| Next changeset 1:7ae426ca9054 (2016-06-26) |
|
Commit message:
planemo upload commit b529f45bf9fecbac1457a65b6b81e3b95200fced |
|
added:
LICENSE README.rst arguments.png create_shed.sh demo.png monarch-genes-for-diseases.xml monarch-genes-for-phenotypes.xml monarch-homologues.xml monarch-phenopackets.xml monarch-phenotypes-for-disease.xml monarch-variants-for-diseases.xml monarch-variants-for-phenotypes.xml requirements.txt test-data/2-diseases-overlap.tsv test-data/2-diseases.tsv test-data/2-genes.tsv test-data/2-phenotypes.tsv test-data/disease.tsv test-data/empty.tsv test-data/gene.tsv test-data/genes-for-2-diseases-intersection.tsv test-data/genes-for-2-diseases-union.tsv test-data/genes-for-2-diseases.tsv test-data/genes-for-2-phenotypes-intersection.tsv test-data/genes-for-2-phenotypes-union.tsv test-data/genes-for-diseases.tsv test-data/genes-for-phenotype.tsv test-data/homologues-for-gene.tsv test-data/homologues-for-genes-intersection.tsv test-data/homologues-for-genes-union.tsv test-data/phenotype.tsv test-data/phenotypes-for-disease.tsv test-data/phenotypes-for-diseases-intersection.tsv test-data/phenotypes-for-diseases-union.tsv test-data/phenotypes-for-variant.json test-data/phenotypes-for-variants-intersection.json test-data/phenotypes-for-variants-union.json test-data/variants-for-disease.tsv test-data/variants-for-diseases-intersection.tsv test-data/variants-for-diseases-union.tsv test-data/variants-for-phenotype.tsv test-data/variants-for-phenotypes-intersection.tsv test-data/variants-for-phenotypes-union.tsv test.txt |
| b |
| diff -r 000000000000 -r 850bb90bd667 LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Sun Jun 26 16:00:28 2016 -0400 |
| b |
| @@ -0,0 +1,27 @@ +Copyright (c) 2016, Nathan Dunn +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +* Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +* Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +* Neither the name of galaxy-monarch-curl nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
| b |
| diff -r 000000000000 -r 850bb90bd667 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Sun Jun 26 16:00:28 2016 -0400 |
| [ |
| @@ -0,0 +1,11 @@ + + +This project wraps the Gene Ontology SOLR services (GOLR) exposed by the [Monarch initiative](https://monarchinitiative.org). + +# Gene Ontology Curl + + planemo serve + + + + |
| b |
| diff -r 000000000000 -r 850bb90bd667 arguments.png |
| b |
| Binary file arguments.png has changed |
| b |
| diff -r 000000000000 -r 850bb90bd667 create_shed.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/create_shed.sh Sun Jun 26 16:00:28 2016 -0400 |
| b |
| @@ -0,0 +1,5 @@ +planemo shed_init --name=geneontology \ + --owner=nathandunn \ + --description="Enriches Related biological data using ontology driven data." \ + --long_description="Tool Suite that Pulls related Variants, Phenotypes, Diseases, Genes, and Homologes" \ + --category="Web Services" |
| b |
| diff -r 000000000000 -r 850bb90bd667 demo.png |
| b |
| Binary file demo.png has changed |
| b |
| diff -r 000000000000 -r 850bb90bd667 monarch-genes-for-diseases.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/monarch-genes-for-diseases.xml Sun Jun 26 16:00:28 2016 -0400 |
| [ |
| @@ -0,0 +1,67 @@ +<tool id="monarch-genes-for-diseases" name="Pull Genes from Diseases" version="0.1.0"> + <requirements/> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ +#set conditional = "%20" + str($conditional1) + "%20" +#set prefix = "object_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') + $suffix + #end for +#end for + +curl -s 'https://solr.monarchinitiative.org/solr/golr/select?defType=edismax&qt=standard&indent=on&wt=csv&rows=100000&start=0&fl=subject,subject_label,subject_taxon,subject_taxon_label,relation,relation_label,object,object_label,evidence,evidence_label,source,is_defined_by,qualifier&facet=true&facet.mincount=1&facet.sort=count&json.nl=arrarr&facet.limit=25&facet.method=enum&csv.encapsulator=&csv.separator=%09&csv.header=true&csv.mv.separator=%7C&fq=($inputString)&fq=subject_category:%22gene%22&fq=object_category:%22disease%22&facet.field=subject_taxon_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="genes-for-diseases.tsv"/> + </test> + <test> + <param name="input1" value="2-diseases.tsv"/> + <param name="conditional1" value="OR"/> + <output name="output1" file="genes-for-2-diseases.tsv"/> + </test> + <test> + <param name="input1" value="2-diseases.tsv"/> + <param name="conditional1" value="AND"/> + <output name="output1" file="empty.tsv"/> + </test> + <test> + <param name="input1" value="2-diseases-overlap.tsv"/> + <param name="conditional1" value="AND"/> + <output name="output1" file="genes-for-2-diseases-intersection.tsv"/> + </test> + <test> + <param name="input1" value="2-diseases-overlap.tsv"/> + <param name="conditional1" value="OR"/> + <output name="output1" file="genes-for-2-diseases-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,relation,relation_label,object,object_label,evidence,evidence_label,source,is_defined_by,qualifier + ]]></help> + <citations> + <citation type="doi">doi:10.1038/nprot.2015.124</citation> + </citations> +</tool> |
| b |
| diff -r 000000000000 -r 850bb90bd667 monarch-genes-for-phenotypes.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/monarch-genes-for-phenotypes.xml Sun Jun 26 16:00:28 2016 -0400 |
| [ |
| @@ -0,0 +1,57 @@ +<tool id="monarch-genes-for-phenotypes" name="Pull Genes from Phenotypes" version="0.1.0"> + <requirements/> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ +#set conditional = "%20" + str($conditional1) + "%20" +#set prefix = "object_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') + $suffix + #end for +#end for + +curl -s 'https://solr.monarchinitiative.org/solr/golr/select?defType=edismax&qt=standard&indent=on&wt=csv&rows=100000&start=0&fl=subject,subject_label,subject_taxon,subject_taxon_label,relation,relation_label,object,object_label,evidence,evidence_label,source,is_defined_by,qualifier&facet=true&facet.mincount=1&facet.sort=count&json.nl=arrarr&facet.limit=25&facet.method=enum&csv.encapsulator=&csv.separator=%09&csv.header=true&csv.mv.separator=%7C&fq=($inputString)&fq=subject_category:%22gene%22&facet.field=subject_taxon_label&q=*:*' | tail -n +2 > $output1 + ]]></command> + <inputs> + <param name="input1" type="data" format="tabular" multiple="true" label="Phenotypes" /> + <param name="conditional1" type="select" multiple="false" display="radio" label="Conditional"> + <option value="AND">and</option> + <option value="OR">or</option> + </param> + </inputs> + <outputs> + <data name="output1" type="data" format="tabular" /> + </outputs> + <tests> + <test> + <param name="input1" value="phenotype.tsv"/> + <param name="conditional1" value="OR"/> + <output name="output1" file="genes-for-phenotype.tsv"/> + </test> + <test> + <param name="input1" value="2-phenotypes.tsv"/> + <param name="conditional1" value="AND"/> + <output name="output1" file="genes-for-2-phenotypes-intersection.tsv"/> + </test> + <test> + <param name="input1" value="2-phenotypes.tsv"/> + <param name="conditional1" value="OR"/> + <output name="output1" file="genes-for-2-phenotypes-union.tsv"/> + </test> + </tests> + <help><![CDATA[ + Pulls data from monarch web services as TSV given a phenotype. + subject,subject_label,subject_taxon,subject_taxon_label,relation,relation_label,object,object_label,evidence,evidence_label,source,is_defined_by,qualifier + ]]></help> + <citations> + <citation type="doi">doi:10.1038/nprot.2015.124</citation> + </citations> +</tool> |
| b |
| diff -r 000000000000 -r 850bb90bd667 monarch-homologues.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/monarch-homologues.xml Sun Jun 26 16:00:28 2016 -0400 |
| [ |
| @@ -0,0 +1,57 @@ +<tool id="monarch-homologues" name="Pull Homologue Information from Monarch" version="0.1.0"> + <requirements/> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ +#set conditional = "%20" + str($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') + $suffix + #end for +#end for + +curl -s 'https://solr.monarchinitiative.org/solr/golr/select?defType=edismax&qt=standard&indent=on&wt=csv&rows=100000&start=0&fl=object,object_label,object_taxon,object_taxon_label,relation,relation_label,evidence,evidence_label,source,is_defined_by,qualifier&facet=true&facet.mincount=1&facet.sort=count&json.nl=arrarr&facet.limit=25&facet.method=enum&csv.encapsulator=&csv.separator=%09&csv.header=true&csv.mv.separator=%7C&fq=($inputString)&fq=object_category:%22gene%22&fq=relation_closure:%22RO:HOM0000001%22&facet.field=subject_taxon_closure_label&facet.field=object_taxon_closure_label&q=*:*' | tail -n +2 > $output1 + ]]></command> + <inputs> + <param name="input1" type="data" format="tabular" multiple="true" label="Gene" /> + <param name="conditional1" type="select" multiple="false" display="radio" label="Conditional"> + <option value="AND">and</option> + <option value="OR">or</option> + </param> + </inputs> + <outputs> + <data name="output1" type="data" format="tabular" /> + </outputs> + <tests> + <test> + <param name="input1" value="gene.tsv"/> + <param name="conditional1" value="OR"/> + <output name="output1" file="homologues-for-gene.tsv"/> + </test> + <test> + <param name="input1" value="2-genes.tsv"/> + <param name="conditional1" value="OR"/> + <output name="output1" file="homologues-for-genes-union.tsv"/> + </test> + <test> + <param name="input1" value="2-genes.tsv"/> + <param name="conditional1" value="AND"/> + <output name="output1" file="homologues-for-genes-intersection.tsv"/> + </test> + </tests> + <help><![CDATA[ + Pulls data from monarch web services as TSV given a gene. + object,object_label,object_taxon,object_taxon_label,relation,relation_label,evidence,evidence_label,source,is_defined_by,qualifier + ]]></help> + <citations> + <citation type="doi">doi:10.1038/nprot.2015.124</citation> + </citations> +</tool> |
| b |
| diff -r 000000000000 -r 850bb90bd667 monarch-phenopackets.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/monarch-phenopackets.xml Sun Jun 26 16:00:28 2016 -0400 |
| [ |
| @@ -0,0 +1,72 @@ +<tool id="monarch-phenotypes-for-disease" name="Pull Diseases from Phenotypes" version="0.1.0"> + <requirements/> + <stdio> + <exit_code range="1:"/> + </stdio> + <command><![CDATA[ +#set conditional = "%20" + str($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') + $suffix + #end for +#end for + +curl -s 'https://monarchinitiative.org/phenopacket?q=*:*&fq=($inputString)&sfq=subject_category:%22variant%22&personality=variant_phenotype' > $output1 + ]]></command> + <inputs> + <param name="input1" type="data" format="tabular" multiple="true" label="Variant"/> + <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="json"/> + </outputs> + <tests> + <test> + <param name="input1" value="phenotype.tsv"/> + <param name="conditional1" value="OR"/> + <!--<output name="output1" file="phenotypes-for-variant.json"/>--> + <output name="output1"> + <assert_contents> + <has_text text='phenopacket":{"phenotype_profile":[{"entity":"ClinVarVariant:217207"'/> + </assert_contents> + </output> + </test> + <test> + <param name="input1" value="2-phenotypes.tsv"/> + <param name="conditional1" value="AND"/> + <!--<output name="output1" file="phenotypes-for-variants-intersection.json"/>--> + <output name="output1"> + <assert_contents> + <has_text text='phenopacket":{"phenotype_profile":[{"entity":"ClinVarVariant:217207"'/> + </assert_contents> + </output> + </test> + <test> + <param name="input1" value="2-phenotypes.tsv"/> + <param name="conditional1" value="OR"/> + <!--<output name="output1" file="phenotypes-for-variants-union.json"/>--> + <output name="output1"> + <assert_contents> + <has_text text='phenopacket":{"phenotype_profile":[{"entity":"ClinVarVariant:217207"'/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + Pulls phenopacket from data from monarch web services from one or more variants. + https://github.com/phenopackets/phenopacket-format/wiki/Getting-Started + ]]></help> + <citations> + <citation type="doi">doi:10.1038/nprot.2015.124</citation> + </citations> +</tool> |
| b |
| diff -r 000000000000 -r 850bb90bd667 monarch-phenotypes-for-disease.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/monarch-phenotypes-for-disease.xml Sun Jun 26 16:00:28 2016 -0400 |
| [ |
| @@ -0,0 +1,57 @@ +<tool id="monarch-phenotypes-for-disease" name="Pull Diseases from Phenotypes" 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') + $suffix + #end for +#end for + +curl -s 'https://solr.monarchinitiative.org/solr/golr/select?defType=edismax&qt=standard&indent=on&wt=csv&rows=100000&start=0&fl=subject,subject_label,relation,relation_label,object,object_label,evidence,evidence_label,source,is_defined_by,qualifier&facet=true&facet.mincount=1&facet.sort=count&json.nl=arrarr&facet.limit=25&facet.method=enum&csv.encapsulator=&csv.separator=%09&csv.header=true&csv.mv.separator=%7C&fq=($inputString)&fq=object_category:%22phenotype%22&fq=subject_category:%22disease%22&facet.field=subject_taxon_closure_label&facet.field=object_taxon_closure_label&q=*:*' | tail -n +2 > $output1 + ]]></command> + <inputs> + <param name="input1" type="data" format="tabular" multiple="true" label="Disease" /> + <param name="conditional1" type="select" multiple="false" display="radio" label="Conditional"> + <option value="AND">and</option> + <option value="OR">or</option> + </param> + </inputs> + <outputs> + <data name="output1" type="data" format="tabular" /> + </outputs> + <tests> + <test> + <param name="input1" value="disease.tsv"/> + <param name="conditional1" value="OR"/> + <output name="output1" file="phenotypes-for-disease.tsv"/> + </test> + <test> + <param name="input1" value="2-diseases-overlap.tsv"/> + <param name="conditional1" value="AND"/> + <output name="output1" file="phenotypes-for-diseases-intersection.tsv"/> + </test> + <test> + <param name="input1" value="2-diseases-overlap.tsv"/> + <param name="conditional1" value="OR"/> + <output name="output1" file="phenotypes-for-diseases-union.tsv"/> + </test> + </tests> + <help><![CDATA[ + Pulls data from monarch web services as TSV given a disease. + subject,subject_label,relation,relation_label,object,object_label,evidence,evidence_label,source,is_defined_by,qualifier + ]]></help> + <citations> + <citation type="doi">doi:10.1038/nprot.2015.124</citation> + </citations> +</tool> |
| b |
| diff -r 000000000000 -r 850bb90bd667 monarch-variants-for-diseases.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/monarch-variants-for-diseases.xml Sun Jun 26 16:00:28 2016 -0400 |
| [ |
| @@ -0,0 +1,57 @@ +<tool id="monarch-variants-for-diseases" name="Pull Variants from Diseases" version="0.1.0"> + <requirements/> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ +#set conditional = "%20" + str($conditional1) + "%20" +#set prefix = "object_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') + $suffix + #end for +#end for + +curl -s 'https://solr.monarchinitiative.org/solr/golr/select?defType=edismax&qt=standard&indent=on&wt=csv&rows=100000&start=0&fl=subject,subject_label,subject_taxon,subject_taxon_label,subject_gene,subject_gene_label,relation,relation_label,object,object_label,evidence,evidence_label,source,is_defined_by,qualifier&facet=true&facet.mincount=1&facet.sort=count&json.nl=arrarr&facet.limit=25&facet.method=enum&csv.encapsulator=&csv.separator=%09&csv.header=true&csv.mv.separator=%7C&fq=($inputString)&fq=subject_category:%22variant%22&fq=object_category:%22disease%22&facet.field=subject_taxon_label&q=*:*' | tail -n +2 > $output1 + ]]></command> + <inputs> + <param name="input1" type="data" format="tabular" multiple="true" label="Disease" /> + <param name="conditional1" type="select" multiple="false" display="radio" label="Conditional"> + <option value="AND">and</option> + <option value="OR">or</option> + </param> + </inputs> + <outputs> + <data name="output1" type="data" format="tabular" /> + </outputs> + <tests> + <test> + <param name="input1" value="disease.tsv"/> + <param name="conditional1" value="OR"/> + <output name="output1" file="variants-for-disease.tsv"/> + </test> + <test> + <param name="input1" value="2-diseases-overlap.tsv"/> + <param name="conditional1" value="AND"/> + <output name="output1" file="variants-for-diseases-intersection.tsv"/> + </test> + <test> + <param name="input1" value="2-diseases-overlap.tsv"/> + <param name="conditional1" value="OR"/> + <output name="output1" file="variants-for-diseases-union.tsv"/> + </test> + </tests> + <help><![CDATA[ + Pulls data from monarch web services as TSV given a disease. + subject,subject_label,subject_taxon,subject_taxon_label,subject_gene,subject_gene_label,relation,relation_label,object,object_label,evidence,evidence_label,source,is_defined_by,qualifier + ]]></help> + <citations> + <citation type="doi">doi:10.1038/nprot.2015.124</citation> + </citations> +</tool> |
| b |
| diff -r 000000000000 -r 850bb90bd667 monarch-variants-for-phenotypes.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/monarch-variants-for-phenotypes.xml Sun Jun 26 16:00:28 2016 -0400 |
| [ |
