| Previous changeset 6:307ec8cd152e (2016-06-29) Next changeset 8:15016fee2bc4 (2016-08-22) |
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Commit message:
planemo upload commit cc498cdcd54060998f80018b8f2dc92345adc414 |
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modified:
README.rst monarch-pathways-for-diseases.xml monarch-phenopackets.xml 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-union.tsv test-data/pathways-for-disease.tsv test-data/pathways-for-diseases-intersection.tsv test-data/pathways-for-diseases-union.tsv test-data/pathways-for-gene.tsv test-data/pathways-for-genes-union.tsv test-data/phenotypes-for-disease.tsv test-data/phenotypes-for-diseases-intersection.tsv test-data/phenotypes-for-diseases-union.tsv 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 |
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added:
output.json test-data/pathway-disease.tsv test-data/pathway-diseases-overlap.tsv |
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| diff -r 307ec8cd152e -r 61d8060bf2ed README.rst --- a/README.rst Wed Jun 29 14:17:39 2016 -0400 +++ b/README.rst Mon Aug 22 12:41:24 2016 -0400 |
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| @@ -10,3 +10,39 @@ .. .. image:: arguments.png +# To Update + +planemo test + +If one of them fails, then we have to make sure that the different tests are just data being updated, but not an error: + + +should be non-zero. + +For each xml test do: + + planemo test monarch-phenotypes-for-disease.xml --update_test_data + +which will update the test data + +If the test data is non-empty: + + git status | grep modified | cut -c14-1000 | xargs wc -l + +then commit. + + +# Send to the Toolset + +Using this reference for publishing: http://planemo.readthedocs.io/en/latest/publishing.html + + planemo shed_lint --tools + + planemo shed_diff --shed_target toolshed + + planemo shed_update --check_diff --shed_target toolshed + + planemo shed_test --shed_target toolshed + + + |
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| diff -r 307ec8cd152e -r 61d8060bf2ed monarch-pathways-for-diseases.xml --- a/monarch-pathways-for-diseases.xml Wed Jun 29 14:17:39 2016 -0400 +++ b/monarch-pathways-for-diseases.xml Mon Aug 22 12:41:24 2016 -0400 |
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| @@ -32,17 +32,17 @@ </outputs> <tests> <test> - <param name="input1" value="disease.tsv"/> + <param name="input1" value="pathway-disease.tsv"/> <param name="conditional1" value="OR"/> <output name="output1" file="pathways-for-disease.tsv"/> </test> <test> - <param name="input1" value="2-diseases-overlap.tsv"/> + <param name="input1" value="pathway-diseases-overlap.tsv"/> <param name="conditional1" value="AND"/> <output name="output1" file="pathways-for-diseases-intersection.tsv"/> </test> <test> - <param name="input1" value="2-diseases-overlap.tsv"/> + <param name="input1" value="pathway-diseases-overlap.tsv"/> <param name="conditional1" value="OR"/> <output name="output1" file="pathways-for-diseases-union.tsv"/> </test> |
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| diff -r 307ec8cd152e -r 61d8060bf2ed monarch-phenopackets.xml --- a/monarch-phenopackets.xml Wed Jun 29 14:17:39 2016 -0400 +++ b/monarch-phenopackets.xml Mon Aug 22 12:41:24 2016 -0400 |
| [ |
| @@ -37,7 +37,7 @@ <!--<output name="output1" file="phenotypes-for-variant.json"/>--> <output name="output1"> <assert_contents> - <has_text text='phenopacket":{"phenotype_profile":[{"entity":"ClinVarVariant:217207"'/> + <has_text text='phenopacket":{"phenotype_profile":[{"entity":"'/> </assert_contents> </output> </test> @@ -47,7 +47,7 @@ <!--<output name="output1" file="phenotypes-for-variants-intersection.json"/>--> <output name="output1"> <assert_contents> - <has_text text='phenopacket":{"phenotype_profile":[{"entity":"ClinVarVariant:217207"'/> + <has_text text='{"phenopacket":{"phenotype_profile":[{"entity":"'/> </assert_contents> </output> </test> @@ -57,7 +57,7 @@ <!--<output name="output1" file="phenotypes-for-variants-union.json"/>--> <output name="output1"> <assert_contents> - <has_text text='phenopacket":{"phenotype_profile":[{"entity":"ClinVarVariant:217207"'/> + <has_text text='{"phenopacket":{"phenotype_profile":[{"entity":"'/> </assert_contents> </output> </test> |
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| diff -r 307ec8cd152e -r 61d8060bf2ed output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/output.json Mon Aug 22 12:41:24 2016 -0400 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"phenopacket":{"phenotype_profile":[{"entity":"PMID:24725409","phenotype":{"types":[{"id":"MGI:5751490","label":"Ush1c<tm1Xzl>/Ush1c<tm1Xzl> [involves: 129S1/Sv * 129X1/SvJ]"}]}},{"entity":"PMID:6961458","phenotype":{"types":[{"id":"Coriell:GM02362","label":"NIGMS-GM02362"}]}},{"entity":"PMID:9284099","phenotype":{"types":[{"id":"MGI:2175832","label":"Dsg3<bal-Pas>/Dsg3<bal-Pas> [129S2.Cg-Dsg3<bal-Pas>]"}]}},{"entity":"PMID:15268757","phenotype":{"types":[{"id":"Coriell:AG10578","label":"NIA-AG10578"}]}},{"entity":"PMID:7881425","phenotype":{"types":[{"id":"Coriell:GM00443","label":"NIGMS-GM00443"}]}},{"entity":"PMID:10634254","phenotype":{"types":[{"id":"Coriell:GM15009","label":"NIGMS-GM15009"}]}},{"entity":"PMID:26823433","phenotype":{"types":[{"id":"ZFIN:ZDB-FISH-160503-4","label":"<cz3334Tg>/<?>; <czt13Tg>/<?>; tp53<zdf1>/tp53<zdf1> [n.s.]"}]}},{"entity":"_:genid439539","phenotype":{"types":[{"id":"OMIA-breed:40","label":"Merino (sheep)"}]}},{"entity":"PMID:6087154","phenotype":{"types":[{"id":"Coriell:GM02292","label":"NIGMS-GM02292"}]}},{"entity":"MGI:62294","phenotype":{"types":[{"id":"MGI:3587737","label":"Nhs<Xcat>/0 [involves: DBA/2 * T STOCK]"}]}},{"entity":"_:genid438854","phenotype":{"types":[{"id":"OMIA-breed:161","label":"Siamese (domestic cat)"}]}},{"entity":"PMID:10649495","phenotype":{"types":[{"id":"Coriell:GM20273","label":"NIGMS-GM20273"}]}},{"entity":"PMID:14993615","phenotype":{"types":[{"id":"Coriell:GM04860","label":"NIGMS-GM04860"}]}},{"entity":"PMID:11697802","phenotype":{"types":[{"id":"MGI:2174799","label":"Vdr<tm1Ska>/Vdr<tm1Ska> [involves: C57BL/6 * CBA]"}]}},{"entity":"PMID:23742761","phenotype":{"types":[{"id":"MGI:5529680","label":"Rps6ka3<tm1.1Kry>/Rps6ka3<tm1.1Kry> [B6.129X1(Cg)-Rps6ka3<tm1.1Kry>]"}]}},{"entity":"PMID:2880399","phenotype":{"types":[{"id":"Coriell:AG09750","label":"NIA-AG09750"}]}},{"entity":"PMID:24629673","phenotype":{"types":[{"id":"MGI:1930937","label":"Psen1<tm1Mpm>"}]}},{"entity":"PMID:8910459","phenotype":{"types":[{"id":"Coriell:GM05653","label":"NIGMS-GM05653"}]}},{"entity":"PMID:20696775","phenotype":{"types":[{"id":"MGI:5428441","label":"Aire<tm1.1Doi>/Aire<tm1.1Doi>; Il1r1<tm1Imx>/Il1r1<+> [involves: 129S2/SvPas * 129S7/SvEvBrd * NOD]"}]}},{"entity":"_:genid439269","phenotype":{"types":[{"id":"OMIA-breed:17","label":"Hereford (cattle)"}]}},{"entity":"PMID:21748598","phenotype":{"types":[{"id":"http://www.monarchinitiative.org/_NCBITaxon7227-with-FlyBaseFBal0285342","label":"Hsap\\\\FUS[WT.Scer\\\\UAS.T:Disc\\\\RFP,T:Ivir\\\\HA1] fly"}]}},{"entity":"PMID:15615772","phenotype":{"types":[{"id":"MGI:2662716","label":"Plau<tm1Mlg>/Plau<tm1Mlg> [involves: 129S2/SvPas * C57BL/6]"}]}},{"entity":"PMID:25740694","phenotype":{"types":[{"id":"MGI:2158456","label":"Akt2<tm1.1Mbb>"}]}},{"entity":"PMID:21982178","phenotype":{"types":[{"id":"ZFIN:ZDB-FISH-150901-12774","label":"WT; tbx5a<MO1-tbx5a>"}]}},{"entity":"PMID:17187063","phenotype":{"types":[{"id":"http://www.monarchinitiative.org/_NCBITaxon7227-with-FlyBaseFBal0126525","label":"Hsap\\\\MAPT[V337M.Scer\\\\UAS] fly"}]}},{"entity":"PMID:21715426","phenotype":{"types":[{"id":"ZFIN:ZDB-FISH-150901-12774","label":"WT; tbx5a<MO1-tbx5a>"}]}},{"entity":"PMID:24423645","phenotype":{"types":[{"id":"MGI:5604251","label":"Mfsd8<tm1a(EUCOMM)Hmgu>/Mfsd8<tm1a(EUCOMM)Hmgu> [involves: C57BL/6N]"}]}},{"entity":"PMID:3790722","phenotype":{"types":[{"id":"Coriell:GM08014","label":"NIGMS-GM08014"}]}},{"entity":"PMID:4206317","phenotype":{"types":[{"id":"OMIA-breed:149","label":"Saint Bernard (dog)"}]}},{"entity":"PMID:15647265","phenotype":{"types":[{"id":"MGI:1857229","label":"Nos3<tm1Unc>"}]}},{"entity":"PMID:17567478","phenotype":{"types":[{"id":"MGI:3806986","label":"Pten<tm2Mak>/Pten<tm2Mak>; Tg(Alb-cre)21Mgn/0 [involves: 129P2/OlaHsd * C57BL/6 * DBA]"}]}},{"entity":"PMID:21324362","phenotype":{"types":[{"id":"MGI:5749790","label":"Tg(Camk2a-MAPT)601Ymot/0 [involves: C57BL/6 * C57BL/6J]"}]}},{"entity":"PMID:21109326","phenotype"'..b'790","phenotype":{"types":[{"id":"MGI:1930203","label":"Tg(MMTVneu)202Mul"}]}},{"entity":"PMID:16281288","phenotype":{"types":[{"id":"MGI:5140950","label":"Cdh23<v-bus>/Cdh23<v-bus> [involves: KYF/MsIdr]"}]}},{"entity":"PMID:22160706","phenotype":{"types":[{"id":"MGI:2174786","label":"Trp73<tm1Fmc>/Trp73<tm1Fmc> [involves: 129S4/SvJae]"}]}},{"entity":"PMID:9312059","phenotype":{"types":[{"id":"Coriell:GM02530","label":"NIGMS-GM02530"}]}},{"entity":"PMID:6667451","phenotype":{"types":[{"id":"Coriell:GM04408","label":"NIGMS-GM04408"}]}},{"entity":"PMID:22859742","phenotype":{"types":[{"id":"MGI:2655355","label":"MGI:2655355"}]}},{"entity":"PMID:14751570","phenotype":{"types":[{"id":"MGI:3764489","label":"Phex<Hyp>/0 [B6.Cg-Phex<Hyp>/J]"}]}},{"entity":"PMID:22423108","phenotype":{"types":[{"id":"http://www.monarchinitiative.org/_NCBITaxon7227-with-FlyBaseFBal0249097","label":"Hsap\\\\LRRK2[G2019S.Scer\\\\UAS.T:Zzzz\\\\FLAG] fly"}]}},{"entity":"PMID:17030179","phenotype":{"types":[{"id":"MGI:4361196","label":"Tg(Krt19-Wnt1)2Maos/0; Tg(Krt19-Ptgs2,Krt19-Ptges)8Tko/0 [involves: C3H * C57BL/6]"}]}},{"entity":"PMID:17428816","phenotype":{"types":[{"id":"MGI:3712038","label":"Opa1<Q285X>/Opa1<+> [involves: C3HeB/FeJ * C57BL/6JCrl]"}]}},{"entity":"PMID:12719382","phenotype":{"types":[{"id":"MGI:3622353","label":"Foxc2<tm1Miu>/Foxc2<+> [involves: 129P2/OlaHsd * C57BL/6 * C57BL/6J]"}]}},{"entity":"PMID:16875466","phenotype":{"types":[{"id":"MGI:3699323","label":"Bckdk<Gt(VICT48)710Lex>/Bckdk<Gt(VICT48)710Lex> [B6.129S5/SvEvBrd-Bckdk<Gt(VICT48)710Lex>]"}]}},{"entity":"PMID:7651536","phenotype":{"types":[{"id":"Coriell:AG09905","label":"NIA-AG09905"}]}},{"entity":"_:genid448596","phenotype":{"types":[{"id":"OMIA-breed:86","label":"Holstein (cattle)"}]}},{"entity":"PMID:21824387","phenotype":{"types":[{"id":"MGI:1856332","label":"Dmd<mdx-5Cv>"}]}},{"entity":"PMID:22068627","phenotype":{"types":[{"id":":_NCBITaxon6239-with-_WBGene00006444-unspecified","label":"some variant of shn-1 worm"}]}},{"entity":"PMID:11714835","phenotype":{"types":[{"id":"MGI:3623449","label":"Ifng<tm1Ts>/Ifng<tm1Ts> [NOD.129S7(B6)-Ifng<tm1Ts>/DvsJ]"}]}},{"entity":"PMID:3343337","phenotype":{"types":[{"id":"Coriell:GM03896","label":"NIGMS-GM03896"}]}},{"entity":"PMID:27030752","phenotype":{"types":[{"id":"MGI:3814564","label":"Tg(MT1A-Dyrk1a)#Xest"}]}},{"entity":"PMID:11258627","phenotype":{"types":[{"id":"Coriell:GM20411","label":"NIGMS-GM20411"}]}},{"entity":"PMID:590190","phenotype":{"types":[{"id":"MGI:3042606","label":"Prop1<df>/Prop1<df> [STOCK Prop1<df>]"}]}},{"entity":"PMID:19641140","phenotype":{"types":[{"id":"MGI:3815114","label":"Ccl2<tm1Rol>/Ccl2<tm1Rol> [B6.129S4-Ccl2<tm1Rol>]"}]}},{"entity":"MGI:63130","phenotype":{"types":[{"id":"MGI:2657281","label":"Zic3<Bn>/Zic3<+> [BNT/LeJ]"}]}},{"entity":"PMID:16039562","phenotype":{"types":[{"id":"MGI:2385631","label":"Tg(APPSWE)2576Kha"}]}},{"entity":"PMID:17052657","phenotype":{"types":[{"id":"Coriell:ND02759","label":"NINDS-ND02759"}]}},{"entity":"PMID:9382875","phenotype":{"types":[{"id":"MGI:3813319","label":"Tg(SOD1*G93A)<dl>1Gur/0 [involves: C57BL/6 * SJL]"}]}},{"entity":"PMID:1680289","phenotype":{"types":[{"id":"Coriell:GM02471","label":"NIGMS-GM02471"}]}},{"entity":"PMID:8440653","phenotype":{"types":[{"id":"OMIA-breed:26","label":"Rambouillet (sheep)"}]}},{"entity":"PMID:15269252","phenotype":{"types":[{"id":"MGI:3038333","label":"Rp1<tm1Jnz>/Rp1<tm1Jnz> [involves: 129S7/SvEvBrd]"}]}},{"entity":"PMID:2491017","phenotype":{"types":[{"id":"Coriell:GM01695","label":"NIGMS-GM01695"}]}},{"entity":"PMID:26251041","phenotype":{"types":[{"id":"http://www.monarchinitiative.org/_NCBITaxon7227-with-FlyBaseFBal0316899","label":"Hsap\\\\VPS35[D620N.Scer\\\\UAS] fly"}]}}],"schema":"phenopacket-level-1"},"params":{"q":"*:*","fq":"(subject_closure:\\"HP:0002548\\")","personality":"variant_phenotype","showEmptyFields":false},"name":"Monarch Application","date":"Mon Aug 22 2016 09:12:35 GMT-0700 (PDT)"}\n\\ No newline at end of file\n' |
