| Previous changeset 8:15016fee2bc4 (2016-08-22) |
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Commit message:
planemo upload commit f59eaefa6c10f425809c7cb6d2e3df6164fa3a15 |
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modified:
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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| diff -r 15016fee2bc4 -r 5fa1f0ca69cc test-data/genes-for-2-diseases-intersection.tsv --- a/test-data/genes-for-2-diseases-intersection.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/genes-for-2-diseases-intersection.tsv Sun Sep 25 21:59:32 2016 -0400 |
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| @@ -1,18 +1,18 @@ -NCBIGene:126 ADH1C NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset ECO:0000220 sequencing assay evidence http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred -NCBIGene:2747 GLUD2 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset PMID:19826450 http://data.monarchinitiative.org/ttl/clinvar.ttl inferred -NCBIGene:5071 PARK2 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/coriell.ttl inferred -NCBIGene:7345 UCHL1 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/ctd.ttl inferred -NCBIGene:4929 NR4A2 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred -NCBIGene:1621 DBH NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/ctd.ttl inferred -NCBIGene:4729 NDUFV2 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/ctd.ttl inferred -NCBIGene:26281 FGF20 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/ctd.ttl inferred -NCBIGene:6311 ATXN2 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset ECO:0000220 sequencing assay evidence http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl inferred -NCBIGene:9627 SNCAIP NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred -NCBIGene:120892 LRRK2 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset PMID:27111571 http://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 inferred -NCBIGene:6622 SNCA NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/coriell.ttl inferred -NCBIGene:6908 TBP NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset ECO:0000220 sequencing assay evidence http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred -NCBIGene:4137 MAPT NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset ECO:0000220 sequencing assay evidence http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred -NCBIGene:2629 GBA NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset ECO:0000220 sequencing assay evidence http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/coriell.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl inferred NCBIGene:23317 DNAJC13 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset PMID:24218364 http://data.monarchinitiative.org/ttl/clinvar.ttl inferred NCBIGene:4535 ND1 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset PMID:7624338 http://data.monarchinitiative.org/ttl/clinvar.ttl inferred NCBIGene:1815 DRD4 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/ctd.ttl inferred +NCBIGene:120892 LRRK2 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset PMID:27111571 http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/coriell.ttl inferred +NCBIGene:9627 SNCAIP NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred +NCBIGene:4137 MAPT NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset ECO:0000220 sequencing assay evidence http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred +NCBIGene:2629 GBA NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset ECO:0000220 sequencing assay evidence http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/coriell.ttl inferred +NCBIGene:5071 PARK2 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/coriell.ttl inferred +NCBIGene:26281 FGF20 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/ctd.ttl inferred +NCBIGene:6311 ATXN2 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset ECO:0000220 sequencing assay evidence http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl inferred +NCBIGene:4729 NDUFV2 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/ctd.ttl inferred +NCBIGene:1621 DBH NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/ctd.ttl inferred +NCBIGene:4929 NR4A2 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred +NCBIGene:7345 UCHL1 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/ctd.ttl inferred +NCBIGene:6908 TBP NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset ECO:0000220 sequencing assay evidence http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred +NCBIGene:126 ADH1C NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset ECO:0000220 sequencing assay evidence http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl inferred +NCBIGene:2747 GLUD2 NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset ECO:0000220 sequencing assay evidence PMID:19826450 http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/kegg.ttl inferred +NCBIGene:6622 SNCA NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/coriell.ttl inferred |
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| diff -r 15016fee2bc4 -r 5fa1f0ca69cc test-data/genes-for-2-diseases-union.tsv --- a/test-data/genes-for-2-diseases-union.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/genes-for-2-diseases-union.tsv Sun Sep 25 21:59:32 2016 -0400 |
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| b"@@ -1,121 +1,126 @@\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/ttl/ctd.ttl\tinferred\n-NCBIGene:120892\tLRRK2\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19915575|PMID:20205471|PMID:25149416|PMID:23628791|PM"..b"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+NCBIGene:9829\tDNAJC6\tNCBITaxon:9606\tHomo sapiens\t\t\tUMLS:CN202824\tYoung-onset Parkinson disease\tECO:0000322\timported manually asserted information used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl\tinferred\n+NCBIGene:116442\tRAB39B\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:311510\tParkinsonism, early onset with mental retardation\tECO:0000322|ECO:0000220\timported manually asserted information used in automatic assertion|sequencing assay evidence\tPMID:25434005|PMID:4025396\thttp://data.monarchinitiative.org/ttl/orphanet.ttl|http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:6622\tSNCA\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168601\tParkinson disease 1\tECO:0000220\tsequencing assay evidence\tPMID:14593171|PMID:20437567|PMID:18852445|PMID:18195271|PMID:11376188|PMID:15451225|PMID:17251522|PMID:18852448|PMID:24936070|PMID:19632874|PMID:23427326|PMID:24158909|PMID:18852449|PMID:17489854|PMID:15451224|PMID:9499430|PMID:11261505|PMID:9506559|PMID:10417297|PMID:17625105|PMID:16358335|PMID:20340137|PMID:9197268|PMID:14755720|PMID:9462735|PMID:9827625|PMID:24158904|PMID:23526723|PMID:18704525\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|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+FlyBase:FBgn0015623\tCpr\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+FlyBase:FBgn0001218\tHsc70-3\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+MGI:1857323\tUp\tNCBITaxon:10090\tMus musculus\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:6622\tSNCA\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:24833599|PMID:12732244|PMID:22166454|PMID:15099020|PMID:17690948|PMID:25064009|PMID:22043175|PMID:18353766|PMID:22185909|PMID:20664293|PMID:22110584|PMID:14535945|PMID:25631236|PMID:21245015|PMID:17131421|PMID:12885775|PMID:25149416|PMID:18841091|PMID:21892157|PMID:19915576|PMID:25106480|PMID:19915575|PMID:12151787|PMID:11535288|PMID:22355530|PMID:20711177|PMID:18322262\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:102464833\tMIR6084\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:21366594|PMID:24374061|PMID:25149416|PMID:22043175|PMID:17010972\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n" |
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| diff -r 15016fee2bc4 -r 5fa1f0ca69cc test-data/genes-for-2-diseases.tsv --- a/test-data/genes-for-2-diseases.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/genes-for-2-diseases.tsv Sun Sep 25 21:59:32 2016 -0400 |
| b |
| b"@@ -1,127 +1,132 @@\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: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 "..b":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+NCBIGene:27235\tCOQ2\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:607426\tCoenzyme Q10 Deficiency, Primary, 1\tECO:0000220\tsequencing assay evidence\tPMID:17855635|PMID:17332895|PMID:16400613|PMID:17374725|PMID:17855635|PMID:16116126|PMID:20495179|PMID:17855635|PMID:16400613\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:9829\tDNAJC6\tNCBITaxon:9606\tHomo sapiens\t\t\tUMLS:CN202824\tYoung-onset Parkinson disease\tECO:0000322\timported manually asserted information used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl\tinferred\n+NCBIGene:116442\tRAB39B\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:311510\tParkinsonism, early onset with mental retardation\tECO:0000322|ECO:0000220\timported manually asserted information used in automatic assertion|sequencing assay evidence\tPMID:25434005|PMID:4025396\thttp://data.monarchinitiative.org/ttl/orphanet.ttl|http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:6622\tSNCA\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168601\tParkinson disease 1\tECO:0000220\tsequencing assay evidence\tPMID:14593171|PMID:20437567|PMID:18852445|PMID:18195271|PMID:11376188|PMID:15451225|PMID:17251522|PMID:18852448|PMID:24936070|PMID:19632874|PMID:23427326|PMID:24158909|PMID:18852449|PMID:17489854|PMID:15451224|PMID:9499430|PMID:11261505|PMID:9506559|PMID:10417297|PMID:17625105|PMID:16358335|PMID:20340137|PMID:9197268|PMID:14755720|PMID:9462735|PMID:9827625|PMID:24158904|PMID:23526723|PMID:18704525\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|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+FlyBase:FBgn0015623\tCpr\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+FlyBase:FBgn0001218\tHsc70-3\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+MGI:1857323\tUp\tNCBITaxon:10090\tMus musculus\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:6622\tSNCA\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:24833599|PMID:12732244|PMID:22166454|PMID:15099020|PMID:17690948|PMID:25064009|PMID:22043175|PMID:18353766|PMID:22185909|PMID:20664293|PMID:22110584|PMID:14535945|PMID:25631236|PMID:21245015|PMID:17131421|PMID:12885775|PMID:25149416|PMID:18841091|PMID:21892157|PMID:19915576|PMID:25106480|PMID:19915575|PMID:12151787|PMID:11535288|PMID:22355530|PMID:20711177|PMID:18322262\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:102464833\tMIR6084\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:21366594|PMID:24374061|PMID:25149416|PMID:22043175|PMID:17010972\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n" |
| b |
| diff -r 15016fee2bc4 -r 5fa1f0ca69cc test-data/genes-for-2-phenotypes-intersection.tsv --- a/test-data/genes-for-2-phenotypes-intersection.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/genes-for-2-phenotypes-intersection.tsv Sun Sep 25 21:59:32 2016 -0400 |
| b |
