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Changeset 2:3107c58d5c85 (2016-06-27)

Previous changeset 1:7ae426ca9054 (2016-06-26) Next changeset 3:52d9016a156f (2016-06-27)

Commit message:
planemo upload commit 24de1c1405f1f79859f764da60ba068f2dc88cc6

modified:
README.rst

added:
monarch-pathways-for-diseases.xml
monarch-pathways-for-genes.xml
test-data/pathway-gene.tsv
test-data/pathway-genes.tsv
test-data/pathways-for-disease.tsv
test-data/pathways-for-diseases-intersection.tsv
test-data/pathways-for-diseases-union.tsv
test-data/pathways-for-gene.tsv
test-data/pathways-for-genes-intersection.tsv
test-data/pathways-for-genes-union.tsv

diff -r 7ae426ca9054 -r 3107c58d5c85 README.rst
--- a/README.rst Sun Jun 26 16:24:15 2016 -0400
+++ b/README.rst Mon Jun 27 09:39:52 2016 -0400

[

@@ -1,13 +1,12 @@

-This project wraps the Gene Ontology SOLR services (GOLR) exposed by the [Monarch initiative](https://monarchinitiative.org).
+This project wraps the Gene Ontology SOLR services (GOLR) exposed by the      `Monarch initiative <https://monarchinitiative.org>`_

-[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.56412.svg)](http://dx.doi.org/10.5281/zenodo.56412)
-
-# Gene Ontology Curl
+.. image:: https://zenodo.org/badge/doi/10.5281/zenodo.56412.svg
+   :target: http://dx.doi.org/10.5281/zenodo.56412

-    planemo serve
+.. image:: demo.png

-![Demo](demo.png)
-![Arguments](arguments.png)
+.. image:: arguments.png

+

diff -r 7ae426ca9054 -r 3107c58d5c85 monarch-pathways-for-diseases.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/monarch-pathways-for-diseases.xml Mon Jun 27 09:39:52 2016 -0400

[

@@ -0,0 +1,57 @@
+<tool id="monarch-variants-for-diseases" name="Pull Variants from Diseases" version="0.1.0">
+    <requirements/>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+ <command><![CDATA[
+#set conditional = "%20" + str($conditional1) + "%20"
+#set prefix = "subject_closure:%22"
+#set suffix = "%22"
+#set inputString = ""
+#for inputFile in $input1
+  #set inputs = open(str($inputFile),'r').read().split(",")
+  #for input in $inputs
+    #if $inputString != ""
+      #set inputString = $inputString + $conditional
+    #end if
+    #set inputString = $inputString + $prefix + str($input).strip(' \t\n\r') + $suffix
+  #end for
+#end for
+
+curl -s 'https://solr.monarchinitiative.org/solr/golr/select?defType=edismax&qt=standard&indent=on&wt=csv&rows=100000&start=0&fl=object,object_label,relation,relation_label,subject,subject_label,evidence,evidence_label,source,is_defined_by,qualifier&facet=true&facet.mincount=1&facet.sort=count&json.nl=arrarr&facet.limit=25&facet.method=enum&csv.encapsulator=&csv.separator=%09&csv.header=true&csv.mv.separator=%7C&fq=($inputString)&fq=object_category:%22pathway%22&fq=subject_category:%22disease%22&facet.field=subject_taxon_closure_label&facet.field=object_taxon_closure_label&q=*:*'| tail -n +2 > $output1
+ ]]></command>
+ <inputs>
+        <param  name="input1" type="data" format="tabular" multiple="true"  label="Disease" />
+ <param  name="conditional1" type="select" multiple="false" display="radio" label="Conditional">
+ <option value="AND">and</option>
+ <option value="OR">or</option>
+ </param>
+    </inputs>
+    <outputs>
+         <data name="output1" type="data" format="tabular" />
+    </outputs>
+ <tests>
+ <test>
+ <param name="input1" value="disease.tsv"/>
+ <param name="conditional1" value="OR"/>
+ <output name="output1" file="pathways-for-disease.tsv"/>
+ </test>
+ <test>
+ <param name="input1" value="2-diseases-overlap.tsv"/>
+ <param name="conditional1" value="AND"/>
+ <output name="output1" file="pathways-for-diseases-intersection.tsv"/>
+ </test>
+ <test>
+ <param name="input1" value="2-diseases-overlap.tsv"/>
+ <param name="conditional1" value="OR"/>
+ <output name="output1" file="pathways-for-diseases-union.tsv"/>
+ </test>
+ </tests>
+    <help><![CDATA[
+        Pulls pathway data from monarch web services as TSV given a disease.
+ object,object_label,relation,relation_label,subject,subject_label,evidence,evidence_label,source,is_defined_by,qualifier
+    ]]></help>
+ <citations>
+ <citation type="doi">doi:10.5281/zenodo.56412</citation>
+    </citations>
+</tool>

diff -r 7ae426ca9054 -r 3107c58d5c85 monarch-pathways-for-genes.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/monarch-pathways-for-genes.xml Mon Jun 27 09:39:52 2016 -0400