| @@ -0,0 +1,58 @@ +<tool id="monarch-variants-for-phenotypes" name="Pull Variants from Phenotypes" version="0.1.0"> + <requirements/> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ +#set conditional = "%20" + str($conditional1) + "%20" +#set prefix = "object_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') + $suffix + #end for +#end for + +curl -s 'https://solr.monarchinitiative.org/solr/golr/select?defType=edismax&qt=standard&indent=on&wt=csv&rows=100000&start=0&fl=subject,subject_label,subject_taxon,subject_taxon_label,subject_gene,subject_gene_label,relation,relation_label,object,object_label,evidence,evidence_label,source,is_defined_by,qualifier&facet=true&facet.mincount=1&facet.sort=count&json.nl=arrarr&facet.limit=25&facet.method=enum&csv.encapsulator=&csv.separator=%09&csv.header=true&csv.mv.separator=%7C&fq=($inputString)&fq=subject_category:%22variant%22&facet.field=subject_taxon_label&q=*:*' | tail -n +2 > $output1 + ]]></command> + <inputs> + <param name="input1" type="data" format="tabular" multiple="true" label="Phenotypes" /> + <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="phenotype.tsv"/> + <param name="conditional1" value="OR"/> + <output name="output1" file="variants-for-phenotype.tsv"/> + </test> + <test> + <param name="input1" value="2-phenotypes.tsv"/> + <param name="conditional1" value="AND"/> + <output name="output1" file="variants-for-phenotypes-intersection.tsv"/> + </test> + <test> + <param name="input1" value="2-phenotypes.tsv"/> + <param name="conditional1" value="OR"/> + <output name="output1" file="variants-for-phenotypes-union.tsv"/> + </test> + </tests> + <help><![CDATA[ + Pulls data from monarch web services as TSV given a disease.. + + subject subject_label relation relation_label object object_label evidence evidence_label source is_defined_by qualifier + ]]></help> + <citations> + <citation type="doi">doi:10.1038/nprot.2015.124</citation> + </citations> +</tool> |
| b |
| diff -r 000000000000 -r 850bb90bd667 requirements.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/requirements.txt Sun Jun 26 16:00:28 2016 -0400 |
| b |
| @@ -0,0 +1,1 @@ +planemo |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/2-diseases-overlap.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2-diseases-overlap.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| @@ -0,0 +1,1 @@ +DOID:14330,OMIM:168600 |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/2-diseases.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2-diseases.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| @@ -0,0 +1,1 @@ +DOID:14330,OMIM:607426 |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/2-genes.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2-genes.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| @@ -0,0 +1,1 @@ +NCBIGene:11132,NCBIGene:84290 \ No newline at end of file |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/2-phenotypes.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2-phenotypes.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| @@ -0,0 +1,1 @@ +HP:0000739,MP:0001363 \ No newline at end of file |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/disease.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/disease.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| @@ -0,0 +1,1 @@ +DOID:14330 |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/gene.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| @@ -0,0 +1,1 @@ +NCBIGene:11132 \ No newline at end of file |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/genes-for-2-diseases-intersection.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genes-for-2-diseases-intersection.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| @@ -0,0 +1,23 @@ +NCBIGene:4729 NDUFV2 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/ctd.ttl inferred +NCBIGene:6622 SNCA NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/coriell.ttl inferred +NCBIGene:5071 parkin RBR E3 ubiquitin protein ligase NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/coriell.ttl inferred +NCBIGene:6315 ATXN8OS NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl inferred +NCBIGene:2747 GLUD2 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl inferred +NCBIGene:4287 ATXN3 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl inferred +NCBIGene:203228 chromosome 9 open reading frame 72 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/coriell.ttl inferred +NCBIGene:6311 ATXN2 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset ECO:0000220 sequencing assay evidence http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl inferred +NCBIGene:26281 fibroblast growth factor 20 NCBITaxon:9606 Homo sapiens 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 +NCBIGene:4929 NR4A2 NCBITaxon:9606 Homo sapiens 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/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred +NCBIGene:7345 UCHL1 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/ctd.ttl inferred +NCBIGene:126 ADH1C NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset ECO:0000220 sequencing assay evidence http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred +NCBIGene:6908 TATA-box binding protein NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset ECO:0000220 sequencing assay evidence http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred +NCBIGene:1621 dopamine beta-hydroxylase (dopamine beta-monooxygenase) NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/ctd.ttl inferred +NCBIGene:627 BDNF NCBITaxon:9606 Homo sapiens 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 inferred +NCBIGene:4535 ND1 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl inferred +NCBIGene:23317 DNAJC13 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl inferred +NCBIGene:1815 dopamine receptor D4 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/ctd.ttl inferred +NCBIGene:120892 leucine-rich repeat kinase 2 NCBITaxon:9606 Homo sapiens 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/coriell.ttl inferred +NCBIGene:9627 synuclein alpha interacting protein NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred +NCBIGene:4137 microtubule associated protein tau NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset ECO:0000220 sequencing assay evidence http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred +NCBIGene:497258 BDNF-AS NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl inferred +NCBIGene:2629 GBA NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset ECO:0000220 sequencing assay evidence http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/coriell.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl inferred |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/genes-for-2-diseases-union.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genes-for-2-diseases-union.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| b"@@ -0,0 +1,130 @@\n+NCBIGene:37853\tMlp60A\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:39002\tPrm\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:627\tBDNF\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19276553\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:3630\tinsulin\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19276553\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:2944\tGSTM1\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:17449559\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:33824\tGpdh\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4137\tmicrotubule associated protein tau\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:260540\tParkinson-Dementia Syndrome\tECO:0000220|ECO:0000322\tsequencing assay evidence|imported manually asserted information used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl|http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4729\tNDUFV2\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:1565\tCYP2D6\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:15174030|PMID:14991823\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:3482\tinsulin like growth factor 2 receptor\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19276553\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4842\tnitric oxide synthase 1 (neuronal)\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:26383258\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:5243\tATP binding cassette subfamily B member 1\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:20558393\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:5071\tparkin RBR E3 ubiquitin protein ligase\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:15882845|PMID:19946270|PMID:25149416|PMID:22043175|PMID:16573651|PMID:12588799|PMID:22841634|PMID:24582596|PMID:15198987|PMID:17010972|PMID:23628791\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4129\tMAOB\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:21318773\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:6622\tSNCA\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/coriell.ttl\tinferred\n+NCBIGene:43497\tObp99b\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4137\tmicrotubule associated protein tau\tNCBITaxon:9606\tHomo sapiens\t\t\tOrphanet:240112\tProgressive supranuclear palsy - progressive non fluent aphasia\tECO:0000322\timported manually asserted information used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl\tinferred\n+NCBIGene:31826\trdgA\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's dise"..b"iens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:20711177\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:2580\tGAK\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:20711177\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:11315\tparkinson protein 7\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:105500\tAmyotrophic Lateral Sclerosis-Parkinsonism/Dementia Complex 1\tECO:0000323\timported automatically asserted information used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl\tinferred\n+NCBIGene:44643\tCnx99A\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:2941\tGSTA4\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:16510128\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4541\tMT-ND6\tNCBITaxon:9606\tHomo sapiens\t\t\tOrphanet:2828\tYoung-onset Parkinson disease\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:33883\tCpr\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:126\tADH1C\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:556500\tParkinson Disease, Mitochondrial\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:4571\tMT-TP\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:556500\tParkinson Disease, Mitochondrial\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:4137\tmicrotubule associated protein tau\tNCBITaxon:9606\tHomo sapiens\t\t\tOrphanet:240103\tProgressive supranuclear palsy - corticobasal syndrome\tECO:0000322\timported manually asserted information used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl\tinferred\n+NCBIGene:6888\tTALDO1\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:23233872\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:1906\tendothelin 1\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19276553\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:11315\tparkinson protein 7\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:606324\tParkinson Disease 7, Autosomal Recessive Early-Onset\tECO:0000220\tsequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:38990\tCpr66D\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:1356\tceruloplasmin (ferroxidase)\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19159062|PMID:25758665\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:54822\tTRPM7\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:105500\tAmyotrophic Lateral Sclerosis-Parkinsonism/Dementia Complex 1\tECO:0000220|ECO:0000323\tsequencing assay evidence|imported automatically asserted information used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl|http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:65018\tPINK1\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:22043175|PMID:17010972|PMID:25149416|PMID:21366594|PMID:24374061\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n" |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/genes-for-2-diseases.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genes-for-2-diseases.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| b"@@ -0,0 +1,136 @@\n+NCBIGene:37853\tMlp60A\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:39002\tPrm\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:627\tBDNF\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19276553\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:3630\tinsulin\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19276553\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:2944\tGSTM1\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:17449559\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:33824\tGpdh\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4137\tmicrotubule associated protein tau\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:260540\tParkinson-Dementia Syndrome\tECO:0000220|ECO:0000322\tsequencing assay evidence|imported manually asserted information used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl|http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4729\tNDUFV2\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:1565\tCYP2D6\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:15174030|PMID:14991823\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:3482\tinsulin like growth factor 2 receptor\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19276553\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:27235\tCOQ2\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:607426\tCoenzyme Q10 Deficiency, Primary, 1\tECO:0000220\tsequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4842\tnitric oxide synthase 1 (neuronal)\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:26383258\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:5243\tATP binding cassette subfamily B member 1\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:20558393\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:5071\tparkin RBR E3 ubiquitin protein ligase\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:15882845|PMID:19946270|PMID:25149416|PMID:22043175|PMID:16573651|PMID:12588799|PMID:22841634|PMID:24582596|PMID:15198987|PMID:17010972|PMID:23628791\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4129\tMAOB\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:21318773\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:6622\tSNCA\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/coriell.ttl\tinferred\n+NCBIGene:23590\tPDSS1\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:607426\tCoenzyme Q10 Deficiency, Primary, 1\t\t\t\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:43497\tObp99b\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tEC"..b"AK\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:20711177\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:11315\tparkinson protein 7\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:105500\tAmyotrophic Lateral Sclerosis-Parkinsonism/Dementia Complex 1\tECO:0000323\timported automatically asserted information used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl\tinferred\n+NCBIGene:44643\tCnx99A\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:2941\tGSTA4\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:16510128\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4541\tMT-ND6\tNCBITaxon:9606\tHomo sapiens\t\t\tOrphanet:2828\tYoung-onset Parkinson disease\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:33883\tCpr\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:126\tADH1C\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:556500\tParkinson Disease, Mitochondrial\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:4571\tMT-TP\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:556500\tParkinson Disease, Mitochondrial\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:4137\tmicrotubule associated protein tau\tNCBITaxon:9606\tHomo sapiens\t\t\tOrphanet:240103\tProgressive supranuclear palsy - corticobasal syndrome\tECO:0000322\timported manually asserted information used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl\tinferred\n+NCBIGene:6888\tTALDO1\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:23233872\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:1906\tendothelin 1\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19276553\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:11315\tparkinson protein 7\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:606324\tParkinson Disease 7, Autosomal Recessive Early-Onset\tECO:0000220\tsequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:38990\tCpr66D\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:1356\tceruloplasmin (ferroxidase)\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19159062|PMID:25758665\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:54840\taprataxin\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:607426\tCoenzyme Q10 Deficiency, Primary, 1\t\t\t\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:54822\tTRPM7\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:105500\tAmyotrophic Lateral Sclerosis-Parkinsonism/Dementia Complex 1\tECO:0000220|ECO:0000323\tsequencing assay evidence|imported automatically asserted information used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl|http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:65018\tPINK1\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:22043175|PMID:17010972|PMID:25149416|PMID:21366594|PMID:24374061\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n" |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/genes-for-2-phenotypes-intersection.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genes-for-2-phenotypes-intersection.