biothings / myvariant.info

MyVariant.info: A BioThings API for human variant annotations
http://myvariant.info
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Add CURIE ID support for some myvariant identifiers #186

Closed newgene closed 3 months ago

newgene commented 5 months ago

With the latest biothings sdk release (0.12.4+), we can now add the CURIE ID support for MyVariant API:

We currently have these in the config_web.py:

ANNOTATION_ID_REGEX_LIST = [
    (re.compile(r'rs[0-9]+', re.I), 'dbsnp.rsid'),
    (re.compile(r'rcv[0-9\.]+', re.I), 'clinvar.rcv.accession'),
    (re.compile(r'var_[0-9]+', re.I), 'uniprot.humsavar.ftid')
]

We can consider adding the support for these CURIE ID patterns:

DBSNP:rs110000   `dbsnp.rsid`
CLINVAR:\d+    `clinvar.variant_id`
CAID:CA\d+  `clingen.caid`               # clingen source is hg38 only 

This query can help get some example ids:

https://myvariant.info/v1/query?q=_exists_:clingen.caid%20AND%20_exists_:clinvar&fields=dbsnp.rsid,clingen,clinvar.variant_id,clinvar.rcv.accession&assembly=hg38