Adding 4 dynamic subsets and reports. Fixes #960

EnvironmentOntology · Jun 3, 2020 · a5b43bd · a5b43bd
1 parent af70239
commit a5b43bd
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Showing 17 changed files with 100,165 additions and 2 deletions.
diff --git a/src/envo/Makefile b/src/envo/Makefile
@@ -180,7 +180,8 @@ $(ONT)-full.owl: $(SRC) $(OTHER_SRC)
 ## Note we also include TSV as a format
 
 
-SUBSETS = envo-basic EnvO-Lite-GSC envoEmpo envoAstro envoPolar envoEmpo envoOmics envoCesab environmental_hazards
+SUBSETS = envo-basic EnvO-Lite-GSC envoEmpo envoAstro envoPolar envoEmpo envoOmics envoCesab environmental_hazards \
+   biome-hierarchy feature-hierarchy material-hierarchy process-hierarchy
 
 SUBSET_ROOTS = $(patsubst %, subsets/%, $(SUBSETS))
 SUBSET_FILES = $(foreach n,$(SUBSET_ROOTS), $(foreach f,$(FORMATS_INCL_TSV), $(n).$(f)))
@@ -189,7 +190,7 @@ SUBSET_FILES = $(foreach n,$(SUBSET_ROOTS), $(foreach f,$(FORMATS_INCL_TSV), $(n
 all_subsets: $(SUBSET_FILES)
 
 subsets/%.tsv: subsets/%.owl
-	$(ROBOT) export -i $< -c "ID|label|definition" -e $@
+	$(ROBOT) export -i $< -c "ID|label|SubClassOf [ID]|SubClassOf [LABEL]|SYNONYMS|definition|inSubset" -e $@
 #	$(ROBOT) query -f tsv -i $< -s ./sparql/labels.sparql $@
 
 envo-simple.owl: envo-base.owl
@@ -210,6 +211,42 @@ subsets/envo-basic.obo: envo-simple.owl
 #pato-lite.obo:
 #	$(OWLTOOLS) $(OBO)/pato.obo --make-subset-by-properties -o -f obo $@
 
+subsets/biome-hierarchy.owl: envo.owl
+	robot filter --input $< \
+	--term ENVO:00000428  \
+	--term IAO:0000115  \
+	--select "annotations self descendants" \
+	--signature true \
+	--output $@
+.PRECIOUS: subsets/biome-hierarchy.owl
+
+subsets/feature-hierarchy.owl: envo.owl
+	robot filter --input $< \
+	--term ENVO:01000813  \
+	--term IAO:0000115  \
+	--select "annotations self descendants" \
+	--signature true \
+	--output $@
+.PRECIOUS: subsets/feature-hierarchy.owl
+
+subsets/material-hierarchy.owl: envo.owl
+	robot filter --input $< \
+	--term ENVO:00010483  \
+	--term IAO:0000115  \
+	--select "annotations self descendants" \
+	--signature true \
+	--output $@
+.PRECIOUS: subsets/material-hierarchy.owl
+
+subsets/process-hierarchy.owl: envo.owl
+	robot filter --input $< \
+	--term ENVO:02500000  \
+	--term IAO:0000115  \
+	--select "annotations self descendants" \
+	--signature true \
+	--output $@
+.PRECIOUS: subsets/process-hierarchy.owl
+
 release-diffs:
 	cd diffs && make
 

diff --git a/src/envo/subsets/biome-hierarchy.json b/src/envo/subsets/biome-hierarchy.json
diff --git a/src/envo/subsets/biome-hierarchy.obo b/src/envo/subsets/biome-hierarchy.obo
diff --git a/src/envo/subsets/biome-hierarchy.owl b/src/envo/subsets/biome-hierarchy.owl
diff --git a/src/envo/subsets/biome-hierarchy.tsv b/src/envo/subsets/biome-hierarchy.tsv