Merge pull request #32 from mcwdsi/fix-units

Fix problems with clinical drug strength units
mcwdsi · Jul 25, 2024 · 1cb7ad6 · 1cb7ad6
2 parents 5787d54 + a4d25bb
commit 1cb7ad6
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diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md
@@ -19,7 +19,9 @@ These are the current imports in DRON
 | ro | http://purl.obolibrary.org/obo/ro.owl | slme |
 | apollo_sv | http://purl.obolibrary.org/obo/apollo_sv.owl | None |
 | go | http://purl.obolibrary.org/obo/go.owl | None |
+| iao | http://purl.obolibrary.org/obo/iao.owl | None |
 | obi | http://purl.obolibrary.org/obo/obi.owl | None |
+| uo | http://purl.obolibrary.org/obo/uo.owl | custom |
 | ogms | http://purl.obolibrary.org/obo/ogms.owl | None |
 | bfo | http://purl.obolibrary.org/obo/bfo.owl | slme |
 | omo | http://purl.obolibrary.org/obo/omo.owl | mirror |

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=                c15ccab5eeab92844591b6c33e398db0bdeaa3b472273506368bae37fe44271e
+CONFIG_HASH=                082560e7167e4c838bb11575d493a5b738d1886fb5b1721258c2e706584f371f
 
 
 # ----------------------------------------
@@ -165,7 +165,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  ro apollo_sv go obi ogms bfo omo chebi pr
+IMPORTS =  ro apollo_sv go iao obi uo ogms bfo omo chebi pr
 
 IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -393,6 +393,10 @@ $(IMPORTDIR)/ro_import.owl: $(MIRRORDIR)/ro.owl $(IMPORTDIR)/ro_terms_combined.t
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
 		$(ANNOTATE_CONVERT_FILE); fi
 
+## Module for ontology: uo
+
+$(IMPORTDIR)/uo_import.owl: $(MIRRORDIR)/uo.owl
+	echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in dron.Makefile!" && false
 ## Module for ontology: bfo
 
 $(IMPORTDIR)/bfo_import.owl: $(MIRRORDIR)/bfo.owl $(IMPORTDIR)/bfo_terms_combined.txt
@@ -511,6 +515,14 @@ mirror-go: | $(TMPDIR)
 	$(ROBOT) convert -i $(TMPDIR)/go-download.owl -o $(TMPDIR)/$@.owl
 
 
+## ONTOLOGY: iao
+.PHONY: mirror-iao
+.PRECIOUS: $(MIRRORDIR)/iao.owl
+mirror-iao: | $(TMPDIR)
+	curl -L $(OBOBASE)/iao.owl --create-dirs -o $(TMPDIR)/iao-download.owl --retry 4 --max-time 200 && \
+	$(ROBOT) convert -i $(TMPDIR)/iao-download.owl -o $(TMPDIR)/$@.owl
+
+
 ## ONTOLOGY: obi
 .PHONY: mirror-obi
 .PRECIOUS: $(MIRRORDIR)/obi.owl
@@ -519,6 +531,14 @@ mirror-obi: | $(TMPDIR)
 	$(ROBOT) convert -i $(TMPDIR)/obi-download.owl -o $(TMPDIR)/$@.owl
 
 
+## ONTOLOGY: uo
+.PHONY: mirror-uo
+.PRECIOUS: $(MIRRORDIR)/uo.owl
+mirror-uo: | $(TMPDIR)
+	curl -L $(OBOBASE)/uo.owl --create-dirs -o $(TMPDIR)/uo-download.owl --retry 4 --max-time 200 && \
+	$(ROBOT) convert -i $(TMPDIR)/uo-download.owl -o $(TMPDIR)/$@.owl
+
+
 ## ONTOLOGY: ogms
 .PHONY: mirror-ogms
 .PRECIOUS: $(MIRRORDIR)/ogms.owl

diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml
@@ -12,6 +12,8 @@
   <uri name="http://purl.obolibrary.org/obo/dron/imports/go_import.owl" uri="imports/go_import.owl"/>
   <uri name="http://purl.obolibrary.org/obo/dron/imports/obi_import.owl" uri="imports/obi_import.owl"/>
   <uri name="http://purl.obolibrary.org/obo/dron/imports/ogms_import.owl" uri="imports/ogms_import.owl"/>
+  <uri name="http://purl.obolibrary.org/obo/dron/imports/iao_import.owl" uri="imports/iao_import.owl"/>
+  <uri name="http://purl.obolibrary.org/obo/dron/imports/uo_import.owl" uri="imports/uo_import.owl"/>
 
