期刊
JOURNAL OF INTEGRATIVE BIOINFORMATICS
卷 18, 期 3, 页码 -出版社
WALTER DE GRUYTER GMBH
DOI: 10.1515/jib-2021-0020
关键词
biosimulation modeling; COMBINE standards; metadata; semantics
资金
- NIH [P41 GM109824]
- Federal Ministry of Education and Research (BMBF, Germany) [031L0054]
The specification provides a technical guideline for encoding standardized annotations in computational biomedical models and their associated files, promoting model reuse and enabling semantic comparisons.
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 names paces, and introduces omex-library.org 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.
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