Merge pull request #115 from berkeleybop/114-update-build-and-qc-make…

…file-targets

update build and qc Makefile targets

src/ontology/Makefile

@@ -700,4 +700,6 @@ Tricks:
 endef
 export data
 
-include aio.Makefile
+include aio.Makefile
+
+make-aio: clean clean-extras remove-old-input components-from-new-input all

src/ontology/aio.Makefile

@@ -38,3 +38,35 @@ components/%.owl: components/%.csv
 	  -t $< \
 	  annotate --annotation-file aio-annotations.ttl \
 	  -o $@
+
+clean-extras:
+	rm -rf aio.db aio-root-statistics* aio-2024-06-26.owl current-vs-2024-06-26-diff*
+
+remove-old-input:
+	rm -rf aio-src.csv
+	rm -rf components/aio-component.owl
+
+components-from-new-input: remove-old-input
+	make aio-src.csv
+	make components/aio-component.owl
+
+aio.db: aio.owl # requires that rdftab and relation0graph have been installed locally and are on the default path
+	poetry run semsql make $@
+	rm -rf aio-relation-graph.tsv.gz
+
+aio-root-statistics.tsv: aio.db # could use sqlite:obo:aio if the file in the BBOP S3 bucket is new enough
+	poetry run runoak \
+		--input $< statistics \
+		-O tsv -o $@ $$(poetry run runoak --input $< roots | cut -f 1 | sed '1d' | tr '\n' ' ')
+
+aio-root-statistics-transposed-filtered.tsv: aio-root-statistics.tsv
+	python ../scripts/transpose_filter_statistics.py < $< > $@
+
+aio-2024-06-26.owl:
+	wget -O $@ "https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/v2024-06-26/aio.owl"
+
+current-vs-2024-06-26-diff.txt: aio.owl aio-2024-06-26.owl
+	robot diff --left $< --right aio-2024-06-26.owl --output $@
+
+current-vs-2024-06-26-diff-skip-defs.txt: current-vs-2024-06-26-diff.txt
+	cat $< | grep -v IAO_0000115 > $@

src/scripts/transpose_filter_statistics.py

@@ -0,0 +1,7 @@
+import sys
+
+prefixes = ('id', 'class_count', 'subclass_of_axiom_count', 'distinct_synonym_count')
+lines = [line.strip().split('\t') for line in sys.stdin]
+transposed = zip(*lines)
+filtered = [row for row in transposed if row[0] in prefixes]
+print('\n'.join('\t'.join(item for item in row) for row in filtered))

src/sparql/subclass-label-compatibility.rq

@@ -0,0 +1,15 @@
+PREFIX  obo:  <http://purl.obolibrary.org/obo/>
+PREFIX  rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+SELECT  ?parent ?parent_label ?child ?child_def
+WHERE
+  { ?child  rdfs:subClassOf  ?parent
+    MINUS
+      { ?child  rdfs:subClassOf  <http://www.w3.org/2002/07/owl#Thing> }
+    FILTER isURI(?parent)
+    OPTIONAL
+      { ?child  obo:IAO_0000115  ?child_def }
+    OPTIONAL
+      { ?parent rdfs:label ?parent_label }
+  }
+ORDER BY ?parent ?child