How Open Target to track ClinVar and OMIM update?

General
1

Dear Team,

I know ClinVar are updated very frequently, I am wondering how Open Target to track these update? The latest ClinVar are usually be loaded when Open Target are updated, corrected?

Thanks.

Shicheng

2

Hi @Shicheng_Guo,

ClinVar data is processed by the EVA team using the CMAT toolkit developed by them for Open Targets. At the time of running, this pipeline always ingests the latest ClinVar FTP release from this FTP directory: Index of /pub/clinvar/xml

After the pipeline is run, several things need to happen: the EVA team perform manual curation, generate evidence strings, and submit them to us at Open Targets. We then QC the data, aggregate it with the other evidence evidence sources, and perform a release. Because of this, the ClinVar data in the latest Open Targets release might not always correspond to the latest data available from ClinVar directly at the time when the release is being performed.

Hope that helps, please let me know if you have any more questions or concerns.

With kind regards,
Kirill

1 Like