Google BigQuery
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
associationByOverallDirect dataset to return a list of targets associated with psoriasis (EFO_0000676) and the overall association score.SELECT
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
FROM
`open-targets-prod.platform.associationByOverallDirect` AS associations
JOIN
`open-targets-prod.platform.diseases` AS diseases
ON
associations.diseaseId = diseases.id
JOIN
`open-targets-prod.platform.targets` AS targets
ON
associations.targetId = targets.id
WHERE
associations.diseaseId='EFO_0000676'
ORDER BY
associations.score DESC
Similarly, you can use our
molecule dataset and pass a list of drug trade names to find relevant information:DECLARE
my_drug_list ARRAY<STRING>;
SET
my_drug_list = [ 'Premarin',
'Calcium disodium versenate',
'Keytruda',
'Vioxx',
'Humira' ];
SELECT
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,
FROM
`open-targets-prod.platform.molecule`,
UNNEST (tradeNames.list) AS tradeNameList
WHERE
(tradeNameList.element) IN UNNEST(my_drug_list)
For more information on how to use BigQuery to access Platform data and example queries based on actual use cases and research questions, check out the Open Targets Community and our Google Cloud dataset homepage.
Last modified 1yr ago