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Nat Protoc. 2012 Mar 1;7(3):579-93. doi: 10.1038/nprot.2012.002.

Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation.

Author information

  • 1Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Gatersleben, Germany. junkera@ipk-gatersleben.de

Abstract

The Systems Biology Graphical Notation (SBGN) is an emerging standard for the uniform representation of biological processes and networks. By using examples from gene regulation and metabolism, this protocol shows the construction of SBGN maps by either manual drawing or automatic translation using the tool SBGN-ED. In addition, it discusses the enrichment of SBGN maps with different kinds of -omics data to bring numerical data into the context of these networks in order to facilitate the interpretation of experimental data. Finally, the export of such maps to public websites, including clickable images, supports the communication of results within the scientific community. With regard to the described functionalities, other tools partially overlap with SBGN-ED. However, currently, SBGN-ED is the only tool that combines all of these functions, including the representation in SBGN, data mapping and website export. This protocol aims to assist scientists with the step-by-step procedure, which altogether takes ∼90 min.

PMID:
22383037
[PubMed - indexed for MEDLINE]
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