University of Washington, Seattle, USA.
Humboldt University, Berlin, Germany.
J Integr Bioinform. 2021 Oct 20;18(3):20210020. doi: 10.1515/jib-2021-0020.
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 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.
一种对计算生物医学模型及其相关文件进行注释的标准化方法，可以促进研究小组之间模型的重复使用和可重复性，增强模型和数据的搜索和检索，并实现模型之间的语义比较。受这些潜在益处的启发，并在计算生物学网络（COMBINE）社区的共识指导下，我们为在 Open Modeling and EXchange (OMEX) 格式档案中进行注释制定了一个规范。本文详细介绍了该规范的 1.2 版本，该版本基于去年在本期刊上发布的 1.0 版本。特别是，这个版本包括了一组初始的模型级注释（而 v1.0 仅在更小的规模上描述了注释）。此外，这个版本使用了名称空间的最佳实践，并引入了 omex-library.org 作为所有注释的通用根。在 OMEX 档案中分发建模项目是 COMBINE 建立的最佳实践，这里提出的 OMEX 元数据规范为注释各种标准化模型表示提供了一种协调一致的、由社区驱动的方法。该规范作为开发可以支持该标准的软件工具的技术指南，从而鼓励模型重用、发现和语义分析的广泛发展。