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| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/genes-for-2-diseases-intersection.tsv --- a/test-data/genes-for-2-diseases-intersection.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/genes-for-2-diseases-intersection.tsv Mon Aug 22 12:41:24 2016 -0400 |
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| b'@@ -1,23 +1,18 @@\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: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:5071\tparkin RBR E3 ubiquitin protein ligase\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:6315\tATXN8OS\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/clinvar.ttl\tinferred\n-NCBIGene:2747\tGLUD2\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/clinvar.ttl\tinferred\n-NCBIGene:4287\tATXN3\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/clinvar.ttl\tinferred\n-NCBIGene:203228\tchromosome 9 open reading frame 72\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:6311\tATXN2\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\tECO:0000220\tsequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl\tinferred\n-NCBIGene:26281\tfibroblast growth factor 20\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/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-NCBIGene:4929\tNR4A2\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/clinvar.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:126\tADH1C\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\tECO:0000220\tsequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:2747\tGLUD2\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\tPMID:19826450\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:5071\tPARK2\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:7345\tUCHL1\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:126\tADH1C\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\tECO:0000220\tsequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-NCBIGene:6908\tTATA-box binding protein\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-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:1621\tdopamine beta-hydroxylase (dopamine beta-monooxygenase)\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:627\tBDNF\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitia'..b'm.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-NCBIGene:4137\tmicrotubule associated protein tau\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-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:497258\tBDNF-AS\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n-NCBIGene:2629\tGBA\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\tECO:0000220\tsequencing assay evidence\t\thttp://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\tinferred\n+NCBIGene:4929\tNR4A2\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:1621\tDBH\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: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:26281\tFGF20\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:6311\tATXN2\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\tECO:0000220\tsequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl\tinferred\n+NCBIGene:9627\tSNCAIP\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:120892\tLRRK2\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\tPMID:27111571\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/coriell.ttl|http://data.monarchinitiative.org/ttl/clinvar.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:6908\tTBP\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\tECO:0000220\tsequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:4137\tMAPT\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\tECO:0000220\tsequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:2629\tGBA\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\tECO:0000220\tsequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/coriell.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl\tinferred\n+NCBIGene:23317\tDNAJC13\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\tPMID:24218364\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:4535\tND1\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\tPMID:7624338\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:1815\tDRD4\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n' |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/genes-for-2-diseases-union.tsv --- a/test-data/genes-for-2-diseases-union.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/genes-for-2-diseases-union.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| b"@@ -1,130 +1,121 @@\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:126\tADH1C\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\tECO:0000220\tsequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:55737\tVPS35\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:614203\tParkinson Disease 17\tECO:0000220\tsequencing assay evidence\tPMID:21763483|PMID:18342564|PMID:22991136|PMID:22517097|PMID:22801713\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:3313\tHSPA9\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:16565515\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:55532\tSLC30A10\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:25149416\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:135138\tPACRG\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\tPMID:16328510\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:3643\tINSR\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:120892\tLRRK2\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:607060\tautosomal dominant Parkinson disease 8\tECO:0000220\tsequencing assay evidence\tPMID:16533964|PMID:18704525|PMID:23075850|PMID:21115957|PMID:16728648|PMID:17353388|PMID:9276200|PMID:16003110|PMID:15680455|PMID:15541309|PMID:19020907|PMID:16311269|PMID:15541308|PMID:16003110|PMID:16436782|PMID:17050822|PMID:15929036|PMID:16436781|PMID:16269541|PMID:19020907|PMID:17215492|PMID:18591067|PMID:20008657|PMID:15852371|PMID:17060595|PMID:16401756|PMID:16966502|PMID:15541309|PMID:19667187|PMID:17938369|PMID:15541309|PMID:7898705|PMID:16533964|PMID:15811455|PMID:19283415|PMID:15732108|PMID:15680456|PMID:19308469|PMID:15880653|PMID:16321986|PMID:16157909|PMID:15541309|PMID:18981379|PMID:16240353|PMID:15541308|PMID:17060595|PMID:16269541|PMID:16960813|PMID:16145815|PMID:15680457|PMID:16172858|PMID:15726496\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:6622\tSNCA\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:605543\tParkinson Disease 4, Autosomal Dominant\tECO:0000220\tsequencing assay evidence\tPMID:17251522|PMID:15159488|PMID:14593171|PMID:14755720|PMID:8285594\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:2747\tGLUD2\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\tPMID:19826450\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:4128\tMAOA\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:3569\tIL6\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:31826\trdgA\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:4803\tNGF\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19276553\thttp://data.monarchinitiative.org"..b"narchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:39826\tfax\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:6571\tSLC18A2\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:16112329\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:8398\tPLA2G6\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:612953\tParkinson disease 14\tECO:0000220\tsequencing assay evidence\tPMID:18981035|PMID:20938027|PMID:18570303|PMID:20886109|PMID:18570303|PMID:18570303|PMID:20938027|PMID:18981035|PMID:20938027|PMID:26633545|PMID:21700586\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:2629\tGBA\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\tECO:0000220\tsequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/coriell.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl\tinferred\n+NCBIGene:1981\tEIF4G1\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:614251\tParkinson disease 18\tECO:0000220\tsequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl\tinferred\n+NCBIGene:6128\tRPL6\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:38418\tkst\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:23317\tDNAJC13\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\tPMID:24218364\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:4535\tND1\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\tPMID:7624338\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:43690\tchp\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:6147\tRPL23A\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:100861548\tPINK1-AS\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\tPMID:18685134|PMID:15349871|PMID:15087508|PMID:15955953|PMID:15596610|PMID:15349870|PMID:18524835|PMID:18003639|PMID:15087508|PMID:15349870|PMID:16207731|PMID:15824318|PMID:16207731|PMID:17030667|PMID:18704525|PMID:16769864|PMID:15970950\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:1815\tDRD4\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:4576\tTRNT\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:556500\tParkinson disease, mitochondrial\t\t\t\thttp://data.monarchinitiative.org/ttl/kegg.ttl\tinferred\n+NCBIGene:3481\tIGF2\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:6531\tSLC6A3\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:613135\tParkinsonism-Dystonia, Infantile\tECO:0000220|ECO:0000322\tsequencing assay evidence|imported manually asserted information used in automatic assertion\tPMID:21112253|PMID:22279524|PMID:19478460|PMID:19478460|PMID:21112253|PMID:21112253\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/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n" |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/genes-for-2-diseases.tsv --- a/test-data/genes-for-2-diseases.