search

clingen-data-model / clinvar-ingest-reports

ClinGen generates several google sheet based reports from the ClinVar ingested data that originates from the Broad BigQuery data.
0 stars 0 forks source link

ClinVar ingest v2 - Somatic XML release 2023 Q4 #50

Open larrybabb opened 1 year ago

larrybabb commented 1 year ago

The clinvar-ingest service will break by Start of Year 2024 based on ClinVar's recent announcement...

Dear colleague,

We anticipate changes to the ClinVar XML files and our submission spreadsheet templates in the fall of 2023 to improve support for classifications of somatic variants in ClinVar. Submission of somatic variants through the API and the submission wizard will be added in 2024.

To help our users and submitters prepare for this change, we are providing a preview of submission spreadsheet templates, updated XSDs, sample XMLs, and supporting documentation on GitHub. The documentation includes:

a preview of the updated XSDs for both RCV and VCVXMLs a list of changes to both XSDs sample XMLs for both RCV and VCV a note explaining Classification on ClinVar aggregated records IMPORTANT: The sample XML is fake data, for testing purposes only! All of the data in the sample XML is fake, including the submitters, the variants, the tumor types, and all supporting data. It is dummy data only to demonstrate what kind of data would be in each field and so that you have test data to use when updating your code. Do NOT incorporate this data into your production system.

Once the new XML format is available, we will support the old XML format through the end of 2023. We encourage our XML users to start the transition to the new XML format as soon as you can, and to contact us at clinvar@ncbi.nlm.nih.gov with any questions.

Please share this information with your colleagues, including your bioinformatics team!

Sincerely,

The ClinVar Team

larrybabb commented 1 year ago

There is planning and urgency around figuring out how we will handle this forthcoming change.

In the meantime, I respectfully requested that clinvar give us at least 6 months after they release the first "production" XML change before stopping production of the current XML format. They seem set on only supporting the current format until EOY 2023. I suspect it will be pretty late into 2023 before the stable version of this file format is made available.

Their expectation (I believe) is that we assume the current proposed XML file format is the final design and that we should all assume it will be ready on day 1. History proves otherwise.