Genetic constraint data in BigQuery

Data Access Google BigQuery/Cloud
1

I am interested in the “genetic constraints” info available from the Open Targets Platform. However, this bit of info seems like it is not available in BigQuery (platform release version 21.11).

Would it be possible to add it or should I fetch this directly from gnomAD?

This question was sent to the Open Targets helpdesk and has been posted here so answers can benefit the whole Community of users.

2

Hello,

Yes, the genetic constraint data for targets is available in Google BigQuery in the constraint field in the open-targets-prod.platform.targets table.

Here is a sample query to find the genetic constraint data for MTOR (ENSG00000198793):

SELECT
  targets.id,
  targets.approvedSymbol,
  gnomADConstraintList.element.constraintType,
  gnomADConstraintList.element.score,
  gnomADConstraintList.element.exp,
  gnomADConstraintList.element.obs,
  gnomADConstraintList.element.oe,
  gnomADConstraintList.element.oeLower,
  gnomADConstraintList.element.oeUpper,
  gnomADConstraintList.element.upperRank,
  gnomADConstraintList.element.upperBin,
  gnomADConstraintList.element.upperBin6
FROM
  `open-targets-prod.platform.targets` AS targets,
  UNNEST (targets.constraint.list) AS gnomADConstraintList
WHERE
  targets.id = 'ENSG00000198793'

Alternatively, you can also use targets datasets in either JSON or Parquet formats and query for the constraint field to find the same information.