Gennari, JH, König, M, Misirli, G, Neal, ML, Nickerson, DP and Waltemath, D (2021) OMEX metadata specification (version 1.2). Journal of integrative bioinformatics, 18 (3). ISSN 1613-4516

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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.

Item Type: Article
Additional Information: Open Access. © 2021 John H. Gennari et al., published by De Gruyter.This work is licensed under the Creative Commons Attribution4.0 International License.
Uncontrolled Keywords: biosimulation modeling; COMBINE standards; metadata; semantics
Subjects: Q Science > Q Science (General)
Q Science > QA Mathematics
T Technology > T Technology (General)
Divisions: Faculty of Natural Sciences > School of Computing and Mathematics
Related URLs:
Depositing User: Symplectic
Date Deposited: 04 Nov 2021 15:23
Last Modified: 11 Feb 2022 11:31

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