| b'@@ -1,206 +1,207 @@\n-MGI:99402\tAdora2a\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:9262401\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-MGI:2682328\tAtmin\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:20889973\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-MGI:108067\tNkx2-1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:17182767\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-MGI:105089\tHsd17b4\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:23777740\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-MGI:1329003\tGalr3\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:24782539\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-MGI:1351641\tNaglu\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:10588735\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-MGI:88495\tCrem\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:18562617\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-MGI:109483\tRnf103\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:18958194\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-MGI:104629\tPenk\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:11172058\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-MGI:1918639\tChd6\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000059\texperimental phenotypic evidence\tPMID:20111866\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-MGI:98331\tSnap25\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:19043548|PMID:21949876\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-MGI:2447658\tDisc1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000059\texperimental phenotypic evidence\tPMID:26728762\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-MGI:108471\tNtan1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:10805755\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-MGI:104615\tCnr1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:12405999|PMID:23785142|PMID:11823890|PMID:15078564\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-MGI:1932872\tCtns\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:12370309\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-MGI:109583\tPten\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000059\texperimental phenotypic evidence\tPMID:16675393\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-MGI:88497\tCrhbp\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000059\texperimental phenotypic evidence\tPMID:10500222\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-MGI:98824\tTrhr\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:17666589\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-MGI:94862\tSlc6a3\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000059\texperimental phenotypic evidence\tPMID:12617953\thttp://data.monarc'..b'\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:23268962\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:3584508\tKcnh5\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000059\texperimental phenotypic evidence\t\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:95819\tGrin1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:19915563\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:108058\tAdm\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:18723674\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:2449712\tFev\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:20818386|PMID:12546819\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:108471\tNtan1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:10805755\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:104615\tCnr1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:12405999|PMID:11823890|PMID:15078564|PMID:23785142\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:1932872\tCtns\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:12370309\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:1919835\tLypd1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:19246390\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:2671987\tShank2\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:22699619|PMID:22699620\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:2447658\tDisc1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000059\texperimental phenotypic evidence\tPMID:26728762\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:1355296\tPark2\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000059\texperimental phenotypic evidence\tPMID:17883413\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:1929864\tMyg1\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000059\texperimental phenotypic evidence\tPMID:19818808\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:99926\tmt-Atp8\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:19037013\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:1351345\tGrm8\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:16045496\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:95809\tGria2\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:16099814|PMID:16216087\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+NCBIGene:497068\tCLN6\tNCBITaxon:9615\tCanis lupus familiaris\t\t\tMP:0001363\tincreased anxiety-related response\t\t\tPMID:21234413\thttp://data.monarchinitiative.org/ttl/monarch.ttl|http://data.monarchinitiative.org/ttl/omia.ttl\tinferred\n+MGI:1342774\tPpargc1a\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000059\texperimental phenotypic evidence\tPMID:15760270\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:1101358\tNpepps\tNCBITaxon:10090\tMus musculus\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000059\texperimental phenotypic evidence\tPMID:10407043\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n' |
| b |
| diff -r 15016fee2bc4 -r 5fa1f0ca69cc test-data/genes-for-2-phenotypes-union.tsv --- a/test-data/genes-for-2-phenotypes-union.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/genes-for-2-phenotypes-union.tsv Sun Sep 25 21:59:32 2016 -0400 |
| b |
| b'@@ -1,591 +1,607 @@\n-MGI:95459\tZfp521\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001364\tdecreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:24676388\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-NCBIGene:3145\tHMBS\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0000739\tAnxiety\tECO:0000322|ECO:0000501|ECO:0000220\timported manually asserted information used in automatic assertion|evidence used in automatic assertion|sequencing assay evidence\tPMID:8270256|PMID:15534187|PMID:8270254|PMID:8270254|PMID:8270254|PMID:1714233|PMID:1714233|PMID:8401516|PMID:8262514|PMID:8270254|PMID:8270254|PMID:1496994|PMID:1301948|PMID:2243128|PMID:8096492|PMID:2227955|PMID:14970743|PMID:9225970|PMID:2025226|PMID:9225970|PMID:9225970|PMID:8096492|PMID:8262523|PMID:12566739|PMID:1577472|PMID:2864531|PMID:10494093|PMID:1427766|PMID:7962538|PMID:10408772|PMID:8270254|PMID:17298217|PMID:8270254|PMID:2243128|PMID:1577472|PMID:2243128|PMID:8270254|PMID:8270254|PMID:1714233|PMID:8270254|PMID:2789372|PMID:1714233|PMID:1961762|PMID:8270256|PMID:8262523|PMID:7757070|PMID:1301948|PMID:1427766|PMID:8270254|PMID:8262523|PMID:8262523|PMID:8262523\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/coriell.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-NCBIGene:55869\tHDAC8\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246|ECO:0000322\tcomputational combinatorial evidence used in automatic assertion|imported manually asserted information used in automatic assertion\tPMID:19330433|PMID:17845236|PMID:18430761|PMID:19309268|PMID:17640042\thttp://data.monarchinitiative.org/ttl/orphanet.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-MGI:99402\tAdora2a\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:9262401\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-NCBIGene:6390\tSDHB\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000220|ECO:0000501|ECO:0000220|ECO:0000246\tsequencing assay evidence|evidence used in automatic assertion|sequencing assay evidence|computational combinatorial evidence used in automatic assertion\tPMID:19389109|PMID:12000816|PMID:18057081|PMID:14685938|PMID:20503330|PMID:16405730|PMID:11404820|PMID:14715873|PMID:12000816|PMID:12213855|PMID:14685938|PMID:16317055|PMID:16258955|PMID:24523625|PMID:21348866|PMID:15531530|PMID:11404820|PMID:490809|PMID:12000816|PMID:16405730|PMID:12000816|PMID:17474956|PMID:14685938|PMID:24523625|PMID:12000816|PMID:11404820|PMID:18419787|PMID:12000816|PMID:14605591|PMID:16405730|PMID:1576030|PMID:18057081|PMID:6829807|PMID:12000816|PMID:9509062|PMID:19569019|PMID:14685938|PMID:21173220|PMID:12213855|PMID:21173220|PMID:12000816|PMID:11404820\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-NCBIGene:9568\tGABBR2\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246|ECO:0000220\tcomputational combinatorial evidence used in automatic assertion|sequencing assay evidence\tPMID:15289208|PMID:7559318|PMID:2209418|PMID:20639284|PMID:1845224\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-MGI:106677\tSlc18a2\tNCBITaxon:10090\tMus musculus\t\t\tMP:0001364\tdecreased anxiety-related response\tECO:0000059\texperimental phenotypic evidence\tPMID:21814181\thttp://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-NCBIGene:5506\tPPP1R3A\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:'..b'D:18493213|PMID:1349576|PMID:24368688|PMID:16879198|PMID:23430918|PMID:9634518|PMID:23430918|PMID:23500595|PMID:9634518|PMID:2574153|PMID:15503242|PMID:23932990|PMID:3093157|PMID:19609714|PMID:15171997|PMID:8406445|PMID:2884570|PMID:21147011|PMID:24350308|PMID:23430547|PMID:9950317|PMID:2606484|PMID:24350308|PMID:8889590|PMID:8533759|PMID:24048906|PMID:23792259|PMID:9391881|PMID:9634518|PMID:23500595|PMID:8268925|PMID:8098245|PMID:1639423|PMID:23430918|PMID:8533759|PMID:2574002|PMID:8981952|PMID:23932990|PMID:22698810|PMID:22841515|PMID:24350308|PMID:8304187|PMID:1671881|PMID:1998345|PMID:21462123|PMID:8990021|PMID:18590700|PMID:2574153|PMID:1358789|PMID:19099685|PMID:1671810|PMID:23430918|PMID:7668259|PMID:20140859|PMID:8268925|PMID:24350308|PMID:17630668|PMID:2309142|PMID:16256386|PMID:1301942|PMID:23500595|PMID:1975096|PMID:12640344|PMID:23074961|PMID:8659548|PMID:9781015|PMID:17935162|PMID:11461196|PMID:15464430|PMID:8535445|PMID:11326337|PMID:8831077|PMID:24350308|PMID:9521426|PMID:23357515|PMID:9642259|PMID:10693064|PMID:24350308|PMID:23074961|PMID:8051931|PMID:23357515|PMID:8889590|PMID:24510552|PMID:11385716|PMID:11524738|PMID:12655550|PMID:8116675|PMID:1312992|PMID:23430918|PMID:22526846|PMID:17924342|PMID:8535445|PMID:17096675|PMID:17924342|PMID:23357515|PMID:3615198|PMID:19609714|PMID:24350308|PMID:12655553|PMID:23430918|PMID:2063869|PMID:18294361|PMID:12655553|PMID:16256386|PMID:1301193|PMID:10693064|PMID:21307867|PMID:23430547|PMID:2564729|PMID:8632937|PMID:1682495|PMID:10394930|PMID:12501224|PMID:19147918|PMID:18346471|PMID:19394257|PMID:21147011|PMID:8487271|PMID:10471838|PMID:8406445|PMID:22513348|PMID:9298832|PMID:23792259|PMID:12649065|PMID:23792259|PMID:1355066|PMID:23500595|PMID:9452062|PMID:20140859|PMID:18247293|PMID:11678552|PMID:17924342|PMID:23430918|PMID:17096675|PMID:21871829|PMID:20920871|PMID:1769645|PMID:1363837|PMID:9429153|PMID:1355066|PMID:1301947|PMID:22526846|PMID:2006152|PMID:15503242|PMID:24350308|PMID:1975559|PMID:24301756|PMID:9781015|PMID:1363838|PMID:23357515|PMID:9298832|PMID:17924342|PMID:1997387|PMID:17935162|PMID:21953985|PMID:16198137|PMID:10693064|PMID:2014036|PMID:22513348|PMID:12501224|PMID:8097423|PMID:23074961|PMID:8533759|PMID:9949232|PMID:22526846|PMID:24368688|PMID:1769645|PMID:24401910|PMID:22112818|PMID:23500595|PMID:2840952|PMID:24350308|PMID:17935162|PMID:23764561|PMID:2035532|PMID:9634518|PMID:23932990|PMID:23932990|PMID:20920871|PMID:19147918|PMID:19609714|PMID:9391881|PMID:12655553|PMID:8406445|PMID:17096675|PMID:17513426|PMID:18538294|PMID:19062537|PMID:2574153|PMID:22333022|PMID:23856132|PMID:9012412|PMID:10394930|PMID:7807961|PMID:17935162|PMID:10679941|PMID:24368688|PMID:11678552|PMID:11385716|PMID:17096675|PMID:2014802|PMID:16256386|PMID:2063869|PMID:10479481|PMID:15633889|PMID:23932990|PMID:12655546|PMID:8098245|PMID:9284280|PMID:19292873|PMID:12655553|PMID:17935162|PMID:3008810|PMID:18299955|PMID:21307867|PMID:23430547|PMID:10394930|PMID:18294361|PMID:21462123|PMID:24350308|PMID:19147918|PMID:18294361|PMID:8370573|PMID:22763404|PMID:1601425|PMID:17096675|PMID:16143554|PMID:12655550|PMID:7913581|PMID:2574153|PMID:8831077|PMID:18798839|PMID:12905706|PMID:21147011|PMID:10394930|PMID:2564729|PMID:19292873|PMID:23430918|PMID:17096675|PMID:21147011|PMID:24401910|PMID:1769645|PMID:9450182|PMID:20187763|PMID:11696894|PMID:9634518|PMID:24350308|PMID:16256386|PMID:1563085|PMID:1671810|PMID:12655553|PMID:18294361\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+NCBIGene:5063\tPAK3\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0000739\tAnxiety\tECO:0000220|ECO:0000269\tsequencing assay evidence|experimental evidence used in manual assertion\tPMID:17853471|PMID:8826460|PMID:10946356|PMID:9332663|PMID:18523455|PMID:12884430|PMID:9731525\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 15016fee2bc4 -r 5fa1f0ca69cc test-data/genes-for-diseases.tsv --- a/test-data/genes-for-diseases.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/genes-for-diseases.tsv Sun Sep 25 21:59:32 2016 -0400 |
| b |
| b"@@ -1,121 +1,126 @@\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/ttl/ctd.ttl\tinferred\n-NCBIGene:120892\tLRRK2\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:19915575|PMID:20205471|PMID:25149416|PMID:23628791|PM"..b"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+NCBIGene:9829\tDNAJC6\tNCBITaxon:9606\tHomo sapiens\t\t\tUMLS:CN202824\tYoung-onset Parkinson disease\tECO:0000322\timported manually asserted information used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl\tinferred\n+NCBIGene:116442\tRAB39B\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:311510\tParkinsonism, early onset with mental retardation\tECO:0000322|ECO:0000220\timported manually asserted information used in automatic assertion|sequencing assay evidence\tPMID:25434005|PMID:4025396\thttp://data.monarchinitiative.org/ttl/orphanet.ttl|http://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl\tinferred\n+NCBIGene:6622\tSNCA\tNCBITaxon:9606\tHomo sapiens\t\t\tOMIM:168601\tParkinson disease 1\tECO:0000220\tsequencing assay evidence\tPMID:14593171|PMID:20437567|PMID:18852445|PMID:18195271|PMID:11376188|PMID:15451225|PMID:17251522|PMID:18852448|PMID:24936070|PMID:19632874|PMID:23427326|PMID:24158909|PMID:18852449|PMID:17489854|PMID:15451224|PMID:9499430|PMID:11261505|PMID:9506559|PMID:10417297|PMID:17625105|PMID:16358335|PMID:20340137|PMID:9197268|PMID:14755720|PMID:9462735|PMID:9827625|PMID:24158904|PMID:23526723|PMID:18704525\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|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+FlyBase:FBgn0015623\tCpr\tNCBITaxon:7227\tDrosophila melanogaster\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+FlyBase:FBgn0001218\tHsc70-3\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+MGI:1857323\tUp\tNCBITaxon:10090\tMus musculus\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:18353766\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:6622\tSNCA\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:24833599|PMID:12732244|PMID:22166454|PMID:15099020|PMID:17690948|PMID:25064009|PMID:22043175|PMID:18353766|PMID:22185909|PMID:20664293|PMID:22110584|PMID:14535945|PMID:25631236|PMID:21245015|PMID:17131421|PMID:12885775|PMID:25149416|PMID:18841091|PMID:21892157|PMID:19915576|PMID:25106480|PMID:19915575|PMID:12151787|PMID:11535288|PMID:22355530|PMID:20711177|PMID:18322262\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+NCBIGene:102464833\tMIR6084\tNCBITaxon:9606\tHomo sapiens\t\t\tDOID:14330\tParkinson's disease\tECO:0000033\ttraceable author statement\tPMID:21366594|PMID:24374061|PMID:25149416|PMID:22043175|PMID:17010972\thttp://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n" |
| b |
| diff -r 15016fee2bc4 -r 5fa1f0ca69cc test-data/genes-for-phenotype.tsv --- a/test-data/genes-for-phenotype.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/genes-for-phenotype.tsv Sun Sep 25 21:59:32 2016 -0400 |
| b |
| b'@@ -1,10 +1,14 @@\n-NCBIGene:6872\tTAF1\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\tPMID:17273961\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:0000269|ECO:0000220\texperimental evidence used in manual assertion|sequencing assay evidence\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:7054\tTH\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000304|ECO:0000322|ECO:0000220\ttraceable author statement used in manual assertion|imported manually asserted information used in automatic assertion|sequencing assay evidence\tPMID:20198643|PMID:10407773|PMID:11281275|PMID:11246459|PMID:7814018|PMID:8817341|PMID:11246459|PMID:11246459|PMID:11246459|PMID:9235905|PMID:9732974|PMID:17696123|PMID:9732974|PMID:24753243|PMID:10407773|PMID:9703425|PMID:10407773|PMID:8528210|PMID:10585338|PMID:10407773|PMID:20430833\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: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/hpoa.ttl\tinferred\n+NCBIGene:120892\tLRRK2\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:17215492|PMID:16401756|PMID:23075850|PMID:19283415|PMID:17353388|PMID:17050822|PMID:19020907|PMID:20008657|PMID:18591067|PMID:16172858|PMID:18981379|PMID:15541309|PMID:16436782|PMID:16269541|PMID:9276200|PMID:15680457|PMID:17060595|PMID:19308469|PMID:15726496|PMID:16960813|PMID:15541309|PMID:16966502|PMID:19667187|PMID:15880653|PMID:15852371|PMID:16436781|PMID:16269541|PMID:16533964|PMID:15811455|PMID:16321986|PMID:15541308|PMID:18704525|PMID:16157909|PMID:16533964|PMID:15680456|PMID:16003110|PMID:15541308|PMID:15541309|PMID:15541309|PMID:19020907|PMID:15929036|PMID:17060595|PMID:21115957|PMID:16240353|PMID:16728648|PMID:16003110|PMID:7898705|PMID:16311269|PMID:15680455|PMID:16145815|PMID:17938369|PMID:15732108\thttp://data.monarchinitiative.org/ttl/omim.ttl|http://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+NCBIGene:291\tSLC25A4\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000322|ECO:0000501\timported manually asserted information used in automatic assertion|evidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+NCBIGene:56652\tPEO1\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000322|ECO:0000501\timported manually asserted information used in automatic assertion|evidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/orphanet.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:0000304|ECO:0000322|ECO:0000220|ECO:0000220\ttraceable author statement used in manual assertion|imported manually a'..b'c 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+NCBIGene:6872\tTAF1\tNCBITaxon:9606\tHomo sapiens\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000322|ECO:0000220|ECO:0000304\timported manually asserted information used in automatic assertion|sequencing assay evidence|traceable author statement used in manual assertion\tPMID:17273961\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' |
| b |
| diff -r 15016fee2bc4 -r 5fa1f0ca69cc test-data/homologues-for-gene.tsv --- a/test-data/homologues-for-gene.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/homologues-for-gene.tsv Sun Sep 25 21:59:32 2016 -0400 |
| b |
| @@ -1,30 +1,27 @@ +NCBIGene:716360 CAPN10 NCBITaxon:9544 Macaca mulatta RO:HOM0000020 in 1 to 1 orthology relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct NCBIGene:25801 GCA NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:10016 PDCD6 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct NCBIGene:388743 CAPN8 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct -NCBIGene:10016 PDCD6 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct -NCBIGene:716360 CAPN10 NCBITaxon:9544 Macaca mulatta RO:HOM0000020 in 1 to 1 orthology relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct NCBIGene:841981 DEK1 NCBITaxon:3702 Arabidopsis thaliana RO:HOM0000017 in orthology relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct NCBIGene:100379827 capn10 NCBITaxon:8364 Xenopus (Silurana) tropicalis RO:HOM0000020 in 1 to 1 orthology relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:789674 CAPN10 NCBITaxon:9913 Bos taurus RO:HOM0000020 in 1 to 1 orthology relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct NCBIGene:825 CAPN3 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct -NCBIGene:789674 CAPN10 NCBITaxon:9913 Bos taurus RO:HOM0000020 in 1 to 1 orthology relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct NCBIGene:824 CAPN2 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +MGI:1344392 Capn10 NCBITaxon:10090 Mus musculus RO:HOM0000020 in 1 to 1 orthology relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct NCBIGene:79747 ADGB NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct -MGI:1344392 Capn10 NCBITaxon:10090 Mus musculus RO:HOM0000020 in 1 to 1 orthology relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct -NCBIGene:726 CAPN5 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct -NCBIGene:823 CAPN1 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct NCBIGene:92291 CAPN13 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct -NCBIGene:607311 CAPN10 NCBITaxon:9615 Canis lupus familiaris RO:HOM0000020 in 1 to 1 orthology relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct -NCBIGene:84290 CAPNS2 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct -NCBIGene:6650 CAPN15 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:823 CAPN1 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:726 CAPN5 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct NCBIGene:11131 CAPN11 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct -NCBIGene:178385 tra-3 NCBITaxon:6239 Caenorhabditis elegans RO:HOM0000017 in orthology relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:6650 CAPN15 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:607311 CAPN10 NCBITaxon:9615 Canis lupus familiaris RO:HOM0000020 in 1 to 1 orthology relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct NCBIGene:63834 Capn10 NCBITaxon:10116 Rattus norvegicus RO:HOM0000020 in 1 to 1 orthology relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct -NCBIGene:23473 CAPN7 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct -NCBIGene:147968 CAPN12 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct NCBIGene:440854 CAPN14 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct NCBIGene:827 CAPN6 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct NCBIGene:10753 CAPN9 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:23473 CAPN7 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:147968 CAPN12 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct NCBIGene:570311 capn10 NCBITaxon:7955 Danio rerio RO:HOM0000017 in orthology relationship with ECO:0000080|ECO:0000031 phylogenetic evidence|protein BLAST evidence used in manual assertion ZFIN:ZDB-PUB-030905-1 http://data.monarchinitiative.org/ttl/panther.ttl|http://data.monarchinitiative.org/ttl/zfin.ttl direct -NCBIGene:553115 PEF1 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct -NCBIGene:826 CAPNS1 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct NCBIGene:6717 SRI NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct NCBIGene:100022544 CAPN10 NCBITaxon:13616 Monodelphis domestica RO:HOM0000020 in 1 to 1 orthology relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct +NCBIGene:553115 PEF1 NCBITaxon:9606 Homo sapiens RO:HOM0000011 in paralogy relationship with ECO:0000080 phylogenetic evidence http://data.monarchinitiative.org/ttl/panther.ttl direct |
