SemGen: a tool for semantics-based annotation and composition of biosimulation models.
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ABSTRACT: Summary
As the number and complexity of biosimulation models grows, so do demands for tools that can help users understand models and compose more comprehensive and accurate systems from existing models. SemGen is a tool for semantics-based annotation and composition of biosimulation models designed to address this demand. A key SemGen capability is to decompose and then integrate models across existing model exchange formats including SBML and CellML. To support this capability, we use semantic annotations to explicitly capture the underlying biological and physical meanings of the entities and processes that are modeled. SemGen leverages annotations to expose a model's biological and computational architecture and to help automate model composition.Availability and implementation
SemGen is freely available at https://github.com/SemBioProcess/SemGen.Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Neal ML
PROVIDER: S-EPMC6499248 | biostudies-literature | 2019 May
REPOSITORIES: biostudies-literature
Publications
SemGen: a tool for semantics-based annotation and composition of biosimulation models.
Neal Maxwell L ML Thompson Christopher T CT Kim Karam G KG James Ryan C RC Cook Daniel L DL Carlson Brian E BE Gennari John H JH
Bioinformatics (Oxford, England) 20190501 9
<h4>Summary</h4>As the number and complexity of biosimulation models grows, so do demands for tools that can help users understand models and compose more comprehensive and accurate systems from existing models. SemGen is a tool for semantics-based annotation and composition of biosimulation models designed to address this demand. A key SemGen capability is to decompose and then integrate models across existing model exchange formats including SBML and CellML. To support this capability, we use ...[more]
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