Identifier for this specification is: https://identifiers.org/combine.specifications:omex-metadata
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.
OMEX metadata is defined in a set of specification documents that describe the elements of the language and its syntax.
The latest specifications are available here:
- OMEX metadata 1.2: https://identifiers.org/combine.specifications:omex-metadata.1.2
- OMEX metadata 1.0: https://identifiers.org/combine.specifications:omex-metadata.1.0
OMEX Metadata development is discussed on the combine-annot mailing list at https://groups.google.com/forum/#!forum/combine-annot.
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.
Neal ML, Gennari JH, Waltemath D, Nickerson DP, König M. 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. PMID: 32589606; PMCID: PMC7756623.
Gennari JH, König M, Misirli G, Neal ML, Nickerson DP, Waltemath D. OMEX metadata specification (version 1.2). J Integr Bioinform. 2021 Oct 20;18(3):20210020. doi: 10.1515/jib-2021-0020. PMID: 34668356; PMCID: PMC8560343.
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.