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/genes-for-2-diseases.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| b"@@ -1,136 +1,127 @@\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:126\tADH1C\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\tECO:0000220\tsequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:55737\tVPS35\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:614203\tParkinson Disease 17\tECO:0000220\tsequencing assay evidence\tPMID:21763483|PMID:18342564|PMID:22991136|PMID:22517097|PMID:22801713\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:3313\tHSPA9\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:16565515\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:55532\tSLC30A10\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:25149416\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:135138\tPACRG\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\tPMID:16328510\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:3643\tINSR\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:56997\tADCK3\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:607426\tCoenzyme Q10 Deficiency, Primary, 1\tECO:0000033\ttraceable author statement\tPMID:18319072\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:57107\tPDSS2\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:120892\tLRRK2\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:607060\tautosomal dominant Parkinson disease 8\tECO:0000220\tsequencing assay evidence\tPMID:16533964|PMID:18704525|PMID:23075850|PMID:21115957|PMID:16728648|PMID:17353388|PMID:9276200|PMID:16003110|PMID:15680455|PMID:15541309|PMID:19020907|PMID:16311269|PMID:15541308|PMID:16003110|PMID:16436782|PMID:17050822|PMID:15929036|PMID:16436781|PMID:16269541|PMID:19020907|PMID:17215492|PMID:18591067|PMID:20008657|PMID:15852371|PMID:17060595|PMID:16401756|PMID:16966502|PMID:15541309|PMID:19667187|PMID:17938369|PMID:15541309|PMID:7898705|PMID:16533964|PMID:15811455|PMID:19283415|PMID:15732108|PMID:15680456|PMID:19308469|PMID:15880653|PMID:16321986|PMID:16157909|PMID:15541309|PMID:18981379|PMID:16240353|PMID:15541308|PMID:17060595|PMID:16269541|PMID:16960813|PMID:16145815|PMID:15680457|PMID:16172858|PMID:15726496\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:6622\tSNCA\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:605543\tParkinson Disease 4, Autosomal Dominant\tECO:0000220\tsequencing assay evidence\tPMID:17251522|PMID:15159488|PMID:14593171|PMID:14755720|PMID:8285594\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:2747\tGLUD2\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\tPMID:19826450\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:57017\tCOQ9\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:4128\tMAOA\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:3569\tIL6\tNCBITaxon:960"..b"narchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:39826\tfax\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:6571\tSLC18A2\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:16112329\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:8398\tPLA2G6\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:612953\tParkinson disease 14\tECO:0000220\tsequencing assay evidence\tPMID:18981035|PMID:20938027|PMID:18570303|PMID:20886109|PMID:18570303|PMID:18570303|PMID:20938027|PMID:18981035|PMID:20938027|PMID:26633545|PMID:21700586\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:2629\tGBA\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\tECO:0000220\tsequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/coriell.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl\tinferred\n+NCBIGene:1981\tEIF4G1\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:614251\tParkinson disease 18\tECO:0000220\tsequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl\tinferred\n+NCBIGene:6128\tRPL6\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:38418\tkst\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:23317\tDNAJC13\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\tPMID:24218364\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:4535\tND1\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\tPMID:7624338\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:43690\tchp\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:6147\tRPL23A\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:100861548\tPINK1-AS\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\tPMID:18685134|PMID:15349871|PMID:15087508|PMID:15955953|PMID:15596610|PMID:15349870|PMID:18524835|PMID:18003639|PMID:15087508|PMID:15349870|PMID:16207731|PMID:15824318|PMID:16207731|PMID:17030667|PMID:18704525|PMID:16769864|PMID:15970950\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:1815\tDRD4\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:4576\tTRNT\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:556500\tParkinson disease, mitochondrial\t\t\t\thttp://data.monarchinitiative.org/ttl/kegg.ttl\tinferred\n+NCBIGene:3481\tIGF2\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:6531\tSLC6A3\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:613135\tParkinsonism-Dystonia, Infantile\tECO:0000220|ECO:0000322\tsequencing assay evidence|imported manually asserted information used in automatic assertion\tPMID:21112253|PMID:22279524|PMID:19478460|PMID:19478460|PMID:21112253|PMID:21112253\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/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n" |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/genes-for-2-phenotypes-intersection.tsv --- a/test-data/genes-for-2-phenotypes-intersection.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/genes-for-2-phenotypes-intersection.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| b'@@ -1,245 +1,206 @@\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:000136'..b'l/mgi_slim.ttl\tdirect\n+MGI:107501\tKcnj11\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:16530794\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:2150393\tGrin3b\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:17880385\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:1919764\tFgfbp3\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:20851768\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:2685783\tBaiap3\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000059\texperimental phenotypic evidence\tPMID:23698091\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:2441758\tGpr26\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000059\texperimental phenotypic evidence\tPMID:21924326\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:2664186\tNpas4\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:18815592\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:2151070\tOphn1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000059\texperimental phenotypic evidence\tPMID:17728457\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:2442233\tArhgef9\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000059\texperimental phenotypic evidence\tPMID:17690689\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:2442233\tArhgef9\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:17690689\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:5308748\tBhv31\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\t\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:95811\tGria4\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:20662939\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:1861942\tGtf2ird1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:22652393\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:94876\tDdc\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:23275025\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:99479\tCckbr\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:12459512\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:95623\tGabrg2\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:15850489\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:101916\tFabp7\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:16882015\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:1858193\tFolh1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:16190866\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:95832\tGrn\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:17764761\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:2139279\tHrh3\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:15078574\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n' |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/genes-for-2-phenotypes-union.tsv --- a/test-data/genes-for-2-phenotypes-union.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/genes-for-2-phenotypes-union.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| b'@@ -1,637 +1,591 @@\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\tdecreas'..b'1942\tGtf2ird1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:22652393\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:88495\tCrem\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001364\tdecreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:10570204\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:1915541\tMto1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001364\tdecreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:25506927\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+NCBIGene:114798\tSLITRK1\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:1564054|PMID:8425124|PMID:8173824|PMID:20351724|PMID:20063404|PMID:17035247|PMID:18413575|PMID:23418216\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+MGI:94876\tDdc\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:23275025\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:99479\tCckbr\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:12459512\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:95623\tGabrg2\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:15850489\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:88065\tAraf\tNCBITaxon:10090\tMus musculus\t\t\tHP:0000739\tAnxiety\tECO:0000059\texperimental phenotypic evidence\tPMID:8805280\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:3045350\tOlfm2\tNCBITaxon:10090\tMus musculus\t\t\tHP:0000739\tAnxiety\tECO:0000059\texperimental phenotypic evidence\tPMID:25218043\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:101916\tFabp7\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:16882015\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:1858193\tFolh1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:16190866\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+NCBIGene:3651\tPDX1\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:22397240|PMID:2209327|PMID:12429356|PMID:9428966|PMID:22188726\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+MGI:1924933\tEhmt1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001364\tdecreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:20005824|PMID:19896504\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+NCBIGene:2820\tGPD2\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:22397240|PMID:2209327|PMID:12429356|PMID:9428966|PMID:9070847|PMID:22188726\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+MGI:95832\tGrn\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:17764761\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:2139279\tHrh3\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:15078574\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n' |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/genes-for-diseases.tsv --- a/test-data/genes-for-diseases.