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| b'@@ -0,0 +1,245 @@\n+MGI:109178\tFgf13\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:22726441\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1270850\tSlc6a2\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:23580201\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1913894\tUba6\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:23499007\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:96918\tMas1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:9565612\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:95819\tGrin1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:19915563\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:2143311\tBbs4\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:16794820\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:101922\tTnc\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:16553788\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:2441758\tGpr26\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:21924326\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1922391\tRasd2\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:15199135\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:95821\tGrin2b\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:20357110\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1916933\tEmc10\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:20562862|MGI:3510987\thttp://data.monarchinitiative.org/ttl/mgi.ttl|http://data.monarchinitiative.org/ttl/mmrrc.ttl\tdirect\n+MGI:96559\tIl6\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006|ECO:0000006\texperimental evidence|experimental evidence\tPMID:16843000|PMID:12946594|PMID:19378383\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1096362\tNrxn2\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:25423136\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1100881\tPrss12\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tMGI:3604450\thttp://data.monarchinitiative.org/ttl/mgi.ttl|http://data.monarchinitiative.org/ttl/mmrrc.ttl\tdirect\n+MGI:95394\tEno2\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:23487260\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1922459\tSv2c\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:23458503\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:2651811\tTph2\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006|ECO:0000006\texperimental evidence|experimental evidence\tPMID:18212115|PMID:18212115\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:2443472\tAtf7\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:19893493\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1328355\tWfs1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:19477223\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:2443963\tCadps2\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\t'..b'90\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006|ECO:0000006|ECO:0000006|ECO:0000006\texperimental evidence|experimental evidence|experimental evidence|experimental evidence\tPMID:19158294|PMID:19158294|PMID:18832146|PMID:10571233\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:102707\tEfna2\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:25281279\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:88497\tCrhbp\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:10500222|PMID:10500222\thttp://data.monarchinitiative.org/ttl/mgi.ttl|http://data.monarchinitiative.org/ttl/mmrrc.ttl\tdirect\n+MGI:88105\tAtp1a1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tMGI:3609573\thttp://data.monarchinitiative.org/ttl/mgi.ttl|http://data.monarchinitiative.org/ttl/mmrrc.ttl\tdirect\n+MGI:2152453\tGsk3a\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:20357757\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:105089\tHsd17b4\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006|ECO:0000006\texperimental evidence|experimental evidence\tPMID:23777740|PMID:23777740\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:96916\tMaob\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:15272015\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1929258\tKcnip3\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:19223600\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:104510\tMyo7a\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tMGI:63673\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1861234\tWt\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:13834122\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1201414\tCer1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tMGI:3604450\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1277959\tDlg4\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:23268962\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:98735\tTh\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:16723393\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:104735\tGt(ROSA)26Sor\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:21885734\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:95819\tGrin1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:19915563\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:3584508\tKcnh5\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tMGI:3604450\thttp://data.monarchinitiative.org/ttl/mgi.ttl|http://data.monarchinitiative.org/ttl/mmrrc.ttl\tdirect\n+MGI:95583\tFshr\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:14502087\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:88470\tComt\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:9707588\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1098271\tRgs2\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:11027316\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n' |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/genes-for-2-phenotypes-union.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genes-for-2-phenotypes-union.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| b'@@ -0,0 +1,637 @@\n+MGI:3589233\ttmgc58\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001364\tdecreased anxiety-related response\tECO:0000006\texperimental evidence\tMGI:3053008|PMID:17629744\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:109178\tFgf13\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:22726441\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1270850\tSlc6a2\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:23580201\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1913894\tUba6\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:23499007\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:2156367\tTlr3\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001364\tdecreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:20713712\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:96918\tMas1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:9565612\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+NCBIGene:8131\tNPRL3\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000213|ECO:0000246\tcombinatorial evidence used in automatic assertion|computational combinatorial evidence used in automatic assertion\tPMID:21099065|PMID:3375880|PMID:23406172|PMID:17938043|PMID:9491171|PMID:21425450\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+MGI:95389\tEn1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001364\tdecreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:19679071\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+NCBIGene:11132\tCAPN10\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:9428966|PMID:22397240|PMID:2209327|PMID:22188726|PMID:12429356\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+MGI:95819\tGrin1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:19915563\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+NCBIGene:6331\tSCN5A\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000220|ECO:0000246\tsequencing assay evidence|computational combinatorial evidence used in automatic assertion\tPMID:1759138|PMID:9172914|PMID:9602186|PMID:22796196|PMID:17854255\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+NCBIGene:6391\tsuccinate dehydrogenase complex, subunit C, integral membrane protein, 15kDa\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000220|ECO:0000501\tsequencing assay evidence|evidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+NCBIGene:2554\tGABRA1\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000322|ECO:0000246\timported manually asserted information used in automatic assertion|computational combinatorial evidence used in automatic assertion\tPMID:11319492|PMID:21703932|PMID:21683658|PMID:19453714|PMID:21041102\thttp://data.monarchinitiative.org/ttl/orphanet.ttl|http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+MGI:97535\tPdyn\tNCBITaxon:10090\tMus musculus\t\t\tHP:0000739\tAnxiety\tECO:0000006\texperimental evidence\tPMID:12843270\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:88227\tC3\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001364\tdecreased'..b'ssertion|evidence used in automatic assertion|sequencing assay evidence|evidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl|http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+MGI:3584508\tKcnh5\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tMGI:3604450\thttp://data.monarchinitiative.org/ttl/mgi.ttl|http://data.monarchinitiative.org/ttl/mmrrc.ttl\tdirect\n+MGI:5646421\tMbt3\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001364\tdecreased anxiety-related response\tECO:0000006\texperimental evidence\tMGI:4940633\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:5515454\tM1073b\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001364\tdecreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:16109771\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+NCBIGene:5573\tPRKAR1A\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0000739\tAnxiety\tECO:0000220|ECO:0000501\tsequencing assay evidence|evidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+NCBIGene:5982\tRFC2\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246|ECO:0000322\tcomputational combinatorial evidence used in automatic assertion|imported manually asserted information used in automatic assertion\tPMID:12730029|PMID:21211940|PMID:22048961|PMID:21328569|PMID:22371147\thttp://data.monarchinitiative.org/ttl/orphanet.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+MGI:95583\tFshr\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:14502087\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:88470\tComt\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:9707588\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:2139535\tTprn\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001364\tdecreased anxiety-related response\tECO:0000059|ECO:0000059|ECO:0000006\texperimental phenotypic evidence|experimental phenotypic evidence|experimental evidence\tMGI:5576271\thttp://data.monarchinitiative.org/ttl/mgi.ttl|http://data.monarchinitiative.org/ttl/impc.ttl\tinferred\n+NCBIGene:3172\tHNF4A\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246|ECO:0000220\tcomputational combinatorial evidence used in automatic assertion|sequencing assay evidence\tPMID:9428966|PMID:22188726|PMID:12429356|PMID:22397240|PMID:2209327\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+MGI:97597\tPrkcg\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001364\tdecreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:10979601\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:95575\tFosb\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001364\tdecreased anxiety-related response\tECO:0000006|ECO:0000006\texperimental evidence|experimental evidence\tPMID:21679928|PMID:21679928\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+NCBIGene:3767\tpotassium channel, inwardly rectifying subfamily J, member 11\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000220|ECO:0000246\tsequencing assay evidence|computational combinatorial evidence used in automatic assertion\tPMID:9428966|PMID:22188726|PMID:12429356|PMID:22397240|PMID:2209327\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/hpoa.ttl\tinferred\n+MGI:1098271\tRgs2\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:11027316\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n' |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/genes-for-diseases.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genes-for-diseases.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| b"@@ -0,0 +1,130 @@\n+NCBIGene:37853\tMlp60A\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:39002\tPrm\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:627\tBDNF\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19276553\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:3630\tinsulin\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19276553\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:2944\tGSTM1\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:17449559\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:33824\tGpdh\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4137\tmicrotubule associated protein tau\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:260540\tParkinson-Dementia Syndrome\tECO:0000220|ECO:0000322\tsequencing assay evidence|imported manually asserted information used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl|http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4729\tNDUFV2\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:1565\tCYP2D6\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:15174030|PMID:14991823\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:3482\tinsulin like growth factor 2 receptor\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19276553\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4842\tnitric oxide synthase 1 (neuronal)\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:26383258\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:5243\tATP binding cassette subfamily B member 1\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:20558393\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:5071\tparkin RBR E3 ubiquitin protein ligase\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:15882845|PMID:19946270|PMID:25149416|PMID:22043175|PMID:16573651|PMID:12588799|PMID:22841634|PMID:24582596|PMID:15198987|PMID:17010972|PMID:23628791\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4129\tMAOB\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:21318773\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:6622\tSNCA\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/coriell.ttl\tinferred\n+NCBIGene:43497\tObp99b\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4137\tmicrotubule associated protein tau\tNCBITaxon:9606\tHomo sapiens\t\t\tOrphanet:240112\tProgressive supranuclear palsy - progressive non fluent aphasia\tECO:0000322\timported manually asserted information used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl\tinferred\n+NCBIGene:31826\trdgA\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's dise"..b"iens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:20711177\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:2580\tGAK\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:20711177\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:11315\tparkinson protein 7\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:105500\tAmyotrophic Lateral Sclerosis-Parkinsonism/Dementia Complex 1\tECO:0000323\timported automatically asserted information used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl\tinferred\n+NCBIGene:44643\tCnx99A\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:2941\tGSTA4\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:16510128\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4541\tMT-ND6\tNCBITaxon:9606\tHomo sapiens\t\t\tOrphanet:2828\tYoung-onset Parkinson disease\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:33883\tCpr\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:126\tADH1C\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:556500\tParkinson Disease, Mitochondrial\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:4571\tMT-TP\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:556500\tParkinson Disease, Mitochondrial\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:4137\tmicrotubule associated protein tau\tNCBITaxon:9606\tHomo sapiens\t\t\tOrphanet:240103\tProgressive supranuclear palsy - corticobasal syndrome\tECO:0000322\timported manually asserted information used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl\tinferred\n+NCBIGene:6888\tTALDO1\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:23233872\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:1906\tendothelin 1\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19276553\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:11315\tparkinson protein 7\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:606324\tParkinson Disease 7, Autosomal Recessive Early-Onset\tECO:0000220\tsequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:38990\tCpr66D\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:1356\tceruloplasmin (ferroxidase)\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19159062|PMID:25758665\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:54822\tTRPM7\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:105500\tAmyotrophic Lateral Sclerosis-Parkinsonism/Dementia Complex 1\tECO:0000220|ECO:0000323\tsequencing assay evidence|imported automatically asserted information used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl|http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:65018\tPINK1\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:22043175|PMID:17010972|PMID:25149416|PMID:21366594|PMID:24374061\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n" |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/genes-for-phenotype.