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. 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.
Highlights
1.1 MotivationMetadata annotations enhance the interoperability, reusability, comparability, and comprehension of computational models in biology
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
The following is an example singular semantic annotation indicating that the model element with metadata ID “meta0013” from the model file “MyModel.sbml” represents adenosine triphosphate: OMEXmodel:meta0013 bqbiol:is chebi
Summary
Metadata annotations enhance the interoperability, reusability, comparability, and comprehension of computational models in biology. Annotations can capture the biological meaning of what a model simulates, specify precisely the components comprising a model, describe a model’s provenance, provide layout information for visualizing a model’s architecture, etc. These annotations can be leveraged to make it easier for researchers to find and re-purpose models, re-combine models and model parts, and integrate models across repositories and experimental data stores. Realizing the potential benefits of annotation requires the development of standards that adhere to a community-based annotation protocol Without such standards, researchers must account for a variety of annotation formats and approaches, a situation that can become prohibitively cumbersome and which can defeat the purpose of annotating a model. Our hope is that community-wide adherence to this specification will significantly advance the community’s ability to discover relevant models and data sets as well as to re-purpose/re-combine models and model components
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