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monarch-initiative / dipper

Data Ingestion Pipeline for Monarch
https://dipper.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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Morpholinos are appearing as variants in the app. #751

Open mbrush opened 7 years ago

mbrush commented 7 years ago

For example, the variant tab here (https://monarchinitiative.org/gene/ZFIN:ZDB-GENE-030131-3776) lists three morpholinos as variants.

Tracked the problem to the cypher queries that do not exclude morpholinos from being loaded into solr. e.g. the variant-gene query here (https://github.com/monarch-initiative/configs/blob/master/SciGraph/golr/queries/variant-gene.yaml) needs to add a filter to prevent morpholinos from being returned.

Ultimately we may get other types of gene knockdown reagents such as dsRNA, RNAi. So the solution shouldn't be specific to morpholinos. Consult with @mbrush as to a grouping class that could be implemented in GENO to collect all of these and exclude them collectively. Or come up with some other more elegant way to buidl a cypher query that ensures only 'variants' are returned from such queries.

TomConlin commented 5 years ago

should move to https://github.com/monarch-initiative/monarch-cypher-queries

kshefchek commented 5 years ago

Moving to dipper as this is an issue across multiple sources. We have a fix in ClinVar but it is a hack. Ideally there would be a relation that would allow us to disambiguate a variant or genotype that affects the function of a gene. And perhaps a subproperty when a variant/genotype affects the function of just one gene.

TomConlin commented 5 years ago

Is there also a front end conservation such as where these induced variants should go?