Update OBI import module using ODK's make base option to get proper…

… parents as the base file is not yet pre-reasoned, as it should be (see also: obi-ontology/obi#1815)
nmrML · Aug 21, 2024 · fd1a5e3 · fd1a5e3
1 parent 5f8c927
commit fd1a5e3
Showing 5 changed files with 101 additions and 18 deletions.
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -10,7 +10,7 @@
 # More information: https://github.com/INCATools/ontology-development-kit/
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                063948980a77d2cae11b525e208d573c79ba7ada9bb786ef8519bf6438fdc969
+CONFIG_HASH=                6bdc85a714f6ee8c03d73f3362a5362d0fe4354c253f35c4f4b4b4d4482f0e4a
 
 
 # ----------------------------------------
@@ -455,8 +455,8 @@ mirror-iao: | $(TMPDIR)
 .PHONY: mirror-obi
 .PRECIOUS: $(MIRRORDIR)/obi.owl
 mirror-obi: | $(TMPDIR)
-	curl -L $(OBOBASE)/obi/obi-base.owl --create-dirs -o $(TMPDIR)/obi-download.owl --retry 4 --max-time 200 && \
-	$(ROBOT) convert -i $(TMPDIR)/obi-download.owl -o $(TMPDIR)/$@.owl
+	curl -L $(OBOBASE)/obi.owl --create-dirs -o $(TMPDIR)/obi-download.owl --retry 4 --max-time 200 && \
+	$(ROBOT) remove -i $(TMPDIR)/obi-download.owl --base-iri $(OBOBASE)/OBI --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: chebi

diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl
diff --git a/src/ontology/imports/obi_remove_list.txt b/src/ontology/imports/obi_remove_list.txt
@@ -10,7 +10,6 @@ OBI:0000684 # 'specimen collection objective'
 OBI:0001933 # 'value specification'
 OBI:0000017 # 'regulatory role'
 OBI:0000947 # 'service provider role'
-OBI:0000832 # 'measurement device'
 OBI:0002989 # 'material supplier'
 OBI:0000450 # 'regulatory agency'
 IAO:0000009

diff --git a/src/ontology/nmrCV-odk.yaml b/src/ontology/nmrCV-odk.yaml
@@ -32,7 +32,6 @@ robot_java_args: '-Xmx16G'  # max RAM to be used by Robot in ODK
 use_templates: TRUE
 
 
-## NMR specific Settings ##
 
 import_group:
   products:
@@ -46,7 +45,7 @@ import_group:
   #- id: chmo
   #- id: pato
   - id: obi
-    use_base: true
+    make_base: true
     module_type: custom
   - id: chebi
     is_large: true

diff --git a/src/ontology/nmrCV.Makefile b/src/ontology/nmrCV.Makefile
@@ -10,7 +10,7 @@
 
 $(IMPORTDIR)/obi_import.owl: $(MIRRORDIR)/obi.owl $(IMPORTDIR)/obi_terms.txt
 	if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
-        extract -T $(IMPORTDIR)/obi_terms.txt --force true --copy-ontology-annotations true --individuals minimal --intermediates minimal --method BOT \
+        extract -T $(IMPORTDIR)/obi_terms.txt --force true --copy-ontology-annotations true --individuals minimal --method BOT \
         query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
         remove -T $(IMPORTDIR)/obi_remove_list.txt --select "self descendants instances" --signature true \
         $(ANNOTATE_CONVERT_FILE); fi