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.
Highlights
1.1 MotivationMetadata annotations enhance the interoperability, reusability, comparability, and comprehension of computational biological models
Note that the generic Resource Description Framework (RDF) resource entity 0 needs to be created when encoding the Composite semantic annotations (CSAs). This is required because there are no structures in the CellML schema that represent physical entities, so they are instantiated as RDF resources in the Open Modeling and EXchange (OMEX) metadata document
The example semantic annotation above is for a physical property of a physical entity, the physical properties simulated in models or measured experimentally can be those of physical processes such as chemical reactions, transport of solutes, flow of fluids in vessels, etc
Summary
Metadata annotations enhance the interoperability, reusability, comparability, and comprehension of computational biological models. 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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