Open modeling and exchange (OMEX) metadata specification version 1.0

J Integr Bioinform. 2020 Jun 25;17(2-3):20200020. doi: 10.1515/jib-2020-0020.


A standardized approach to annotating computational biomedical models and their associated files can facilitate model reuse and reproducibility among research groups, enhance search and retrieval of models and data, and enable semantic comparisons between models. Motivated by these potential benefits and guided by consensus across the COmputational Modeling in BIology NEtwork (COMBINE) community, we have developed a specification for encoding annotations in Open Modeling and EXchange (OMEX)-formatted archives. Distributing modeling projects within these archives is a best practice established by COMBINE, and the OMEX metadata specification presented here provides a harmonized, community-driven approach for annotating a variety of standardized model and data representation formats within an archive. The specification primarily includes technical guidelines for encoding archive metadata, so that software tools can more easily utilize and exchange it, thereby spurring broad advancements in model reuse, discovery, and semantic analyses.

Keywords: data integration; metadata; semantics; simulation.

MeSH terms

  • Computational Biology
  • Metadata*
  • Reproducibility of Results
  • Semantics
  • Software*