We are currently working through a bug (#1565) that prevents users from downloading certain data tables from the user interface, such as known drugs for a given disease. We aim to have it resolved for our next release, at the end of June.
In the meantime, how else can you access this data?
One way to access the data is to use our data downloads, specifically the KnownDrugsAggregated dataset, available in JSON or Parquet format from the FTP. For more information, and for sample Python and R scripts, check out our dataset documentation.
You can also use our BigQuery instance — open-targets-prod — to retrieve the data using an SQL query.
Here is an example query for a single disease, EFO_1001947, which you can run directly here:
SELECT targetId, approvedSymbol, approvedName, diseaseId, label, drugId, prefName, drugType, mechanismOfAction, phase, status, urlList.element.niceName, urlList.element.url, FROM `open-targets-prod.platform_21_04.knownDrugsAggregated`, UNNEST (urls.list) as urlList WHERE diseaseId='EFO_1001947' ORDER BY phase desc
You’ll notice that the number returned by BigQuery (175) is different from the number returned on the childhood T acute lymphoblastic leukemia profile page (138). This is because in BigQuery, the script has been set to return separate rows for each source entry in the
urls.list array, whereas in the web interface, we aggregate the data in the Source column (e.g. 2 references).
@irene recently resolved a similar question, this time extracting the list of known drugs for multiple targets: