Computational Biology and Informatics Lab (CBIL)
ErythronDB website and database available as docker build Thursday, February 9, 2023 The original ErythronDB website was retired at the end of 2022. The site can be built using code available here.
CBIL site migration to GitHub complete Tuesday, December 20, 2022 Selected content from the www.cbil.upenn.edu site has been migrated to https://cstoeckert.github.io./ Links to tools and databases now point to summaries or a Content Not Available page. The original CBIL site has been repointed to the GitHub site and the CBIL server hosting the web pages for projects will be shut down later this week.
New release of the TURBO ontology Thursday, June 9, 2022 The TURBO ontology supporting the Semantic Engine application has been updated and refactored using the ODK. Details of the new release are here.
New release of the VEuPathDB ontology Thursday, June 8, 2022 A new release is available of the VEuPathDB ontology supporting the VEuPathDB, ClinEpiDB, and MicrobiomeDB projects. Details of the new release are here.
CBIL site content moving to GitHub Thursday, January 6, 2022 - 10:01 Selected content from the www.cbil.upenn.edu site will be migrated to https://cstoeckert.github.io./ over the course of 2022. Once the migration is complete, the original CBIL site will be shut down.
New release of OBIB Monday, August 9, 2021 - 11:45 We made a new release of the Ontology for Biobanking earlier this year (2021-02-02). The release includes new imports from OBI, updates of deprecated terms, new terms and fixes including those fixes identified by the OBO Foundry dashboard.
A novel tool for standardizing clinical data in a semantically rich model Monday, January 4, 2021 - 11:25 As part of our TURBO project, we recently published a paper on “A novel tool for standardizing clinical data in a semantically rich model” in the Journal of Biomedical Informatics (https://www.sciencedirect.com/science/article/pii/S2590177X20300214). Our article is open access and our tool is at https://github.com/PennTURBO/semantic-engine.
GUS now on GitHub Monday, January 4, 2021 - 11:16 The Genomics Unified Schema (GUS) relational database system has been actively developed and maintained for some time by project members of VEuPathDB ( http://veupathdb.org). In 2020, the code base for GUS was moved from subversion to GitHub. GUS repositories are https://github.com/VEuPathDB/GusSchema and https://github.com/VEuPathDB/GusAppFramework.