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Published December 18, 2016 | Published
Journal Article Open

SBML Level 3 package: Groups, Version 1 Release 1


Biological models often contain components that have relationships with each other, or that modelers want to treat as belonging to groups with common characteristics or shared metadata. The SBML Level 3 Version 1 Core specification does not provide an explicit mechanism for expressing such relationships, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The SBML Groups package for SBML Level 3 adds the necessary features to SBML to allow grouping of model components to be expressed. Such groups do not affect the mathematical interpretation of a model, but they do provide a way to add information that can be useful for modelers and software tools. The SBML Groups package enables a modeler to include definitions of groups and nested groups, each of which may be annotated to convey why that group was created, and what it represents.

Additional Information

Copyright 2016 The Author(s). Published by Journal of Integrative Bioinformatics. This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License (http://creativecommons.org/licenses/by-nc-nd/3.0/). Work such as this does not take place in a vacuum; many people contributed ideas and discussions that shaped the Groups proposal that you see before you. We particularly thank Nicolas Le Novère, Frank Bergmann, Sarah Keating, Allyson Lister, Robert Phair, Sven Sahle, Stefan Hoops, Chris Myers, and the members of the sbml-discuss and sbml-groups mailing lists for suggestions and comments. We would also like to thank Andreas Dräeger, Ben Heavner, Brett Olivier, Kieran Smallbone, and Anna Zhukova for their work in implementing 'Groups' support in their own software tools, with Brett in particular investigating implementaton of the 'nested groups' aspect of the specification. This work was funded by the National Institutes of Health (USA) under grant R01 GM070923.

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