Chunlei Wu

Results 67 comments of Chunlei Wu

@SusiJo the issue with oncoKB is their license. We may not be able to incorporate their data into our API.

@erikyao Looks like `post_download` or `post_dump` might be the good place to add the md5 check for a data src like dbsnp: https://github.com/biothings/biothings.api/blob/181a36fc2d5f782bb3608ec032891b0eaa9e7e1d/biothings/hub/dataload/dumper.py#L162-L172

see an example here from mychem: https://github.com/biothings/mychem.info/commit/79f704b4424036d06014798a2f143bcfab4617e8 and a small change https://github.com/biothings/mychem.info/commit/6fa89376efff4fb1886253f18f97d11d9e1b8889

We can provide a "data plugin" available for standalone myvariant.info instance when users have the permission to use HGMD. But it won't available in public myvariant.info API due to the...

Another possible option is we can provide a parser, but standalone instance users (in-house, not the public one) who do have the HGMD license, can get the dumped HGMD-RPO file...

@andrewsu can you please locate the particular data file at https://portals.broadinstitute.org/ccle/data?

also parameters implemented in https://github.com/biothings/mygene.py/issues/11

@NikkiBytes let's make the `taxid` field as an integer.

One way doing this is to use EBI's OLS API to get the children GO IDs and then query MyGene.info API: https://www.ebi.ac.uk/ols/docs/api