Genetic disorder of ClinVar in EVA

General
1

Dear Team,

I find lots of records in ClinVar from EVA, like the below. I am wondering is there any plan to make this one more explicit in our next update/version?

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Meanwhile, It looks some significant result from ClinVar is not showed in OT as below.

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@Shicheng_Guo Regarding your first question: unfortunately ClinVar contains a lot of entries with very nonspecific terms such as “Inborn genetic diseases” and the like, which don’t contain any actual disease information and get mapped into the root ontology term “genetic disorder”. This is an example for three of the RCVs on your first screenshot which I randomly checked:

There is nothing we can do on our side, because there’s no disease information to extract from these terms. It would be great if ClinVar didn’t allow such non-specific submissions because they are nearly useless, but this is outside of our control.

As for the second question you raised, I’m currently looking into it.

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@Shicheng_Guo I have now checked the second issue. The reason is version sync. The term “hypercholanemia, familial, 2” only appeared in EFO in version 3.60.0, which was released on the 15th of November 2023. However, when we were preparing the 23.12 release, the EFO version was fixed at 3.58.0. (We need to freeze the versions of external data sources and ontologies in advance, so that we can do data preparation and appropriate QC in time.) So this term should appear starting from the next release.

I’ll be marking this discussion as answered, but please let me know if you have any further questions or concerns.

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Awesome!! Thank you Kirill!! Happy New Year!!

It looks EFO is also mainly leading by Open Targets. I am wondering How frequently EFO will be updated? each quarter or each month? I notice the latest version is 3.61.0

Thanks.

Shicheng

6

@Shicheng_Guo EFO isn’t directly developed by Open Targets, however, it’s developed by SPOT, which is another team at EBI: Services | EMBL’s European Bioinformatics Institute

You can find their GitHub with source code, issues and release notes here: Releases · EBISPOT/efo · GitHub. As you can see, they are doing the releases roughly monthly.

Please let me know if you have any further questions.

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Do we have a Github project for Open Targets?

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@Shicheng_Guo Yes, all Open Targets repositories live under Open Targets · GitHub. Please let me know if you are interested in any project in particular