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genes-for-phenotype.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| @@ -0,0 +1,10 @@ +NCBIGene:26058 GRB10 interacting GYF protein 2 NCBITaxon:9606 Homo sapiens HP:0002548 Parkinsonism with favorable response to dopaminergic medication ECO:0000220|ECO:0000269 sequencing assay evidence|experimental evidence used in manual assertion PMID:18358451 http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl inferred +NCBIGene:5428 polymerase (DNA directed), gamma NCBITaxon:9606 Homo sapiens HP:0002548 Parkinsonism with favorable response to dopaminergic medication ECO:0000501|ECO:0000220 evidence used in automatic assertion|sequencing assay evidence http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl inferred +NCBIGene:2643 GCH1 NCBITaxon:9606 Homo sapiens HP:0002548 Parkinsonism with favorable response to dopaminergic medication ECO:0000220|ECO:0000304 sequencing assay evidence|traceable author statement used in manual assertion http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl inferred +NCBIGene:25793 F-box protein 7 NCBITaxon:9606 Homo sapiens HP:0002548 Parkinsonism with favorable response to dopaminergic medication ECO:0000322|ECO:0000220|ECO:0000501 imported manually asserted information used in automatic assertion|sequencing assay evidence|evidence used in automatic assertion http://data.monarchinitiative.org/ttl/orphanet.ttl|http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl inferred +NCBIGene:23400 ATP13A2 NCBITaxon:9606 Homo sapiens HP:0002548 Parkinsonism with favorable response to dopaminergic medication ECO:0000220|ECO:0000322|ECO:0000220|ECO:0000304 sequencing assay evidence|imported manually asserted information used in automatic assertion|sequencing assay evidence|traceable author statement used in manual assertion http://data.monarchinitiative.org/ttl/orphanet.ttl|http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl inferred +NCBIGene:7054 TH NCBITaxon:9606 Homo sapiens HP:0002548 Parkinsonism with favorable response to dopaminergic medication ECO:0000322|ECO:0000304|ECO:0000220 imported manually asserted information used in automatic assertion|traceable author statement used in manual assertion|sequencing assay evidence http://data.monarchinitiative.org/ttl/orphanet.ttl|http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl inferred +NCBIGene:27429 HTRA2 NCBITaxon:9606 Homo sapiens HP:0002548 Parkinsonism with favorable response to dopaminergic medication ECO:0000220|ECO:0000304 sequencing assay evidence|traceable author statement used in manual assertion http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl inferred +NCBIGene:120892 leucine-rich repeat kinase 2 NCBITaxon:9606 Homo sapiens HP:0002548 Parkinsonism with favorable response to dopaminergic medication ECO:0000501|ECO:0000220 evidence used in automatic assertion|sequencing assay evidence 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/hpoa.ttl inferred +NCBIGene:6872 TATA-box binding protein associated factor 1 NCBITaxon:9606 Homo sapiens HP:0002548 Parkinsonism with favorable response to dopaminergic medication ECO:0000304|ECO:0000220 traceable author statement used in manual assertion|sequencing assay evidence http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl inferred +NCBIGene:6622 SNCA NCBITaxon:9606 Homo sapiens HP:0002548 Parkinsonism with favorable response to dopaminergic medication ECO:0000501|ECO:0000322 evidence used in automatic assertion|imported manually asserted information used in automatic assertion http://data.monarchinitiative.org/ttl/orphanet.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl inferred |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/homologues-for-gene.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/homologues-for-gene.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| @@ -0,0 +1,30 @@ +NCBIGene:607311 CAPN10 NCBITaxon:9615 Canis lupus familiaris RO:HOM0000020 in 1 to 1 orthology relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:84290 CAPNS2 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +WormBase:WBGene00006606 tra-3 NCBITaxon:6239 Caenorhabditis elegans RO:HOM0000017 in orthology relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:6650 calpain 15 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:11131 CAPN11 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:79747 ADGB NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +MGI:1344392 Capn10 NCBITaxon:10090 Mus musculus RO:HOM0000020 in 1 to 1 orthology relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:63834 Capn10 NCBITaxon:10116 Rattus norvegicus RO:HOM0000020 in 1 to 1 orthology relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:147968 calpain 12 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:23473 CAPN7 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:440854 CAPN14 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:10753 CAPN9 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:570311 capn10 NCBITaxon:7955 Danio rerio RO:HOM0000020 in 1 to 1 orthology relationship with ECO:0000031|ECO:0000080 protein BLAST evidence used in manual assertion|phylogenetic evidence ZFIN:ZDB-PUB-030905-1 http://data.monarchinitiative.org/ttl/panther.ttl|http://data.monarchinitiative.org/ttl/zfin.ttl direct +NCBIGene:827 CAPN6 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:553115 PEF1 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:826 CAPNS1 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:100022544 CAPN10 NCBITaxon:13616 Monodelphis domestica RO:HOM0000020 in 1 to 1 orthology relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:6717 SRI NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:10016 PDCD6 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:388743 CAPN8 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:25801 GCA NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:824 CAPN2 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:716360 CAPN10 NCBITaxon:9544 Macaca mulatta RO:HOM0000020 in 1 to 1 orthology relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:841981 DEK1 NCBITaxon:3702 Arabidopsis thaliana RO:HOM0000017 in orthology relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:789674 CAPN10 NCBITaxon:9913 Bos taurus RO:HOM0000020 in 1 to 1 orthology relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:825 calpain 3 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:100379827 capn10 NCBITaxon:8364 Xenopus tropicalis RO:HOM0000020 in 1 to 1 orthology relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:726 CAPN5 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:823 calpain 1, (mu/I) large subunit NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:92291 CAPN13 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/homologues-for-genes-union.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/homologues-for-genes-union.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| b'@@ -0,0 +1,58 @@\n+NCBIGene:607311\tCAPN10\tNCBITaxon:9615\tCanis lupus familiaris\tRO:HOM0000020\tin 1 to 1 orthology relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:84290\tCAPNS2\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+ZFIN:ZDB-GENE-030131-5206\tcapns1b\tNCBITaxon:7955\tDanio rerio\tRO:HOM0000017\tin orthology relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+WormBase:WBGene00006606\ttra-3\tNCBITaxon:6239\tCaenorhabditis elegans\tRO:HOM0000017\tin orthology relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:6650\tcalpain 15\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:10753\tCAPN9\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:388743\tCAPN8\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+MGI:1916793\tCapns2\tNCBITaxon:10090\tMus musculus\tRO:HOM0000020\tin 1 to 1 orthology relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:11131\tCAPN11\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:79747\tADGB\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+MGI:1344392\tCapn10\tNCBITaxon:10090\tMus musculus\tRO:HOM0000020\tin 1 to 1 orthology relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:6717\tSRI\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:825\tcalpain 3\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:79747\tADGB\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:823\tcalpain 1, (mu/I) large subunit\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080|ECO:0000079\tphylogenetic evidence|affinity chromatography evidence\tPMID:26186194\thttp://data.monarchinitiative.org/ttl/panther.ttl|http://data.monarchinitiative.org/ttl/biogrid.ttl\tdirect\n+NCBIGene:6650\tcalpain 15\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:63834\tCapn10\tNCBITaxon:10116\tRattus norvegicus\tRO:HOM0000020\tin 1 to 1 orthology relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+ZFIN:ZDB-GENE-030113-3\tcapns1a\tNCBITaxon:7955\tDanio rerio\tRO:HOM0000017\tin orthology relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:147968\tcalpain 12\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:553115\tPEF1\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:23473\tCAPN7\tNC'..b'ylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:826\tCAPNS1\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080|ECO:0000079\tphylogenetic evidence|affinity chromatography evidence\tPMID:26186194\thttp://data.monarchinitiative.org/ttl/panther.ttl|http://data.monarchinitiative.org/ttl/biogrid.ttl\tdirect\n+NCBIGene:25801\tGCA\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:824\tCAPN2\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:92291\tCAPN13\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:716360\tCAPN10\tNCBITaxon:9544\tMacaca mulatta\tRO:HOM0000020\tin 1 to 1 orthology relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:11131\tCAPN11\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:841981\tDEK1\tNCBITaxon:3702\tArabidopsis thaliana\tRO:HOM0000017\tin orthology relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:820192\tAT3G10300\tNCBITaxon:3702\tArabidopsis thaliana\tRO:HOM0000017\tin orthology relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:726\tCAPN5\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:23473\tCAPN7\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:789674\tCAPN10\tNCBITaxon:9913\tBos taurus\tRO:HOM0000020\tin 1 to 1 orthology relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:825\tcalpain 3\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:100145791\tcapns1\tNCBITaxon:8364\tXenopus tropicalis\tRO:HOM0000017\tin orthology relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:11132\tCAPN10\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:100379827\tcapn10\tNCBITaxon:8364\tXenopus tropicalis\tRO:HOM0000020\tin 1 to 1 orthology relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:824\tCAPN2\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:726\tCAPN5\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:823\tcalpain 1, (mu/I) large subunit\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:92291\tCAPN13\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:10016\tPDCD6\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n' |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/phenotype.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phenotype.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| @@ -0,0 +1,1 @@ +HP:0002548 \ No newline at end of file |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/phenotypes-for-disease.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phenotypes-for-disease.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| b"@@ -0,0 +1,283 @@\n+DOID:14330\tParkinson's disease\tRO:0002200\thas phenotype\tHP:0002019\tConstipation\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:12814332|PMID:21560061|PMID:23408927|PMID:22021174|PMID:19717168\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:613135\tParkinsonism-Dystonia, Infantile\tRO:0002200\thas phenotype\tHP:0002067\tBradykinesia\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:614251\tParkinson Disease 18, Autosomal Dominant, Susceptibility to\tRO:0002200\thas phenotype\tHP:0002063\tRigidity\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:614203\tParkinson Disease 17\tRO:0002200\thas phenotype\tHP:0100660\tDyskinesia\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:168600\tParkinson Disease, Late-Onset\tRO:0002200\thas phenotype\tHP:0002015\tDysphagia\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:614251\tParkinson Disease 18, Autosomal Dominant, Susceptibility to\tRO:0002200\thas phenotype\tHP:0002322\tResting tremor\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:605543\tParkinson Disease 4, Autosomal Dominant\tRO:0002200\thas phenotype\tHP:0001824\tWeight loss\tECO:0000304\ttraceable author statement used in manual assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:606324\tParkinson Disease 7, Autosomal Recessive Early-Onset\tRO:0002200\thas phenotype\tHP:0000739\tAnxiety\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:168100\tParalysis Agitans, Juvenile, of Hunt\tRO:0002200\thas phenotype\tHP:0001300\tParkinsonism\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\tRO:0002200\thas phenotype\tHP:0001332\tDystonia\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:613135\tParkinsonism-Dystonia, Infantile\tRO:0002200\thas phenotype\tHP:0002020\tGastroesophageal reflux\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:614251\tParkinson Disease 18, Autosomal Dominant, Susceptibility to\tRO:0002200\thas phenotype\tHP:0100315\tLewy bodies\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+DOID:14330\tParkinson's disease\tRO:0002200\thas phenotype\tHP:0000011\tNeurogenic bladder\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:22331071|PMID:12922929|PMID:12756142|PMID:1965204|PMID:16855424\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+DOID:14330\tParkinson's disease\tRO:0002200\thas phenotype\tHP:0001824\tWeight loss\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:20028343|PMID:16773618|PMID:15595933|PMID:11241387|PMID:21192784\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:606693\tKufor-Rakeb syndrome\tRO:0002200\thas phenotype\tHP:0000605\tSupranuclear gaze palsy\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:168601\tautosomal dominant Parkinson disease 1\tRO:0002200\thas phenotype\tHP:0000012\tUrinary urgency\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:168600\tParkinson Disease, Late-Onset\tRO:0002200\thas phenotype\tHP:0001621\tWeak voice\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:168600\tParkinson Disease, Late-Onset\tRO:0002200\thas phenotype\tHP:0100315\tLewy bodies\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:605543\tParkinson Di"..b"Juvenile, of Hunt\tRO:0002200\thas phenotype\tHP:0002063\tRigidity\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+DOID:14330\tParkinson's disease\tRO:0002200\thas phenotype\tHP:0001332\tDystonia\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:2515718|PMID:6231489|PMID:22976499|PMID:2579626|PMID:7715793\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:614251\tParkinson Disease 18, Autosomal Dominant, Susceptibility to\tRO:0002200\thas phenotype\tHP:0002067\tBradykinesia\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:606693\tKufor-Rakeb syndrome\tRO:0002200\thas phenotype\tHP:0000514\tSlow saccadic eye movements\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:614203\tParkinson Disease 17\tRO:0002200\thas phenotype\tHP:0002172\tPostural instability\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:614203\tParkinson Disease 17\tRO:0002200\thas phenotype\tHP:0001300\tParkinsonism\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:615528\tParkinson Disease 19, Juvenile-Onset\tRO:0002200\thas phenotype\tHP:0002172\tPostural instability\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:105500\tAmyotrophic Lateral Sclerosis-Parkinsonism/Dementia Complex 1\tRO:0002200\thas phenotype\tHP:0001283\tBulbar palsy\tECO:0000304\ttraceable author statement used in manual assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\tRO:0002200\thas phenotype\tHP:0001288\tGait disturbance\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+DOID:14330\tParkinson's disease\tRO:0002200\thas phenotype\tHP:0000751\tPersonality changes\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:21560061|PMID:16908734|PMID:21845593|PMID:9426865|PMID:18346925\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:616361\tParkinson Disease 21\tRO:0002200\thas phenotype\tHP:0002172\tPostural instability\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+DOID:14330\tParkinson's disease\tRO:0002200\thas phenotype\tHP:0002321\tVertigo\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:19479494|PMID:21843110|PMID:19768728|PMID:2515717|PMID:12814332\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:607688\tParkinson Disease 11, Autosomal Dominant, Susceptibility to\tRO:0002200\thas phenotype\tHP:0002322\tResting tremor\tECO:0000269\texperimental evidence used in manual assertion\tPMID:18358451\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+DOID:14330\tParkinson's disease\tRO:0002200\thas phenotype\tHP:0000746\tDelusions\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:12814332|PMID:16239760|PMID:7652084|PMID:19507125|PMID:20538500\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+DOID:14330\tParkinson's disease\tRO:0002200\thas phenotype\tHP:0000822\tHypertension\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:18166127|PMID:20032288|PMID:11041086|PMID:17761552|PMID:17514358\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:605543\tParkinson Disease 4, Autosomal Dominant\tRO:0002200\thas phenotype\tHP:0100315\tLewy bodies\tECO:0000304\ttraceable author statement used in manual assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+DOID:14330\tParkinson's disease\tRO:0002200\thas phenotype\tHP:0000012\tUrinary urgency\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:3942028|PMID:14521485|PMID:18327532|PMID:19908315|PMID:11570707\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n" |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/phenotypes-for-diseases-intersection.