Merge pull request #72 from monarch-initiative/boom

DO NOT MERGE YET: building mondo using kboom method

.travis.yml

@@ -0,0 +1,28 @@
+language: java
+jdk:
+  - openjdk7
+
+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/*
+
+# command to run tests
+script: cd src/mondo && make test
+
+#after_success:
+#  coveralls
+
+# whitelist
+branches:
+  only:
+    - master
+
+notifications:
+  email:
+    - cjmungall@lbl.gov
+

README.md

@@ -1,3 +1,4 @@
+[![Build Status](https://travis-ci.org/cmungall/monarch-disease-ontology.svg?branch=master)](https://travis-ci.org/cmungall/monarch-disease-ontology)
 [![DOI](https://zenodo.org/badge/13996/cmungall/monarch-disease-ontology.svg)](https://zenodo.org/badge/latestdoi/13996/cmungall/monarch-disease-ontology)
 
 ## Editors Instructions

src/clusters/omimclusters_bridge_to_doid.obo

@@ -336,7 +336,6 @@ id: DC:0000659 ! Muscular Dystrophy-Dystroglycanopathy, Type A
 is_a: DOID:0050588 ! muscular dystrophy-dystroglycanopathy
 is_a: DOID:9884 ! muscular dystrophy
 
-
 [Term]
 id: DC:0000634 ! Autoimmune Thyroid Disease, Susceptibility to
 is_a: DOID:7188 ! autoimmune thyroiditis

src/doid/fix-xrefs.pl

@@ -1,5 +1,11 @@
 #!/usr/bin/perl
 while(<>) {
     s@^xref: ORDO:@xref: Orphanet:@g;
+    s@^xref: ICD10CM:@xref: ICD10:@g;
+    s@^xref: ICD9CM:@xref: ICD9:@g;
+    s@^xref: SNOMEDCT_\w+:@xref: SCTID:@g;
+    s@^xref: UMLS_CUI:@xref: UMLS:@g;
+    s@^xref: MSH:@xref: MESH:@g;
+    s@^xref: NCI:@xref: NCIT:@g;
     print $_;
 }

src/genereviews/Makefile

@@ -0,0 +1,2 @@
+genereviews.ttl:
+	wget http://data.monarchinitiative.org/ttl/genereviews.ttl -O $@

src/medgen/Makefile

@@ -1,3 +1,6 @@
+MEDGEN = medgen-disease-extract.obo
+
+all: $(MEDGEN)
 
 fetch:
 	wget -r -np ftp://ftp.ncbi.nlm.nih.gov/pub/medgen/
@@ -13,3 +16,21 @@ medgen-disease-extract.obo: medgen.obo
 
 #medgen-disease-subset.obo: medgen-disease-extract.obo
 #	
+
+mg.pro: medgenid_count.txt
+	cut -f1 $<  | tbl2p -p mg > $@
+
+unmapped.tsv:
+	blip-findall -i medgen-disease-extract.obo  -i xrefs-medgen.obo -r mondo -i mg.pro "mg(X),\+entity_xref(_,X),class(X)" -select X -label > $@
+
+mg_cat.tsv:
+	blip-findall -i medgen.obo  -i xrefs-medgen.obo -r mondo -i mg.pro "mg(X),entity_partition(X,S)" -select X-S -no_pred -label > $@
+
+medgenid_count_labeled.txt: medgenid_count.txt
+	blip labelify -i medgen.obo $< > $@
+
+align-medgen.tsv: $(MEDGEN)
+	blip-findall -debug index -i ../mondo/super_ignore.pro -u metadata_nlp -i $< -r mondo -goal index_entity_pair_label_match "class(X),id_idspace(X,'UMLS'),entity_pair_label_reciprocal_best_intermatch(X,Y,S)" -select "m(X,Y,S)" -use_tabs -label -no_pred > $@.tmp && sort -u $@.tmp > $@
+
+xrefs-%.obo:  align-%.tsv
+	cut -f1-4 $^  | sort -u| tbl2obolinks.pl --swap --rel xref - > $@

src/medic/mesh-antislim.obo

@@ -0,0 +1,24 @@
+format-version: 1.2
+ontology: mondo/mesh-antislim
+subsetdef: mesh_antislim "MESH antislim"
+
+[Term]
+id: MESH:C ! Diseases
+name: Diseases
+subset: mesh_antislim
+
+[Term]
+id: MESH:D010335 ! Pathologic Processes
+name: Pathologic Processes
+subset: mesh_antislim
+
+[Term]
+id: MESH:D012816 ! Signs and Symptoms
+name: Signs and Symptoms
+subset: mesh_antislim
+
+[Term]
+id: MESH:D013568 ! Pathological Conditions, Signs and Symptoms
+name: Pathological Conditions, Signs and Symptoms
+subset: mesh_antislim
+

src/medic/transform-ctd.pl

@@ -0,0 +1,22 @@
+#!/usr/bin/perl
+
+print "ontology: mesh\n";
+while(<>) {
+    chomp;
+    if (m@^id: (\S+)@) {
+        $id = $1;
+    }
+    if ($id =~ /OMIM/) {
+        next if m@^name:@;
+        next if m@^synonym:@;
+    }
+    if (m@^synonym: "(.*)"\s+\S+\s+\[@) {
+        my $s = $1;
+        if ($s !~ /[a-z]/) {
+            next;
+        }
+    }
+    s@^alt_id:@xref:@;
+    s@ EXACT @ RELATED @;
+    print "$_\n";
+}