +309,18 @@ $(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/%.owl $(IMPORTDIR)/%_terms_combined.txt
 
 .PRECIOUS: $(IMPORTDIR)/%_import.owl
 
+## Module for ontology: bfo-2020
+
+$(IMPORTDIR)/bfo-2020_import.owl: $(MIRRORDIR)/bfo-2020.owl $(IMPORTDIR)/bfo-2020_terms_combined.txt
+	if [ $(IMP) = true ]; then $(ROBOT) merge -i $< query --update ../sparql/preprocess-module.ru --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru  \
+    $(ANNOTATE_CONVERT_FILE); fi
+
+## Module for ontology: omo
+
+$(IMPORTDIR)/omo_import.owl: $(MIRRORDIR)/omo.owl $(IMPORTDIR)/omo_terms_combined.txt
+	if [ $(IMP) = true ]; then $(ROBOT) merge -i $< query --update ../sparql/preprocess-module.ru --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru  \
+    $(ANNOTATE_CONVERT_FILE); fi
+
 
 .PHONY: refresh-imports
 refresh-imports:
@@ -340,12 +352,11 @@ IMP_LARGE=true # Global parameter to bypass handling of large imports
 
 
 
-## ONTOLOGY: bfo
-.PHONY: mirror-bfo
-.PRECIOUS: $(MIRRORDIR)/bfo.owl
-mirror-bfo: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/bfo.owl --create-dirs -o $(MIRRORDIR)/bfo.owl --retry 4 --max-time 200 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/bfo.owl -o $@.tmp.owl &&\
+## ONTOLOGY: bfo-2020
+.PHONY: mirror-bfo-2020
+.PRECIOUS: $(MIRRORDIR)/bfo-2020.owl
+mirror-bfo-2020: | $(TMPDIR)
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I https://raw.githubusercontent.com/BFO-ontology/BFO-2020/master/21838-2/owl/bfo-2020.owl -o $@.tmp.owl &&\
 		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
@@ -367,15 +378,6 @@ mirror-obi: | $(TMPDIR)
 		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
-## ONTOLOGY: omrse
-.PHONY: mirror-omrse
-.PRECIOUS: $(MIRRORDIR)/omrse.owl
-mirror-omrse: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/omrse.owl --create-dirs -o $(MIRRORDIR)/omrse.owl --retry 4 --max-time 200 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/omrse.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
-
-
 $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
 	if [ $(IMP) = true ] && [ $(MIR) = true ] && [ -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
@@ -396,10 +398,6 @@ $(SUBSETDIR)/%.owl: $(ONT).owl | $(SUBSETDIR)
 .PRECIOUS: $(SUBSETDIR)/%.owl
 
 
-$(SUBSETDIR)/%.json: $(SUBSETDIR)/%.owl
-	$(ROBOT) convert --input $< --check false -f json -o $@.tmp.json &&\
-	mv $@.tmp.json $@
-
 
 # ---------------------------------------------
 # Sparql queries: Table exports / Query Reports
@@ -419,14 +417,6 @@ endif
 # ----------------------------------------
 
 
-$(ONT)-base.json: $(ONT)-base.owl
-	$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
-		convert --check false -f json -o $@.tmp.json &&\
-		mv $@.tmp.json $@
-$(ONT)-full.json: $(ONT)-full.owl
-	$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
-		convert --check false -f json -o $@.tmp.json &&\
-		mv $@.tmp.json $@
 # ----------------------------------------
 # Release artefacts: main release artefacts
 # ----------------------------------------
@@ -435,10 +425,6 @@ $(ONT).owl: $(ONT)-full.owl
 	$(ROBOT) annotate --input $< --ontology-iri $(URIBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
 		convert -o $@.tmp.owl && mv $@.tmp.owl $@
 
-$(ONT).json: $(ONT).owl
-	$(ROBOT) annotate --input $< --ontology-iri $(URIBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
-		convert --check false -f json -o $@.tmp.json &&\
-		mv $@.tmp.json $@
 # -----------------------------------------------------
 # Release artefacts: variants (base, full, simple, etc)
 # -----------------------------------------------------

diff --git a/src/ontology/ODKRepo-edit.owl b/src/ontology/ODKRepo-edit.owl
@@ -1,4 +1,3 @@
-
 Prefix(:=<http://purl.obolibrary.org/obo/ODKRepo.owl#>)
 Prefix(dce:=<http://purl.org/dc/elements/1.1/>)
 Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
@@ -10,42 +9,44 @@ Prefix(dcterms:=<http://purl.org/dc/terms/>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/ODKRepo.owl>
-
-Import(<http://purl.obolibrary.org/obo/ODKRepo/imports/bfo_import.owl>)
-
-Import(<http://purl.obolibrary.org/obo/ODKRepo/imports/omo_import.owl>)
-
-Import(<http://purl.obolibrary.org/obo/ODKRepo/imports/obi_import.owl>)
-
-Import(<http://purl.obolibrary.org/obo/ODKRepo/imports/omrse_import.owl>)
-
-
+Import(<http://purl.obolibrary.org/obo/ODKRepo/releases/2023-04-20/imports/bfo-2020_import.owl>)
+Import(<http://purl.obolibrary.org/obo/ODKRepo/releases/2023-04-20/imports/obi_import.owl>)
+Import(<http://purl.obolibrary.org/obo/ODKRepo/releases/2023-04-20/imports/omo_import.owl>)
 Annotation(dcterms:description "None")
 Annotation(dcterms:license <https://creativecommons.org/licenses/unspecified>)
 Annotation(dcterms:title "ODK test repository")
 