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/genes-for-diseases.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| b"@@ -1,130 +1,121 @@\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:126\tADH1C\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\tECO:0000220\tsequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:55737\tVPS35\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:614203\tParkinson Disease 17\tECO:0000220\tsequencing assay evidence\tPMID:21763483|PMID:18342564|PMID:22991136|PMID:22517097|PMID:22801713\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:3313\tHSPA9\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:16565515\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:55532\tSLC30A10\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:25149416\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:135138\tPACRG\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\tPMID:16328510\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:3643\tINSR\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:120892\tLRRK2\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:607060\tautosomal dominant Parkinson disease 8\tECO:0000220\tsequencing assay evidence\tPMID:16533964|PMID:18704525|PMID:23075850|PMID:21115957|PMID:16728648|PMID:17353388|PMID:9276200|PMID:16003110|PMID:15680455|PMID:15541309|PMID:19020907|PMID:16311269|PMID:15541308|PMID:16003110|PMID:16436782|PMID:17050822|PMID:15929036|PMID:16436781|PMID:16269541|PMID:19020907|PMID:17215492|PMID:18591067|PMID:20008657|PMID:15852371|PMID:17060595|PMID:16401756|PMID:16966502|PMID:15541309|PMID:19667187|PMID:17938369|PMID:15541309|PMID:7898705|PMID:16533964|PMID:15811455|PMID:19283415|PMID:15732108|PMID:15680456|PMID:19308469|PMID:15880653|PMID:16321986|PMID:16157909|PMID:15541309|PMID:18981379|PMID:16240353|PMID:15541308|PMID:17060595|PMID:16269541|PMID:16960813|PMID:16145815|PMID:15680457|PMID:16172858|PMID:15726496\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:6622\tSNCA\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:605543\tParkinson Disease 4, Autosomal Dominant\tECO:0000220\tsequencing assay evidence\tPMID:17251522|PMID:15159488|PMID:14593171|PMID:14755720|PMID:8285594\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:2747\tGLUD2\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\tPMID:19826450\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:4128\tMAOA\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:3569\tIL6\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:31826\trdgA\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:4803\tNGF\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19276553\thttp://data.monarchinitiative.org"..b"narchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:39826\tfax\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:6571\tSLC18A2\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:16112329\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:8398\tPLA2G6\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:612953\tParkinson disease 14\tECO:0000220\tsequencing assay evidence\tPMID:18981035|PMID:20938027|PMID:18570303|PMID:20886109|PMID:18570303|PMID:18570303|PMID:20938027|PMID:18981035|PMID:20938027|PMID:26633545|PMID:21700586\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:2629\tGBA\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\tECO:0000220\tsequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/coriell.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl\tinferred\n+NCBIGene:1981\tEIF4G1\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:614251\tParkinson disease 18\tECO:0000220\tsequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl\tinferred\n+NCBIGene:6128\tRPL6\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:38418\tkst\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:23317\tDNAJC13\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\tPMID:24218364\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:4535\tND1\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\tPMID:7624338\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:43690\tchp\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:6147\tRPL23A\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:100861548\tPINK1-AS\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\tPMID:18685134|PMID:15349871|PMID:15087508|PMID:15955953|PMID:15596610|PMID:15349870|PMID:18524835|PMID:18003639|PMID:15087508|PMID:15349870|PMID:16207731|PMID:15824318|PMID:16207731|PMID:17030667|PMID:18704525|PMID:16769864|PMID:15970950\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:1815\tDRD4\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:4576\tTRNT\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:556500\tParkinson disease, mitochondrial\t\t\t\thttp://data.monarchinitiative.org/ttl/kegg.ttl\tinferred\n+NCBIGene:3481\tIGF2\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:6531\tSLC6A3\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:613135\tParkinsonism-Dystonia, Infantile\tECO:0000220|ECO:0000322\tsequencing assay evidence|imported manually asserted information used in automatic assertion\tPMID:21112253|PMID:22279524|PMID:19478460|PMID:19478460|PMID:21112253|PMID:21112253\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/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n" |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/genes-for-phenotype.tsv --- a/test-data/genes-for-phenotype.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/genes-for-phenotype.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| b'@@ -1,10 +1,10 @@\n-NCBIGene:26058\tGRB10 interacting GYF protein 2\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000220|ECO:0000269\tsequencing assay evidence|experimental evidence used in manual assertion\tPMID:18358451\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-NCBIGene:5428\tpolymerase (DNA directed), gamma\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000501|ECO:0000220\tevidence used in automatic assertion|sequencing assay evidence\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:2643\tGCH1\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000220|ECO:0000304\tsequencing assay evidence|traceable author statement used in manual 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:25793\tF-box protein 7\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000322|ECO:0000220|ECO:0000501\timported manually asserted information 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-NCBIGene:23400\tATP13A2\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000220|ECO:0000322|ECO:0000220|ECO:0000304\tsequencing assay evidence|imported manually asserted information used in automatic assertion|sequencing assay evidence|traceable author statement used in manual 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-NCBIGene:7054\tTH\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000322|ECO:0000304|ECO:0000220\timported manually asserted information used in automatic assertion|traceable author statement used in manual assertion|sequencing assay evidence\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-NCBIGene:27429\tHTRA2\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000220|ECO:0000304\tsequencing assay evidence|traceable author statement used in manual 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:120892\tleucine-rich repeat kinase 2\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000501|ECO:0000220\tevidence used in automatic assertion|sequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-NCBIGene:6872\tTATA-box binding protein associated factor 1\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000304|ECO:0000220\ttraceable author statement used in manual assertion|sequencing assay evidence\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitia'..b'tive.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+NCBIGene:27429\tHTRA2\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000220|ECO:0000304\tsequencing assay evidence|traceable author statement used in manual assertion\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+NCBIGene:7054\tTH\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000322|ECO:0000304|ECO:0000220\timported manually asserted information used in automatic assertion|traceable author statement used in manual assertion|sequencing assay evidence\tPMID:17696123|PMID:10407773|PMID:8817341|PMID:9235905|PMID:7814018|PMID:20198643|PMID:10407773|PMID:9703425|PMID:9732974|PMID:20430833|PMID:9732974|PMID:11246459|PMID:24753243|PMID:10407773|PMID:11246459|PMID:11246459|PMID:10407773|PMID:11281275|PMID:10585338|PMID:11246459|PMID:8528210\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+NCBIGene:23400\tATP13A2\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000322|ECO:0000220|ECO:0000220|ECO:0000304\timported manually asserted information used in automatic assertion|sequencing assay evidence|sequencing assay evidence|traceable author statement used in manual assertion\tPMID:21724849|PMID:16964263|PMID:22388936|PMID:16964263|PMID:26633545|PMID:26633545|PMID:495089|PMID:20853184|PMID:21724849|PMID:16964263|PMID:21094623|PMID:17485642|PMID:21724849|PMID:20310007\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+NCBIGene:25793\tFBXO7\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000322|ECO:0000220|ECO:0000501\timported manually asserted information used in automatic assertion|sequencing assay evidence|evidence used in automatic assertion\tPMID:18513678|PMID:19038853|PMID:19038853|PMID:19038853\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+NCBIGene:5428\tPOLG\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000220|ECO:0000501\tsequencing assay evidence|evidence used in automatic assertion\tPMID:17420318|PMID:15351195|PMID:12210792|PMID:2067633|PMID:12210792|PMID:14467368|PMID:11897778|PMID:11431686|PMID:2725645\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+NCBIGene:2643\tGCH1\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000220|ECO:0000304\tsequencing assay evidence|traceable author statement used in manual assertion\tPMID:9667588|PMID:11486899|PMID:17111153|PMID:9576537|PMID:11359069|PMID:12391354|PMID:11026444|PMID:9576537|PMID:9576537|PMID:7874165|PMID:7874165|PMID:10732814|PMID:10078749|PMID:10732814|PMID:7874165|PMID:7874165|PMID:10208576\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+NCBIGene:26058\tGIGYF2\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000220|ECO:0000269\tsequencing assay evidence|experimental evidence used in manual assertion\tPMID:18358451\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n' |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/homologues-for-gene.tsv --- a/test-data/homologues-for-gene.