[

@@ -0,0 +1,59 @@
+<tool id="monarch-variants-for-diseases" name="Pull Variants from Diseases" version="0.1.0">
+    <requirements/>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+ <command><![CDATA[
+#set conditional = "%20" + str($conditional1) + "%20"
+#set prefix = "subject_closure:%22"
+#set suffix = "%22"
+#set inputString = ""
+#for inputFile in $input1
+  #set inputs = open(str($inputFile),'r').read().split(",")
+  #for input in $inputs
+    #if $inputString != ""
+      #set inputString = $inputString + $conditional
+    #end if
+    #set inputString = $inputString + $prefix + str($input).strip(' \t\n\r') + $suffix
+  #end for
+#end for
+
+curl -s 'https://solr.monarchinitiative.org/solr/golr/select?defType=edismax&qt=standard&indent=on&wt=csv&rows=100000&start=0&fl=object,object_label,relation,relation_label,subject,subject_label,evidence,evidence_label,source,is_defined_by,qualifier&facet=true&facet.mincount=1&facet.sort=count&json.nl=arrarr&facet.limit=25&facet.method=enum&csv.encapsulator=&csv.separator=%09&csv.header=true&csv.mv.separator=%7C&fq=($inputString)&fq=object_category:%22pathway%22&facet.field=subject_taxon_closure_label&facet.field=object_taxon_closure_label&q=*:*' | tail -n +2 > $output1
+
+
+ ]]></command>
+ <inputs>
+        <param  name="input1" type="data" format="tabular" multiple="true"  label="Disease" />
+ <param  name="conditional1" type="select" multiple="false" display="radio" label="Conditional">
+ <option value="AND">and</option>
+ <option value="OR">or</option>
+ </param>
+    </inputs>
+    <outputs>
+         <data name="output1" type="data" format="tabular" />
+    </outputs>
+ <tests>
+ <test>
+ <param name="input1" value="pathway-gene.tsv"/>
+ <param name="conditional1" value="OR"/>
+ <output name="output1" file="pathways-for-gene.tsv"/>
+ </test>
+ <test>
+ <param name="input1" value="pathway-genes.tsv"/>
+ <param name="conditional1" value="AND"/>
+ <output name="output1" file="pathways-for-genes-intersection.tsv"/>
+ </test>
+ <test>
+ <param name="input1" value="pathway-genes.tsv"/>
+ <param name="conditional1" value="OR"/>
+ <output name="output1" file="pathways-for-genes-union.tsv"/>
+ </test>
+ </tests>
+    <help><![CDATA[
+        Pulls data from monarch web services as TSV given a disease.
+ subject,subject_label,subject_taxon,subject_taxon_label,subject_gene,subject_gene_label,relation,relation_label,object,object_label,evidence,evidence_label,source,is_defined_by,qualifier
+    ]]></help>
+ <citations>
+ <citation type="doi">doi:10.5281/zenodo.56412</citation>
+    </citations>
+</tool>

diff -r 7ae426ca9054 -r 3107c58d5c85 test-data/pathway-gene.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pathway-gene.tsv Mon Jun 27 09:39:52 2016 -0400

@@ -0,0 +1,1 @@
+NCBIGene:675
\ No newline at end of file

diff -r 7ae426ca9054 -r 3107c58d5c85 test-data/pathway-genes.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pathway-genes.tsv Mon Jun 27 09:39:52 2016 -0400

