First pass at matching between obo-core classes and (a) existing OBOs

(b) external resources [sio,wikidata,biotop,mesh,...]
See beckyjackson#1
beckyjackson#2
Still to do OBOFoundry#14 UMLS

I also include an import in manual-core that brings in the matches;
we indicate these as skos annotations to avoid 'polluting' core
note a bug in the owlapi means we lose some axiom annotations on these.

.gitignore

@@ -5,3 +5,4 @@ src/ontology/build/*.rq
 src/ontology/build/*.ttl
 src/ontology/catalog-v001.xml
 src/ontology/imports/catalog-v001.xml
+RDF-Cache/

Makefile

@@ -82,3 +82,19 @@ templates/human.tsv:
 .PHONY: templates/science.tsv
 templates/science.tsv:
 	curl "$(SCIENCE_SHEET)" > $@
+
+# ---------- ALIGNMENT ---------- #
+# Currentlh this requires installing some tools - I will set up a docker for running these...
+
+XONTS = ro sio biotop bfoc mesh chebi blmod common_core
+all_matches: $(patsubst %, matches/matches-%.tsv, $(XONTS))
+
+matches/matches-%.tsv: manual-core.owl
+	rdfmatch -d rdf_matcher -G imports/matches-$*.owl --predicate skos:exactMatch --prefix CORE -f tsv -l -A ~/repos/onto-mirror/void.ttl -i prefixes.ttl -i $< -i $* new_match > $@.tmp &&   cut -f1-4 $@.tmp | sort -u > $@
+
+# match to wikidata
+matches/wd-closematches.ttl: manual-core.owl
+	wd-ontomatch -d ontomatcher -i $< -a wikidata_ontomatcher:cached_db_file=$@ -e match_classes
+
+matches/wd-align.tsv: manual-core.owl matches/wd-closematches.ttl
+	rdfmatch -d rdf_matcher -G imports/matches-wd.owl --predicate skos:closeMatch --prefix CORE -f tsv -l -A ~/repos/onto-mirror/void.ttl -i prefixes.ttl -i $< -i wd-closematches.ttl exact > $@.tmp &&  cut -f1-9,11,15-19 $@.tmp > $@

catalog-v001.xml

@@ -1,12 +1,22 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
-    <group id="Folder Repository, directory=, recursive=true, Auto-Update=true, version=2" prefer="public" xml:base="">
-        <uri id="Automatically generated entry, Timestamp=1553804231012" name="http://purl.obolibrary.org/obo/obo-core.owl" uri="obo-core.owl"/>
-        <uri id="Automatically generated entry, Timestamp=1553804231012" name="http://purl.obolibrary.org/obo/obo-core/modules/biological.owl" uri="modules/biological.owl"/>
-        <uri id="Automatically generated entry, Timestamp=1553804231012" name="http://purl.obolibrary.org/obo/obo-core/modules/generic.owl" uri="modules/generic.owl"/>
-        <uri id="Automatically generated entry, Timestamp=1553804231012" name="http://purl.obolibrary.org/obo/obo-core/modules/human.owl" uri="modules/human.owl"/>
-        <uri id="Automatically generated entry, Timestamp=1553804231012" name="http://purl.obolibrary.org/obo/obo-core/modules/physical.owl" uri="modules/physical.owl"/>
-        <uri id="Automatically generated entry, Timestamp=1553804231012" name="http://purl.obolibrary.org/obo/obo-core/modules/science.owl" uri="modules/science.owl"/>
-        <uri id="Automatically generated entry, Timestamp=1553804231012" name="http://www.semanticweb.org/tauber/ontologies/2019/2/untitled-ontology-528" uri="manual-core.owl"/>
+    <group id="Folder Repository, directory=, recursive=true, Auto-Update=false, version=2" prefer="public" xml:base="">
+        <uri id="Automatically generated entry, Timestamp=1562295109044" name="http://purl.obolibrary.org/obo/obo-core.owl" uri="obo-core.owl"/>
+        <uri id="Automatically generated entry, Timestamp=1562295109044" name="http://purl.obolibrary.org/obo/obo-core/modules/biological.owl" uri="modules/biological.owl"/>
+        <uri id="Automatically generated entry, Timestamp=1562295109044" name="http://purl.obolibrary.org/obo/obo-core/modules/generic.owl" uri="modules/generic.owl"/>
+        <uri id="Automatically generated entry, Timestamp=1562295109044" name="http://purl.obolibrary.org/obo/obo-core/modules/human.owl" uri="modules/human.owl"/>
+        <uri id="Automatically generated entry, Timestamp=1562295109044" name="http://purl.obolibrary.org/obo/obo-core/modules/physical.owl" uri="modules/physical.owl"/>
+        <uri id="Automatically generated entry, Timestamp=1562295109044" name="http://purl.obolibrary.org/obo/obo-core/modules/science.owl" uri="modules/science.owl"/>
+        <uri id="Automatically generated entry, Timestamp=1562295109044" name="http://www.semanticweb.org/tauber/ontologies/2019/2/untitled-ontology-528" uri="manual-core.owl"/>
+        <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/core/imports/matches-bfoc.owl" uri="./imports/matches-bfoc.owl"/>
+        <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/core/imports/matches-biotop.owl" uri="./imports/matches-biotop.owl"/>
+        <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/core/imports/matches-blmod.owl" uri="./imports/matches-blmod.owl"/>
+        <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/core/imports/matches-chebi.owl" uri="./imports/matches-chebi.owl"/>
+        <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/core/imports/matches-common_core.owl" uri="./imports/matches-common_core.owl"/>
+        <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/core/imports/matches-mesh.owl" uri="./imports/matches-mesh.owl"/>
+        <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/core/imports/matches-ro.owl" uri="./imports/matches-ro.owl"/>
+        <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/core/imports/matches-sio.owl" uri="./imports/matches-sio.owl"/>
+        <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/core/imports/matches-obi.owl" uri="./imports/matches-obi.owl"/>
+        <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/core/imports/matches-ogms.owl" uri="./imports/matches-ogms.owl"/>
     </group>
 </catalog>

imports/matches-bfoc.owl

@@ -0,0 +1,27 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE rdf:RDF [
+    <!ENTITY rdf 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'>
+    <!ENTITY skos 'http://www.w3.org/2004/02/skos/core#'>
+]>
+
+<rdf:RDF
+    xmlns:rdf="&rdf;"
+    xmlns:skos="&skos;"
+>
+<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CORE_0000001">
+  <skos:exactMatch rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
+</rdf:Description>
+
+<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CORE_0000006">
+  <skos:exactMatch rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
+</rdf:Description>
+
+<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CORE_0000031">
+  <skos:exactMatch rdf:resource="http://purl.obolibrary.org/obo/BFO_0000141"/>
+</rdf:Description>
+
+<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CORE_0000034">
+  <skos:exactMatch rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+</rdf:Description>
+
+</rdf:RDF>