Abstract
AbstractThe 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).
Highlights
Introduction and motivationAnnotations encode meta-information in SBML models
The Resource Description Framework (RDF) Primer generalises the concept of a “web resource” to represent information about things that can be identified on the web, even when they cannot be directly retrieved on the web
The basic concept of RDF is the identification of things using Uniform Resource Identifiers (URIs)
Summary
Version number and date of public release This is version 1 of the Annotation package proposal. It reflects the results of the Annotation package meeting, 19–21 May 2010. URL or this version of the proposal Annot package proposal version 1 (2011-02). URL for the previous version of this proposal None
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