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phenotypes-for-diseases-intersection.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| @@ -0,0 +1,22 @@ +OMIM:168600 Parkinson Disease, Late-Onset RO:0002200 has phenotype HP:0002015 Dysphagia ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct +OMIM:168600 Parkinson Disease, Late-Onset RO:0002200 has phenotype HP:0001621 Weak voice ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct +OMIM:168600 Parkinson Disease, Late-Onset RO:0002200 has phenotype HP:0100315 Lewy bodies ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct +OMIM:168600 Parkinson Disease, Late-Onset RO:0002200 has phenotype HP:0002172 Postural instability ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct +OMIM:168600 Parkinson Disease, Late-Onset RO:0002200 has phenotype HP:0007311 Short stepped shuffling gait ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct +OMIM:168600 Parkinson Disease, Late-Onset RO:0002200 has phenotype HP:0001300 Parkinsonism ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct +OMIM:168600 Parkinson Disease, Late-Onset RO:0002200 has phenotype HP:0000716 Depression ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct +OMIM:168600 Parkinson Disease, Late-Onset RO:0002200 has phenotype HP:0001260 Dysarthria ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct +OMIM:168600 Parkinson Disease, Late-Onset RO:0002200 has phenotype HP:0000012 Urinary urgency ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct +OMIM:168600 Parkinson Disease, Late-Onset RO:0002200 has phenotype HP:0002019 Constipation ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct +OMIM:168600 Parkinson Disease, Late-Onset RO:0002200 has phenotype HP:0000751 Personality changes ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct +OMIM:168600 Parkinson Disease, Late-Onset RO:0002200 has phenotype HP:0002360 Sleep disturbance ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct +OMIM:168600 Parkinson Disease, Late-Onset RO:0002200 has phenotype HP:0011960 Substantia nigra gliosis ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct +OMIM:168600 Parkinson Disease, Late-Onset RO:0002200 has phenotype HP:0000726 Dementia ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct +OMIM:168600 Parkinson Disease, Late-Onset RO:0002200 has phenotype HP:0000738 Hallucinations ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct +OMIM:168600 Parkinson Disease, Late-Onset RO:0002200 has phenotype HP:0000298 Mask-like facies ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct +OMIM:168600 Parkinson Disease, Late-Onset RO:0002200 has phenotype HP:0002529 Neuronal loss in central nervous system ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct +OMIM:168600 Parkinson Disease, Late-Onset RO:0002200 has phenotype HP:0001332 Dystonia ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct +OMIM:168600 Parkinson Disease, Late-Onset RO:0002200 has phenotype HP:0002322 Resting tremor ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct +OMIM:168600 Parkinson Disease, Late-Onset RO:0002200 has phenotype HP:0002459 Dysautonomia ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct +OMIM:168600 Parkinson Disease, Late-Onset RO:0002200 has phenotype HP:0002063 Rigidity ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct +OMIM:168600 Parkinson Disease, Late-Onset RO:0002200 has phenotype HP:0002067 Bradykinesia ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/phenotypes-for-diseases-union.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phenotypes-for-diseases-union.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| b"@@ -0,0 +1,283 @@\n+DOID:14330\tParkinson's disease\tRO:0002200\thas phenotype\tHP:0002019\tConstipation\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:12814332|PMID:21560061|PMID:23408927|PMID:22021174|PMID:19717168\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:613135\tParkinsonism-Dystonia, Infantile\tRO:0002200\thas phenotype\tHP:0002067\tBradykinesia\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:614251\tParkinson Disease 18, Autosomal Dominant, Susceptibility to\tRO:0002200\thas phenotype\tHP:0002063\tRigidity\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:614203\tParkinson Disease 17\tRO:0002200\thas phenotype\tHP:0100660\tDyskinesia\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:168600\tParkinson Disease, Late-Onset\tRO:0002200\thas phenotype\tHP:0002015\tDysphagia\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:614251\tParkinson Disease 18, Autosomal Dominant, Susceptibility to\tRO:0002200\thas phenotype\tHP:0002322\tResting tremor\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:605543\tParkinson Disease 4, Autosomal Dominant\tRO:0002200\thas phenotype\tHP:0001824\tWeight loss\tECO:0000304\ttraceable author statement used in manual assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:606324\tParkinson Disease 7, Autosomal Recessive Early-Onset\tRO:0002200\thas phenotype\tHP:0000739\tAnxiety\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:168100\tParalysis Agitans, Juvenile, of Hunt\tRO:0002200\thas phenotype\tHP:0001300\tParkinsonism\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\tRO:0002200\thas phenotype\tHP:0001332\tDystonia\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:613135\tParkinsonism-Dystonia, Infantile\tRO:0002200\thas phenotype\tHP:0002020\tGastroesophageal reflux\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:614251\tParkinson Disease 18, Autosomal Dominant, Susceptibility to\tRO:0002200\thas phenotype\tHP:0100315\tLewy bodies\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+DOID:14330\tParkinson's disease\tRO:0002200\thas phenotype\tHP:0000011\tNeurogenic bladder\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:22331071|PMID:12922929|PMID:12756142|PMID:1965204|PMID:16855424\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+DOID:14330\tParkinson's disease\tRO:0002200\thas phenotype\tHP:0001824\tWeight loss\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:20028343|PMID:16773618|PMID:15595933|PMID:11241387|PMID:21192784\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:606693\tKufor-Rakeb syndrome\tRO:0002200\thas phenotype\tHP:0000605\tSupranuclear gaze palsy\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:168601\tautosomal dominant Parkinson disease 1\tRO:0002200\thas phenotype\tHP:0000012\tUrinary urgency\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:168600\tParkinson Disease, Late-Onset\tRO:0002200\thas phenotype\tHP:0001621\tWeak voice\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:168600\tParkinson Disease, Late-Onset\tRO:0002200\thas phenotype\tHP:0100315\tLewy bodies\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:605543\tParkinson Di"..b"Juvenile, of Hunt\tRO:0002200\thas phenotype\tHP:0002063\tRigidity\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+DOID:14330\tParkinson's disease\tRO:0002200\thas phenotype\tHP:0001332\tDystonia\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:2515718|PMID:6231489|PMID:22976499|PMID:2579626|PMID:7715793\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:614251\tParkinson Disease 18, Autosomal Dominant, Susceptibility to\tRO:0002200\thas phenotype\tHP:0002067\tBradykinesia\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:606693\tKufor-Rakeb syndrome\tRO:0002200\thas phenotype\tHP:0000514\tSlow saccadic eye movements\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:614203\tParkinson Disease 17\tRO:0002200\thas phenotype\tHP:0002172\tPostural instability\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:614203\tParkinson Disease 17\tRO:0002200\thas phenotype\tHP:0001300\tParkinsonism\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:615528\tParkinson Disease 19, Juvenile-Onset\tRO:0002200\thas phenotype\tHP:0002172\tPostural instability\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:105500\tAmyotrophic Lateral Sclerosis-Parkinsonism/Dementia Complex 1\tRO:0002200\thas phenotype\tHP:0001283\tBulbar palsy\tECO:0000304\ttraceable author statement used in manual assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\tRO:0002200\thas phenotype\tHP:0001288\tGait disturbance\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+DOID:14330\tParkinson's disease\tRO:0002200\thas phenotype\tHP:0000751\tPersonality changes\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:21560061|PMID:16908734|PMID:21845593|PMID:9426865|PMID:18346925\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:616361\tParkinson Disease 21\tRO:0002200\thas phenotype\tHP:0002172\tPostural instability\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+DOID:14330\tParkinson's disease\tRO:0002200\thas phenotype\tHP:0002321\tVertigo\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:19479494|PMID:21843110|PMID:19768728|PMID:2515717|PMID:12814332\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:607688\tParkinson Disease 11, Autosomal Dominant, Susceptibility to\tRO:0002200\thas phenotype\tHP:0002322\tResting tremor\tECO:0000269\texperimental evidence used in manual assertion\tPMID:18358451\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+DOID:14330\tParkinson's disease\tRO:0002200\thas phenotype\tHP:0000746\tDelusions\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:12814332|PMID:16239760|PMID:7652084|PMID:19507125|PMID:20538500\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+DOID:14330\tParkinson's disease\tRO:0002200\thas phenotype\tHP:0000822\tHypertension\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:18166127|PMID:20032288|PMID:11041086|PMID:17761552|PMID:17514358\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:605543\tParkinson Disease 4, Autosomal Dominant\tRO:0002200\thas phenotype\tHP:0100315\tLewy bodies\tECO:0000304\ttraceable author statement used in manual assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+DOID:14330\tParkinson's disease\tRO:0002200\thas phenotype\tHP:0000012\tUrinary urgency\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:3942028|PMID:14521485|PMID:18327532|PMID:19908315|PMID:11570707\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n" |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/phenotypes-for-variant.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phenotypes-for-variant.json Sun Jun 26 16:00:28 2016 -0400 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"phenopacket":{"phenotype_profile":[{"entity":"ClinVarVariant:217207","phenotype":{"types":[{"id":"HP:0010535","label":"Sleep apnea"}]}},{"entity":"FlyBase:FBal0213223","phenotype":{"types":[{"id":"FBcv:0000352","label":"partially lethal - majority die"}]}},{"entity":"ClinVarVariant:11487","phenotype":{"types":[{"id":"HP:0001829","label":"Foot polydactyly"}]}},{"entity":"http://www.monarchinitiative.org/_WBGene00022219-WBRNAi00094335","phenotype":{"types":[{"id":"WBPhenotype:0000508","label":"nonsense mRNA accumulation"}]}},{"entity":"FlyBase:FBal0204990","phenotype":{"types":[{"id":"FBcv:0002039","label":"some die during pupal stage"}]}},{"entity":"FlyBase:FBal0094697","phenotype":{"types":[{"id":"FBcv:0000395","label":"locomotor rhythm defective"}]}},{"entity":"ClinVarVariant:126392","phenotype":{"types":[{"id":"HP:0001433","label":"Hepatosplenomegaly"}]}},{"entity":"ClinVarVariant:167486","phenotype":{"types":[{"id":"HP:0000083","label":"Renal insufficiency"}]}},{"entity":"ClinVarVariant:161253","phenotype":{"types":[{"id":"HP:0011096","label":"Peripheral demyelination"}]}},{"entity":"ClinVarVariant:24488","phenotype":{"types":[{"id":"HP:0000517","label":"Abnormality of the lens"}]}},{"entity":"ClinVarVariant:10038","phenotype":{"types":[{"id":"HP:0003149","label":"Hyperuricosuria"}]}},{"entity":"ClinVarVariant:120292","phenotype":{"types":[{"id":"HP:0003560","label":"Muscular dystrophy"}]}},{"entity":"ClinVarVariant:91630","phenotype":{"types":[{"id":"HP:0003002","label":"Breast carcinoma"}]}},{"entity":"ClinVarVariant:188714","phenotype":{"types":[{"id":"HP:0002015","label":"Dysphagia"}]}},{"entity":"ClinVarVariant:65078","phenotype":{"types":[{"id":"HP:0002514","label":"Cerebral calcification"}]}},{"entity":"ClinVarVariant:13919","phenotype":{"types":[{"id":"HP:0002527","label":"Falls"}]}},{"entity":"ClinVarVariant:166796","phenotype":{"types":[{"id":"HP:0008872","label":"Feeding difficulties in infancy"}]}},{"entity":"ClinVarVariant:53300","phenotype":{"types":[{"id":"HP:0003040","label":"Arthropathy"}]}},{"entity":"ClinVarVariant:49671","phenotype":{"types":[{"id":"HP:0002888","label":"Ependymoma"}]}},{"entity":"ClinVarVariant:6383","phenotype":{"types":[{"id":"HP:0002758","label":"Osteoarthritis"}]}},{"entity":"ClinVarVariant:12869","phenotype":{"types":[{"id":"HP:0000272","label":"Malar flattening"}]}},{"entity":"ClinVarVariant:3241","phenotype":{"types":[{"id":"HP:0003560","label":"Muscular dystrophy"}]}},{"entity":"MGI:1856875","phenotype":{"types":[{"id":"MP:0000377","label":"abnormal hair follicle morphology"}]}},{"entity":"ClinVarVariant:24448","phenotype":{"types":[{"id":"HP:0000545","label":"Myopia"}]}},{"entity":"NCBIGene:553991","phenotype":{"types":[{"id":"HP:0003805","label":"Rimmed vacuoles"}]}},{"entity":"ClinVarVariant:35614","phenotype":{"types":[{"id":"HP:0001518","label":"Small for gestational age"}]}},{"entity":"ClinVarVariant:24856","phenotype":{"types":[{"id":"HP:0001636","label":"Tetralogy of Fallot"}]}},{"entity":"ClinVarVariant:135244","phenotype":{"types":[{"id":"HP:0100819","label":"Intestinal fistula"}]}},{"entity":"MGI:3702572","phenotype":{"types":[{"id":"MP:0001327","label":"decreased retinal photoreceptor cell number"}]}},{"entity":"ClinVarVariant:204248","phenotype":{"types":[{"id":"HP:0001824","label":"Weight loss"}]}},{"entity":"http://www.monarchinitiative.org/_WBGene00002981-WBRNAi00083915","phenotype":{"types":[{"id":"WBPhenotype:0001171","label":"shortened life span"}]}},{"entity":"ClinVarVariant:10490","phenotype":{"types":[{"id":"HP:0010864","label":"Intellectual disability, severe"}]}},{"entity":"http://www.monarchinitiative.org/_WBGene00007201-WBRNAi00062819","phenotype":{"types":[{"id":"WBPhenotype:0000691","label":"gonad development variant"}]}},{"entity":"MGI:2182460","phenotype":{"types":[{"id":"HP:0000708","label":"Behavioral abnormality"}]}},{"entity":"dbSNP:rs2202157","phenotype":{"types":[{"id":"HP:0009733","label":"Glioma"}]}},{"entity":"ClinVarVari'..b'}},{"entity":"ClinVarVariant:12791","phenotype":{"types":[{"id":"HP:0001250","label":"Seizures"}]}},{"entity":"ClinVarVariant:101135","phenotype":{"types":[{"id":"HP:0000212","label":"Gingival overgrowth"}]}},{"entity":"ClinVarVariant:189852","phenotype":{"types":[{"id":"HP:0002384","label":"Focal seizures with impairment of consciousness or awareness"}]}},{"entity":"AQTL:20678","phenotype":{"types":[{"id":"AQTLTrait:10","label":"Backfat at last lumbar"}]}},{"entity":"ClinVarVariant:13340","phenotype":{"types":[{"id":"HP:0004808","label":"Acute myeloid leukemia"}]}},{"entity":"ClinVarVariant:40490","phenotype":{"types":[{"id":"HP:0100495","label":"Mastocytosis"}]}},{"entity":"ClinVarVariant:94601","phenotype":{"types":[{"id":"HP:0003560","label":"Muscular dystrophy"}]}},{"entity":"WormBase:WBVar00531947","phenotype":{"types":[{"id":"WBPhenotype:0000138","label":"lipid composition variant"}]}},{"entity":"MGI:3712283","phenotype":{"types":[{"id":"MP:0006316","label":"increased urine sodium level"}]}},{"entity":"http://www.monarchinitiative.org/_WBGene00017983-WBRNAi00075550","phenotype":{"types":[{"id":"WBPhenotype:0000032","label":"sick"}]}},{"entity":"ClinVarVariant:44631","phenotype":{"types":[{"id":"HP:0000179","label":"Thick lower lip vermilion"}]}},{"entity":"MGI:5317762","phenotype":{"types":[{"id":"HP:0000204","label":"Cleft upper lip"}]}},{"entity":"MGI:2153094","phenotype":{"types":[{"id":"HP:0001397","label":"Hepatic steatosis"}]}},{"entity":"MGI:5467564","phenotype":{"types":[{"id":"MP:0002083","label":"premature death"}]}},{"entity":"ClinVarVariant:132733","phenotype":{"types":[{"id":"HP:0100777","label":"Exostoses"}]}},{"entity":"ClinVarVariant:53794","phenotype":{"types":[{"id":"HP:0002105","label":"Hemoptysis"}]}},{"entity":"ClinVarVariant:1568","phenotype":{"types":[{"id":"HP:0002014","label":"Diarrhea"}]}},{"entity":"ClinVarVariant:5502","phenotype":{"types":[{"id":"HP:0200094","label":"Frontal open bite"}]}},{"entity":"MGI:3043520","phenotype":{"types":[{"id":"MP:0004952","label":"increased spleen weight"}]}},{"entity":"MGI:2157350","phenotype":{"types":[{"id":"GO:0030900PHENOTYPE","label":"forebrain development phenotype"}]}},{"entity":"ClinVarVariant:17189","phenotype":{"types":[{"id":"HP:0000768","label":"Pectus carinatum"}]}},{"entity":"ClinVarVariant:18025","phenotype":{"types":[{"id":"HP:0004850","label":"Recurrent deep vein thrombosis"}]}},{"entity":"http://www.monarchinitiative.org/_WBGene00006975-WBRNAi00081919","phenotype":{"types":[{"id":"WBPhenotype:0001595","label":"somatic transgene silencing variant"}]}},{"entity":"ClinVarVariant:100719","phenotype":{"types":[{"id":"HP:0001250","label":"Seizures"}]}},{"entity":"ClinVarVariant:9454","phenotype":{"types":[{"id":"HP:0000529","label":"Progressive visual loss"}]}},{"entity":"ClinVarVariant:53366","phenotype":{"types":[{"id":"HP:0002630","label":"Fat malabsorption"}]}},{"entity":"http://www.monarchinitiative.org/_WBGene00004453-WBRNAi00072949","phenotype":{"types":[{"id":"WBPhenotype:0000062","label":"lethal"}]}},{"entity":"ClinVarVariant:204127","phenotype":{"types":[{"id":"HP:0001513","label":"Obesity"}]}},{"entity":"ClinVarVariant:1236","phenotype":{"types":[{"id":"HP:0001270","label":"Motor delay"}]}},{"entity":"ClinVarVariant:48912","phenotype":{"types":[{"id":"HP:0002086","label":"Abnormality of the respiratory system"}]}},{"entity":"ClinVarVariant:8212","phenotype":{"types":[{"id":"HP:0001000","label":"Abnormality of skin pigmentation"}]}},{"entity":"ClinVarVariant:30180","phenotype":{"types":[{"id":"HP:0000272","label":"Malar flattening"}]}},{"entity":"http://www.monarchinitiative.org/_WBGene00007030-WBRNAi00026587","phenotype":{"types":[{"id":"HP:0001508","label":"Failure to thrive"}]}}],"schema":"phenopacket-level-1"},"params":{"q":"*:*","fq":"(subject_closure:\\"HP:0002548\\")","personality":"variant_phenotype","showEmptyFields":false},"name":"Monarch Application","date":"Sun Jun 26 2016 12:07:13 GMT-0700 (PDT)"}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/phenotypes-for-variants-intersection.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phenotypes-for-variants-intersection.json Sun Jun 26 16:00:28 2016 -0400 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"phenopacket":{"phenotype_profile":[{"entity":"ClinVarVariant:217207","phenotype":{"types":[{"id":"HP:0010535","label":"Sleep apnea"}]}},{"entity":"FlyBase:FBal0213223","phenotype":{"types":[{"id":"FBcv:0000352","label":"partially lethal - majority die"}]}},{"entity":"ClinVarVariant:11487","phenotype":{"types":[{"id":"HP:0001829","label":"Foot polydactyly"}]}},{"entity":"http://www.monarchinitiative.org/_WBGene00022219-WBRNAi00094335","phenotype":{"types":[{"id":"WBPhenotype:0000508","label":"nonsense mRNA accumulation"}]}},{"entity":"FlyBase:FBal0204990","phenotype":{"types":[{"id":"FBcv:0002039","label":"some die during pupal stage"}]}},{"entity":"FlyBase:FBal0094697","phenotype":{"types":[{"id":"FBcv:0000395","label":"locomotor rhythm defective"}]}},{"entity":"ClinVarVariant:126392","phenotype":{"types":[{"id":"HP:0001433","label":"Hepatosplenomegaly"}]}},{"entity":"ClinVarVariant:167486","phenotype":{"types":[{"id":"HP:0000083","label":"Renal insufficiency"}]}},{"entity":"ClinVarVariant:161253","phenotype":{"types":[{"id":"HP:0011096","label":"Peripheral demyelination"}]}},{"entity":"ClinVarVariant:24488","phenotype":{"types":[{"id":"HP:0000517","label":"Abnormality of the lens"}]}},{"entity":"ClinVarVariant:10038","phenotype":{"types":[{"id":"HP:0003149","label":"Hyperuricosuria"}]}},{"entity":"ClinVarVariant:120292","phenotype":{"types":[{"id":"HP:0003560","label":"Muscular dystrophy"}]}},{"entity":"ClinVarVariant:91630","phenotype":{"types":[{"id":"HP:0003002","label":"Breast carcinoma"}]}},{"entity":"ClinVarVariant:188714","phenotype":{"types":[{"id":"HP:0002015","label":"Dysphagia"}]}},{"entity":"ClinVarVariant:65078","phenotype":{"types":[{"id":"HP:0002514","label":"Cerebral calcification"}]}},{"entity":"ClinVarVariant:13919","phenotype":{"types":[{"id":"HP:0002527","label":"Falls"}]}},{"entity":"ClinVarVariant:166796","phenotype":{"types":[{"id":"HP:0008872","label":"Feeding difficulties in infancy"}]}},{"entity":"ClinVarVariant:53300","phenotype":{"types":[{"id":"HP:0003040","label":"Arthropathy"}]}},{"entity":"ClinVarVariant:49671","phenotype":{"types":[{"id":"HP:0002888","label":"Ependymoma"}]}},{"entity":"ClinVarVariant:6383","phenotype":{"types":[{"id":"HP:0002758","label":"Osteoarthritis"}]}},{"entity":"ClinVarVariant:12869","phenotype":{"types":[{"id":"HP:0000272","label":"Malar flattening"}]}},{"entity":"ClinVarVariant:3241","phenotype":{"types":[{"id":"HP:0003560","label":"Muscular dystrophy"}]}},{"entity":"MGI:1856875","phenotype":{"types":[{"id":"MP:0000377","label":"abnormal hair follicle morphology"}]}},{"entity":"ClinVarVariant:24448","phenotype":{"types":[{"id":"HP:0000545","label":"Myopia"}]}},{"entity":"NCBIGene:553991","phenotype":{"types":[{"id":"HP:0003805","label":"Rimmed vacuoles"}]}},{"entity":"ClinVarVariant:35614","phenotype":{"types":[{"id":"HP:0001518","label":"Small for gestational age"}]}},{"entity":"ClinVarVariant:24856","phenotype":{"types":[{"id":"HP:0001636","label":"Tetralogy of Fallot"}]}},{"entity":"ClinVarVariant:135244","phenotype":{"types":[{"id":"HP:0100819","label":"Intestinal fistula"}]}},{"entity":"MGI:3702572","phenotype":{"types":[{"id":"MP:0001327","label":"decreased retinal photoreceptor cell number"}]}},{"entity":"ClinVarVariant:204248","phenotype":{"types":[{"id":"HP:0001824","label":"Weight loss"}]}},{"entity":"http://www.monarchinitiative.org/_WBGene00002981-WBRNAi00083915","phenotype":{"types":[{"id":"WBPhenotype:0001171","label":"shortened life span"}]}},{"entity":"ClinVarVariant:10490","phenotype":{"types":[{"id":"HP:0010864","label":"Intellectual disability, severe"}]}},{"entity":"http://www.monarchinitiative.org/_WBGene00007201-WBRNAi00062819","phenotype":{"types":[{"id":"WBPhenotype:0000691","label":"gonad development variant"}]}},{"entity":"MGI:2182460","phenotype":{"types":[{"id":"HP:0000708","label":"Behavioral abnormality"}]}},{"entity":"dbSNP:rs2202157","phenotype":{"types":[{"id":"HP:0009733","label":"Glioma"}]}},{"entity":"ClinVarVari'..b',"phenotype":{"types":[{"id":"HP:0001250","label":"Seizures"}]}},{"entity":"ClinVarVariant:101135","phenotype":{"types":[{"id":"HP:0000212","label":"Gingival overgrowth"}]}},{"entity":"ClinVarVariant:189852","phenotype":{"types":[{"id":"HP:0002384","label":"Focal seizures with impairment of consciousness or awareness"}]}},{"entity":"AQTL:20678","phenotype":{"types":[{"id":"AQTLTrait:10","label":"Backfat at last lumbar"}]}},{"entity":"ClinVarVariant:13340","phenotype":{"types":[{"id":"HP:0004808","label":"Acute myeloid leukemia"}]}},{"entity":"ClinVarVariant:40490","phenotype":{"types":[{"id":"HP:0100495","label":"Mastocytosis"}]}},{"entity":"ClinVarVariant:94601","phenotype":{"types":[{"id":"HP:0003560","label":"Muscular dystrophy"}]}},{"entity":"WormBase:WBVar00531947","phenotype":{"types":[{"id":"WBPhenotype:0000138","label":"lipid composition variant"}]}},{"entity":"MGI:3712283","phenotype":{"types":[{"id":"MP:0006316","label":"increased urine sodium level"}]}},{"entity":"http://www.monarchinitiative.org/_WBGene00017983-WBRNAi00075550","phenotype":{"types":[{"id":"WBPhenotype:0000032","label":"sick"}]}},{"entity":"ClinVarVariant:44631","phenotype":{"types":[{"id":"HP:0000179","label":"Thick lower lip vermilion"}]}},{"entity":"MGI:5317762","phenotype":{"types":[{"id":"HP:0000204","label":"Cleft upper lip"}]}},{"entity":"MGI:2153094","phenotype":{"types":[{"id":"HP:0001397","label":"Hepatic steatosis"}]}},{"entity":"MGI:5467564","phenotype":{"types":[{"id":"MP:0002083","label":"premature death"}]}},{"entity":"ClinVarVariant:132733","phenotype":{"types":[{"id":"HP:0100777","label":"Exostoses"}]}},{"entity":"ClinVarVariant:53794","phenotype":{"types":[{"id":"HP:0002105","label":"Hemoptysis"}]}},{"entity":"ClinVarVariant:1568","phenotype":{"types":[{"id":"HP:0002014","label":"Diarrhea"}]}},{"entity":"ClinVarVariant:5502","phenotype":{"types":[{"id":"HP:0200094","label":"Frontal open bite"}]}},{"entity":"MGI:3043520","phenotype":{"types":[{"id":"MP:0004952","label":"increased spleen weight"}]}},{"entity":"MGI:2157350","phenotype":{"types":[{"id":"GO:0030900PHENOTYPE","label":"forebrain development phenotype"}]}},{"entity":"ClinVarVariant:17189","phenotype":{"types":[{"id":"HP:0000768","label":"Pectus carinatum"}]}},{"entity":"ClinVarVariant:18025","phenotype":{"types":[{"id":"HP:0004850","label":"Recurrent deep vein thrombosis"}]}},{"entity":"http://www.monarchinitiative.org/_WBGene00006975-WBRNAi00081919","phenotype":{"types":[{"id":"WBPhenotype:0001595","label":"somatic transgene silencing variant"}]}},{"entity":"ClinVarVariant:100719","phenotype":{"types":[{"id":"HP:0001250","label":"Seizures"}]}},{"entity":"ClinVarVariant:9454","phenotype":{"types":[{"id":"HP:0000529","label":"Progressive visual loss"}]}},{"entity":"ClinVarVariant:53366","phenotype":{"types":[{"id":"HP:0002630","label":"Fat malabsorption"}]}},{"entity":"http://www.monarchinitiative.org/_WBGene00004453-WBRNAi00072949","phenotype":{"types":[{"id":"WBPhenotype:0000062","label":"lethal"}]}},{"entity":"ClinVarVariant:204127","phenotype":{"types":[{"id":"HP:0001513","label":"Obesity"}]}},{"entity":"ClinVarVariant:1236","phenotype":{"types":[{"id":"HP:0001270","label":"Motor delay"}]}},{"entity":"ClinVarVariant:48912","phenotype":{"types":[{"id":"HP:0002086","label":"Abnormality of the respiratory system"}]}},{"entity":"ClinVarVariant:8212","phenotype":{"types":[{"id":"HP:0001000","label":"Abnormality of skin pigmentation"}]}},{"entity":"ClinVarVariant:30180","phenotype":{"types":[{"id":"HP:0000272","label":"Malar flattening"}]}},{"entity":"http://www.monarchinitiative.org/_WBGene00007030-WBRNAi00026587","phenotype":{"types":[{"id":"HP:0001508","label":"Failure to thrive"}]}}],"schema":"phenopacket-level-1"},"params":{"q":"*:*","fq":"(subject_closure:\\"HP:0000739\\" AND subject_closure:\\"MP:0001363\\")","personality":"variant_phenotype","showEmptyFields":false},"name":"Monarch Application","date":"Sun Jun 26 2016 12:07:31 GMT-0700 (PDT)"}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/phenotypes-for-variants-union.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phenotypes-for-variants-union.json Sun Jun 26 16:00:28 2016 -0400 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"phenopacket":{"phenotype_profile":[{"entity":"ClinVarVariant:217207","phenotype":{"types":[{"id":"HP:0010535","label":"Sleep apnea"}]}},{"entity":"FlyBase:FBal0213223","phenotype":{"types":[{"id":"FBcv:0000352","label":"partially lethal - majority die"}]}},{"entity":"ClinVarVariant:11487","phenotype":{"types":[{"id":"HP:0001829","label":"Foot polydactyly"}]}},{"entity":"http://www.monarchinitiative.org/_WBGene00022219-WBRNAi00094335","phenotype":{"types":[{"id":"WBPhenotype:0000508","label":"nonsense mRNA accumulation"}]}},{"entity":"FlyBase:FBal0204990","phenotype":{"types":[{"id":"FBcv:0002039","label":"some die during pupal stage"}]}},{"entity":"FlyBase:FBal0094697","phenotype":{"types":[{"id":"FBcv:0000395","label":"locomotor rhythm defective"}]}},{"entity":"ClinVarVariant:126392","phenotype":{"types":[{"id":"HP:0001433","label":"Hepatosplenomegaly"}]}},{"entity":"ClinVarVariant:167486","phenotype":{"types":[{"id":"HP:0000083","label":"Renal insufficiency"}]}},{"entity":"ClinVarVariant:161253","phenotype":{"types":[{"id":"HP:0011096","label":"Peripheral demyelination"}]}},{"entity":"ClinVarVariant:24488","phenotype":{"types":[{"id":"HP:0000517","label":"Abnormality of the lens"}]}},{"entity":"ClinVarVariant:10038","phenotype":{"types":[{"id":"HP:0003149","label":"Hyperuricosuria"}]}},{"entity":"ClinVarVariant:120292","phenotype":{"types":[{"id":"HP:0003560","label":"Muscular dystrophy"}]}},{"entity":"ClinVarVariant:91630","phenotype":{"types":[{"id":"HP:0003002","label":"Breast carcinoma"}]}},{"entity":"ClinVarVariant:188714","phenotype":{"types":[{"id":"HP:0002015","label":"Dysphagia"}]}},{"entity":"ClinVarVariant:65078","phenotype":{"types":[{"id":"HP:0002514","label":"Cerebral calcification"}]}},{"entity":"ClinVarVariant:13919","phenotype":{"types":[{"id":"HP:0002527","label":"Falls"}]}},{"entity":"ClinVarVariant:166796","phenotype":{"types":[{"id":"HP:0008872","label":"Feeding difficulties in infancy"}]}},{"entity":"ClinVarVariant:53300","phenotype":{"types":[{"id":"HP:0003040","label":"Arthropathy"}]}},{"entity":"ClinVarVariant:49671","phenotype":{"types":[{"id":"HP:0002888","label":"Ependymoma"}]}},{"entity":"ClinVarVariant:6383","phenotype":{"types":[{"id":"HP:0002758","label":"Osteoarthritis"}]}},{"entity":"ClinVarVariant:12869","phenotype":{"types":[{"id":"HP:0000272","label":"Malar flattening"}]}},{"entity":"ClinVarVariant:3241","phenotype":{"types":[{"id":"HP:0003560","label":"Muscular dystrophy"}]}},{"entity":"MGI:1856875","phenotype":{"types":[{"id":"MP:0000377","label":"abnormal hair follicle morphology"}]}},{"entity":"ClinVarVariant:24448","phenotype":{"types":[{"id":"HP:0000545","label":"Myopia"}]}},{"entity":"NCBIGene:553991","phenotype":{"types":[{"id":"HP:0003805","label":"Rimmed vacuoles"}]}},{"entity":"ClinVarVariant:35614","phenotype":{"types":[{"id":"HP:0001518","label":"Small for gestational age"}]}},{"entity":"ClinVarVariant:24856","phenotype":{"types":[{"id":"HP:0001636","label":"Tetralogy of Fallot"}]}},{"entity":"ClinVarVariant:135244","phenotype":{"types":[{"id":"HP:0100819","label":"Intestinal fistula"}]}},{"entity":"MGI:3702572","phenotype":{"types":[{"id":"MP:0001327","label":"decreased retinal photoreceptor cell number"}]}},{"entity":"ClinVarVariant:204248","phenotype":{"types":[{"id":"HP:0001824","label":"Weight loss"}]}},{"entity":"http://www.monarchinitiative.org/_WBGene00002981-WBRNAi00083915","phenotype":{"types":[{"id":"WBPhenotype:0001171","label":"shortened life span"}]}},{"entity":"ClinVarVariant:10490","phenotype":{"types":[{"id":"HP:0010864","label":"Intellectual disability, severe"}]}},{"entity":"http://www.monarchinitiative.org/_WBGene00007201-WBRNAi00062819","phenotype":{"types":[{"id":"WBPhenotype:0000691","label":"gonad development variant"}]}},{"entity":"MGI:2182460","phenotype":{"types":[{"id":"HP:0000708","label":"Behavioral abnormality"}]}},{"entity":"dbSNP:rs2202157","phenotype":{"types":[{"id":"HP:0009733","label":"Glioma"}]}},{"entity":"ClinVarVari'..b'","phenotype":{"types":[{"id":"HP:0001250","label":"Seizures"}]}},{"entity":"ClinVarVariant:101135","phenotype":{"types":[{"id":"HP:0000212","label":"Gingival overgrowth"}]}},{"entity":"ClinVarVariant:189852","phenotype":{"types":[{"id":"HP:0002384","label":"Focal seizures with impairment of consciousness or awareness"}]}},{"entity":"AQTL:20678","phenotype":{"types":[{"id":"AQTLTrait:10","label":"Backfat at last lumbar"}]}},{"entity":"ClinVarVariant:13340","phenotype":{"types":[{"id":"HP:0004808","label":"Acute myeloid leukemia"}]}},{"entity":"ClinVarVariant:40490","phenotype":{"types":[{"id":"HP:0100495","label":"Mastocytosis"}]}},{"entity":"ClinVarVariant:94601","phenotype":{"types":[{"id":"HP:0003560","label":"Muscular dystrophy"}]}},{"entity":"WormBase:WBVar00531947","phenotype":{"types":[{"id":"WBPhenotype:0000138","label":"lipid composition variant"}]}},{"entity":"MGI:3712283","phenotype":{"types":[{"id":"MP:0006316","label":"increased urine sodium level"}]}},{"entity":"http://www.monarchinitiative.org/_WBGene00017983-WBRNAi00075550","phenotype":{"types":[{"id":"WBPhenotype:0000032","label":"sick"}]}},{"entity":"ClinVarVariant:44631","phenotype":{"types":[{"id":"HP:0000179","label":"Thick lower lip vermilion"}]}},{"entity":"MGI:5317762","phenotype":{"types":[{"id":"HP:0000204","label":"Cleft upper lip"}]}},{"entity":"MGI:2153094","phenotype":{"types":[{"id":"HP:0001397","label":"Hepatic steatosis"}]}},{"entity":"MGI:5467564","phenotype":{"types":[{"id":"MP:0002083","label":"premature death"}]}},{"entity":"ClinVarVariant:132733","phenotype":{"types":[{"id":"HP:0100777","label":"Exostoses"}]}},{"entity":"ClinVarVariant:53794","phenotype":{"types":[{"id":"HP:0002105","label":"Hemoptysis"}]}},{"entity":"ClinVarVariant:1568","phenotype":{"types":[{"id":"HP:0002014","label":"Diarrhea"}]}},{"entity":"ClinVarVariant:5502","phenotype":{"types":[{"id":"HP:0200094","label":"Frontal open bite"}]}},{"entity":"MGI:3043520","phenotype":{"types":[{"id":"MP:0004952","label":"increased spleen weight"}]}},{"entity":"MGI:2157350","phenotype":{"types":[{"id":"GO:0030900PHENOTYPE","label":"forebrain development phenotype"}]}},{"entity":"ClinVarVariant:17189","phenotype":{"types":[{"id":"HP:0000768","label":"Pectus carinatum"}]}},{"entity":"ClinVarVariant:18025","phenotype":{"types":[{"id":"HP:0004850","label":"Recurrent deep vein thrombosis"}]}},{"entity":"http://www.monarchinitiative.org/_WBGene00006975-WBRNAi00081919","phenotype":{"types":[{"id":"WBPhenotype:0001595","label":"somatic transgene silencing variant"}]}},{"entity":"ClinVarVariant:100719","phenotype":{"types":[{"id":"HP:0001250","label":"Seizures"}]}},{"entity":"ClinVarVariant:9454","phenotype":{"types":[{"id":"HP:0000529","label":"Progressive visual loss"}]}},{"entity":"ClinVarVariant:53366","phenotype":{"types":[{"id":"HP:0002630","label":"Fat malabsorption"}]}},{"entity":"http://www.monarchinitiative.org/_WBGene00004453-WBRNAi00072949","phenotype":{"types":[{"id":"WBPhenotype:0000062","label":"lethal"}]}},{"entity":"ClinVarVariant:204127","phenotype":{"types":[{"id":"HP:0001513","label":"Obesity"}]}},{"entity":"ClinVarVariant:1236","phenotype":{"types":[{"id":"HP:0001270","label":"Motor delay"}]}},{"entity":"ClinVarVariant:48912","phenotype":{"types":[{"id":"HP:0002086","label":"Abnormality of the respiratory system"}]}},{"entity":"ClinVarVariant:8212","phenotype":{"types":[{"id":"HP:0001000","label":"Abnormality of skin pigmentation"}]}},{"entity":"ClinVarVariant:30180","phenotype":{"types":[{"id":"HP:0000272","label":"Malar flattening"}]}},{"entity":"http://www.monarchinitiative.org/_WBGene00007030-WBRNAi00026587","phenotype":{"types":[{"id":"HP:0001508","label":"Failure to thrive"}]}}],"schema":"phenopacket-level-1"},"params":{"q":"*:*","fq":"(subject_closure:\\"HP:0000739\\" OR subject_closure:\\"MP:0001363\\")","personality":"variant_phenotype","showEmptyFields":false},"name":"Monarch Application","date":"Sun Jun 26 2016 12:08:27 GMT-0700 (PDT)"}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/variants-for-disease.