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/homologues-for-gene.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| b'@@ -1,30 +1,30 @@\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-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: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: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: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+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+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: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:100379827\tcapn10\tNCBITaxon:8364\tXenopus (Silurana) 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:825\tCAPN3\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: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: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: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\tCAPN1\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: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://d'..b' 1 orthology relationship with\tECO:0000031|ECO:0000080\tprotein BLAST evidence used in manual assertion|phylogenetic evidence\tZFIN:ZDB-PUB-030905-1\thttp://data.monarchinitiative.org/ttl/panther.ttl|http://data.monarchinitiative.org/ttl/zfin.ttl\tdirect\n-NCBIGene:827\tCAPN6\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:570311\tcapn10\tNCBITaxon:7955\tDanio rerio\tRO:HOM0000017\tin orthology relationship with\tECO:0000080|ECO:0000031\tphylogenetic evidence|protein BLAST evidence used in manual assertion\tZFIN:ZDB-PUB-030905-1\thttp://data.monarchinitiative.org/ttl/panther.ttl|http://data.monarchinitiative.org/ttl/zfin.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:826\tCAPNS1\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: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:100022544\tCAPN10\tNCBITaxon:13616\tMonodelphis domestica\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: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-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-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: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: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: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: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: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' |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/homologues-for-genes-union.tsv --- a/test-data/homologues-for-genes-union.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/homologues-for-genes-union.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| b'@@ -1,58 +1,61 @@\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: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: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:826\tCAPNS1\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000079|ECO:0000080\taffinity chromatography evidence|phylogenetic evidence\tPMID:26186194\thttp://data.monarchinitiative.org/ttl/panther.ttl|http://data.monarchinitiative.org/ttl/biogrid.ttl\tdirect\n+NCBIGene:440854\tCAPN14\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 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: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: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: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: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:100379827\tcapn10\tNCBITaxon:8364\tXenopus (Silurana) 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:825\tCAPN3\tNCB'..b'Homo 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+NCBIGene:100022544\tCAPN10\tNCBITaxon:13616\tMonodelphis domestica\tRO:HOM0000020\tin 1 to 1 orthology relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n+NCBIGene:100518072\tCAPNS2\tNCBITaxon:9823\tSus scrofa\tRO:HOM0000020\tin 1 to 1 orthology relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n' |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/pathway-disease.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pathway-disease.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| @@ -0,0 +1,1 @@ +Orphanet:183524 |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/pathway-diseases-overlap.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pathway-diseases-overlap.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| @@ -0,0 +1,1 @@ +Orphanet:183524,DOID:0080010 |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/pathways-for-disease.tsv --- a/test-data/pathways-for-disease.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/pathways-for-disease.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| b"@@ -1,99 +1,30 @@\n-KEGG-path:ko05010\tAlzheimer's disease\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko01100\tMetabolic pathways\tRO:0002331\tinvolved in\tOrphanet:2828\tYoung-onset Parkinson disease\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko04010\tMAPK signaling pathway\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-http://www.reactome.org/PathwayBrowser/#REACT_71\tGene Expression\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko04120\tUbiquitin mediated proteolysis\tRO:0002331\tinvolved in\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko04141\tProtein processing in endoplasmic reticulum\tRO:0002331\tinvolved in\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko05010\tAlzheimer's disease\tRO:0002331\tinvolved in\tOMIM:556500\tParkinson Disease, Mitochondrial\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko05010\tAlzheimer's disease\tRO:0002331\tinvolved in\tOMIM:168601\tautosomal dominant Parkinson disease 1\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko00591\tLinoleic acid metabolism\tRO:0002331\tinvolved in\tOMIM:612953\tParkinson Disease 14, Autosomal Recessive\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko00250\tAlanine, aspartate and glutamate metabolism\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-http://www.reactome.org/PathwayBrowser/#REACT_11123\tMembrane Trafficking\tRO:0002331\tinvolved in\tOMIM:615528\tParkinson Disease 19, Juvenile-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-http://www.reactome.org/PathwayBrowser/#REACT_17015\tMetabolism of proteins\tRO:0002331\tinvolved in\tOMIM:614251\tParkinson Disease 18, Autosomal Dominant, Susceptibility to\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko04964\tProximal tubule bicarbonate reclamation\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko00562\tInositol phosphate metabolism\tRO:0002331\tinvolved in\tOMIM:615530\tParkinson Disease 20, Early-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred"..b'903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:22558097\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map00983\tDrug metabolism - other enzymes\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:22558097\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map05120\tEpithelial cell signaling in Helicobacter pylori infection\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map05110\tVibrio cholerae infection\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map00190\tOxidative phosphorylation\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map04142\tLysosome\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map00500\tStarch and sucrose metabolism\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:22558097\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map04740\tOlfactory transduction\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:23406172\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map04145\tPhagosome\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+REACT:15518\tTransmembrane transport of small molecules\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map04144\tEndocytosis\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:25670933\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map01100\tMetabolic pathways\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213|ECO:0000213\tcombinatorial evidence used in automatic assertion|combinatorial evidence used in automatic assertion\tPMID:22558097|PMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map00980\tMetabolism of xenobiotics by cytochrome P450\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:22558097\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+REACT:71\tGene Expression\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:24058526\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n' |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/pathways-for-diseases-intersection.tsv --- a/test-data/pathways-for-diseases-intersection.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/pathways-for-diseases-intersection.