Add a base file

.gitignore

@@ -8,9 +8,9 @@ catalog-v001.xml
 graphviz-images/
 junk/
 lib/
-mro-import.owl
 mro.xlsx
 mro.owl
+mro-base.owl
 iedb.zip
 reference/
 src/.cache/

Makefile

@@ -45,7 +45,7 @@ SHELL := bash
 
 OBO = http://purl.obolibrary.org/obo
 LIB = lib
-ROBOT := java -jar build/robot.jar
+ROBOT := java -jar build/robot.jar --prefix "REO: $(OBO)/REO_"
 TODAY := $(shell date +%Y-%m-%d)
 
 tables = external core genetic-locus haplotype serotype chain molecule haplotype-molecule serotype-molecule mutant-molecule evidence chain-sequence
@@ -234,8 +234,6 @@ update-mamu-alleles: src/update_mamu_alleles.py ontology/chain-sequence.tsv onto
 mro.owl: build/mro-import.owl index.tsv $(build_files) ontology/metadata.ttl | build/robot.jar
 	$(ROBOT) template \
 	--input $< \
-	--prefix "MRO: $(OBO)/MRO_" \
-	--prefix "REO: $(OBO)/REO_" \
 	--template index.tsv \
 	$(templates) \
 	--merge-before \
@@ -249,6 +247,18 @@ mro.owl: build/mro-import.owl index.tsv $(build_files) ontology/metadata.ttl | b
 	--annotation-file ontology/metadata.ttl \
 	--output $@
 
+mro-base.owl: mro.owl index.tsv $(build_files) ontology/metadata-base.ttl | build/robot.jar
+	$(ROBOT) template \
+	--input $< \
+	--template index.tsv \
+	$(foreach i,$(filter-out build/external.tsv,$(build_files)),--template $(i)) \
+	annotate \
+	--ontology-iri "$(OBO)/mro/mro-base.owl" \
+	--version-iri "$(OBO)/mro/$(shell date +%Y-%m-%d)/mro-base.owl" \
+	--annotation owl:versionInfo "$(shell date +%Y-%m-%d)" \
+	--annotation-file ontology/metadata-base.ttl \
+	--output $@
+
 build/mro-import.owl: build/eco-import.ttl build/iao-import.ttl build/obi-import.ttl build/ro-import.ttl ontology/import.txt | build/robot.jar
 	$(ROBOT) merge \
 	--input build/eco-import.ttl \
@@ -308,7 +318,6 @@ IEDB_TARGETS := build/mro-iedb.owl \
 # extended version for IEDB use
 build/mro-iedb.owl: mro.owl iedb/iedb.tsv iedb/iedb-manual.tsv | build/robot.jar iedb
 	$(ROBOT) template \
-	--prefix "MRO: $(OBO)/MRO_" \
 	--input $< \
 	--template $(word 2,$^) \
 	--template $(word 3,$^) \
@@ -370,15 +379,9 @@ update-iedb: $(IEDB_TARGETS)
 
 VERIFY_QUERIES = $(wildcard src/verify/*.rq)
 
-build/mro-base.owl: mro.owl | build/robot.jar
-	$(ROBOT) remove --input $< \
-	--base-iri $(OBO)/MRO_ \
-	--axioms external \
-	--output $@
-
 # Run a series of standard OBO checks
 .PRECIOUS: build/report.csv
-build/report.csv: build/mro-base.owl | build/robot.jar
+build/report.csv: mro-base.owl | build/robot.jar
 	$(ROBOT) report --input $< --print 10 --output $@
 
 # Run a series of MRO-specific queries as checks
@@ -419,6 +422,7 @@ prepare:
 .PHONY: clean
 clean:
 	rm -rf mro.owl
+	rm -rf mro-base.owl
 	rm -rf build
 	rm -f iedb.zip
 	rm -f mro.owl.gz
@@ -445,7 +449,7 @@ build/release-notes.txt: | build
 # GITHUB_TOKEN env variable must be set to a PAT with "repo" permissions
 # https://docs.github.com/en/free-pro-team@latest/github/authenticating-to-github/creating-a-personal-access-token
 .PHONY: release
-release: mro.owl iedb.zip build/release-notes.txt
+release: mro.owl mro-base.owl iedb.zip build/release-notes.txt
 	gh release create v$(TODAY) mro.owl iedb.zip \
 	-t "$(TODAY) Release" \
 	-F build/release-notes.txt

ontology/metadata-base.ttl

@@ -0,0 +1,8 @@
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix dc:   <http://purl.org/dc/elements/1.1/> .
+@prefix dct:  <http://purl.org/dc/terms/> .
+
+<http://purl.obolibrary.org/obo/mro/mro-base.owl>
+  dc:title "MHC Restriction Ontology (Base Version)" ;
+  dc:description "The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions. The base version contains all and only native axioms." ;
+  dct:license <http://creativecommons.org/licenses/by/3.0/> .