@@ -0,0 +1,1 @@
+NCBIGene:675,NCBIGene:11186
\ No newline at end of file

diff -r 7ae426ca9054 -r 3107c58d5c85 test-data/pathways-for-disease.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pathways-for-disease.tsv Mon Jun 27 09:39:52 2016 -0400

b"@@ -0,0 +1,99 @@\n+KEGG-path:ko05010\tAlzheimer's disease\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:ko01100\tMetabolic pathways\tRO:0002331\tinvolved in\tOrphanet:2828\tYoung-onset Parkinson disease\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:ko04010\tMAPK signaling pathway\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+http://www.reactome.org/PathwayBrowser/#REACT_71\tGene Expression\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:ko04120\tUbiquitin mediated proteolysis\tRO:0002331\tinvolved in\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:ko04141\tProtein processing in endoplasmic reticulum\tRO:0002331\tinvolved in\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:ko05010\tAlzheimer's disease\tRO:0002331\tinvolved in\tOMIM:556500\tParkinson Disease, Mitochondrial\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:ko05010\tAlzheimer's disease\tRO:0002331\tinvolved in\tOMIM:168601\tautosomal dominant Parkinson disease 1\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:ko00591\tLinoleic acid metabolism\tRO:0002331\tinvolved in\tOMIM:612953\tParkinson Disease 14, Autosomal Recessive\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:ko00250\tAlanine, aspartate and glutamate metabolism\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+http://www.reactome.org/PathwayBrowser/#REACT_11123\tMembrane Trafficking\tRO:0002331\tinvolved in\tOMIM:615528\tParkinson Disease 19, Juvenile-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+http://www.reactome.org/PathwayBrowser/#REACT_17015\tMetabolism of proteins\tRO:0002331\tinvolved in\tOMIM:614251\tParkinson Disease 18, Autosomal Dominant, Susceptibility to\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:ko04964\tProximal tubule bicarbonate reclamation\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:ko00562\tInositol phosphate metabolism\tRO:0002331\tinvolved in\tOMIM:615530\tParkinson Disease 20, Early-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n"..b"var.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:ko04664\tFc epsilon RI signaling pathway\tRO:0002331\tinvolved in\tOMIM:612953\tParkinson Disease 14, Autosomal Recessive\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:ko04070\tPhosphatidylinositol signaling system\tRO:0002331\tinvolved in\tOMIM:615530\tParkinson Disease 20, Early-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:ko05012\tParkinson's disease\tRO:0002331\tinvolved in\tOMIM:606324\tParkinson Disease 7, Autosomal Recessive Early-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+http://www.reactome.org/PathwayBrowser/#REACT_6900\tImmune System\tRO:0002331\tinvolved in\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:ko05010\tAlzheimer's disease\tRO:0002331\tinvolved in\tOMIM:605543\tParkinson Disease 4, Autosomal Dominant\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+http://www.reactome.org/PathwayBrowser/#REACT_1788\tTranscription\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:ko05016\tHuntington's disease\tRO:0002331\tinvolved in\tOMIM:556500\tParkinson Disease, Mitochondrial\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:ko00010\tGlycolysis / Gluconeogenesis\tRO:0002331\tinvolved in\tOMIM:556500\tParkinson Disease, Mitochondrial\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+http://www.reactome.org/PathwayBrowser/#REACT_6900\tImmune System\tRO:0002331\tinvolved in\tOMIM:612953\tParkinson Disease 14, Autosomal Recessive\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:ko00071\tFatty acid degradation\tRO:0002331\tinvolved in\tOMIM:556500\tParkinson Disease, Mitochondrial\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:ko03013\tRNA transport\tRO:0002331\tinvolved in\tOMIM:614251\tParkinson Disease 18, Autosomal Dominant, Susceptibility to\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:ko05012\tParkinson's disease\tRO:0002331\tinvolved in\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:ko00980\tMetabolism of xenobiotics by cytochrome P450\tRO:0002331\tinvolved in\tOMIM:556500\tParkinson Disease, Mitochondrial\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:ko04141\tProtein processing in endoplasmic reticulum\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n"

diff -r 7ae426ca9054 -r 3107c58d5c85 test-data/pathways-for-diseases-intersection.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pathways-for-diseases-intersection.tsv Mon Jun 27 09:39:52 2016 -0400