 <!--  <uri name="http://purl.obolibrary.org/obo/dron/dron-chebi.owl" uri="components/dron-chebi.owl"/>-->
 

diff --git a/src/ontology/dron-edit.owl b/src/ontology/dron-edit.owl
@@ -16,11 +16,13 @@ Import(<http://purl.obolibrary.org/obo/dron/imports/apollo_sv_import.owl>)
 Import(<http://purl.obolibrary.org/obo/dron/imports/bfo_import.owl>)
 Import(<http://purl.obolibrary.org/obo/dron/imports/chebi_import.owl>)
 Import(<http://purl.obolibrary.org/obo/dron/imports/go_import.owl>)
+Import(<http://purl.obolibrary.org/obo/dron/imports/iao_import.owl>)
 Import(<http://purl.obolibrary.org/obo/dron/imports/obi_import.owl>)
 Import(<http://purl.obolibrary.org/obo/dron/imports/ogms_import.owl>)
 Import(<http://purl.obolibrary.org/obo/dron/imports/omo_import.owl>)
 Import(<http://purl.obolibrary.org/obo/dron/imports/pr_import.owl>)
 Import(<http://purl.obolibrary.org/obo/dron/imports/ro_import.owl>)
+Import(<http://purl.obolibrary.org/obo/dron/imports/uo_import.owl>)
 Annotation(dcterms:creator "Eric Joseph")
 Annotation(dcterms:creator "Josh Hanna")
 Annotation(dcterms:creator "Mathias Brochhausen")

diff --git a/src/ontology/dron-odk.yaml b/src/ontology/dron-odk.yaml
@@ -31,7 +31,10 @@ import_group:
       slme_individuals: exclude
     - id: apollo_sv
     - id: go
+    - id: iao
     - id: obi
+    - id: uo
+      module_type: custom
     - id: ogms
     - id: bfo
       module_type: slme

diff --git a/src/ontology/dron.Makefile b/src/ontology/dron.Makefile
@@ -3,6 +3,18 @@
 ## If you need to customize your Makefile, make
 ## changes here rather than in the main Makefile
 
+##########################
+#### Custom UO Import ####
+##########################
+
+$(IMPORTDIR)/uo_import.owl: $(MIRRORDIR)/uo.owl $(IMPORTDIR)/uo_terms_combined.txt
+	if [ $(IMP) = true ]; then $(ROBOT) merge -i $< \
+		query --update ../sparql/preprocess-module.ru \
+		remove --base-iri "$(OBOBASE)/UO_" --axioms external --preserve-structure false --trim false \
+		extract --method MIREOT --upper-term UO:0000000 $(patsubst %, --lower-term %, $(ANNOTATION_PROPERTIES)) --lower-terms $(IMPORTDIR)/uo_terms_combined.txt \
+		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
+		$(ANNOTATE_CONVERT_FILE); fi
+
 ##################################
 #### Custom release artefacts ####
 ##################################
@@ -33,7 +45,7 @@ $(TMPDIR)/ldtab.jar: | $(TMPDIR)
 LDTAB := java -jar $(TMPDIR)/ldtab.jar
 
 # Load DrOn templates into SQLite.
-$(TMPDIR)/dron.db: $(SCRIPTSDIR)/create-dron-tables.sql $(SCRIPTSDIR)/load-dron-tables.sql $(SCRIPTSDIR)/index-dron-tables.sql
+$(TMPDIR)/dron.db: $(SCRIPTSDIR)/create-dron-tables.sql $(SCRIPTSDIR)/load-dron-tables.sql $(SCRIPTSDIR)/index-dron-tables.sql $(TEMPLATEDIR)/*.tsv
 	rm -f $@
 	sqlite3 $@ < $<
 	sqlite3 $@ < $(word 2,$^)

diff --git a/src/ontology/imports/external_import.owl b/src/ontology/imports/external_import.owl
@@ -97,6 +97,12 @@ Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000057>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002211>))
 Declaration(DataProperty(<http://purl.obolibrary.org/obo/OBI_0001937>))
 Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/UO_0000022>))
+Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/UO_0000040>))
+Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/UO_0000098>))
+Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/UO_0000176>))
+Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/UO_0000187>))
+Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/UO_0000201>))
+Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/UO_0010073>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/BFO_0000179>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/BFO_0000180>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000111>))