-
-Declaration(Class(<http://purl.obolibrary.org/obo/ODKREPO_0000000>))
+Declaration(Class(<http:/purl.obolibrary.org/obo/ODKREPO_0000001>))
 Declaration(AnnotationProperty(dcterms:description))
 Declaration(AnnotationProperty(dcterms:license))
 Declaration(AnnotationProperty(dcterms:title))
-
 ############################
 #   Annotation Properties
 ############################
 
+# Annotation Property: dcterms:description (description)
+
 AnnotationAssertion(rdfs:label dcterms:description "description")
+
+# Annotation Property: dcterms:license (license)
+
 AnnotationAssertion(rdfs:label dcterms:license "license")
+
+# Annotation Property: dcterms:title (title)
+
 AnnotationAssertion(rdfs:label dcterms:title "title")
 
+
+
 ############################
 #   Classes
 ############################
 
-# Class: <http://purl.obolibrary.org/obo/ODKREPO_0000000> (root node)
-
-AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ODKREPO_0000000> "root node"@en)
+# Class: <http:/purl.obolibrary.org/obo/ODKREPO_0000001> (health intervention)
 
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http:/purl.obolibrary.org/obo/ODKREPO_0000001> "A planned process that is an intervention."@en)
+AnnotationAssertion(rdfs:label <http:/purl.obolibrary.org/obo/ODKREPO_0000001> "health intervention"@en)
+SubClassOf(<http:/purl.obolibrary.org/obo/ODKREPO_0000001> <http://purl.obolibrary.org/obo/OBI_0000011>)
 
-)
 
+)
diff --git a/src/ontology/ODKRepo-odk.yaml b/src/ontology/ODKRepo-odk.yaml
@@ -10,11 +10,12 @@ release_artefacts:
 primary_release: full
 export_formats:
   - owl
-  - json
 import_group:
   products:
-    - id: bfo
+    - id: bfo-2020
+      module_type: mirror
+      mirror_from: "https://raw.githubusercontent.com/BFO-ontology/BFO-2020/master/21838-2/owl/bfo-2020.owl"
     - id: omo
+      module_type: mirror
     - id: obi
-    - id: omrse
 robot_java_args: "-Xmx8G"
diff --git a/src/ontology/ODKRepo.Makefile b/src/ontology/ODKRepo.Makefile
@@ -3,4 +3,20 @@
 ## If you need to customize your Makefile, make
 ## changes here rather than in the main Makefile
 
+## ONTOLOGY: obi without individuals
+.PHONY: mirror-obi
+.PRECIOUS: $(MIRRORDIR)/obi.owl
+mirror-obi: | $(TMPDIR)
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/obi.owl --create-dirs -o $(MIRRORDIR)/obi.owl --retry 4 --max-time 200 &&\
+	$(ROBOT) convert -i $(MIRRORDIR)/obi.owl -o $@.tmp.owl &&\
+	$(ROBOT) remove -i $@.tmp.owl --select individuals -o $@.tmp.owl &&\
+	mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
+## ONTOLOGY: omo
+.PHONY: mirror-omo
+.PRECIOUS: $(MIRRORDIR)/omo.owl
+mirror-omo: | $(TMPDIR)
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/omo.owl --create-dirs -o $(MIRRORDIR)/omo.owl --retry 4 --max-time 200 &&\
+		$(ROBOT) convert -i $(MIRRORDIR)/omo.owl -o $@.tmp.owl &&\
+		$(ROBOT) remove -i $@.tmp.owl --select individuals -o $@.tmp.owl &&\
+		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml
@@ -1,23 +1,7 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
-<group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public" xml:base="">
-
-
-  <uri name="http://purl.obolibrary.org/obo/ODKRepo/imports/bfo_import.owl" uri="imports/bfo_import.owl"/>
-  <uri name="http://purl.obolibrary.org/obo/ODKRepo/imports/bfo_import.obo" uri="imports/bfo_import.obo"/>
-
-  <uri name="http://purl.obolibrary.org/obo/ODKRepo/imports/omo_import.owl" uri="imports/omo_import.owl"/>
-  <uri name="http://purl.obolibrary.org/obo/ODKRepo/imports/omo_import.obo" uri="imports/omo_import.obo"/>
-
-  <uri name="http://purl.obolibrary.org/obo/ODKRepo/imports/obi_import.owl" uri="imports/obi_import.owl"/>
-  <uri name="http://purl.obolibrary.org/obo/ODKRepo/imports/obi_import.obo" uri="imports/obi_import.obo"/>
-
-  <uri name="http://purl.obolibrary.org/obo/ODKRepo/imports/omrse_import.owl" uri="imports/omrse_import.owl"/>
-  <uri name="http://purl.obolibrary.org/obo/ODKRepo/imports/omrse_import.obo" uri="imports/omrse_import.obo"/>
-
-
-
-
-
-</group>
-</catalog>
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
+    <uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/obo/ODKRepo/releases/2023-04-20/imports/obi_import.owl" uri="imports/obi_import.owl"/>
+    <uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/obo/ODKRepo/releases/2023-04-20/imports/omo_import.owl" uri="imports/omo_import.owl"/>
+    <uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/obo/ODKRepo/releases/2023-04-20/imports/bfo-2020_import.owl" uri="imports/bfo-2020_import.owl"/>
+    <group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public" xml:base=""/>
+</catalog>