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Version 1.4.0

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@Genarito Genarito released this 15 Jun 20:43
· 1 commit to master since this release
1.4.0
7a4e792

This release updates BioAPI’s database import pipeline, dependencies, and documentation, with a focus on OncoKB and STRING data processing.

Highlights

  • Updated Python dependencies for both the API and genomic ETL tools
  • Improved OncoKB import support, including new XLSX-to-JSON processing for precision oncology therapies
  • Added a new STRING import script and improved duplicate handling during import
  • Corrected and refactored the BioMart/CiVIC gene data retrieval script
  • Updated deployment and project documentation to match the new database sources and filenames
  • Upgraded MongoDB from 6.0.12 to 8.3.2
  • Upgraded NGINX from 1.23.3 to 1.31

Technical changes

  • Fixed the OncoKB collection name used by the API
  • Updated OncoKB import scripts and dataset filenames
  • Refactored cancer gene list parsing for newer OncoKB formats
  • Updated the HGNC download source
  • Removed legacy bundled OncoKB data files
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