Skip to content

Conversation

@bencap
Copy link
Collaborator

@bencap bencap commented Dec 18, 2025

This pull request adds a script that exports variants from a given score set URN into a CSV/TSV with appropriate format to submit to ClinVar.

Run the script with

with_mavedb_db_session poetry run python3 -m mavedb.scripts.tabular_clinvar_submission <score set URN> ./output-directory --format csv

A few outstanding questions remain:

  • For the Condition ID and Condition Value, we are generating MedGen and C0012634 (the generic 'disease' condition) for all score sets. We should verify this condition is appropriate.
  • For Assay Type, we should talk with ClinVar about their various allowed assay types shown here: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/functional_assay_types.txt. These assay types don't seem to have an appropriate ontology for certain assays in MaveDB, such as Label-Seq or VAMP-Seq.
  • For Molecular Phenotype Measured, we should talk with ClinVar about an appropriate ontology for the field. We should also ensure we have a robust decision tree for moving from our controlled keywords for molecular phenotype to whatever we decide on with ClinVar.
  • We should ensure that the score set method and primary publication are appropriate to send as the method and method citation.
  • We should discuss how to handle score sets with categorical calibrations, as ClinVar's submission format only seems to accept range based calibrations.
  • We should go through the other blank columns and verify these do not require submission values.

@bencap bencap linked an issue Dec 18, 2025 that may be closed by this pull request
@bencap bencap force-pushed the feature/bencap/538/categorical-calibrations branch from d524416 to 4962f4f Compare December 18, 2025 20:43
@bencap bencap force-pushed the feature/bencap/599/script-for-tabular-clinvar-submission branch 2 times, most recently from 0d1726f to dddae2b Compare December 18, 2025 20:52
Work in progress script for ClinVar tabular file generation in a format
appropriate for submission. Some outstanding questions remain to be
resolved, specifically around the ontologies desired for submission
and the handling of categorical scoring ranges.
@bencap bencap force-pushed the feature/bencap/599/script-for-tabular-clinvar-submission branch from dddae2b to f529aad Compare December 23, 2025 16:24
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

ClinVar submission exploration

2 participants