| b |
| diff -r 15016fee2bc4 -r 5fa1f0ca69cc test-data/homologues-for-genes-union.tsv --- a/test-data/homologues-for-genes-union.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/homologues-for-genes-union.tsv Sun Sep 25 21:59:32 2016 -0400 |
| b |
| b'@@ -1,61 +1,27 @@\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: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: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: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: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\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:100145791\tcapns1\tNCBITaxon:8364\tXenopus (Silurana) 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:187448\tM04F3.4\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:100014285\tCAPNS1\tNCBI'..b'tp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n-NCBIGene:553115\tPEF1\tNCBITaxon:9606\tHomo sapiens\tRO:HOM0000011\tin paralogy relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n-ZFIN:ZDB-GENE-030113-3\tcapns1a\tNCBITaxon:7955\tDanio rerio\tRO:HOM0000017\tin orthology relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.ttl\tdirect\n-NCBIGene:147968\tCAPN12\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:548915\tcapns2\tNCBITaxon:8364\tXenopus (Silurana) tropicalis\tRO:HOM0000017\tin orthology relationship with\tECO:0000080\tphylogenetic evidence\t\thttp://data.monarchinitiative.org/ttl/panther.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: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: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: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:147968\tCAPN12\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: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: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: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:830295\tAT5G04170\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: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: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: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 15016fee2bc4 -r 5fa1f0ca69cc test-data/pathways-for-disease.tsv --- a/test-data/pathways-for-disease.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/pathways-for-disease.tsv Sun Sep 25 21:59:32 2016 -0400 |
| b |
| b'@@ -1,30 +1,30 @@\n-KEGG-path:map05152\tTuberculosis\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:111217\tMetabolism\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:24058526|PMID:22558097\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:map00040\tPentose and glucuronate interconversions\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:map00053\tAscorbate and aldarate 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-REACT:R-HSA-1989781\tPPARA activates gene expression\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213|ECO:0000304\tcombinatorial evidence used in automatic assertion|traceable author statement used in manual assertion\tPMID:22558097\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/reactome.ttl\tinferred\n-KEGG-path:map04976\tBile secretion\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-KEGG-path:map02010\tABC transporters\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-KEGG-path:map00982\tDrug metabolism - 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-KEGG-path:map05323\tRheumatoid arthritis\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:map04966\tCollecting duct acid secretion\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:111102\tSignal Transduction\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213|ECO:0000213|ECO:0000213\tcombinatorial evidence used in automatic assertion|combinatorial evidence used in automatic assertion|combinatorial evidence used in automatic assertion\tPMID:23406172|PMID:25670933|PMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map00140\tSteroid hormone biosynthesis\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:map00830\tRetinol 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\tinfe'..b'903\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: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+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: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 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+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: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: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: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' |
| b |
| diff -r 15016fee2bc4 -r 5fa1f0ca69cc test-data/pathways-for-diseases-intersection.tsv --- a/test-data/pathways-for-diseases-intersection.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/pathways-for-diseases-intersection.tsv Sun Sep 25 21:59:32 2016 -0400 |
| b |
| b'@@ -1,30 +1,30 @@\n-KEGG-path:map05152\tTuberculosis\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:111217\tMetabolism\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:24058526|PMID:22558097\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:map00040\tPentose and glucuronate interconversions\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:map00053\tAscorbate and aldarate 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-REACT:R-HSA-1989781\tPPARA activates gene expression\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213|ECO:0000304\tcombinatorial evidence used in automatic assertion|traceable author statement used in manual assertion\tPMID:22558097\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/reactome.ttl\tinferred\n-KEGG-path:map04976\tBile secretion\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-KEGG-path:map02010\tABC transporters\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-KEGG-path:map00982\tDrug metabolism - 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-KEGG-path:map05323\tRheumatoid arthritis\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:map04966\tCollecting duct acid secretion\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:111102\tSignal Transduction\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213|ECO:0000213|ECO:0000213\tcombinatorial evidence used in automatic assertion|combinatorial evidence used in automatic assertion|combinatorial evidence used in automatic assertion\tPMID:23406172|PMID:25670933|PMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map00140\tSteroid hormone biosynthesis\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:map00830\tRetinol 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\tinfe'..b'903\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: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+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: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 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+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: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: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: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' |
| b |
| diff -r 15016fee2bc4 -r 5fa1f0ca69cc test-data/pathways-for-diseases-union.tsv --- a/test-data/pathways-for-diseases-union.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/pathways-for-diseases-union.tsv Sun Sep 25 21:59:32 2016 -0400 |
| b |
| b'@@ -1,30 +1,30 @@\n-KEGG-path:map05152\tTuberculosis\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:111217\tMetabolism\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:24058526|PMID:22558097\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n-KEGG-path:map00040\tPentose and glucuronate interconversions\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:map00053\tAscorbate and aldarate 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-REACT:R-HSA-1989781\tPPARA activates gene expression\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213|ECO:0000304\tcombinatorial evidence used in automatic assertion|traceable author statement used in manual assertion\tPMID:22558097\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/reactome.ttl\tinferred\n-KEGG-path:map04976\tBile secretion\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-KEGG-path:map02010\tABC transporters\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-KEGG-path:map00982\tDrug metabolism - 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-KEGG-path:map05323\tRheumatoid arthritis\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:map04966\tCollecting duct acid secretion\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:111102\tSignal Transduction\tRO:0002331\tinvolved in\tOMIM:603903\tSickle Cell Anemia\tECO:0000213|ECO:0000213|ECO:0000213\tcombinatorial evidence used in automatic assertion|combinatorial evidence used in automatic assertion|combinatorial evidence used in automatic assertion\tPMID:23406172|PMID:25670933|PMID:21326311\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/ctd.ttl\tinferred\n+KEGG-path:map00140\tSteroid hormone biosynthesis\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:map00830\tRetinol 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\tinfe'..b'903\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: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+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: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 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+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: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: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: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' |
| b |
| diff -r 15016fee2bc4 -r 5fa1f0ca69cc test-data/pathways-for-gene.tsv --- a/test-data/pathways-for-gene.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/pathways-for-gene.tsv Sun Sep 25 21:59:32 2016 -0400 |
