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biothings / pending.api

Set of standalone APIs built with the BioThings SDK for the Translator Project
https://biothings.ncats.io
Apache License 2.0
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create new API for gene-disease associations from AGR #28

Closed andrewsu closed 3 years ago

andrewsu commented 3 years ago

The Alliance for Genome Resources (AGR) maintains a list of gene-disease associations for seven organisms (including human, mouse, rat, fly, worm, zebrafish, and yeast) at https://www.alliancegenome.org/downloads. Files can be downloaded in either JSON or TSV. I don't think these data have been imported into any other biothings API. They are candidates for inclusion in mygene.info and mydisease.info, but as a starting point we should create a pending API. This would be incredibly useful for Translator...

sierra-moxon commented 3 years ago

'DBobjectType' in these files can be one of several values: 'gene', 'allele', 'affected genomic model'. 'DBobjectType' = 'gene' rows/objects are probably the ones you are looking for.

('affected genomic model' DBobjecType, is a grouping class for 'genotype', 'strain', 'population' or 'genotype + sequence targeting reagents like morpholinos, crisprs and talens'. 'affected genomic model' objects represent animal 'models of' a human disease).

If you need more information about how the gene->disease annotations are made (these are a result of curation at either the gene, allele, or affected genomic model levels), please do let me know. Here's one paper that describes MGI's approach.

tokebe commented 3 years ago

Thank you, I've included filtering to only inlcude 'DBobjectType' == 'gene' rows in the parser. I think I have it working, though please let me know if I missed anything. I just updated my PR with an example output document in case that's useful.

erikyao commented 3 years ago

Hi @tokebe, sorry we cannot deploy the new API due to some minor technical issues in the new biothings API v0.10 (see this comment). Will keep you updated. Thank you!

erikyao commented 3 years ago

It's published! Check https://pending.biothings.io/agr

Please let me know if you found anything wrong. Thank you!

andrewsu commented 3 years ago

looks good to me! @colleenXu can you create a new issue to create a smartAPI record for this new API? prioritize as you see fit..

colleenXu commented 3 years ago

Added an issue about this here: https://github.com/biothings/BioThings_Explorer_TRAPI/issues/260