From cdf013d6a19a23091de1bdbde84dd666f61d4317 Mon Sep 17 00:00:00 2001
From: Anita Caron <anitacaron@users.noreply.github.com>
Date: Mon, 26 Jun 2023 15:32:53 +0100
Subject: [PATCH] add common-anatomy.owl artifact

---
 .gitignore                   |  1 +
 src/ontology/Makefile        | 11 ++++++++++-
 src/ontology/uberon-odk.yaml |  1 +
 src/ontology/uberon.Makefile | 10 ++++++++++
 4 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index bd2f91d38d..05b083ca9e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -204,6 +204,7 @@ uberon-base.obo
 uberon-basic.*
 uberon-full.*
 uberon-simple.*
+common-anatomy.*
 patterns/definitions.owl
 patterns/pattern.owl
 subsets/*.json
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
index 84a536a80a..4a755541d7 100644
--- a/src/ontology/Makefile
+++ b/src/ontology/Makefile
@@ -62,7 +62,7 @@ PATTERN_RELEASE_FILES=      $(PATTERNDIR)/definitions.owl $(PATTERNDIR)/pattern.
 
 FORMATS = $(sort  owl obo json owl)
 FORMATS_INCL_TSV = $(sort $(FORMATS) tsv)
-RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic ext basic composite-metazoan composite-metazoan-basic composite-vertebrate composite-vertebrate-basic )
+RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic ext basic composite-metazoan composite-metazoan-basic composite-vertebrate composite-vertebrate-basic common-anatomy )
 
 # ----------------------------------------
 # Top-level targets
@@ -703,6 +703,12 @@ composite-vertebrate-basic.json: composite-vertebrate-basic.owl
 	$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
 		convert --check false -f json -o $@.tmp.json &&\
 		mv $@.tmp.json $@
+common-anatomy.obo: common-anatomy.owl
+	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo
+common-anatomy.json: common-anatomy.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
 # ----------------------------------------
@@ -791,6 +797,9 @@ composite-vertebrate.owl:
 
 composite-vertebrate-basic.owl:
 	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false
+
+common-anatomy.owl:
+	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false
 # ----------------------------------------
 # Debugging Tools
 # ----------------------------------------
diff --git a/src/ontology/uberon-odk.yaml b/src/ontology/uberon-odk.yaml
index 823459f78b..3e399e3adb 100644
--- a/src/ontology/uberon-odk.yaml
+++ b/src/ontology/uberon-odk.yaml
@@ -26,6 +26,7 @@ release_artefacts:
   - custom-composite-metazoan-basic
   - custom-composite-vertebrate
   - custom-composite-vertebrate-basic
+  - custom-common-anatomy
 edit_format: obo
 import_group:
   use_base_merging: TRUE
diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile
index 2f30bfb758..a338850582 100644
--- a/src/ontology/uberon.Makefile
+++ b/src/ontology/uberon.Makefile
@@ -254,6 +254,16 @@ subsets/cumbo.obo: subsets/cumbo.owl
 #supercheck.owl: $(TMPDIR)/unreasoned.owl
 #	owltools $(UCAT) $< $(COMPONENTSDIR)/phenoscape-ext.owl --merge-support-ontologies --expand-macros --assert-inferred-subclass-axioms --useIsInferred -o -f functional $@
 
+# ----------------------------------------
+# STEP 6: Create common anatomy subset
+# ----------------------------------------
+
+common-anatomy.owl: $(ONT).owl
+	$(OWLTOOLS) $< --extract-ontology-subset --fill-gaps --subset common_anatomy -o $@.tmp.owl && mv $@.tmp.owl $@ &&\
+	$(ROBOT) annotate --input $@ --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@.tmp.owl && mv $@.tmp.owl $@
+.PRECIOUS: common-anatomy.owl
+	
+
 
 # ----------------------------------------
 # IMPORTS