Google BigQuery

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Google BigQuery
To support more complex queries and advanced informatics workflows that use Google Cloud services, the Open Targets Platform data is also available via our Google BigQuery instance - open-targets-prod.
What is Google BigQuery?
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.
BigQuery access points
Open Targets has uploaded all of our data to Google BigQuery. You can run queries via:
​Cloud Console​
​Command line bq tool​
​Client libraries, including Python​
For more information on BiqQuery, please review the BigQuery documentation.
Example BigQuery SQL queries
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. 
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SELECT
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  associations.targetId AS target_id,
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  targets.approvedSymbol AS target_approved_symbol,
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  associations.diseaseId AS disease_id,
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  diseases.name AS disease_name,
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  associations.score AS overall_association_score
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FROM
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  `open-targets-prod.platform_21_06.associationByOverallDirect` AS associations
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JOIN
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  `open-targets-prod.platform_21_06.diseases` AS diseases
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ON
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  associations.diseaseId = diseases.id
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JOIN
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  `open-targets-prod.platform_21_06.targets` AS targets
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ON
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  associations.targetId = targets.id
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WHERE
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  associations.diseaseId='EFO_0000676'
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ORDER BY
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  associations.score DESC
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​Run this query in BigQuery​
Similarly, you can use our molecule dataset and pass a list of drug trade names to find relevant information:
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DECLARE
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  my_drug_list ARRAY<STRING>;
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SET
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  my_drug_list = [ 'Premarin',
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  'Calcium disodium versenate',
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  'Keytruda',
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  'Vioxx',
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  'Humira' ];
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SELECT
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  id AS drug_id,
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  name AS drug_chembl_name,
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  tradeNameList.element AS drug_trade_name,
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  drugType AS drug_type,
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  isApproved AS drug_is_approved,
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  blackBoxWarning AS drug_blackbox_warning,
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  hasBeenWithdrawn AS drug_withdrawn,
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FROM
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  `open-targets-prod.platform_21_06.molecule`,
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  UNNEST (tradeNames.list) AS tradeNameList
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WHERE
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  (tradeNameList.element) IN UNNEST(my_drug_list)
Copied!
​Run this query in BigQuery​
Tutorials and how-to guides
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.
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Last modified 27d ago
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Contents
What is Google BigQuery?
BigQuery access points
Example BigQuery SQL queries
Tutorials and how-to guides