| b |
| @@ -1,6 +1,6 @@ -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:map03440 Homologous recombination 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 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:map05212 Pancreatic cancer 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:675 BRCA2 http://data.monarchinitiative.org/ttl/ctd.ttl direct |
| b |
| diff -r 15016fee2bc4 -r 5fa1f0ca69cc test-data/pathways-for-genes-union.tsv --- a/test-data/pathways-for-genes-union.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/pathways-for-genes-union.tsv Sun Sep 25 21:59:32 2016 -0400 |
| b |
| @@ -1,9 +1,9 @@ -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 +KEGG-path:map03440 Homologous recombination 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:216 DNA Repair 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:map05219 Bladder cancer RO:0002331 involved in NCBIGene:11186 RASSF1 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 +KEGG-path:map05212 Pancreatic cancer 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: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 |
| b |
| diff -r 15016fee2bc4 -r 5fa1f0ca69cc test-data/phenotypes-for-disease.tsv --- a/test-data/phenotypes-for-disease.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/phenotypes-for-disease.tsv Sun Sep 25 21:59:32 2016 -0400 |
| b |
| b"@@ -1,283 +1,302 @@\n-OMIM:168600\tParkinson Disease, Late-Onset\tRO:0002200\thas phenotype\tHP:0000726\tDementia\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:0002172\tPostural instability\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:3747258|PMID:20055267|PMID:17048150|PMID:22130147|PMID:12948464\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n-OMIM:612953\tParkinson disease 14\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:260300\tautosomal recessive early-onset Parkinson disease 15\tRO:0002200\thas phenotype\tHP:0002071\tAbnormality of extrapyramidal motor function\tECO:0000304\ttraceable author statement used in manual assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n-OMIM:615530\tParkinson disease 20, early-onset\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-DOID:14330\tParkinson's disease\tRO:0002200\thas phenotype\tHP:0000012\tUrinary urgency\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:18327532|PMID:14521485|PMID:19908315|PMID:11570707|PMID:3942028\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n-OMIM:168600\tParkinson Disease, Late-Onset\tRO:0002200\thas phenotype\tHP:0002529\tNeuronal loss in central nervous system\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:0002067\tBradykinesia\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:0100543\tCognitive impairment\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:17516457|PMID:18178571|PMID:20832408|PMID:18682443|PMID:9387801\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n-OMIM:606693\tParkinson disease 9\tRO:0002200\thas phenotype\tHP:0000458\tAnosmia\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:0002312\tClumsiness\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:0004409\tHyposmia\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:0000473\tTorticollis\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n-OMIM:260300\tautosomal recessive early-onset Parkinson disease 15\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:0002172\tPostural instability\tECO:0000501\tevidence used in automatic assertion\t\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-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:168100\tParalysis Agitans, Juvenile, of Hunt\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:606324\tParkinson disease 7\tRO:0002200\thas phenotype\tHP:0002063\tRigidity\tECO:0000304\ttrac"..b"sed in manual assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n-OMIM:168601\tParkinson disease 1\tRO:0002200\thas phenotype\tHP:0001260\tDysarthria\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n-OMIM:607060\tautosomal dominant Parkinson disease 8\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: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-DOID:14330\tParkinson's disease\tRO:0002200\thas phenotype\tHP:0002019\tConstipation\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:21560061|PMID:23408927|PMID:22021174|PMID:19717168|PMID:12814332\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:614251\tParkinson disease 18\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: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: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:606324\tParkinson disease 7\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:614251\tParkinson disease 18\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:614251\tParkinson disease 18\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: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:613135\tParkinsonism-Dystonia, Infantile\tRO:0002200\thas phenotype\tHP:0002194\tDelayed gross motor development\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: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+OMIM:612953\tAdult-onset dystonia-parkinsonism\tRO:0002200\thas phenotype\tHP:0001268\tMental deterioration\tECO:0000304\ttraceable author statement used in manual assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n" |
| b |
| diff -r 15016fee2bc4 -r 5fa1f0ca69cc test-data/phenotypes-for-diseases-intersection.tsv --- a/test-data/phenotypes-for-diseases-intersection.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/phenotypes-for-diseases-intersection.tsv Sun Sep 25 21:59:32 2016 -0400 |
| b |
| @@ -1,22 +1,22 @@ -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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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 15016fee2bc4 -r 5fa1f0ca69cc test-data/phenotypes-for-diseases-union.tsv --- a/test-data/phenotypes-for-diseases-union.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/phenotypes-for-diseases-union.tsv Sun Sep 25 21:59:32 2016 -0400 |
| b |
| b"@@ -1,283 +1,302 @@\n-OMIM:168600\tParkinson Disease, Late-Onset\tRO:0002200\thas phenotype\tHP:0000726\tDementia\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:0002172\tPostural instability\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:3747258|PMID:20055267|PMID:17048150|PMID:22130147|PMID:12948464\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n-OMIM:612953\tParkinson disease 14\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:260300\tautosomal recessive early-onset Parkinson disease 15\tRO:0002200\thas phenotype\tHP:0002071\tAbnormality of extrapyramidal motor function\tECO:0000304\ttraceable author statement used in manual assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n-OMIM:615530\tParkinson disease 20, early-onset\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-DOID:14330\tParkinson's disease\tRO:0002200\thas phenotype\tHP:0000012\tUrinary urgency\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:18327532|PMID:14521485|PMID:19908315|PMID:11570707|PMID:3942028\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n-OMIM:168600\tParkinson Disease, Late-Onset\tRO:0002200\thas phenotype\tHP:0002529\tNeuronal loss in central nervous system\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:0002067\tBradykinesia\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:0100543\tCognitive impairment\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:17516457|PMID:18178571|PMID:20832408|PMID:18682443|PMID:9387801\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n-OMIM:606693\tParkinson disease 9\tRO:0002200\thas phenotype\tHP:0000458\tAnosmia\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:0002312\tClumsiness\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:0004409\tHyposmia\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:0000473\tTorticollis\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n-OMIM:260300\tautosomal recessive early-onset Parkinson disease 15\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:0002172\tPostural instability\tECO:0000501\tevidence used in automatic assertion\t\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-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:168100\tParalysis Agitans, Juvenile, of Hunt\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:606324\tParkinson disease 7\tRO:0002200\thas phenotype\tHP:0002063\tRigidity\tECO:0000304\ttrac"..b"sed in manual assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n-OMIM:168601\tParkinson disease 1\tRO:0002200\thas phenotype\tHP:0001260\tDysarthria\tECO:0000501\tevidence used in automatic assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n-OMIM:607060\tautosomal dominant Parkinson disease 8\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: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-DOID:14330\tParkinson's disease\tRO:0002200\thas phenotype\tHP:0002019\tConstipation\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:21560061|PMID:23408927|PMID:22021174|PMID:19717168|PMID:12814332\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:614251\tParkinson disease 18\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: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: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:606324\tParkinson disease 7\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:614251\tParkinson disease 18\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:614251\tParkinson disease 18\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: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:613135\tParkinsonism-Dystonia, Infantile\tRO:0002200\thas phenotype\tHP:0002194\tDelayed gross motor development\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: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+OMIM:612953\tAdult-onset dystonia-parkinsonism\tRO:0002200\thas phenotype\tHP:0001268\tMental deterioration\tECO:0000304\ttraceable author statement used in manual assertion\t\thttp://data.monarchinitiative.org/ttl/hpoa.ttl\tdirect\n" |
| b |
| diff -r 15016fee2bc4 -r 5fa1f0ca69cc test-data/variants-for-disease.tsv --- a/test-data/variants-for-disease.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/variants-for-disease.tsv Sun Sep 25 21:59:32 2016 -0400 |
| b |
