# HG changeset patch
# User nathandunn
# Date 1467034792 14400
# Node ID 3107c58d5c85319260b440c2a17107a0c1228462
# Parent  7ae426ca905482ce96a2a48948e38dfb3d7fd201
planemo upload commit 24de1c1405f1f79859f764da60ba068f2dc88cc6

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
@@ -0,0 +1,99 @@
+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:ko01100	Metabolic pathways	RO:0002331	involved in	Orphanet:2828	Young-onset Parkinson disease				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:ko04120	Ubiquitin mediated proteolysis	RO:0002331	involved in	OMIM:600116	Parkinson Disease 2, Autosomal Recessive Juvenile				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:600116	Parkinson Disease 2, Autosomal Recessive Juvenile				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko05010	Alzheimer's disease	RO:0002331	involved in	OMIM:556500	Parkinson Disease, Mitochondrial				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko05010	Alzheimer's disease	RO:0002331	involved in	OMIM:168601	autosomal dominant Parkinson disease 1				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko00591	Linoleic acid metabolism	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				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
+http://www.reactome.org/PathwayBrowser/#REACT_11123	Membrane Trafficking	RO:0002331	involved in	OMIM:615528	Parkinson Disease 19, Juvenile-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_17015	Metabolism of proteins	RO:0002331	involved in	OMIM:614251	Parkinson Disease 18, Autosomal Dominant, Susceptibility to				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:ko00562	Inositol phosphate metabolism	RO:0002331	involved in	OMIM:615530	Parkinson Disease 20, Early-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:ko00970	Aminoacyl-tRNA biosynthesis	RO:0002331	involved in	OMIM:556500	Parkinson Disease, Mitochondrial				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko00982	Drug metabolism - cytochrome P450	RO:0002331	involved in	OMIM:556500	Parkinson Disease, Mitochondrial				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko04972	Pancreatic secretion	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko00590	Arachidonic acid metabolism	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				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:ko04724	Glutamatergic synapse	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko04370	VEGF signaling pathway	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				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:ko05416	Viral myocarditis	RO:0002331	involved in	OMIM:614251	Parkinson Disease 18, Autosomal Dominant, Susceptibility to				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko04144	Endocytosis	RO:0002331	involved in	OMIM:615528	Parkinson Disease 19, Juvenile-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_20679	Amine compound SLC transporters	RO:0002331	involved in	OMIM:613135	Parkinsonism-Dystonia, Infantile				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:612953	Parkinson Disease 14, Autosomal Recessive				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:ko04666	Fc gamma R-mediated phagocytosis	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				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
+http://www.reactome.org/PathwayBrowser/#REACT_111102	Signal Transduction	RO:0002331	involved in	OMIM:614203	Parkinson Disease 17				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
+http://www.reactome.org/PathwayBrowser/#REACT_111102	Signal Transduction	RO:0002331	involved in	OMIM:614251	Parkinson Disease 18, Autosomal Dominant, Susceptibility to				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko00592	alpha-Linolenic acid metabolism	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko00564	Glycerophospholipid metabolism	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				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_15518	Transmembrane transport of small molecules	RO:0002331	involved in	OMIM:613135	Parkinsonism-Dystonia, Infantile				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_71	Gene Expression	RO:0002331	involved in	OMIM:614251	Parkinson Disease 18, Autosomal Dominant, Susceptibility to				http://data.monarchinitiative.org/ttl/omim.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
+http://www.reactome.org/PathwayBrowser/#REACT_111217	Metabolism	RO:0002331	involved in	OMIM:605909	Parkinson Disease 6, Autosomal Recessive Early-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
