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.
Funding source: U.S. National Institutes of Health
Award Identifier / Grant number: P41-EB023912
Funding source: German Federal Ministry of Education and Research (BMBF) as part of the e:Bio program SEMS
Award Identifier / Grant number: FKZ 031 6194
Funding source: Aotearoa Foundation Physiome Fellowship
Funding source: German Federal Ministry of Education and Research (BMBF) as part of the research network Systems Medicine of the Liver (LiSyM)
Award Identifier / Grant number: 031L0054
© 2020 Maxwell L. Neal et al., published by De Gruyter, Berlin/Boston
This work is licensed under the Creative Commons Attribution 4.0 International License.