How to access genetic evidence from Genomics England from 22.09 Platform release

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1

Dear Team,

I am wondering how to download these 35,690 genetic evidence.

Thanks

Shicheng

2

Hi @Shicheng_Guo,

you can filter the evidence dataset on the sourceId field. You can inspect all the different values in this field to extract what is the nomenclature we use for each source.

A snippet in Pyspark would be:

evd = spark.read.parquet('gs://open-targets-data-releases/22.09/output/etl/parquet/evidence')

evd.filter(f.col('sourceId') == 'genomics_england').count()
>> 35690
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3

Thank you so much Irene!! Really appreciated for your swift support!!

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4

Do we have any delay for the ingestion of latest version of Genomics England data?

Thanks.

Shicheng

5

Hi!

Panel App data was updated in September. This version includes less panels but of a better quality. Most importantly, we have included 173 panels signed off by the NHS in their genomic testing strategy to identify rare and inherited diseases.

The evidence in the upcoming will essentially be the same, only considering that the disease mapping will be based on EFO version 3.47.

I hope this answers your question!
Irene

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