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BY 4.0 license Open Access Published by De Gruyter June 25, 2020

Open modeling and exchange (OMEX) metadata specification version 1.0

Maxwell L. Neal ORCID logo EMAIL logo , John H. Gennari ORCID logo , Dagmar Waltemath ORCID logo , David P. Nickerson ORCID logo and Matthias König ORCID logo

Abstract

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.


Corresponding author: Maxwell L. Neal, Seattle Children’s Research Institute, Seattle, USA, E-mail:

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

Received: 2020-04-16
Accepted: 2020-04-26
Published Online: 2020-06-25

© 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.

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