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| b"@@ -1,26 +1,30 @@\n-KEGG-path:ko05010\tAlzheimer's disease\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko04010\tMAPK signaling pathway\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-http://www.reactome.org/PathwayBrowser/#REACT_71\tGene Expression\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko00250\tAlanine, aspartate and glutamate metabolism\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko04964\tProximal tubule bicarbonate reclamation\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko04142\tLysosome\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko05218\tMelanoma\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko00511\tOther glycan degradation\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko01100\tMetabolic pathways\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko05016\tHuntington's disease\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko00910\tNitrogen metabolism\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko00330\tArginine and proline metabolism\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-http://www.reactome.org/PathwayBrowser/#REACT_6900\tImmune System\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko03022\tBasal transcription factors\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko00471\tD-Glutamine and D-glutamate metabolism\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monar"..b'903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:22558097\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map00983\tDrug metabolism - other enzymes\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:22558097\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map05120\tEpithelial cell signaling in Helicobacter pylori infection\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map05110\tVibrio cholerae infection\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map00190\tOxidative phosphorylation\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map04142\tLysosome\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map00500\tStarch and sucrose metabolism\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:22558097\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map04740\tOlfactory transduction\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:23406172\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map04145\tPhagosome\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+REACT:15518\tTransmembrane transport of small molecules\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map04144\tEndocytosis\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:25670933\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map01100\tMetabolic pathways\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213|ECO:0000213\tcombinatorial evidence used in automatic assertion|combinatorial evidence used in automatic assertion\tPMID:22558097|PMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map00980\tMetabolism of xenobiotics by cytochrome P450\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:22558097\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+REACT:71\tGene Expression\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:24058526\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n' |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/pathways-for-diseases-union.tsv --- a/test-data/pathways-for-diseases-union.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/pathways-for-diseases-union.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| b"@@ -1,99 +1,30 @@\n-KEGG-path:ko05010\tAlzheimer's disease\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko01100\tMetabolic pathways\tRO:0002331\tinvolved in\tOrphanet:2828\tYoung-onset Parkinson disease\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko04010\tMAPK signaling pathway\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-http://www.reactome.org/PathwayBrowser/#REACT_71\tGene Expression\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko04120\tUbiquitin mediated proteolysis\tRO:0002331\tinvolved in\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko04141\tProtein processing in endoplasmic reticulum\tRO:0002331\tinvolved in\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko05010\tAlzheimer's disease\tRO:0002331\tinvolved in\tOMIM:556500\tParkinson Disease, Mitochondrial\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko05010\tAlzheimer's disease\tRO:0002331\tinvolved in\tOMIM:168601\tautosomal dominant Parkinson disease 1\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko00591\tLinoleic acid metabolism\tRO:0002331\tinvolved in\tOMIM:612953\tParkinson Disease 14, Autosomal Recessive\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko00250\tAlanine, aspartate and glutamate metabolism\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-http://www.reactome.org/PathwayBrowser/#REACT_11123\tMembrane Trafficking\tRO:0002331\tinvolved in\tOMIM:615528\tParkinson Disease 19, Juvenile-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-http://www.reactome.org/PathwayBrowser/#REACT_17015\tMetabolism of proteins\tRO:0002331\tinvolved in\tOMIM:614251\tParkinson Disease 18, Autosomal Dominant, Susceptibility to\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko04964\tProximal tubule bicarbonate reclamation\tRO:0002331\tinvolved in\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:ko00562\tInositol phosphate metabolism\tRO:0002331\tinvolved in\tOMIM:615530\tParkinson Disease 20, Early-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred"..b'903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:22558097\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map00983\tDrug metabolism - other enzymes\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:22558097\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map05120\tEpithelial cell signaling in Helicobacter pylori infection\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map05110\tVibrio cholerae infection\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map00190\tOxidative phosphorylation\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map04142\tLysosome\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map00500\tStarch and sucrose metabolism\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:22558097\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map04740\tOlfactory transduction\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:23406172\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map04145\tPhagosome\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+REACT:15518\tTransmembrane transport of small molecules\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map04144\tEndocytosis\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:25670933\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map01100\tMetabolic pathways\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213|ECO:0000213\tcombinatorial evidence used in automatic assertion|combinatorial evidence used in automatic assertion\tPMID:22558097|PMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map00980\tMetabolism of xenobiotics by cytochrome P450\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:22558097\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+REACT:71\tGene Expression\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213\tcombinatorial evidence used in automatic assertion\tPMID:24058526\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n' |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/pathways-for-gene.tsv --- a/test-data/pathways-for-gene.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/pathways-for-gene.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| @@ -1,5 +1,6 @@ -http://www.reactome.org/PathwayBrowser/#REACT_115566 Cell Cycle RO:0002331 involved in NCBIGene:675 breast cancer 2 http://data.monarchinitiative.org/ttl/ctd.ttl direct -http://www.reactome.org/PathwayBrowser/#REACT_216 DNA Repair RO:0002331 involved in NCBIGene:675 breast cancer 2 http://data.monarchinitiative.org/ttl/ctd.ttl direct -KEGG-path:ko05212 Pancreatic cancer RO:0002331 involved in NCBIGene:675 breast cancer 2 http://data.monarchinitiative.org/ttl/ctd.ttl direct -KEGG-path:ko05200 Pathways in cancer RO:0002331 involved in NCBIGene:675 breast cancer 2 http://data.monarchinitiative.org/ttl/ctd.ttl direct -KEGG-path:ko03440 Homologous recombination RO:0002331 involved in NCBIGene:675 breast cancer 2 http://data.monarchinitiative.org/ttl/ctd.ttl direct +KEGG-path:map05200 Pathways in cancer RO:0002331 involved in NCBIGene:675 BRCA2 http://data.monarchinitiative.org/ttl/ctd.ttl direct +KEGG-path:map05212 Pancreatic cancer RO:0002331 involved in NCBIGene:675 BRCA2 http://data.monarchinitiative.org/ttl/ctd.ttl direct +REACT:216 DNA Repair RO:0002331 involved in NCBIGene:675 BRCA2 http://data.monarchinitiative.org/ttl/ctd.ttl direct +REACT:200794 Mus musculus biological processes RO:0002331 involved in NCBIGene:675 BRCA2 http://data.monarchinitiative.org/ttl/ctd.ttl direct +KEGG-path:map03440 Homologous recombination RO:0002331 involved in NCBIGene:675 BRCA2 http://data.monarchinitiative.org/ttl/ctd.ttl direct +REACT:115566 Cell Cycle RO:0002331 involved in NCBIGene:675 BRCA2 http://data.monarchinitiative.org/ttl/ctd.ttl direct |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/pathways-for-genes-union.tsv --- a/test-data/pathways-for-genes-union.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/pathways-for-genes-union.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| @@ -1,8 +1,9 @@ -KEGG-path:ko05223 Non-small cell lung cancer RO:0002331 involved in NCBIGene:11186 RASSF1 http://data.monarchinitiative.org/ttl/ctd.ttl direct -http://www.reactome.org/PathwayBrowser/#REACT_115566 Cell Cycle RO:0002331 involved in NCBIGene:675 breast cancer 2 http://data.monarchinitiative.org/ttl/ctd.ttl direct -KEGG-path:ko05219 Bladder cancer RO:0002331 involved in NCBIGene:11186 RASSF1 http://data.monarchinitiative.org/ttl/ctd.ttl direct -http://www.reactome.org/PathwayBrowser/#REACT_216 DNA Repair RO:0002331 involved in NCBIGene:675 breast cancer 2 http://data.monarchinitiative.org/ttl/ctd.ttl direct -KEGG-path:ko05212 Pancreatic cancer RO:0002331 involved in NCBIGene:675 breast cancer 2 http://data.monarchinitiative.org/ttl/ctd.ttl direct -KEGG-path:ko05200 Pathways in cancer RO:0002331 involved in NCBIGene:11186 RASSF1 http://data.monarchinitiative.org/ttl/ctd.ttl direct -KEGG-path:ko05200 Pathways in cancer RO:0002331 involved in NCBIGene:675 breast cancer 2 http://data.monarchinitiative.org/ttl/ctd.ttl direct -KEGG-path:ko03440 Homologous recombination RO:0002331 involved in NCBIGene:675 breast cancer 2 http://data.monarchinitiative.org/ttl/ctd.ttl direct +KEGG-path:map05200 Pathways in cancer RO:0002331 involved in NCBIGene:675 BRCA2 http://data.monarchinitiative.org/ttl/ctd.ttl direct +KEGG-path:map05212 Pancreatic cancer RO:0002331 involved in NCBIGene:675 BRCA2 http://data.monarchinitiative.org/ttl/ctd.ttl direct +KEGG-path:map05223 Non-small cell lung cancer RO:0002331 involved in NCBIGene:11186 RASSF1 http://data.monarchinitiative.org/ttl/ctd.ttl direct +REACT:216 DNA Repair RO:0002331 involved in NCBIGene:675 BRCA2 http://data.monarchinitiative.org/ttl/ctd.ttl direct +REACT:200794 Mus musculus biological processes RO:0002331 involved in NCBIGene:675 BRCA2 http://data.monarchinitiative.org/ttl/ctd.ttl direct +KEGG-path:map03440 Homologous recombination RO:0002331 involved in NCBIGene:675 BRCA2 http://data.monarchinitiative.org/ttl/ctd.ttl direct +REACT:115566 Cell Cycle RO:0002331 involved in NCBIGene:675 BRCA2 http://data.monarchinitiative.org/ttl/ctd.ttl direct +KEGG-path:map05200 Pathways in cancer RO:0002331 involved in NCBIGene:11186 RASSF1 http://data.monarchinitiative.org/ttl/ctd.ttl direct +KEGG-path:map05219 Bladder cancer RO:0002331 involved in NCBIGene:11186 RASSF1 http://data.monarchinitiative.org/ttl/ctd.ttl direct |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/phenotypes-for-disease.tsv --- a/test-data/phenotypes-for-disease.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/phenotypes-for-disease.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| b"@@ -1,283 +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 "..b".