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biothings / myvariant.info

MyVariant.info: A BioThings API for human variant annotations
http://myvariant.info
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Data source: GWAS Central #69

Open newgene opened 5 years ago

newgene commented 5 years ago

https://help.gwascentral.org/data/download/

namespacestd0 commented 5 years ago

I am inclined to think there's no straightforward way to dump this source entirely.

A biomart XML query

https://mart.gwascentral.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query><Query  virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.7" ><Dataset name = "study" interface = "default" ><Filter name = "gene_region" value = "%"/><Attribute name = "identifier" /><Attribute name = "name" /></Dataset></Query>

returns Internal Server Error.

It does mention here regarding

accessing BioMart via the martservice webservices interface

https://mart.gwascentral.org/biomart/mview/help.html

but it seems to be a generic biomart instruction and there is no mention of RESTful APIs similar to: http://uswest.ensembl.org/info/data/biomart/biomart_restful.html.

In MartView, results seem only to be exported by email.

An email I received indicated:

Your query returns more than our threshold of 1,000 results (76,300,402 in total). To gain access to the remaining data please email us at help@gwascentral.org and specify the job ID (0709191252_318)

Maybe we can contact them via email for data download help.