OMEX Metadata Specification
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 COMBINE community, we have developed a specification for encoding annotations in 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.
Normative definitions
OMEX metadata is defined in a set of specification documents that describe the elements of the language and its syntax.
Communication
OMEX Metadata development is discussed on the combine-annot mailing list at https://groups.google.com/forum/#!forum/combine-annot.
Software support
libsemsim, a C/C++ library that supports the OMEX metadata specification is under development at https://github.com/sys-bio/libsemsim.
The SemSim Java API, a Java library that supports the specification is under development at https://github.com/SemBioProcess/SemSim-Java-API.
How to cite OMEX Metadata
This will be updated once an appropriate paper is published.
History
Guided by consensus from the COMBINE community, the OMEX metadata specification has been developed by Maxwell Neal, John Gennari, Dagmar Waltemath, David Nickerson, and Matthias König.