+KEGG-path:ko00190	Oxidative phosphorylation	RO:0002331	involved in	OMIM:556500	Parkinson Disease, Mitochondrial				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_21257	Metabolism of RNA	RO:0002331	involved in	OMIM:614251	Parkinson Disease 18, Autosomal Dominant, Susceptibility to				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko00350	Tyrosine metabolism	RO:0002331	involved in	OMIM:556500	Parkinson Disease, Mitochondrial				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:ko05012	Parkinson's disease	RO:0002331	involved in	OMIM:168601	autosomal dominant Parkinson disease 1				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	Orphanet:2828	Young-onset Parkinson disease				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	Orphanet:2828	Young-onset Parkinson disease				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko04120	Ubiquitin mediated proteolysis	RO:0002331	involved in	Orphanet:2828	Young-onset Parkinson disease				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:ko04010	MAPK signaling pathway	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				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	Orphanet:2828	Young-onset Parkinson disease				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko04270	Vascular smooth muscle contraction	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				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:ko00830	Retinol metabolism	RO:0002331	involved in	OMIM:556500	Parkinson Disease, Mitochondrial				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko05145	Toxoplasmosis	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				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:556500	Parkinson Disease, Mitochondrial				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:607060	autosomal dominant Parkinson disease 8				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:ko05012	Parkinson's disease	RO:0002331	involved in	Orphanet:2828	Young-onset Parkinson disease				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:556500	Parkinson Disease, Mitochondrial				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:605543	Parkinson Disease 4, Autosomal Dominant				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:ko04912	GnRH signaling pathway	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				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:615530	Parkinson Disease 20, Early-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:605909	Parkinson Disease 6, Autosomal Recessive Early-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
+KEGG-path:ko00565	Ether lipid metabolism	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				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:ko04730	Long-term depression	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko04975	Fat digestion and absorption	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				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:614251	Parkinson Disease 18, Autosomal Dominant, Susceptibility to				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:613135	Parkinsonism-Dystonia, Infantile				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:556500	Parkinson Disease, Mitochondrial				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
+KEGG-path:ko00190	Oxidative phosphorylation	RO:0002331	involved in	OMIM:605909	Parkinson Disease 6, Autosomal Recessive Early-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:605909	Parkinson Disease 6, Autosomal Recessive Early-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:612953	Parkinson Disease 14, Autosomal Recessive				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:ko01100	Metabolic pathways	RO:0002331	involved in	OMIM:615530	Parkinson Disease 20, Early-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	Orphanet:2828	Young-onset Parkinson disease				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_1762	3' -UTR-mediated translational regulation	RO:0002331	involved in	OMIM:614251	Parkinson Disease 18, Autosomal Dominant, Susceptibility to				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:610297	Parkinson Disease 13, Autosomal Dominant, Susceptibility to				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:613643	Parkinson Disease 5, Autosomal Dominant, Susceptibility to				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko04664	Fc epsilon RI signaling pathway	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko04070	Phosphatidylinositol signaling system	RO:0002331	involved in	OMIM:615530	Parkinson Disease 20, Early-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:606324	Parkinson Disease 7, Autosomal Recessive Early-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:600116	Parkinson Disease 2, Autosomal Recessive Juvenile				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko05010	Alzheimer's disease	RO:0002331	involved in	OMIM:605543	Parkinson Disease 4, Autosomal Dominant				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:ko05016	Huntington's disease	RO:0002331	involved in	OMIM:556500	Parkinson Disease, Mitochondrial				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko00010	Glycolysis / Gluconeogenesis	RO:0002331	involved in	OMIM:556500	Parkinson Disease, Mitochondrial				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:612953	Parkinson Disease 14, Autosomal Recessive				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko00071	Fatty acid degradation	RO:0002331	involved in	OMIM:556500	Parkinson Disease, Mitochondrial				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko03013	RNA transport	RO:0002331	involved in	OMIM:614251	Parkinson Disease 18, Autosomal Dominant, Susceptibility to				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:600116	Parkinson Disease 2, Autosomal Recessive Juvenile				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko00980	Metabolism of xenobiotics by cytochrome P450	RO:0002331	involved in	OMIM:556500	Parkinson Disease, Mitochondrial				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-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
