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OMEX metadata specification (version 1.2).

Nickerson, DP; Waltemath, D; Gennari, JH; König, M; Misirli, G; Neal, ML

OMEX metadata specification (version 1.2). Thumbnail


DP Nickerson

D Waltemath

JH Gennari

M König

ML Neal


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. This document details version 1.2 of the specification, which builds on version 1.0 published last year in this journal. In particular, this version includes a set of initial model-level annotations (whereas v 1.0 described exclusively annotations at a smaller scale). Additionally, this version uses best practices for namespaces, and introduces as a common root for all annotations. Distributing modeling projects within an OMEX archive 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 representations. This specification acts as a technical guideline for developing software tools that can support this standard, and thereby encourages broad advances in model reuse, discovery, and semantic analyses.


Nickerson, D., Waltemath, D., Gennari, J., König, M., Misirli, G., & Neal, M. (2021). OMEX metadata specification (version 1.2). Journal of Integrative Bioinformatics,

Acceptance Date Aug 27, 2021
Publication Date Oct 20, 2021
Journal Journal of integrative bioinformatics
Print ISSN 1613-4516
Publisher De Gruyter
Keywords biosimulation modeling; COMBINE standards; metadata; semantics
Publisher URL


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