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create new API for gene-disease associations from AGR #28

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andrewsu opened this issue Aug 2, 2021 · 6 comments
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create new API for gene-disease associations from AGR #28

andrewsu opened this issue Aug 2, 2021 · 6 comments
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@erikyao @tokebe
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data source Data source pending to create a new API

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@andrewsu
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andrewsu commented Aug 2, 2021

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...
@newgene newgene added the data source Data source pending to create a new API label Aug 2, 2021
@andrewsu andrewsu mentioned this issue Aug 3, 2021
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@tokebe tokebe mentioned this issue Aug 12, 2021
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@sierra-moxon
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sierra-moxon commented Aug 12, 2021 •
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'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
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tokebe commented Aug 12, 2021

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.

@tokebe tokebe closed this as completed Aug 12, 2021
@tokebe tokebe reopened this Aug 12, 2021
@erikyao erikyao self-assigned this Aug 17, 2021
@erikyao
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erikyao commented Aug 17, 2021 •
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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
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erikyao commented Aug 20, 2021

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

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

@erikyao erikyao closed this as completed Aug 20, 2021
@andrewsu
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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
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Added an issue about this here: biothings/biothings_explorer#260

@andrewsu andrewsu mentioned this issue Sep 21, 2021
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@newgene @andrewsu @sierra-moxon @erikyao @tokebe @colleenXu