SBML Level 3 Package Proposal: Annotation

Hucka, Michael; Laibe, Camille; Juty, Nick; Liebermeister, Wolfram; Keating, Sarah; Lloyd, Catherine; Knuepfer, Christian; Misirli, Goksel; Schulz, Marvin; Waltemath, Dagmar; Taschuk, Morgan; Swainston, Neil; Le Novère, Nicolas; Lister, Allyson; Bergmann, Frank; Henkel, Ron; Krause, Falko; Hoops, Stefan

Abstract

The annotation of Systems Biology Markup Language (SBML) models with semantic terms has been supported for a number of years. The prevalence of such annotated models is growing, with repositories such as Biomodels.net and an increasing number of software tools supporting and encouraging their use and development.With the increasing use of semantic annotations in the context of systems biology modeling has come the realization that the current Core SBML specification defining their use contains limitations that reduce the scope of metadata that can be captured in such models.SBML Level 3 provides the facility to propose and develop optional extensions to the Core specification. One such extension is described here, with an initial proposal of an Annotation package.This proposal extends the current Core annotation specification to provide support for a richer set of semantic annotations while adhering more closely to the existing specification of Resource Description Framework (RDF).

Citation

Hucka, M., Laibe, C., Juty, N., Liebermeister, W., Keating, S., Lloyd, C., Knuepfer, C., Misirli, G., Schulz, M., Waltemath, D., Taschuk, M., Swainston, N., Le Novère, N., Lister, A., Bergmann, F., Henkel, R., Krause, F., & Hoops, S. (in press). SBML Level 3 Package Proposal: Annotation. Nature Proceedings

• Report Type: Technical Standard
• Acceptance Date: Jan 31, 2011
• Online Publication Date: Jan 31, 2011
• Deposit Date: Aug 15, 2023
• Publisher: Nature Publishing Group
• DOI: https://doi.org/10.1038/npre.2011.5610.1
• Keywords: Systems Biology Markup Language; annotation; semantic data; systems biology; standards paper
• Public URL: https://keele-repository.worktribe.com/output/541332
• Additional Information: Received: 31 January 2011; Accepted: 31 January 2011; First Online: 31 January 2011; ; Published as Gold Open Access