Thanks to some assistance from the gnomAD team, we have identified a batch-query API that allows fetching gene constraint information from gnomAD. This reimplements an improved and modernized gene constraint table using the new data source.
"errors":[{"message":"gnomAD v2.1.1 data is not available on reference genome GRCh38"
TODO
At present, gnomAD has no constraint data for GRCh38, even in the v3 dataset. After deconstructing their API calls, it's not clear how to request different datasets. The error message we get on requesting build 38 data refers to dataset 2.1.1, even in gnomad v3. It's possible that the error message is unclear.
We will reach out to the gnomAD team. Since this would be no worse than the current system, it is a target for future improvement, but not a blocker for this release.
Ref: #174
Purpose
Thanks to some assistance from the gnomAD team, we have identified a batch-query API that allows fetching gene constraint information from gnomAD. This reimplements an improved and modernized gene constraint table using the new data source.
Caveats
It appears that gnomAD does not yet have constraint data for build 38. (example: https://gnomad.broadinstitute.org/gene/ENSG00000148737?dataset=gnomad_r3 ) This table will only appear for build 37 datasets. For build 38, the table will not be present on tooltips.
"errors":[{"message":"gnomAD v2.1.1 data is not available on reference genome GRCh38"TODO
At present, gnomAD has no constraint data for GRCh38, even in the v3 dataset. After deconstructing their API calls, it's not clear how to request different datasets. The error message we get on requesting build 38 data refers to dataset 2.1.1, even in gnomad v3. It's possible that the error message is unclear.
We will reach out to the gnomAD team. Since this would be no worse than the current system, it is a target for future improvement, but not a blocker for this release.