@@ -0,0 +1,99 @@
+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:ko01100	Metabolic pathways	RO:0002331	involved in	Orphanet:2828	Young-onset Parkinson disease				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:ko04120	Ubiquitin mediated proteolysis	RO:0002331	involved in	OMIM:600116	Parkinson Disease 2, Autosomal Recessive Juvenile				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:600116	Parkinson Disease 2, Autosomal Recessive Juvenile				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko05010	Alzheimer's disease	RO:0002331	involved in	OMIM:556500	Parkinson Disease, Mitochondrial				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko05010	Alzheimer's disease	RO:0002331	involved in	OMIM:168601	autosomal dominant Parkinson disease 1				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko00591	Linoleic acid metabolism	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				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
+http://www.reactome.org/PathwayBrowser/#REACT_11123	Membrane Trafficking	RO:0002331	involved in	OMIM:615528	Parkinson Disease 19, Juvenile-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_17015	Metabolism of proteins	RO:0002331	involved in	OMIM:614251	Parkinson Disease 18, Autosomal Dominant, Susceptibility to				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:ko00562	Inositol phosphate metabolism	RO:0002331	involved in	OMIM:615530	Parkinson Disease 20, Early-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:ko00970	Aminoacyl-tRNA biosynthesis	RO:0002331	involved in	OMIM:556500	Parkinson Disease, Mitochondrial				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko00982	Drug metabolism - cytochrome P450	RO:0002331	involved in	OMIM:556500	Parkinson Disease, Mitochondrial				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko04972	Pancreatic secretion	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko00590	Arachidonic acid metabolism	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				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:ko04724	Glutamatergic synapse	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko04370	VEGF signaling pathway	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				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:ko05416	Viral myocarditis	RO:0002331	involved in	OMIM:614251	Parkinson Disease 18, Autosomal Dominant, Susceptibility to				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko04144	Endocytosis	RO:0002331	involved in	OMIM:615528	Parkinson Disease 19, Juvenile-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_20679	Amine compound SLC transporters	RO:0002331	involved in	OMIM:613135	Parkinsonism-Dystonia, Infantile				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:612953	Parkinson Disease 14, Autosomal Recessive				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:ko04666	Fc gamma R-mediated phagocytosis	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				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
+http://www.reactome.org/PathwayBrowser/#REACT_111102	Signal Transduction	RO:0002331	involved in	OMIM:614203	Parkinson Disease 17				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
+http://www.reactome.org/PathwayBrowser/#REACT_111102	Signal Transduction	RO:0002331	involved in	OMIM:614251	Parkinson Disease 18, Autosomal Dominant, Susceptibility to				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko00592	alpha-Linolenic acid metabolism	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko00564	Glycerophospholipid metabolism	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				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_15518	Transmembrane transport of small molecules	RO:0002331	involved in	OMIM:613135	Parkinsonism-Dystonia, Infantile				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_71	Gene Expression	RO:0002331	involved in	OMIM:614251	Parkinson Disease 18, Autosomal Dominant, Susceptibility to				http://data.monarchinitiative.org/ttl/omim.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
+http://www.reactome.org/PathwayBrowser/#REACT_111217	Metabolism	RO:0002331	involved in	OMIM:605909	Parkinson Disease 6, Autosomal Recessive Early-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
+KEGG-path:ko00190	Oxidative phosphorylation	RO:0002331	involved in	OMIM:556500	Parkinson Disease, Mitochondrial				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_21257	Metabolism of RNA	RO:0002331	involved in	OMIM:614251	Parkinson Disease 18, Autosomal Dominant, Susceptibility to				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko00350	Tyrosine metabolism	RO:0002331	involved in	OMIM:556500	Parkinson Disease, Mitochondrial				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:ko05012	Parkinson's disease	RO:0002331	involved in	OMIM:168601	autosomal dominant Parkinson disease 1				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	Orphanet:2828	Young-onset Parkinson disease				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	Orphanet:2828	Young-onset Parkinson disease				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko04120	Ubiquitin mediated proteolysis	RO:0002331	involved in	Orphanet:2828	Young-onset Parkinson disease				