| b'@@ -1,117 +1,125 @@\n-ClinVarVariant:2409\tNM_032409.2(PINK1):c.1570_1573dupTTAG (p.Asp525Valfs)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\tPMID:15349871\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-ClinVarVariant:6204\tNM_003560.2(PLA2G6):c.2239C>T (p.Arg747Trp)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:612953\tParkinson disease 14\t\t\tPMID:18981035|PMID:18570303|PMID:20886109|PMID:18570303|PMID:26633545\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-ClinVarVariant:2408\tNM_032409.2(PINK1):c.1040T>C (p.Leu347Pro)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\tPMID:15596610|PMID:15349870|PMID:15824318\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-ClinVarVariant:6203\tNM_003560.2(PLA2G6):c.2222G>A (p.Arg741Gln)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:612953\tParkinson disease 14\t\t\tPMID:18570303|PMID:18981035\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-ClinVarVariant:218884\tNM_001320327.1(CHCHD2):c.300+5G>A\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:616710\tParkinson disease 22, autosomal dominant\t\t\tPMID:26067113|PMID:25662902\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\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-ClinVarVariant:39131\tNM_198578.3(LRRK2):c.1256C>T (p.Ala419Val)\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:218882\tNM_001320327.1(CHCHD2):c.182C>T (p.Thr61Ile)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:616710\tParkinson disease 22, autosomal dominant\t\t\tPMID:25662902|PMID:26067113\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-ClinVarVariant:14011\tSNCA, DUPLICATION\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:168601\tParkinson disease 1\t\t\tPMID:17625105|PMID:18195271|PMID:17251522|PMID:18852448|PMID:18852449|PMID:15451224|PMID:18852445|PMID:15451225|PMID:14593171|PMID:14755720|PMID:16358335\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-ClinVarVariant:2407\tNM_032409.2(PINK1):c.736C>T (p.Arg246Ter)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\tPMID:15349870\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-ClinVarVariant:218883\tNM_001320327.1(CHCHD2):c.434G>A (p.Arg145Gln)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:616710\tParkinson disease 22, autosomal dominant\t\t\tPMID:25662902|PMID:26067113\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-ClinVarVariant:2406\tNM_032409.2(PINK1):c.1311G>A (p.Trp437Ter)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\tPMID:16207731|PMID:15087508|PMID:18524835\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-ClinVarVariant:2405\tNM_032409.2(PINK1):c.813C>A (p.His271Gln)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\tPMID:15349870\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-ClinVarVariant:14009\tSNCA, TRIPLICATION\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:605543\tParkinson Disease 4, Autosomal Dominant\t\t\tPMID:17251522|PMID:8285594|PMID:15159488|PMID:14593171|PMID:14755720\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-OMIM:602544.0002\tPARK2, EX4DEL\t\t\t\t\t\t\tOMIM:600116\tParkinson Di'..b'l\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+ClinVarVariant:2412\tNM_005216.4(DDOST):c.*807_*5409del\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:100861548\tPINK1-AS\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\tNCBIGene:11315\tPARK7\tGENO:0000840\tpathogenic_for_condition\tOMIM:606324\tParkinson disease 7\t\t\tPMID:16240358\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:222070\tNM_020821.2(VPS13C):c.4165G>C (p.Gly1389Arg)\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:54832\tVPS13C\tGENO:0000840\tpathogenic_for_condition\tOMIM:616840\tParkinson Disease 23, Autosomal Recessive Early-Onset\t\t\tPMID:26942284\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:97018\tNM_001044.4(SLC6A3):c.1561C>T (p.Arg521Trp)\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:6531\tSLC6A3\tGENO:0000840\tpathogenic_for_condition\tOMIM:613135\tParkinsonism-Dystonia, Infantile\t\t\tPMID:21112253\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:1220\tATP13A2, 22-BP DUP\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:23400\tATP13A2\tGENO:0000840\tpathogenic_for_condition\tOMIM:606693\tParkinson disease 9\t\t\tPMID:16964263|PMID:21724849\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:222071\tNM_020821.2(VPS13C):c.4777delC (p.Gln1593Lysfs)\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:54832\tVPS13C\tGENO:0000840\tpathogenic_for_condition\tOMIM:616840\tParkinson Disease 23, Autosomal Recessive Early-Onset\t\t\tPMID:26942284\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:1221\tNM_022089.3(ATP13A2):c.1510G>C (p.Gly504Arg)\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:23400\tATP13A2\tGENO:0000840\tpathogenic_for_condition\tOMIM:606693\tParkinson disease 9\t\t\tPMID:17485642\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:4810\tNM_012179.3(FBXO7):c.1144+1G>T\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:25793\tFBXO7\tGENO:0000840\tpathogenic_for_condition\tOMIM:260300\tautosomal recessive early-onset Parkinson disease 15\t\t\tPMID:19038853\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:30368\tPLA2G6, PHE72LEU\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:8398\tPLA2G6\tGENO:0000840\tpathogenic_for_condition\tOMIM:612953\tAdult-onset dystonia-parkinsonism\t\t\tPMID:20938027\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+OMIM:602544.0014\tPARK2, 1-BP DEL, 255A\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:5071\tPARK2\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/coriell.ttl\tinferred\n+ClinVarVariant:2411\tNM_032409.2(PINK1):c.836G>A (p.Arg279His)\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:100861548\tPINK1-AS\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\tNCBIGene:120892\tLRRK2\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\tNCBIGene:120892\tLRRK2\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:2410\tPINK1, 3-BP INS, 1602CAA\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:102464833\tMIR6084\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' |
| b |
| diff -r 15016fee2bc4 -r 5fa1f0ca69cc test-data/variants-for-diseases-intersection.tsv --- a/test-data/variants-for-diseases-intersection.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/variants-for-diseases-intersection.tsv Sun Sep 25 21:59:32 2016 -0400 |
| b |
| @@ -1,12 +1,12 @@ -ClinVarVariant:56171 NM_015268.3(DNAJC13):c.2564A>G (p.Asn855Ser) NCBITaxon:9606 Homo sapiens GENO:0000840 pathogenic_for_condition OMIM:168600 Parkinson Disease, Late-Onset PMID:24218364 http://data.monarchinitiative.org/ttl/clinvar.ttl direct -OMIM:602544.0011 PARK2, ALA82GLU OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred -OMIM:602544.0005 PARK2, EX3DEL OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred -dbSNP:rs34637584 rs34637584-A NCBITaxon:9606 Homo sapiens OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred -OMIM:606463.0003 GBA, ASN370SER OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred -OMIM:163890.0003 SNCA, TRIPLICATION OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred -ClinVarVariant:9726 m.3397A>G NCBITaxon:9606 Homo sapiens GENO:0000840 pathogenic_for_condition OMIM:168600 Parkinson Disease, Late-Onset PMID:7624338 http://data.monarchinitiative.org/ttl/clinvar.ttl direct -ClinVarVariant:29936 NM_012084.3(GLUD2):c.1492T>G (p.Ser498Ala) NCBITaxon:9606 Homo sapiens GENO:0000840 pathogenic_for_condition OMIM:168600 Parkinson Disease, Late-Onset PMID:19826450 http://data.monarchinitiative.org/ttl/clinvar.ttl direct -OMIM:602544.0022 PARK2, EX5-6 DEL OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred -OMIM:602544.0014 PARK2, 1-BP DEL, 255A OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred -OMIM:602544.0017 PARK2, ARG275TRP OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred -ClinVarVariant:225276 NM_198578.3(LRRK2):c.4321C>A (p.Arg1441Ser) NCBITaxon:9606 Homo sapiens GENO:0000840 pathogenic_for_condition OMIM:168600 Parkinson Disease, Late-Onset PMID:27111571 http://data.monarchinitiative.org/ttl/clinvar.ttl direct +ClinVarVariant:29936 NM_012084.3(GLUD2):c.1492T>G (p.Ser498Ala) NCBITaxon:9606 Homo sapiens NCBIGene:2747 GLUD2 GENO:0000840 pathogenic_for_condition OMIM:168600 Parkinson Disease, Late-Onset PMID:19826450 http://data.monarchinitiative.org/ttl/clinvar.ttl direct +OMIM:602544.0022 PARK2, EX5-6 DEL NCBITaxon:9606 Homo sapiens NCBIGene:5071 PARK2 OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred +ClinVarVariant:9726 m.3397A>G NCBITaxon:9606 Homo sapiens NCBIGene:4535 ND1 GENO:0000840 pathogenic_for_condition OMIM:168600 Parkinson Disease, Late-Onset PMID:7624338 http://data.monarchinitiative.org/ttl/clinvar.ttl direct +OMIM:163890.0003 SNCA, TRIPLICATION NCBITaxon:9606 Homo sapiens NCBIGene:6622 SNCA OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred +OMIM:602544.0005 PARK2, EX3DEL NCBITaxon:9606 Homo sapiens NCBIGene:5071 PARK2 OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred +ClinVarVariant:56171 NM_015268.3(DNAJC13):c.2564A>G (p.Asn855Ser) NCBITaxon:9606 Homo sapiens NCBIGene:23317 DNAJC13 GENO:0000840 pathogenic_for_condition OMIM:168600 Parkinson Disease, Late-Onset PMID:24218364 http://data.monarchinitiative.org/ttl/clinvar.ttl direct +OMIM:602544.0011 PARK2, ALA82GLU NCBITaxon:9606 Homo sapiens NCBIGene:5071 PARK2 OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred +dbSNP:rs34637584 rs34637584-A NCBITaxon:9606 Homo sapiens NCBIGene:120892 LRRK2 OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred +OMIM:606463.0003 GBA, ASN370SER NCBITaxon:9606 Homo sapiens NCBIGene:2629 GBA OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred +OMIM:602544.0017 PARK2, ARG275TRP NCBITaxon:9606 Homo sapiens NCBIGene:5071 PARK2 OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred +OMIM:602544.0014 PARK2, 1-BP DEL, 255A NCBITaxon:9606 Homo sapiens NCBIGene:5071 PARK2 OMIM:168600 Parkinson Disease, Late-Onset http://data.monarchinitiative.org/ttl/coriell.ttl inferred +ClinVarVariant:225276 NM_198578.3(LRRK2):c.4321C>A (p.Arg1441Ser) NCBITaxon:9606 Homo sapiens NCBIGene:120892 LRRK2 GENO:0000840 pathogenic_for_condition OMIM:168600 Parkinson Disease, Late-Onset PMID:27111571 http://data.monarchinitiative.org/ttl/clinvar.ttl direct |
| b |
| diff -r 15016fee2bc4 -r 5fa1f0ca69cc test-data/variants-for-diseases-union.tsv --- a/test-data/variants-for-diseases-union.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/variants-for-diseases-union.tsv Sun Sep 25 21:59:32 2016 -0400 |
| b |
