Annotation_G2

improving metadata annotations

A thorough description of the complex annotation within the .smbl-files can be found in the Metadata section. The scope of this particular section was to identify possible shortcomings of the MIRIAM-annotation, that is used in the .sbml-language. As illustrated in figure 1 the guidelines for the general idea of the MIRIAM annotation is to bundle the references, model information and the annotations in one comprehensive tool.

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Figure 1: According to [1] the MIRIAM guidelines are composed of three parts: 1. Reference correspondence, 2. Attribution annotation, and 3. External resource annotation.

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annotation tools

There are different ways of accessing the metadata knitted in the *.sbml-files. You could use

• Notepad ++, v8.1, a free source code editor and Notepad replacement that supports several languages. Here you would only want to make minor channges e.g. correcting URLs oder vCards as you do not have a front end editor.
• SemanticSBML, a tool published in 2009 under GNU public license with a mighty range of MIRIAM-compliant annotation options as describes in [2]. Unfortunately the URL seems to be no longer available.

References:

[1] Combine.org
[2] Liebermeister, Wolfram; Krause, Falko; Uhlendorf, Jannis; Lubitz, Timo; Klipp, Edda (2009): SemanticSBML: a tool for annotating, checking, and merging of biochemical models in SBML format. In: Nat Prec. DOI: 10.1038/npre.2009.3093.1.