@@ -0,0 +1,26 @@
+KEGG-path:ko05010 Alzheimer's disease RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+KEGG-path:ko04010 MAPK signaling pathway RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+http://www.reactome.org/PathwayBrowser/#REACT_71 Gene Expression RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+KEGG-path:ko00250 Alanine, aspartate and glutamate metabolism RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+KEGG-path:ko04964 Proximal tubule bicarbonate reclamation RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+KEGG-path:ko04142 Lysosome RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+KEGG-path:ko05218 Melanoma RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+KEGG-path:ko00511 Other glycan degradation RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+KEGG-path:ko01100 Metabolic pathways RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+KEGG-path:ko05016 Huntington's disease RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+KEGG-path:ko00910 Nitrogen metabolism RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+KEGG-path:ko00330 Arginine and proline metabolism RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+http://www.reactome.org/PathwayBrowser/#REACT_6900 Immune System RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+KEGG-path:ko03022 Basal transcription factors RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+KEGG-path:ko00471 D-Glutamine and D-glutamate metabolism RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+KEGG-path:ko00190 Oxidative phosphorylation RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+KEGG-path:ko05200 Pathways in cancer RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+KEGG-path:ko05012 Parkinson's disease RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+KEGG-path:ko00600 Sphingolipid metabolism RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+http://www.reactome.org/PathwayBrowser/#REACT_578 Apoptosis RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+KEGG-path:ko04810 Regulation of actin cytoskeleton RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+http://www.reactome.org/PathwayBrowser/#REACT_111217 Metabolism RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+KEGG-path:ko04722 Neurotrophin signaling pathway RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+http://www.reactome.org/PathwayBrowser/#REACT_111102 Signal Transduction RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+http://www.reactome.org/PathwayBrowser/#REACT_1788 Transcription RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred
+KEGG-path:ko04141 Protein processing in endoplasmic reticulum RO:0002331 involved in OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred

diff -r 7ae426ca9054 -r 3107c58d5c85 test-data/pathways-for-diseases-union.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pathways-for-diseases-union.tsv Mon Jun 27 09:39:52 2016 -0400

diff -r 7ae426ca9054 -r 3107c58d5c85 test-data/pathways-for-gene.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pathways-for-gene.tsv Mon Jun 27 09:39:52 2016 -0400

@@ -0,0 +1,5 @@
+http://www.reactome.org/PathwayBrowser/#REACT_115566 Cell Cycle RO:0002331 involved in NCBIGene:675 breast cancer 2 http://data.monarchinitiative.org/ttl/ctd.ttl direct
+http://www.reactome.org/PathwayBrowser/#REACT_216 DNA Repair RO:0002331 involved in NCBIGene:675 breast cancer 2 http://data.monarchinitiative.org/ttl/ctd.ttl direct
+KEGG-path:ko05212 Pancreatic cancer RO:0002331 involved in NCBIGene:675 breast cancer 2 http://data.monarchinitiative.org/ttl/ctd.ttl direct
+KEGG-path:ko05200 Pathways in cancer RO:0002331 involved in NCBIGene:675 breast cancer 2 http://data.monarchinitiative.org/ttl/ctd.ttl direct
+KEGG-path:ko03440 Homologous recombination RO:0002331 involved in NCBIGene:675 breast cancer 2 http://data.monarchinitiative.org/ttl/ctd.ttl direct

diff -r 7ae426ca9054 -r 3107c58d5c85 test-data/pathways-for-genes-union.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pathways-for-genes-union.tsv Mon Jun 27 09:39:52 2016 -0400

@@ -0,0 +1,8 @@
+KEGG-path:ko05223 Non-small cell lung cancer RO:0002331 involved in NCBIGene:11186 RASSF1 http://data.monarchinitiative.org/ttl/ctd.ttl direct
+http://www.reactome.org/PathwayBrowser/#REACT_115566 Cell Cycle RO:0002331 involved in NCBIGene:675 breast cancer 2 http://data.monarchinitiative.org/ttl/ctd.ttl direct
+KEGG-path:ko05219 Bladder cancer RO:0002331 involved in NCBIGene:11186 RASSF1 http://data.monarchinitiative.org/ttl/ctd.ttl direct
+http://www.reactome.org/PathwayBrowser/#REACT_216 DNA Repair RO:0002331 involved in NCBIGene:675 breast cancer 2 http://data.monarchinitiative.org/ttl/ctd.ttl direct
+KEGG-path:ko05212 Pancreatic cancer RO:0002331 involved in NCBIGene:675 breast cancer 2 http://data.monarchinitiative.org/ttl/ctd.ttl direct
+KEGG-path:ko05200 Pathways in cancer RO:0002331 involved in NCBIGene:11186 RASSF1 http://data.monarchinitiative.org/ttl/ctd.ttl direct
+KEGG-path:ko05200 Pathways in cancer RO:0002331 involved in NCBIGene:675 breast cancer 2 http://data.monarchinitiative.org/ttl/ctd.ttl direct
+KEGG-path:ko03440 Homologous recombination RO:0002331 involved in NCBIGene:675 breast cancer 2 http://data.monarchinitiative.org/ttl/ctd.ttl direct