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To support more complex queries and advanced informatics workflows that use Google Cloud services, the Open Targets Platform data is also available as a Google Cloud public dataset via our Google BigQuery instance — open-targets-prod.
Google BigQuery is a data warehouse that enables researchers to run super-fast, asynchronous SQL queries using Google's cloud infrastructure. After running your query, you can either export into various formats or copy into a Google Cloud bucket for further downstream analyses.
Open Targets Platform data is publicly accessible as a Google Cloud public dataset. Users only pay for the queries they perform on the data, and through this program, the first 1 TB per month is free.
Open Targets has uploaded all of our data to Google BigQuery. You can run queries via:
Below is a sample query that uses our
associationByOverallDirectdataset to return a list of targets associated with psoriasis (EFO_0000676) and the overall association score.
associations.targetId AS target_id,
targets.approvedSymbol AS target_approved_symbol,
associations.diseaseId AS disease_id,
diseases.name AS disease_name,
associations.score AS overall_association_score
`open-targets-prod.platform.associationByOverallDirect` AS associations
`open-targets-prod.platform.diseases` AS diseases
associations.diseaseId = diseases.id
`open-targets-prod.platform.targets` AS targets
associations.targetId = targets.id
Similarly, you can use our
moleculedataset and pass a list of drug trade names to find relevant information:
my_drug_list = [ 'Premarin',
'Calcium disodium versenate',
id AS drug_id,
name AS drug_chembl_name,
tradeNameList.element AS drug_trade_name,
drugType AS drug_type,
isApproved AS drug_is_approved,
blackBoxWarning AS drug_blackbox_warning,
hasBeenWithdrawn AS drug_withdrawn,
UNNEST (tradeNames.list) AS tradeNameList
(tradeNameList.element) IN UNNEST(my_drug_list)