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/variants-for-disease.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| b'@@ -0,0 +1,316 @@\n+ClinVarVariant:39148\tNM_198578.3(LRRK2):c.2264C>T (p.Pro755Leu)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:7051\tNM_004562.2(PARK2):c.633A>T (p.Lys211Asn)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:1936\tNM_198578.3(LRRK2):c.4321C>G (p.Arg1441Gly)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:4810\tNM_012179.3(FBXO7):c.1144+1G>T\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:260300\tautosomal recessive early-onset Parkinson disease 15\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39147\tNM_198578.3(LRRK2):c.225G>A (p.Ala75=)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39234\tNM_198578.3(LRRK2):c.7155A>G (p.Gly2385=)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:2412\tNM_005216.4(DDOST):c.*807_*5409del\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOrphanet:2828\tYoung-onset Parkinson disease\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:7050\tNM_004562.2(PARK2):c.823C>T (p.Arg275Trp)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:9695\tm.14319T>C\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39128\tNM_198578.3(LRRK2):c.1000G>A (p.Glu334Lys)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39215\tNM_198578.3(LRRK2):c.5620G>T (p.Glu1874Ter)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39195\tNM_198578.3(LRRK2):c.4793T>A (p.Val1598Glu)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:209135\tNM_022089.3(ATP13A2):c.348-9_351del\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:606693\tKufor-Rakeb syndrome\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:4809\tNM_012179.3(FBXO7):c.1492C>T (p.Arg498Ter)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:260300\tautosomal recessive early-onset Parkinson disease 15\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39214\tNM_198578.3(LRRK2):c.5610G>T (p.Leu1870Phe)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:143196\tNM_022089.3(ATP13A2):c.490C>T (p.Arg164Trp)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:606693\tKufor-Rakeb syndrome\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39194\tNM_198578.3(LRRK2):c.4666C>A (p.Leu1556Ile)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:7042\tNM_004562.2(PARK2):c.1358G>A (p.Trp453Ter)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0'..b'clinvar.ttl\tdirect\n+ClinVarVariant:7035\tNM_004562.2(PARK2):c.413-?_534+?del\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\t\thttp://data.monarchinitiative.org/ttl/coriell.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39199\tNM_198578.3(LRRK2):c.4911A>G (p.Lys1637=)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:7055\tPARK2, EX5-6 DEL\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOrphanet:2828\tYoung-onset Parkinson disease\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:14009\tSNCA, TRIPLICATION\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/coriell.ttl\tinferred\n+ClinVarVariant:39170\tNM_198578.3(LRRK2):c.364C= (p.Leu122=)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:12297\tNM_004181.4(UCHL1):c.279C>G (p.Ile93Met)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOrphanet:2828\tYoung-onset Parkinson disease\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39224\tNM_198578.3(LRRK2):c.6356C>T (p.Pro2119Leu)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:14011\tSNCA, DUPLICATION\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:168601\tautosomal dominant Parkinson disease 1\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:2407\tNM_032409.2(PINK1):c.736C>T (p.Arg246Ter)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39131\tNM_198578.3(LRRK2):c.1256C>T (p.Ala419Val)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+dbSNP:rs34637584\trs34637584-A\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:2415\tNM_032409.2(PINK1):c.1366C>T (p.Gln456Ter)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOrphanet:2828\tYoung-onset Parkinson disease\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:7067\tNM_007262.4(PARK7):c.192G>C (p.Glu64Asp)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOrphanet:2828\tYoung-onset Parkinson disease\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:7040\tNM_004562.2(PARK2):c.8-?_171+?del\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOrphanet:2828\tYoung-onset Parkinson disease\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:7038\tNM_004562.2(PARK2):c.245C>A (p.Ala82Glu)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOrphanet:2828\tYoung-onset Parkinson disease\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:2406\tNM_032409.2(PINK1):c.1311G>A (p.Trp437Ter)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+dbSNP:rs6265\trs6265-C\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39130\tNM_198578.3(LRRK2):c.1096G>A (p.Val366Met)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n' |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/variants-for-diseases-intersection.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/variants-for-diseases-intersection.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| @@ -0,0 +1,33 @@ +ClinVarVariant:8113 NM_002973.3(ATXN2):c.496_498CAG(15_24) (p.Gln188_Pro189insGlnGln) NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:9726 m.3397A>G NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:29936 NM_012084.3(GLUD2):c.1492T>G (p.Ser498Ala) NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:4885 FGF20, 951C/T NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:98243 NM_016835.4(MAPT):c.1838_1840delATA (p.Asn613del) NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:4295 NM_001005741.2(GBA):c.1504C>T (p.Arg502Cys) NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:7040 NM_004562.2(PARK2):c.8-?_171+?del NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred +ClinVarVariant:56171 NM_015268.3(DNAJC13):c.2564A>G (p.Asn855Ser) NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:6144 NR_002717.2(ATXN8OS):n.1103_1105CTG(15_40) NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:7038 NM_004562.2(PARK2):c.245C>A (p.Ala82Glu) NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred +ClinVarVariant:96731 NM_198578.3(LRRK2):c.7300A>G (p.Ile2434Val) NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:3551 NM_004993.5(ATXN3):c.892_894CAG(8_36) (p.Gln298_Gln305=) NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:96729 NM_032409.2(PINK1):c.923T>A (p.Leu308Gln) NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:96730 NM_198578.3(LRRK2):c.2352C>A (p.Ser784Arg) NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:7035 NM_004562.2(PARK2):c.413-?_534+?del NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred +ClinVarVariant:96728 NM_032409.2(PINK1):c.644C>T (p.Pro215Leu) NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:38301 NM_001005741.2(GBA):c.1226A>C (p.Asn409Thr) NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:96727 NM_018206.4(VPS35):c.1576C>T (p.Arg526Cys) NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:4288 NM_001005741.2(GBA):c.1448T>C (p.Leu483Pro) NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:1936 NM_198578.3(LRRK2):c.4321C>G (p.Arg1441Gly) NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred +ClinVarVariant:7050 NM_004562.2(PARK2):c.823C>T (p.Arg275Trp) NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred +ClinVarVariant:9449 NM_003194.4(TBP):c.172_174CAG(25_42) (p.Gln95(25_42)) NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:7048 PARK2, 1-BP DEL, 255A NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred +dbSNP:rs34637584 rs34637584-A NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred +ClinVarVariant:7679 NR4A2, 1-BP DEL, -291T NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:7055 PARK2, EX5-6 DEL NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred +ClinVarVariant:96726 NM_007262.4(PARK7):c.399G>C (p.Met133Ile) NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:4335 NM_001005741.2(GBA):c.1444G>A (p.Asp482Asn) NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:6078 NM_005460.3(SNCAIP):c.1861C>T (p.Arg621Cys) NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:31151 NG_031977.1:g.5321_5326GGGGCC(24_?) NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred +ClinVarVariant:7680 NR4A2, -245T-G NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:14009 SNCA, TRIPLICATION NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred +dbSNP:rs6265 rs6265-C NCBITaxon:9606 Homo sapiens RO:0002200 has phenotype OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/clinvar.ttl direct |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/variants-for-diseases-union.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/variants-for-diseases-union.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| b'@@ -0,0 +1,316 @@\n+ClinVarVariant:39148\tNM_198578.3(LRRK2):c.2264C>T (p.Pro755Leu)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:7051\tNM_004562.2(PARK2):c.633A>T (p.Lys211Asn)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:1936\tNM_198578.3(LRRK2):c.4321C>G (p.Arg1441Gly)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:4810\tNM_012179.3(FBXO7):c.1144+1G>T\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:260300\tautosomal recessive early-onset Parkinson disease 15\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39147\tNM_198578.3(LRRK2):c.225G>A (p.Ala75=)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39234\tNM_198578.3(LRRK2):c.7155A>G (p.Gly2385=)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:2412\tNM_005216.4(DDOST):c.*807_*5409del\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOrphanet:2828\tYoung-onset Parkinson disease\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:7050\tNM_004562.2(PARK2):c.823C>T (p.Arg275Trp)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:9695\tm.14319T>C\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39128\tNM_198578.3(LRRK2):c.1000G>A (p.Glu334Lys)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39215\tNM_198578.3(LRRK2):c.5620G>T (p.Glu1874Ter)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39195\tNM_198578.3(LRRK2):c.4793T>A (p.Val1598Glu)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:209135\tNM_022089.3(ATP13A2):c.348-9_351del\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:606693\tKufor-Rakeb syndrome\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:4809\tNM_012179.3(FBXO7):c.1492C>T (p.Arg498Ter)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:260300\tautosomal recessive early-onset Parkinson disease 15\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39214\tNM_198578.3(LRRK2):c.5610G>T (p.Leu1870Phe)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:143196\tNM_022089.3(ATP13A2):c.490C>T (p.Arg164Trp)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:606693\tKufor-Rakeb syndrome\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39194\tNM_198578.3(LRRK2):c.4666C>A (p.Leu1556Ile)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:7042\tNM_004562.2(PARK2):c.1358G>A (p.Trp453Ter)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0'..b'clinvar.ttl\tdirect\n+ClinVarVariant:7035\tNM_004562.2(PARK2):c.413-?_534+?del\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\t\thttp://data.monarchinitiative.org/ttl/coriell.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39199\tNM_198578.3(LRRK2):c.4911A>G (p.Lys1637=)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:7055\tPARK2, EX5-6 DEL\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOrphanet:2828\tYoung-onset Parkinson disease\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:14009\tSNCA, TRIPLICATION\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/coriell.ttl\tinferred\n+ClinVarVariant:39170\tNM_198578.3(LRRK2):c.364C= (p.Leu122=)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:12297\tNM_004181.4(UCHL1):c.279C>G (p.Ile93Met)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOrphanet:2828\tYoung-onset Parkinson disease\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39224\tNM_198578.3(LRRK2):c.6356C>T (p.Pro2119Leu)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:14011\tSNCA, DUPLICATION\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:168601\tautosomal dominant Parkinson disease 1\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:2407\tNM_032409.2(PINK1):c.736C>T (p.Arg246Ter)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39131\tNM_198578.3(LRRK2):c.1256C>T (p.Ala419Val)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+dbSNP:rs34637584\trs34637584-A\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:2415\tNM_032409.2(PINK1):c.1366C>T (p.Gln456Ter)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOrphanet:2828\tYoung-onset Parkinson disease\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:7067\tNM_007262.4(PARK7):c.192G>C (p.Glu64Asp)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOrphanet:2828\tYoung-onset Parkinson disease\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:7040\tNM_004562.2(PARK2):c.8-?_171+?del\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOrphanet:2828\tYoung-onset Parkinson disease\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:7038\tNM_004562.2(PARK2):c.245C>A (p.Ala82Glu)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOrphanet:2828\tYoung-onset Parkinson disease\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:2406\tNM_032409.2(PINK1):c.1311G>A (p.Trp437Ter)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+dbSNP:rs6265\trs6265-C\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39130\tNM_198578.3(LRRK2):c.1096G>A (p.Val366Met)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n' |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/variants-for-phenotype.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/variants-for-phenotype.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| b'@@ -0,0 +1,184 @@\n+ClinVarVariant:13509\tNM_002693.2(POLG):c.2492A>G (p.Tyr831Cys)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:39216\tNM_198578.3(LRRK2):c.5822G>A (p.Arg1941His)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:39156\tNM_198578.3(LRRK2):c.2857T>C (p.Leu953=)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:39146\tNM_198578.3(LRRK2):c.2167A>G (p.Ile723Val)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:39136\tNM_198578.3(LRRK2):c.155C>T (p.Ser52Phe)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:39206\tNM_198578.3(LRRK2):c.5183G>A (p.Arg1728His)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:39246\tNM_198578.3(LRRK2):c.936G>T (p.Ala312=)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:39236\tNM_198578.3(LRRK2):c.7183G>A (p.Glu2395Lys)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:39226\tNM_198578.3(LRRK2):c.6422C>T (p.Thr2141Met)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:39176\tNM_198578.3(LRRK2):c.4111A>G (p.Ile1371Val)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:39166\tNM_198578.3(LRRK2):c.3494T>C (p.Leu1165Pro)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:39186\tNM_198578.3(LRRK2):c.4337C>T (p.Pro1446Leu)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:39196\tNM_198578.3(LRRK2):c.483'..b'tl/hpoa.ttl\tinferred\n+ClinVarVariant:757\tNM_015575.3(GIGYF2):c.1262A>G (p.Lys421Arg)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000269\texperimental evidence used in manual assertion\tPMID:18358451\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:9291\tGCH1, DEL\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000304\ttraceable author statement used in manual assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:9271\tNM_000161.2(GCH1):c.262C>T (p.Arg88Trp)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000304\ttraceable author statement used in manual assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:12324\tNM_199292.2(TH):c.1234C>A (p.Gln412Lys)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000304\ttraceable author statement used in manual assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:12334\tNM_199292.2(TH):c.1076G>T (p.Cys359Phe)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000304\ttraceable author statement used in manual assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:39231\tNM_198578.3(LRRK2):c.683G>C (p.Cys228Ser)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:39241\tNM_198578.3(LRRK2):c.7435A>G (p.Asn2479Asp)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:39201\tNM_198578.3(LRRK2):c.4939T>A (p.Ser1647Thr)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:39221\tNM_198578.3(LRRK2):c.6241A>G (p.Asn2081Asp)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:39211\tNM_198578.3(LRRK2):c.546A>G (p.Lys182=)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:9276\tGCH1, IVS2, A-G, -2\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000304\ttraceable author statement used in manual assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:208620\tNM_000360.3(TH):c.283delG (p.Ala95Argfs)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000304\ttraceable author statement used in manual assertion\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n' |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/variants-for-phenotypes-intersection.