Closed andrewsu closed 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.
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.
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!
It's published! Check https://pending.biothings.io/agr
Please let me know if you found anything wrong. Thank you!
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..
Added an issue about this here: https://github.com/biothings/BioThings_Explorer_TRAPI/issues/260
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...