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:ko04010	MAPK signaling pathway	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				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	Orphanet:2828	Young-onset Parkinson disease				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko04270	Vascular smooth muscle contraction	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				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:ko00830	Retinol metabolism	RO:0002331	involved in	OMIM:556500	Parkinson Disease, Mitochondrial				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko05145	Toxoplasmosis	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				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:556500	Parkinson Disease, Mitochondrial				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:607060	autosomal dominant Parkinson disease 8				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:ko05012	Parkinson's disease	RO:0002331	involved in	Orphanet:2828	Young-onset Parkinson disease				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:556500	Parkinson Disease, Mitochondrial				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:605543	Parkinson Disease 4, Autosomal Dominant				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:ko04912	GnRH signaling pathway	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				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:615530	Parkinson Disease 20, Early-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:605909	Parkinson Disease 6, Autosomal Recessive Early-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
+KEGG-path:ko00565	Ether lipid metabolism	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				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:ko04730	Long-term depression	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko04975	Fat digestion and absorption	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				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:614251	Parkinson Disease 18, Autosomal Dominant, Susceptibility to				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:613135	Parkinsonism-Dystonia, Infantile				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:556500	Parkinson Disease, Mitochondrial				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
+KEGG-path:ko00190	Oxidative phosphorylation	RO:0002331	involved in	OMIM:605909	Parkinson Disease 6, Autosomal Recessive Early-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:605909	Parkinson Disease 6, Autosomal Recessive Early-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:612953	Parkinson Disease 14, Autosomal Recessive				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:ko01100	Metabolic pathways	RO:0002331	involved in	OMIM:615530	Parkinson Disease 20, Early-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	Orphanet:2828	Young-onset Parkinson disease				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_1762	3' -UTR-mediated translational regulation	RO:0002331	involved in	OMIM:614251	Parkinson Disease 18, Autosomal Dominant, Susceptibility to				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:610297	Parkinson Disease 13, Autosomal Dominant, Susceptibility to				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:613643	Parkinson Disease 5, Autosomal Dominant, Susceptibility to				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko04664	Fc epsilon RI signaling pathway	RO:0002331	involved in	OMIM:612953	Parkinson Disease 14, Autosomal Recessive				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko04070	Phosphatidylinositol signaling system	RO:0002331	involved in	OMIM:615530	Parkinson Disease 20, Early-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:606324	Parkinson Disease 7, Autosomal Recessive Early-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:600116	Parkinson Disease 2, Autosomal Recessive Juvenile				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko05010	Alzheimer's disease	RO:0002331	involved in	OMIM:605543	Parkinson Disease 4, Autosomal Dominant				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:ko05016	Huntington's disease	RO:0002331	involved in	OMIM:556500	Parkinson Disease, Mitochondrial				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko00010	Glycolysis / Gluconeogenesis	RO:0002331	involved in	OMIM:556500	Parkinson Disease, Mitochondrial				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:612953	Parkinson Disease 14, Autosomal Recessive				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko00071	Fatty acid degradation	RO:0002331	involved in	OMIM:556500	Parkinson Disease, Mitochondrial				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko03013	RNA transport	RO:0002331	involved in	OMIM:614251	Parkinson Disease 18, Autosomal Dominant, Susceptibility to				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:600116	Parkinson Disease 2, Autosomal Recessive Juvenile				http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl	inferred
+KEGG-path:ko00980	Metabolism of xenobiotics by cytochrome P450	RO:0002331	involved in	OMIM:556500	Parkinson Disease, Mitochondrial				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-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-intersection.tsv
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