Welcome to BioMed Sample Sheet


Project Status

While the cancer and germline TSV sheets, the JSON sheets, and the shortcut modules are useable, this project is still in “pre-release” status. We hope that the API will remain fairly stable but it can (and probably) will change in the future. The main aim of these early releases is for allowing to get feedback.

This document describes the current draft of the biomedical sample sheets.

The project consists of

  • a JSON-based data format for the description of biomedical sample sheets,
  • pre-defined data types to be used in the sample sheets,
  • a Python program for the validation thereof,
  • a Python program for conversion between JSON and TSV-based sample sheets (for easier viewing and editing),
  • a Python library for access of the JSON sheets, and
  • a Python library for simplified access of the JSON sheets for the important cases of matched tumor/normal studies and rare disease studies with pedigree relationships.

Open Questions

  • Keep or drop globally unique PKs from the file names? Random pks make everything very hard to use as files, add complexity to shortcut schemas. Sequential pks at least keep a temporal order.