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monarch-initiative / monarch-legacy

Monarch web application and API
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Remove or differentiate duplicate gene-phenotype and variant-phenotype associations #923

Open mbrush opened 8 years ago

mbrush commented 8 years ago

Related to duplicated gene-disease issue #735.

Recreate: From phenotype http://beta.monarchinitiative.org/phenotype/ZP:0007522, go to Genes tab. Count is 4, but all four are the same gene/association (same gene, phenotype, evidence, and source). Note that these genes are associated with the phenotype based on MO knockdown experiments, and as noted in #922 there are issues labeling/identifying expression variants.

I see duplication of genes to a lesser degree for other phenotypes as well, e.g. http://beta.monarchinitiative.org/phenotype/ZP:0003762 (here the olig2 association with source ZFIN:ZDB-PUB-090309-10 is duplicated)

Also seeing duplication in variants tab for phenootype http://beta.monarchinitiative.org/phenotype/ZP:0007522 (zf15Tg, nrg1 both duplicated).

Duplication also occurring in opposite direction. For example, the phenotype tab for the zf15Tg variant page (http://stage.monarchinitiative.org/variant/ZFIN:ZDB-ALT-050512-10) has the 'abnormal(ly) lacks parts or has fewer parts of type posterior lateral line nerve towards myelinating Schwann cell' phenotype association duplicated three times.

jmcmurry commented 8 years ago

Duplication is also happening in the genotypes tab, eg: http://beta.monarchinitiative.org/gene/NCBIGene:18504#genotypes The vast majority (276/321) of the rows shown are exact duplicates of each other.