ClinVar submission complaints

[alexejknaus]

After generating an XML submission for a single variant, ClinVar issued several complaints:

1. • If it is not too difficult, please include the appropriate submission ID (sub_id="SUB9964212") in the first line of each file. If that is too difficult, we will add it before processing:

How should it be possible to add a submission ID, prior submission?
Suggestion:

• A user starts a ClinVar submission as a dummy in ClinVar, thereby generating a SUB-ID
• The SUB-ID is added into a field in VarFish ClinVar submission tool.

2. • Please include either the trait Preferred name OR Database identifier in ObservedIn (/ClinvarSubmissionSet/ClinvarSubmission/MeasureTrait/ObservedIn/TraitSet/Trait/Name OR /ClinvarSubmissionSet/ClinvarSubmission/MeasureTrait/ObservedIn/TraitSet/Trait/XRef) because we no longer process both Preferred name and Database identifier. HPO Database IDs are preferred.

Please adjust that HPO terms are submitted only in the VarFish ClinVar submission tool, so that instad of
<Trait>
<TraitType val_type="name">Finding</TraitType>
<Name>
<ElementValueType val_type="name">Preferred</ElementValueType>
<ElementValue>Muscular hypotonia of the trunk</ElementValue>
</Name>
<XRef db="HP" id="HP:0008936"/>
</Trait>

it only shows:

<Trait>
<TraitType val_type="name">Finding</TraitType>
<XRef db="HP" id="HP:0008936"/>
</Trait>

3. • Please include either the trait Preferred name and Database identifier in the ClinVarSubmission TraitSet
     (/ClinvarSubmissionSet/ClinvarSubmission/TraitSet/Trait/Name OR /ClinvarSubmissionSet/ClinvarSubmission/TraitSet/Trait/XRef),
     because we no longer process both Preferred name and Database identifier. The Database ID is preferred and can be any of OMIM, MeSH, MedGen, UMLS, Orphanet, HPO, or MONDO IDs.

The reason for missing condition name was that OMIM db was not up-to-date in VarFish. This is requested in another ticket.

[ahujameg]

The XSD schema version for clinvar export used in VarFish is 1.6. The latest schema version in ClinVar is 1.7 where enumeration for Named Protein Variant is added to the list of Trait Types. So the same needs to be updated in Varfish.

[holtgrewe]

Fixed in #226.