| b'@@ -1,117 +1,125 @@\n-ClinVarVariant:2409\tNM_032409.2(PINK1):c.1570_1573dupTTAG (p.Asp525Valfs)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\tPMID:15349871\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-ClinVarVariant:6204\tNM_003560.2(PLA2G6):c.2239C>T (p.Arg747Trp)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:612953\tParkinson disease 14\t\t\tPMID:18981035|PMID:18570303|PMID:20886109|PMID:18570303|PMID:26633545\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-ClinVarVariant:2408\tNM_032409.2(PINK1):c.1040T>C (p.Leu347Pro)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\tPMID:15596610|PMID:15349870|PMID:15824318\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-ClinVarVariant:6203\tNM_003560.2(PLA2G6):c.2222G>A (p.Arg741Gln)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:612953\tParkinson disease 14\t\t\tPMID:18570303|PMID:18981035\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-ClinVarVariant:218884\tNM_001320327.1(CHCHD2):c.300+5G>A\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:616710\tParkinson disease 22, autosomal dominant\t\t\tPMID:26067113|PMID:25662902\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\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-ClinVarVariant:39131\tNM_198578.3(LRRK2):c.1256C>T (p.Ala419Val)\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:218882\tNM_001320327.1(CHCHD2):c.182C>T (p.Thr61Ile)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:616710\tParkinson disease 22, autosomal dominant\t\t\tPMID:25662902|PMID:26067113\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-ClinVarVariant:14011\tSNCA, DUPLICATION\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:168601\tParkinson disease 1\t\t\tPMID:17625105|PMID:18195271|PMID:17251522|PMID:18852448|PMID:18852449|PMID:15451224|PMID:18852445|PMID:15451225|PMID:14593171|PMID:14755720|PMID:16358335\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-ClinVarVariant:2407\tNM_032409.2(PINK1):c.736C>T (p.Arg246Ter)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\tPMID:15349870\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-ClinVarVariant:218883\tNM_001320327.1(CHCHD2):c.434G>A (p.Arg145Gln)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:616710\tParkinson disease 22, autosomal dominant\t\t\tPMID:25662902|PMID:26067113\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-ClinVarVariant:2406\tNM_032409.2(PINK1):c.1311G>A (p.Trp437Ter)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\tPMID:16207731|PMID:15087508|PMID:18524835\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-ClinVarVariant:2405\tNM_032409.2(PINK1):c.813C>A (p.His271Gln)\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:605909\tParkinson Disease 6, Autosomal Recessive Early-Onset\t\t\tPMID:15349870\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-ClinVarVariant:14009\tSNCA, TRIPLICATION\tNCBITaxon:9606\tHomo sapiens\t\t\tGENO:0000840\tpathogenic_for_condition\tOMIM:605543\tParkinson Disease 4, Autosomal Dominant\t\t\tPMID:17251522|PMID:8285594|PMID:15159488|PMID:14593171|PMID:14755720\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n-OMIM:602544.0002\tPARK2, EX4DEL\t\t\t\t\t\t\tOMIM:600116\tParkinson Di'..b'l\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+ClinVarVariant:2412\tNM_005216.4(DDOST):c.*807_*5409del\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:100861548\tPINK1-AS\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\tNCBIGene:11315\tPARK7\tGENO:0000840\tpathogenic_for_condition\tOMIM:606324\tParkinson disease 7\t\t\tPMID:16240358\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:222070\tNM_020821.2(VPS13C):c.4165G>C (p.Gly1389Arg)\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:54832\tVPS13C\tGENO:0000840\tpathogenic_for_condition\tOMIM:616840\tParkinson Disease 23, Autosomal Recessive Early-Onset\t\t\tPMID:26942284\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:97018\tNM_001044.4(SLC6A3):c.1561C>T (p.Arg521Trp)\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:6531\tSLC6A3\tGENO:0000840\tpathogenic_for_condition\tOMIM:613135\tParkinsonism-Dystonia, Infantile\t\t\tPMID:21112253\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:1220\tATP13A2, 22-BP DUP\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:23400\tATP13A2\tGENO:0000840\tpathogenic_for_condition\tOMIM:606693\tParkinson disease 9\t\t\tPMID:16964263|PMID:21724849\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:222071\tNM_020821.2(VPS13C):c.4777delC (p.Gln1593Lysfs)\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:54832\tVPS13C\tGENO:0000840\tpathogenic_for_condition\tOMIM:616840\tParkinson Disease 23, Autosomal Recessive Early-Onset\t\t\tPMID:26942284\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:1221\tNM_022089.3(ATP13A2):c.1510G>C (p.Gly504Arg)\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:23400\tATP13A2\tGENO:0000840\tpathogenic_for_condition\tOMIM:606693\tParkinson disease 9\t\t\tPMID:17485642\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:4810\tNM_012179.3(FBXO7):c.1144+1G>T\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:25793\tFBXO7\tGENO:0000840\tpathogenic_for_condition\tOMIM:260300\tautosomal recessive early-onset Parkinson disease 15\t\t\tPMID:19038853\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+ClinVarVariant:30368\tPLA2G6, PHE72LEU\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:8398\tPLA2G6\tGENO:0000840\tpathogenic_for_condition\tOMIM:612953\tAdult-onset dystonia-parkinsonism\t\t\tPMID:20938027\thttp://data.monarchinitiative.org/ttl/clinvar.ttl\tdirect\n+OMIM:602544.0014\tPARK2, 1-BP DEL, 255A\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:5071\tPARK2\t\t\tOMIM:168600\tParkinson Disease, Late-Onset\t\t\t\thttp://data.monarchinitiative.org/ttl/coriell.ttl\tinferred\n+ClinVarVariant:2411\tNM_032409.2(PINK1):c.836G>A (p.Arg279His)\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:100861548\tPINK1-AS\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\tNCBIGene:120892\tLRRK2\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\tNCBIGene:120892\tLRRK2\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:2410\tPINK1, 3-BP INS, 1602CAA\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:102464833\tMIR6084\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' |
| b |
| diff -r 15016fee2bc4 -r 5fa1f0ca69cc test-data/variants-for-phenotype.tsv --- a/test-data/variants-for-phenotype.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/variants-for-phenotype.tsv Sun Sep 25 21:59:32 2016 -0400 |
| b |
| b'@@ -1,65 +1,65 @@\n-ClinVarVariant:4810\tNM_012179.3(FBXO7):c.1144+1G>T\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:19038853\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-ClinVarVariant:12328\tNM_199292.2(TH):c.1010G>A (p.Arg337His)\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:11246459\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-ClinVarVariant:39215\tNM_198578.3(LRRK2):c.5620G>T (p.Glu1874Ter)\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:1937\tNM_198578.3(LRRK2):c.5096A>G (p.Tyr1699Cys)\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:15541308|PMID:18591067|PMID:15541309|PMID:16003110\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-ClinVarVariant:9283\tNM_000161.2(GCH1):c.671A>G (p.Lys224Arg)\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:9667588|PMID:12391354\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-ClinVarVariant:9273\tGCH1, 2-BP INS\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:12331\tNM_199292.2(TH):c.1198-24T>A\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:11281275\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-ClinVarVariant:21011\tNR_104387.1(TAF1):n.5894C>T\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:9285\tNM_000161.2(GCH1):c.404T>A (p.Ile135Lys)\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:10208576\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-ClinVarVariant:9275\tGCH1, IVS1, 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\tPMID:10732814\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-ClinVarVariant:12333\tTH, -70G-A\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:9235905|PMID:17696123\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-ClinVarVariant:1219\tNM_022089.3(ATP13A2):c.1306+5G>A\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000304\ttraceable author statement used'..b'linvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-ClinVarVariant:209136\tNM_022089.3(ATP13A2):c.943G>A (p.Gly315Arg)\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:26633545\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-ClinVarVariant:4809\tNM_012179.3(FBXO7):c.1492C>T (p.Arg498Ter)\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:19038853\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-ClinVarVariant:13495\tNM_002693.2(POLG):c.2864A>G (p.Tyr955Cys)\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:14467368|PMID:11897778|PMID:11431686|PMID:15351195|PMID:2725645|PMID:12210792|PMID:2067633\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-ClinVarVariant:12330\tNM_199292.2(TH):c.941C>T (p.Thr314Met)\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:11246459\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-ClinVarVariant:39212\tNM_198578.3(LRRK2):c.5605A>G (p.Met1869Val)\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: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+ClinVarVariant:4808\tNM_012179.3(FBXO7):c.1132C>G (p.Arg378Gly)\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:25793\tFBXO7\t\t\tHP:0002548\tParkinsonism with favorable response to dopaminergic medication\tECO:0000501\tevidence used in automatic assertion\tPMID:18513678\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:39131\tNM_198578.3(LRRK2):c.1256C>T (p.Ala419Val)\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:120892\tLRRK2\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 15016fee2bc4 -r 5fa1f0ca69cc test-data/variants-for-phenotypes-intersection.tsv --- a/test-data/variants-for-phenotypes-intersection.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/variants-for-phenotypes-intersection.tsv Sun Sep 25 21:59:32 2016 -0400 |
| b |
| b'@@ -1,351 +1,353 @@\n-MGI:4442238\tChd6<tm1.2Fier>\t\t\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:20111866\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n-MGI:3625122\tIds<tm1Muen>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:16505002\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n-MGI:2679626\tCplx2<tm1Rmnd>\t\t\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:20412316\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n-MGI:3778285\tTg(DRD1-ctxA)7Burt\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:10780249|PMID:10780249\thttp://data.monarchinitiative.org/ttl/mgi.ttl|http://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-MGI:3604494\tGpr19<tm1Dgen>\t\t\t\t\tRO:0002200\thas phenotype\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tMGI:3604450\thttp://data.monarchinitiative.org/ttl/mgi.ttl|http://data.monarchinitiative.org/ttl/mmrrc.ttl\tdirect\n-MGI:5752777\tDisc1<m1H>\t\t\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:26728762\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n-MGI:2386951\tTg(HDexon1)62Gpb\tNCBITaxon:10090\tMus musculus\tNCBIGene:3064\tHTT\tRO:0002200\thas phenotype\tMP:0001363\tincreased anxiety-related response\tECO:0000059|ECO:0000006|ECO:0000006\texperimental phenotypic evidence|experimental evidence|experimental evidence\tPMID:19464370|PMID:19464370|PMID:19464370\thttp://data.monarchinitiative.org/ttl/mgi.ttl|http://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n-MGI:3762618\tGrn<tm1Mni>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:17764761\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n-MGI:3530009\tAtp1a1<Gt(OST31117)Lex>\t\t\t\t\tRO:0002200\thas phenotype\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tMGI:3609573\thttp://data.monarchinitiative.org/ttl/mgi.ttl|http://data.monarchinitiative.org/ttl/mmrrc.ttl\tdirect\n-MGI:2176172\tTg(Nes-cre)1Kln\tNCBITaxon:10090\tMus musculus\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006|ECO:0000006\texperimental evidence|experimental evidence\tPMID:23777740|PMID:20889973\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n-MGI:4837197\tFev<tm2Esd>\t\t\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:20818386\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n-MGI:3512756\tMapt<tm1(cre)Nagy>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:20130183\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n-MGI:2177567\tGad2<tm1Oba>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006|ECO:0000006\texperimental