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+OMIM:168600\tParkinson Disease, Late-Onset\tRO:0002200\thas phenotype\tHP:0000716\tDepression\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:606693\tParkinson disease 9\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:612953\tParkinson disease 14\tRO:0002200\thas phenotype\tHP:0001347\tHyperreflexia\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:0001336\tMyoclonus\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:2350935|PMID:1965204|PMID:12465085|PMID:2067442|PMID:18686651\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n" |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/phenotypes-for-diseases-intersection.tsv --- a/test-data/phenotypes-for-diseases-intersection.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/phenotypes-for-diseases-intersection.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| @@ -1,22 +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: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: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:0002067 Bradykinesia 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: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: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: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: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: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: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: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: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: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: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 +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: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:0000716 Depression ECO:0000501 evidence used in automatic assertion http://data.monarchinitiative.org/ttl/hpoa.ttl direct |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/phenotypes-for-diseases-union.tsv --- a/test-data/phenotypes-for-diseases-union.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/phenotypes-for-diseases-union.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| b"@@ -1,283 +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 "..b".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+OMIM:168600\tParkinson Disease, Late-Onset\tRO:0002200\thas phenotype\tHP:0000716\tDepression\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n+OMIM:606693\tParkinson disease 9\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:612953\tParkinson disease 14\tRO:0002200\thas phenotype\tHP:0001347\tHyperreflexia\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:0001336\tMyoclonus\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:2350935|PMID:1965204|PMID:12465085|PMID:2067442|PMID:18686651\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n" |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/variants-for-disease.tsv --- a/test-data/variants-for-disease.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/variants-for-disease.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| b'@@ -1,316 +1,117 @@\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'..b'condition\tOMIM:168601\tParkinson disease 1\t\t\tPMID:23526723\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\tGENO:0000840\tpathogenic_for_condition\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\tPMID:16769864|PMID:18685134\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:218942\tNM_005397.3(PODXL):c.89_90insGTCGCCCC (p.Gln32Profs)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000841\tlikely_pathogenic_for_condition\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\tPMID:26864383\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:7046\tNM_004562.2(PARK2):c.635G>A (p.Cys212Tyr)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\tPMID:12056932|PMID:11163284\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:189240\tNM_032409.2(PINK1):c.620delG (p.Arg207Glnfs)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:7047\tNM_004562.2(PARK2):c.167T>A (p.Val56Glu)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\tPMID:12056932\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:7048\tPARK2, 1-BP DEL, 255A\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\tPMID:10072423|PMID:12056932\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39183\tNM_198578.3(LRRK2):c.4309A>C (p.Asn1437His)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:30366\tNM_003560.2(PLA2G6):c.1904G>A (p.Arg635Gln)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:612953\tParkinson disease 14\t\t\tPMID:20938027\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:30367\tNM_003560.2(PLA2G6):c.1354C>T (p.Gln452Ter)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:612953\tParkinson disease 14\t\t\tPMID:20938027\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:2412\tNM_005216.4(DDOST):c.*807_*5409del\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\tPMID:15955953\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:60700\tNM_007262.4(PARK7):c.-24+75_-24+92dup\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:606324\tParkinson disease 7\t\t\tPMID:16240358\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:2410\tPINK1, 3-BP INS, 1602CAA\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\tPMID:15970950\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:2411\tNM_032409.2(PINK1):c.836G>A (p.Arg279His)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\tPMID:18704525|PMID:15970950\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:225276\tNM_198578.3(LRRK2):c.4321C>A (p.Arg1441Ser)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\tPMID:27111571\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39164\tNM_198578.3(LRRK2):c.3342A>G (p.Leu1114=)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n' |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/variants-for-diseases-intersection.tsv --- a/test-data/variants-for-diseases-intersection.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/variants-for-diseases-intersection.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| b'@@ -1,33 +1,12 @@\n-ClinVarVariant:8113\tNM_002973.3(ATXN2):c.496_498CAG(15_24) (p.Gln188_Pro189insGlnGln)\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:9726\tm.3397A>G\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:29936\tNM_012084.3(GLUD2):c.1492T>G (p.Ser498Ala)\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:4885\tFGF20, 951C/T\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:98243\tNM_016835.4(MAPT):c.1838_1840delATA (p.Asn613del)\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:4295\tNM_001005741.2(GBA):c.1504C>T (p.Arg502Cys)\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:7040\tNM_004562.2(PARK2):c.8-?_171+?del\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:56171\tNM_015268.3(DNAJC13):c.2564A>G (p.Asn855Ser)\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:6144\tNR_002717.2(ATXN8OS):n.1103_1105CTG(15_40)\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:7038\tNM_004562.2(PARK2):c.245C>A (p.Ala82Glu)\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:96731\tNM_198578.3(LRRK2):c.7300A>G (p.Ile2434Val)\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:3551\tNM_004993.5(ATXN3):c.892_894CAG(8_36) (p.Gln298_Gln305=)\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:96729\tNM_032409.2(PINK1):c.923T>A (p.Leu308Gln)\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:96730\tNM_198578.3(LRRK2):c.2352C>A (p.Ser784Arg)\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:7035\tNM_004562.2(PARK2):c.413-?_534+?del\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:96728\tNM_032409.2(PINK1):c.644C>T (p.Pro215Leu)\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:38301\tNM_001005741.2(GBA):c.1226A>C (p.Asn409Thr)\tNCBITaxon:9606\tHomo sapiens\t\t\tRO:0002200\thas phenotype\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/coriell.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-ClinVarVariant:96727\tNM_018206.4(VPS35):c.1576C>T (p.Arg526Cys)\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:4288\tNM_001005741.2(GBA)'..b'te-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/coriell.ttl\tinferred\n+ClinVarVariant:56171\tNM_015268.3(DNAJC13):c.2564A>G (p.Asn855Ser)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\tPMID:24218364\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+OMIM:602544.0011\tPARK2, ALA82GLU\t\t\t\t\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/coriell.ttl\tinferred\n+OMIM:602544.0005\tPARK2, EX3DEL\t\t\t\t\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/coriell.ttl\tinferred\n dbSNP:rs34637584\trs34637584-A\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:7679\tNR4A2, 1-BP DEL, -291T\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:7055\tPARK2, EX5-6 DEL\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:96726\tNM_007262.4(PARK7):c.399G>C (p.Met133Ile)\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:4335\tNM_001005741.2(GBA):c.1444G>A (p.Asp482Asn)\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:6078\tNM_005460.3(SNCAIP):c.1861C>T (p.Arg621Cys)\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:31151\tNG_031977.1:g.5321_5326GGGGCC(24_?)\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:7680\tNR4A2, -245T-G\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: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-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+OMIM:606463.0003\tGBA, ASN370SER\t\t\t\t\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/coriell.ttl\tinferred\n+OMIM:163890.0003\tSNCA, TRIPLICATION\t\t\t\t\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/coriell.ttl\tinferred\n+ClinVarVariant:9726\tm.3397A>G\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\tPMID:7624338\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:29936\tNM_012084.3(GLUD2):c.1492T>G (p.Ser498Ala)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\tPMID:19826450\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+OMIM:602544.0022\tPARK2, EX5-6 DEL\t\t\t\t\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/coriell.ttl\tinferred\n+OMIM:602544.0014\tPARK2, 1-BP DEL, 255A\t\t\t\t\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/coriell.ttl\tinferred\n+OMIM:602544.0017\tPARK2, ARG275TRP\t\t\t\t\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/coriell.ttl\tinferred\n+ClinVarVariant:225276\tNM_198578.3(LRRK2):c.4321C>A (p.Arg1441Ser)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\tPMID:27111571\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n' |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/variants-for-diseases-union.tsv --- a/test-data/variants-for-diseases-union.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/variants-for-diseases-union.