First pass at mesh mapping

.travis.yml

@@ -1,28 +1,20 @@
-language: java
-jdk:
-  - oraclejdk8
+sudo: required
 
-before_script:
-  - mkdir -p bin
-  - export PATH=$PATH:$PWD/bin
-  - wget http://build.berkeleybop.org/userContent/owltools/owltools -O bin/owltools
-  - wget http://build.berkeleybop.org/userContent/owltools/ontology-release-runner -O bin/ontology-release-runner
-  - wget http://build.berkeleybop.org/userContent/owltools/owltools-runner-all.jar -O bin/owltools-runner-all.jar
-  - wget http://build.berkeleybop.org/userContent/owltools/owltools-oort-all.jar -O bin/owltools-oort-all.jar
-  - chmod +x bin/*
+services:
+  - docker
+
+before_install:
+  - docker pull obolibrary/odkfull
 
 # command to run tests
-script: cd src/ontology && make test
+script: cd src/ontology && sh run.sh make travis_test
 
 #after_success:
 #  coveralls
 
-# whitelist
-branches:
-  only:
-    - master
 
+### Add your own lists here
+### See https://github.com/INCATools/ontology-development-kit/issues/35
 notifications:
   email:
-    - [email protected]
-
+    - [email protected]

src/ontology/Makefile

@@ -37,6 +37,11 @@ imports/%_import.owl: chiro-edit.owl %.owl imports/seed.tsv
 	robot extract -i $*.owl -T imports/seed.tsv -m BOT -O $(OBO)/chiro/$@ -o [email protected] && mv [email protected] $@
 #	owltools --use-catalog $< $(OBO)/$*.owl  --add-imports-from-supports --extract-module -s $(OBO)/$*.owl -c --extract-mingraph  --set-ontology-id $(OBO)/go/extensions/$@ -o $@
 
+imports/chebi-role.owl: chebi.owl
+	robot filter -i $< --term CHEBI:50906 --select "annotations self descendants" \
+	--signature true \
+	--output $@
+
 chebi.owl:
 	wget $(OBO)/chebi.owl
 
@@ -92,3 +97,39 @@ role-xp-unvetted.obo: role-list-mined.txt
 
 chiro-xp.owl: role-xp.obo
 	owltools $< -o -f ofn $@
+
+# ----------------------------------------
+# Mappings
+# ----------------------------------------
+
+imports/mesh-chemrole.owl: mesh-obo.owl
+	robot filter -i $< --term http://id.nlm.nih.gov/mesh/D020164 --select "annotations self descendants" \
+	--signature true \
+	--output $@
+
+imports/ncit-chemeffect.owl: ncit.owl
+	robot filter -i $< --term http://purl.obolibrary.org/obo/NCIT_C19996 --select "annotations self descendants" \
+	--signature true \
+	--output $@
+
+mappings/mesh-chebi-role-mappings.tsv: imports/mesh-chemrole.owl imports/chebi-role.owl
+	rdfmatch -p CHEBI -w mappings/chebi_mesh_weights.pro  -i prefixes.ttl -i $< -i imports/chebi-role.owl match > [email protected] && mv [email protected] $@
+
+mappings/ncit-chebi-role-mappings.tsv: imports/ncit-chemeffect.owl imports/chebi-role.owl
+	rdfmatch -p CHEBI -d rdf_matcher -i prefixes.ttl -i $< -i imports/chebi-role.owl match > [email protected] && mv [email protected] $@
+
+mappings/ncit-mesh-role-mappings.tsv: imports/ncit-chemeffect.owl imports/mesh-chemrole.owl
+	rdfmatch -p NCIT -d rdf_matcher -i prefixes.ttl -i $< -i imports/mesh-chemrole.owl match > [email protected] && mv [email protected] $@
+
+mappings/mesh-chebi-role-mappings-unique.tsv: mappings/mesh-chebi-role-mappings.tsv
+	cut -f1-4 $< | sort -u > $@
+
+mappings/%-ptable.tsv: mappings/%-mappings.tsv
+	python ~/repos/sssom-py/sssom/cli.py ptable --priors 0.01 0.01 0.88 0.1 $< > $@
+
+imports/mesh-chebi-role.owl: imports/mesh-chemrole.owl imports/ncit-chemeffect.owl
+	robot merge -i imports/mesh-chemrole.owl -i imports/ncit-chemeffect.owl -o $@
+
+mappings/mesh-chebi-role-equivs.owl: mappings/mesh-chebi-role-ptable.tsv imports/mesh-chebi-role.owl
+	boomer --ptable $< --ontology imports/mesh-chebi-role.owl --prefixes prefixes.yaml --window-count 20 --runs 20 && robot reason -A EquivalentClass -r elk -i output.ofn  -o $@
+

src/ontology/mappings/chebi_mesh_weights.pro

@@ -0,0 +1,24 @@
+% xrefs
+weight(1.0, [predicate_id='owl:equivalentClass', subject_match_field='oio:hasDbXref', object_match_field='oio:hasDbXref']).
+
+weight(2, [predicate_id='owl:equivalentClass', any_match_field='dc:identifier']).
+weight(2, [predicate_id='owl:equivalentClass', any_match_field='schema:url']).
+
+weight(3, [predicate_id='owl:equivalentClass', any_match_field='rdfs:label']).
+weight(3, [predicate_id='owl:equivalentClass', any_match_field='oio:hasExactSynonym']).
+weight(3, [predicate_id='owl:equivalentClass', any_match_field='skos:exactMatch']).
+weight(2, [predicate_id='owl:equivalentClass', any_match_field='oio:hasRelatedSynonym']).
+
+weight(-2, [predicate_id='owl:equivalentClass', any_match_field='oio:hasNarrowSynonym']).
+weight(-2, [predicate_id='owl:equivalentClass', any_match_field='oio:hasBroadSynonym']).
+
+% lexical is lower, stemmming even lower
+weight(-1.0, [predicate_id='owl:equivalentClass', match_type=['Lexical','Stemming']]).
+weight(-0.5, [predicate_id='owl:equivalentClass', match_type=['Lexical']]).
+
+weight(-1, [match_string=S]) :-  atom_length(S,3).
+weight(-2, [match_string=S]) :-  atom_length(S,2).
+weight(-3, [match_string=S]) :-  atom_length(S,1).
+weight(-99, [match_string=S]) :-  atom_length(S,0).
+
+