evidence|experimental evidence\tPMID:10814732|PMID:10814732\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n-MGI:3608888\tRic8a<tm1Aks>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:16221497\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n-MGI:5515451\tM876b\tNCBITaxon:10090\tMus musculus\tMGI:5515451\tM876b\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:16109771\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n-MGI:5544724\tGbx1<tm1Mrh>\t\t\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:24010020\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n-MGI:4837202\tTg(Fev-cre/ERT2)aEsd\tNCBITaxon:10090\tMus musculus\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:20818386\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n-MGI:4410507\tRnf103<tm1.1Thg>\t\t\t\t\tRO:0002200\thas phenotype\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:18958194|PMID:18958194|PMID:19753093\thttp://data.monarchinitiative.org/ttl/mgi.tt'..b' musculus\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:11124984\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:1857129\tApoe<tm1Unc>\tNCBITaxon:10090\tMus musculus\t\t\tRO:0002200\thas phenotype\tMP:0001363\tincreased anxiety-related response\tECO:0000006|ECO:0000006|ECO:0000006\texperimental evidence|experimental evidence|experimental evidence\tPMID:15708438|PMID:10684907|PMID:15708438|PMID:15304509\thttp://data.monarchinitiative.org/ttl/mgi.ttl|http://data.monarchinitiative.org/ttl/mmrrc.ttl\tdirect\n+MGI:3759300\tDlgap3<tm1Gfng>\tNCBITaxon:10090\tMus musculus\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:17713528\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:2673210\tNpepps<goku>\tNCBITaxon:10090\tMus musculus\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:10407043\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:2384535\tCckbr<tm1Tom>\tNCBITaxon:10090\tMus musculus\t\t\t\t\tMP:0001363\tincreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:12459512\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:3834477\tSlitrk1<tm1Jaru>\tNCBITaxon:10090\tMus musculus\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:3720069\tTg(Thy1-App*R609D*K612E)6Vln\tNCBITaxon:10090\tMus musculus\t\t\tRO:0002200\thas phenotype\tMP:0002797\tincreased thigmotaxis\tECO:0000059|ECO:0000006|ECO:0000006\texperimental phenotypic evidence|experimental evidence|experimental evidence\tPMID:8635459|PMID:8635459|PMID:8635459\thttp://data.monarchinitiative.org/ttl/mgi.ttl|http://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:3513042\tCrhbp<tm1Afs>\tNCBITaxon:10090\tMus musculus\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:5776473\tTg(C9orf72)450BLagi\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:27112497|PMID:27112497\thttp://data.monarchinitiative.org/ttl/mgi.ttl|http://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:5052110\tTg(Mapt-MAPT*)#Hanr\tNCBITaxon:10090\tMus musculus\tNCBIGene:4137\tMAPT\tRO:0002200\thas phenotype\tMP:0001363\tincreased anxiety-related response\tECO:0000059|ECO:0000006\texperimental phenotypic evidence|experimental evidence\tPMID:18490011|PMID:18490011\thttp://data.monarchinitiative.org/ttl/mgi.ttl|http://data.monarchinitiative.org/ttl/mgi_slim.ttl\tdirect\n+MGI:3042719\tNrxn2<tm1Sud>\tNCBITaxon:10090\tMus musculus\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:4949899\tFgfbp3<tm1Tohe>\tNCBITaxon:10090\tMus musculus\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>\tNCBITaxon:10090\tMus musculus\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:3835761\tWfs1<tm1Koks>\tNCBITaxon:10090\tMus musculus\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:19477223\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n+MGI:2181809\tLgals1<tm1Rob>\tNCBITaxon:10090\tMus musculus\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:3512173\tGrin3b<tm1Yaha>\tNCBITaxon:10090\tMus musculus\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' |
| b |
| diff -r 15016fee2bc4 -r 5fa1f0ca69cc test-data/variants-for-phenotypes-union.tsv --- a/test-data/variants-for-phenotypes-union.tsv Mon Aug 22 12:53:55 2016 -0400 +++ b/test-data/variants-for-phenotypes-union.tsv Sun Sep 25 21:59:32 2016 -0400 |
| [ |
| b'@@ -1,2075 +1,2339 @@\n-ClinVarVariant:10985\tNM_005710.2(PQBP1):c.194A>G (p.Tyr65Cys)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000739\tAnxiety\tECO:0000501\tevidence used in automatic assertion\tPMID:6711604|PMID:20410308|PMID:15782410|PMID:16740914\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-MGI:1856628\tDtnbp1<sdy>\t\t\t\t\t\t\tMP:0001364\tdecreased anxiety-related response\tECO:0000006\texperimental evidence\tPMID:25677649\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n-MGI:4442238\tChd6<tm1.2Fier>\t\t\t\t\t\t\tMP:0002797\tincreased thigmotaxis\tECO:0000006\texperimental evidence\tPMID:20111866\thttp://data.monarchinitiative.org/ttl/mgi.ttl\tinferred\n-ClinVarVariant:102736\tNM_000277.1(PAH):c.561G>A (p.Trp187Ter)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000739\tAnxiety\tECO:0000501\tevidence used in automatic assertion\tPMID:8268925|PMID:17502162|PMID:17096675|PMID:24368688|PMID:17935162|PMID:12655553|PMID:23932990|PMID:23430918|PMID:9012412|PMID:9634518|PMID:15503242\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-ClinVarVariant:17258\tNM_000089.3(COL1A2):c.1981G>A (p.Gly661Ser)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tAnxiety (with pheochromocytoma)\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:16137956|PMID:12099988|PMID:75706|PMID:1463018|PMID:21525520|PMID:21847749|PMID:2052622|PMID:8786074\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-ClinVarVariant:5778\tSGCE, 6,872-BP DEL, EX6DEL\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000739\tAnxiety\tECO:0000501\tevidence used in automatic assertion\tPMID:16240355\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-ClinVarVariant:5768\tNM_003919.2(SGCE):c.289C>T (p.Arg97Ter)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000739\tAnxiety\tECO:0000501\tevidence used in automatic assertion\tPMID:11528394|PMID:15728306\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-ClinVarVariant:102696\tNM_000277.1(PAH):c.47_48delCT (p.Ser16Terfs)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000739\tAnxiety\tECO:0000501\tevidence used in automatic assertion\tPMID:23430547|PMID:12655550|PMID:19444284|PMID:19062537|PMID:23357515|PMID:8535445|PMID:16879198|PMID:21147011|PMID:17935162|PMID:12655553|PMID:8535445|PMID:10394930\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n-ClinVarVariant:120292\tNM_000277.1(PAH):c.912+2T>C\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000739\tAnxiety\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:120272\tNM_000277.1(PAH):c.284_285delTCinsCA (p.Ile95Thr)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000739\tAnxiety\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:53501\tNM_000492.3(CFTR):c.2491G>T (p.Glu831Ter)\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:1080\tCFTR\t\t\tHP:0000740\tEpisodic paroxysmal anxiety\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:20949073|PMID:23974870|PMID:10361400|PMID:23974870|PMID:7866213|PMID:20171652|PMID:20495477|PMID:8956039|PMID:12796866|PMID:21296036\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+dbSNP:rs1113932\trs1113932-G\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:23671\tTMEFF2\t\t\tHP:0000740\tEpisodic paroxysmal anxiety\tECO:0000213|ECO:0000246\tcombinatorial evidence used in automatic assertion|computational combinatorial evidence used in automatic assertion\tPMID:21099065|PMID:3375880|PMID:21425450|PMID:9491171|PMID:17938043|PMID:25042611\thttp://data.monarchinitiative.org/ttl/gwascatalog.ttl|http://data.monarchinitiative.org/ttl/hpoa'..b'M_000277.1(PAH):c.1220C>T (p.Pro407Leu)\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:5053\tPAH\t\t\tHP:0000739\tAnxiety\tECO:0000501\tevidence used in automatic assertion\tPMID:9950317\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\tEpisodic paroxysmal anxiety\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:7866213|PMID:20171652|PMID:20495477|PMID:12796866|PMID:10361400\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:2146\tNM_133433.3(NIPBL):c.5167C>T (p.Arg1723Ter)\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:25836\tNIPBL\t\t\tHP:0000740\tEpisodic paroxysmal anxiety\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:15318302|PMID:18430761|PMID:17640042|PMID:17845236|PMID:19309268|PMID:19330433|PMID:15146186\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:13399\tNM_000311.3(PRNP):c.532G>A (p.Asp178Asn)\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:5621\tPRNP\t\t\tHP:0000739\tAnxiety\tECO:0000304\ttraceable author statement used in manual assertion\tPMID:12205650|PMID:9751723|PMID:1469441|PMID:1671983|PMID:19038218|PMID:1671440|PMID:1684756|PMID:1353342|PMID:1353344|PMID:16227536|PMID:7709737|PMID:1353341\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:10589\tNM_000133.3(F9):c.655C>T (p.Gln219Ter)\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:2158\tF9\t\t\tHP:0000740\tEpisodic paroxysmal anxiety\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:3817455|PMID:7875359|PMID:18700841|PMID:10734657|PMID:2773937|PMID:19187190\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:159124\tNM_015384.4(NIPBL):c.4663delG (p.Glu1555Lysfs)\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:25836\tNIPBL\t\t\tHP:0000740\tEpisodic paroxysmal anxiety\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:17845236|PMID:19309268|PMID:19330433|PMID:18430761|PMID:17640042\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:159134\tNM_015384.4(NIPBL):c.5033_5039delCCCAGTG (p.Ala1678Glyfs)\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:25836\tNIPBL\t\t\tHP:0000740\tEpisodic paroxysmal anxiety\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:17845236|PMID:19309268|PMID:19330433|PMID:18430761|PMID:17640042\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:53984\tNM_000492.3(CFTR):c.50delT (p.Phe17Serfs)\tNCBITaxon:9606\tHomo sapiens\t\t\t\t\tHP:0000740\tEpisodic paroxysmal anxiety\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:7866213|PMID:20171652|PMID:20495477|PMID:12796866|PMID:10361400\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:209047\tNM_000492.3(CFTR):c.1210-12[5]\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:1080\tCFTR\t\t\tHP:0000740\tEpisodic paroxysmal anxiety\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:7866213|PMID:20171652|PMID:20495477|PMID:12796866|PMID:10361400\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n+ClinVarVariant:159104\tNM_133433.3(NIPBL):c.4017C>A (p.Tyr1339Ter)\tNCBITaxon:9606\tHomo sapiens\tNCBIGene:25836\tNIPBL\t\t\tHP:0000740\tEpisodic paroxysmal anxiety\tECO:0000246\tcomputational combinatorial evidence used in automatic assertion\tPMID:17845236|PMID:19309268|PMID:19330433|PMID:18430761|PMID:17640042\thttp://data.monarchinitiative.org/ttl/clinvar.ttl|http://data.monarchinitiative.org/ttl/hpoa.ttl\tinferred\n' |