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| b'@@ -1,316 +1,117 @@\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'..b'condition\tOMIM:168601\tParkinson disease 1\t\t\tPMID:23526723\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\tGENO:0000840\tpathogenic_for_condition\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\tPMID:16769864|PMID:18685134\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:218942\tNM_005397.3(PODXL):c.89_90insGTCGCCCC (p.Gln32Profs)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000841\tlikely_pathogenic_for_condition\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\tPMID:26864383\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:7046\tNM_004562.2(PARK2):c.635G>A (p.Cys212Tyr)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\tPMID:12056932|PMID:11163284\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:189240\tNM_032409.2(PINK1):c.620delG (p.Arg207Glnfs)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:7047\tNM_004562.2(PARK2):c.167T>A (p.Val56Glu)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\tPMID:12056932\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:7048\tPARK2, 1-BP DEL, 255A\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:600116\tParkinson Disease 2, Autosomal Recessive Juvenile\t\t\tPMID:10072423|PMID:12056932\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39183\tNM_198578.3(LRRK2):c.4309A>C (p.Asn1437His)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:30366\tNM_003560.2(PLA2G6):c.1904G>A (p.Arg635Gln)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:612953\tParkinson disease 14\t\t\tPMID:20938027\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:30367\tNM_003560.2(PLA2G6):c.1354C>T (p.Gln452Ter)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:612953\tParkinson disease 14\t\t\tPMID:20938027\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:2412\tNM_005216.4(DDOST):c.*807_*5409del\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\tPMID:15955953\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:60700\tNM_007262.4(PARK7):c.-24+75_-24+92dup\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:606324\tParkinson disease 7\t\t\tPMID:16240358\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:2410\tPINK1, 3-BP INS, 1602CAA\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\tPMID:15970950\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:2411\tNM_032409.2(PINK1):c.836G>A (p.Arg279His)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\tPMID:18704525|PMID:15970950\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:225276\tNM_198578.3(LRRK2):c.4321C>A (p.Arg1441Ser)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\tPMID:27111571\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:39164\tNM_198578.3(LRRK2):c.3342A>G (p.Leu1114=)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:607060\tautosomal dominant Parkinson disease 8\t\t\t\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n' |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/variants-for-phenotype.tsv --- a/test-data/variants-for-phenotype.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/variants-for-phenotype.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| b'@@ -1,184 +1,65 @@\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.48'..b'ITaxon: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+ClinVarVariant:9272\tNM_000161.2(GCH1):c.401A>T (p.Asp134Val)\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\tPMID:7874165\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:9862\tTAF1, SVA RETROTRANSPOSON INSERTION\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\tPMID:17273961\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:1936\tNM_198578.3(LRRK2):c.4321C>G (p.Arg1441Gly)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000501\tevidence used in automatic assertion\tPMID:16533964|PMID:15541308|PMID:19020907|PMID:16003110|PMID:19308469\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:39164\tNM_198578.3(LRRK2):c.3342A>G (p.Leu1114=)\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' |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/variants-for-phenotypes-intersection.tsv --- a/test-data/variants-for-phenotypes-intersection.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/variants-for-phenotypes-intersection.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| b'@@ -1,329 +1,351 @@\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:35'..b'3\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tMGI:5000289|PMID:20562862\thttp://data.monarchinitiative.org/ttl/mgi.ttl|http://data.monarchinitiative.org/ttl/mmrrc.ttl\tdirect\n+MGI:3844445\tTg(Thy1-Nlgn2)6Hnes\tNCBITaxon:10090\tMus musculus\t\t\tRO:0002200\thas phenotype\tMP:0001363\tincreased anxiety-related response\tECO:0000006|ECO:0000059\texperimental evidence|experimental phenotypic evidence\tPMID:18550748|PMID:18550748\thttp://data.monarchinitiative.org/ttl/mgi.ttl|http://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:3510602\tTg(Thy1-APP<SL>)28Lpr\tNCBITaxon:10090\tMus musculus\tNCBIGene:351\tAPP\tRO:0002200\thas phenotype\tMP:0001363\tincreased anxiety-related response\tECO:0000006|ECO:0000059\texperimental evidence|experimental phenotypic evidence\tPMID:18184372|PMID:18184372\thttp://data.monarchinitiative.org/ttl/mgi.ttl|http://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:5644306\tBaiap3<tm1Smwk>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:23698091\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:5297824\tLrrc7<tm1.1Mabk>\t\t\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:22072671\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:2178542\tComt<tm1Kara>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:9707588\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1933974\tNtrk2<tm2Kln>\t\t\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006|ECO:0000006\texperimental evidence|experimental evidence\tPMID:18832146|PMID:10571233\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:4438929\tTg(ACTB-Eif4e)#Ppp\tNCBITaxon:10090\tMus musculus\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:26306459\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1861234\tWt\tNCBITaxon:10090\tMus musculus\tMGI:1861234\tWt\tRO:0002200\thas phenotype\tMP:0001363\tincreased anxiety-related response\tECO:0000006|ECO:0000059\texperimental evidence|experimental phenotypic evidence\tPMID:13834122|PMID:13834122\thttp://data.monarchinitiative.org/ttl/mgi.ttl|http://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:3579440\tGabrg2<tm2Geh>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:15850489\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:2386761\tEsr2<tm1Mma>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:11593044\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:4461457\tTg(RP23-326M22)760She\tNCBITaxon:10090\tMus musculus\t\t\tRO:0002200\thas phenotype\tMP:0001363\tincreased anxiety-related response\tECO:0000006|ECO:0000059|ECO:0000006\texperimental evidence|experimental phenotypic evidence|experimental evidence\tPMID:18285828|PMID:18285828|PMID:18285828|PMID:18285828\thttp://data.monarchinitiative.org/ttl/mgi.ttl|http://data.monarchinitiative.org/ttl/mmrrc.ttl|http://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:3604604\tLrp5<tm1Dgen>\t\t\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tMGI:3604450\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:3829789\tTg(YAC18)18Hay\tNCBITaxon:10090\tMus musculus\tNCBIGene:3064\tHTT\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:23001568\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:3057337\tMaoa<K284stop>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:15272015\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:2388020\tPenk<tm1Dwp>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:11172058\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1857158\tDrd1<tm1Jcd>\t\t\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006|ECO:0000006\texperimental evidence|experimental evidence\tPMID:10884517|PMID:10884517\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n' |
| b |
| diff -r 307ec8cd152e -r 61d8060bf2ed test-data/variants-for-phenotypes-union.tsv --- a/test-data/variants-for-phenotypes-union.tsv Wed Jun 29 14:17:39 2016 -0400 +++ b/test-data/variants-for-phenotypes-union.tsv Mon Aug 22 12:41:24 2016 -0400 |
| b |
| b'@@ -1,3347 +1,2075 @@\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.monar'..b'clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:209174\tNM_002501.3(NFIX):c.338_342dupAGATC (p.Arg116Serfs)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000739\tAnxiety\tECO:0000304\ttraceable author statement used in manual assertion\tPMID:26633545\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:56259\tNM_001042432.1(CLN3):c.222+2T>G\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000739\tAnxiety\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:13918\tNM_020630.4(RET):c.1902C>G (p.Cys634Trp)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:17898100|PMID:1576030|PMID:19569019|PMID:17474956|PMID:12000816|PMID:14605591|PMID:7907913|PMID:6829807\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:10217\tNM_000132.3(F8):c.1492G>A (p.Gly498Arg)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:7728145|PMID:6438527|PMID:2378544|PMID:8490618|PMID:15357786|PMID:17498080|PMID:9302853|PMID:10734657\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:53379\tNM_000492.3(CFTR):c.1766+3A>G\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:12796866|PMID:20495477|PMID:7866213|PMID:23974870|PMID:10361400|PMID:20171652\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:5287\tPDE11A, 1-BP DEL, 171T\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000739\tAnxiety\tECO:0000501\tevidence used in automatic assertion\tPMID:16767104\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+dbSNP:rs67072384\trs67072384-T\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246|ECO:0000213\tcomputational combinatorial evidence used in automatic assertion|combinatorial evidence used in automatic assertion\tPMID:17938043|PMID:25670933|PMID:21425450|PMID:21099065|PMID:3375880|PMID:9491171\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:10247\tNM_000132.3(F8):c.2215G>A (p.Glu739Lys)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:2378544|PMID:7728145|PMID:15357786|PMID:17498080|PMID:9302853|PMID:10734657\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:10257\tF8, 1-BP INS, A, CODON 1414\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:2378544|PMID:15357786|PMID:17498080|PMID:9302853|PMID:10734657|PMID:1908096\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:3893\tNM_000520.5(HEXA):c.346+1G>C\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:8355954|PMID:20597919|PMID:16301864|PMID:1833974|PMID:696935|PMID:2739956\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+MGI:1857158\tDrd1<tm1Jcd>\t\t\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006|ECO:0000006\texperimental evidence|experimental evidence\tPMID:10884517|PMID:10884517\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n' |