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/variants-for-phenotypes-intersection.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| b'@@ -0,0 +1,329 @@\n+MGI:3512173\tGrin3b<tm1Yaha>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:17880385\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:3578225\tGsk3a<tm1Dral>\t\t\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:20357757\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:3815322\tGt(ROSA)26Sor<tm1(Crh)Jde>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:21885734\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:4868760\tAtmin<tm1Axbe>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:20889973\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:3640817\tNtrk2<tm1.1Tes>\t\t\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006|ECO:0000006\texperimental evidence|experimental evidence\tPMID:19158294|PMID:19158294\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:4359727\tDp(7Herc2-Mkrn3)1Taku\tNCBITaxon:10090\tMus musculus\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:19563756\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:2178959\tMdk<tm1Tmu>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:10096022\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:3720069\tTg(Thy1-App*R609D*K612E)6Vln\tNCBITaxon:10090\tMus musculus\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006|ECO:0000006\texperimental evidence|experimental evidence\tPMID:8635459|PMID:8635459\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:2183727\tMecp2<tm1Hzo>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:12160743\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1856716\tMyo7a<sh1>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tMGI:63673\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:3603321\tGrm8<tm1Duv>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:16045496\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:2386577\tPax5<tm3Mbu>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006|ECO:0000006\texperimental evidence|experimental evidence\tPMID:23349049|PMID:23349049\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:3513042\tCrhbp<tm1Afs>\t\t\t\t\tRO:0002200\thas phenotype\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:10500222|PMID:10500222\thttp://data.monarchinitiative.org/ttl/mgi.ttl|http://data.monarchinitiative.org/ttl/mmrrc.ttl\tdirect\n+MGI:3834477\tSlitrk1<tm1Jaru>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:18794888\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:4949899\tFgfbp3<tm1Tohe>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:20851768\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:3528874\tKcnip3<tm1Lex>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:19223600\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:3042719\tNrxn2<tm1Sud>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:25423136\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:3835761\tWfs1<tm1Koks>\t\t\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:19477223\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:5052110\tTg(Mapt-MAPT*)#Hanr\tNCBITaxon:10090\tMus musculus\tNCBIGene:4137\tmicrotubule associated protein tau\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:18490011\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:2181809\tLgals1<tm1Rob>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:23118208\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:3575'..b't\n+MGI:3527166\tTh<tm5Rpa>\t\t\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:16723393\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:3720068\tTg(Thy1-App*R609D*K612E)4Vln\tNCBITaxon:10090\tMus musculus\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006|ECO:0000006\texperimental evidence|experimental evidence\tPMID:8635459|PMID:8635459\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:3609234\tApp<tm1Ck>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006|ECO:0000006|ECO:0000006\texperimental evidence|experimental evidence|experimental evidence\tPMID:22336193|PMID:22336193|PMID:24278307\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:5568123\tSv2c<tm1Dda>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:23458503\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:5634938\tTg(Thy1-EGFP/SQSTM1*P392L)#Mcwo\tNCBITaxon:10090\tMus musculus\tNCBIGene:8878\tsequestosome 1\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:23591541\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1857026\tFoxq1<sa>\t\t\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:16109771\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1857572\tIns2<Akita>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:17334640\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:3607718\tsau\tNCBITaxon:10090\tMus musculus\tMGI:3607718\tsau\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:16109771\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:2152583\tAdora2a<tm1Map>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:9262401\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1931877\tVim<tm1Cba>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:9888296\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:3800752\tTg(HTT*97Q)IXwy\tNCBITaxon:10090\tMus musculus\tNCBIGene:3064\thuntingtin\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006|ECO:0000006\texperimental evidence|experimental evidence\tPMID:19464370|PMID:24784230|PMID:20064390|PMID:24784230\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:5503119\tKif13a<tm1.1Noh>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:23438369\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:3759300\tDlgap3<tm1Gfng>\t\t\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:17713528\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:2388144\tRgs2<tm1Pngr>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:11027316\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1857227\tNos1<tm1Plh>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:15158692\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:2182005\tPten<tm2Mak>\t\t\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:16675393\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:5532204\tGtf2i<tm1Vcam>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:20403157\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:5503119\tKif13a<tm1.1Noh>\t\t\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:23438369\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:3604467\tPrss12<tm1Dgen>\t\t\t\t\tRO:0002200\thas phenotype\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tMGI:3604450\thttp://data.monarchinitiative.org/ttl/mgi.ttl|http://data.monarchinitiative.org/ttl/mmrrc.ttl\tdirect\n+MGI:3055492\tBbs4<Gt1Nk>\t\t\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:16794820\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n' |
| b |
| diff -r 000000000000 -r 850bb90bd667 test-data/variants-for-phenotypes-union.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/variants-for-phenotypes-union.tsv Sun Jun 26 16:00:28 2016 -0400 |
| b |
| b'@@ -0,0 +1,3347 @@\n+ClinVarVariant:53226\tNM_000492.3(CFTR):c.1315C>T (p.Pro439Ser)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:20171652|PMID:12796866|PMID:7866213|PMID:20495477|PMID:10361400\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:53236\tNM_000492.3(CFTR):c.1366G>T (p.Val456Phe)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:20171652|PMID:12796866|PMID:7866213|PMID:20495477|PMID:10361400\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:4301\tNM_001005741.2(GBA):c.754T>A (p.Phe252Ile)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:20635362|PMID:9333269|PMID:7554686|PMID:12581195|PMID:23510063\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:4311\tNM_001005741.2(GBA):c.1604G>A (p.Arg535His)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:20635362|PMID:9333269|PMID:7554686|PMID:12581195|PMID:23510063\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:53206\tNM_000492.3(CFTR):c.1175T>C (p.Val392Ala)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:20171652|PMID:12796866|PMID:7866213|PMID:20495477|PMID:10361400\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:4321\tNM_001005741.2(GBA):c.259C>T (p.Arg87Trp)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:20635362|PMID:9333269|PMID:7554686|PMID:12581195|PMID:23510063\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+MGI:4429385\tTg(Htt-ATXN3*148Q)3746Thsc\tNCBITaxon:10090\tMus musculus\tNCBIGene:4287\tATXN3\t\t\tMP:0001364\tdecreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:19699305\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+ClinVarVariant:54057\tNM_000492.3(CFTR):c.775delCinsTCTTCCTCAGATTCATTGTGATTACCTCA (p.Leu259Serfs)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:20171652|PMID:12796866|PMID:7866213|PMID:20495477|PMID:10361400\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:54087\tNM_000492.3(CFTR):c.92G>T (p.Arg31Leu)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:20171652|PMID:12796866|PMID:7866213|PMID:20495477|PMID:10361400\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:54097\tNM_000492.3(CFTR):c.987delA (p.Gly330Glufs)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:20171652|PMID:12796866|PMID:7866213|PMID:20495477|PMID:10361400\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:5779\tNM_003919.2(SGCE):c.619_620delAG (p.Arg207Glyfs)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000739\tAnxiety\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchi'..b'21883167|PMID:22773173|PMID:8539655\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:53656\tNM_000492.3(CFTR):c.3139+101C>G\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:20171652|PMID:12796866|PMID:7866213|PMID:20495477|PMID:10361400\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:159984\tNM_005445.3(SMC3):c.2964T>C (p.Asp988=)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:19309268|PMID:18430761|PMID:17845236|PMID:17640042|PMID:19330433\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:53646\tNM_000492.3(CFTR):c.3068_3072delTAGTG (p.Ile1023Serfs)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:20171652|PMID:12796866|PMID:7866213|PMID:20495477|PMID:10361400\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+MGI:2668495\tSerpini1<tm1Dpw>\t\t\t\t\t\t\tHP:0000739\tAnxiety\tECO:0000006\texperimental evidence\tPMID:12837630\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+ClinVarVariant:53636\tNM_000492.3(CFTR):c.3039delC (p.Tyr1014Thrfs)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:20171652|PMID:12796866|PMID:7866213|PMID:20495477|PMID:10361400\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:159974\tNM_005445.3(SMC3):c.2299T>C (p.Leu767=)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:19309268|PMID:18430761|PMID:17845236|PMID:17640042|PMID:19330433\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:159964\tNM_006306.3(SMC1A):c.855-15C>T\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:19309268|PMID:18430761|PMID:17845236|PMID:17640042|PMID:19330433\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:53626\tNM_000492.3(CFTR):c.3014T>G (p.Ile1005Arg)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:20171652|PMID:12796866|PMID:7866213|PMID:20495477|PMID:10361400\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+MGI:3055492\tBbs4<Gt1Nk>\t\t\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:16794820\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+ClinVarVariant:159954\tNM_006306.3(SMC1A):c.3146G>A (p.Arg1049Gln)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:19309268|PMID:18430761|PMID:17845236|PMID:17640042|PMID:19330433\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:53616\tNM_000492.3(CFTR):c.2989_3139del151 (p.Leu997Alafs)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:20171652|PMID:12796866|PMID:7866213|PMID:20495477|PMID:10361400\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n' |
| b |
| diff -r 000000000000 -r 850bb90bd667 test.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test.txt Sun Jun 26 16:00:28 2016 -0400 |
| b |
| b"@@ -0,0 +1,130 @@\n+NCBIGene:37853\tMlp60A\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:39002\tPrm\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:627\tBDNF\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19276553\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:3630\tinsulin\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19276553\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:2944\tGSTM1\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:17449559\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:33824\tGpdh\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4137\tmicrotubule associated protein tau\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:260540\tParkinson-Dementia Syndrome\tECO:0000220|ECO:0000322\tsequencing assay evidence|imported manually asserted information used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl|http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4729\tNDUFV2\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:1565\tCYP2D6\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:15174030|PMID:14991823\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:3482\tinsulin like growth factor 2 receptor\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19276553\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4842\tnitric oxide synthase 1 (neuronal)\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:26383258\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:5243\tATP binding cassette subfamily B member 1\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:20558393\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:5071\tparkin RBR E3 ubiquitin protein ligase\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:15882845|PMID:19946270|PMID:25149416|PMID:22043175|PMID:16573651|PMID:12588799|PMID:22841634|PMID:24582596|PMID:15198987|PMID:17010972|PMID:23628791\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4129\tMAOB\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:21318773\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:6622\tSNCA\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/coriell.ttl\tinferred\n+NCBIGene:43497\tObp99b\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4137\tmicrotubule associated protein tau\tNCBITaxon:9606\tHomo sapiens\t\t\tOrphanet:240112\tProgressive supranuclear palsy - progressive non fluent aphasia\tECO:0000322\timported manually asserted information used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl\tinferred\n+NCBIGene:31826\trdgA\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's dise"..b"iens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:20711177\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:2580\tGAK\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:20711177\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:11315\tparkinson protein 7\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:105500\tAmyotrophic Lateral Sclerosis-Parkinsonism/Dementia Complex 1\tECO:0000323\timported automatically asserted information used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl\tinferred\n+NCBIGene:44643\tCnx99A\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:2941\tGSTA4\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:16510128\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4541\tMT-ND6\tNCBITaxon:9606\tHomo sapiens\t\t\tOrphanet:2828\tYoung-onset Parkinson disease\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:33883\tCpr\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:126\tADH1C\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:556500\tParkinson Disease, Mitochondrial\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:4571\tMT-TP\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:556500\tParkinson Disease, Mitochondrial\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:4137\tmicrotubule associated protein tau\tNCBITaxon:9606\tHomo sapiens\t\t\tOrphanet:240103\tProgressive supranuclear palsy - corticobasal syndrome\tECO:0000322\timported manually asserted information used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl\tinferred\n+NCBIGene:6888\tTALDO1\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:23233872\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:1906\tendothelin 1\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19276553\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:11315\tparkinson protein 7\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:606324\tParkinson Disease 7, Autosomal Recessive Early-Onset\tECO:0000220\tsequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:38990\tCpr66D\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:1356\tceruloplasmin (ferroxidase)\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19159062|PMID:25758665\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:54822\tTRPM7\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:105500\tAmyotrophic Lateral Sclerosis-Parkinsonism/Dementia Complex 1\tECO:0000220|ECO:0000323\tsequencing assay evidence|imported automatically asserted information used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl|http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:65018\tPINK1\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:22043175|PMID:17010972|PMID:25149416|PMID:21366594|PMID:24374061\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n" |
