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

Nature Protocols volume 7, pages 579–593 (2012)Cite this article

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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.

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Figure 1: Workflow of the creation of interactive, web-based and data-enriched maps using SBGN.
Figure 2: The SBGN Process Description (PD) notation.
Figure 3: Screenshot of the SBGN-ED desktop.
Figure 4: Regulatory interactions between four master regulators of Arabidopsis seed development: LEC1, LEC2, FUS3 and ABI3.
Figure 5
Figure 6: Screenshot of a mapping table.
Figure 7: Manually edited LEC1/AFL-B3 regulatory network of Arabidopsis seed transcription factors enriched by time-resolved expression data.
Figure 8
Figure 9: Metabolic network of the TCA cycle taken from the MetaCrop database, enriched by metabolic measurement data.
Figure 10: Example website.

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Acknowledgements

We are grateful to J. Hüge and B. Junker for helpful discussions and advice.

Author information

Authors and Affiliations

  1. Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Gatersleben, Germany

    Astrid Junker, Hendrik Rohn, Tobias Czauderna, Christian Klukas, Anja Hartmann & Falk Schreiber

  2. Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany

    Falk Schreiber

Authors
  1. Astrid Junker
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  2. Hendrik Rohn
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  3. Tobias Czauderna
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  4. Christian Klukas
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  5. Anja Hartmann
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  6. Falk Schreiber
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Contributions

All authors contributed extensively to the work presented in this paper. A.J. and H.R. wrote the paper. T.C. and C.K. wrote the code. A.H. developed the tutorial. A.H., T.C. and F.S. edited the manuscript. F.S. supervised the project and gave conceptual advice.

Corresponding author

Correspondence to Astrid Junker.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Tutorial

Creating interactive, web-based and data-enriched maps using the Systems Biology Graphical Notation. (PDF 10646 kb)

Supplementary Data 1

LEC1/AFL-B3 regulatory network. This file represents the result of the manual drawing process (Steps 9Ai-xxiv). It can directly be loaded into SBGN-ED for further layouting or data mapping. (ZIP 1 kb)

Supplementary Data 2

TCA cycle metabolic network. This file represents the result of the import of a SBGN style metabolic network from the MetaCrop database (Steps 9Bi-iii). It can directly be loaded into SBGN-ED for further layouting or data mapping. (ZIP 2 kb)

Supplementary Data 3

Excel template with expression data. This template file contains expression data obtained from the Genevestigator database for four transcription factors of the LEC1/AFL-B3 regulatory network. It can directly be used for upload into SBGN-ED and for mapping onto the LEC1/AFL-B3 regulatory network as described in Steps 10Ai-x. (XLS 29 kb)

Supplementary Data 4

Mapping table for mapping of expression data. This mapping table provides alternative IDs (AGI gene IDs for Arabidopsis) for the mapping of expression data on the LEC1/AFL-B3 regulatory network which contains only the gene names. (XLS 26 kb)

Supplementary Data 5

Regulatory network mapping. This file shows the LEC1/AFL-B3 regulatory network enriched by expression data as the result of Steps 10Ai-x. It can directly be loaded into SBGN-ED for further layouting or data mapping. (ZIP 3 kb)

Supplementary Data 6

Excel template with metabolic data. This template file contains metabolite measurement data obtained from literature. It can directly be used for upload into SBGN-ED and for mapping onto the TCA cycle metabolic network as described in Steps 10Bi-iii. (XLS 76 kb)

Supplementary Data 7

Metabolic pathway mapping. This file shows the TCA cycle metabolic network enriched by metabolite data as the result of steps 10Bi-iii. It can directly be loaded into SBGN-ED for further layouting or data mapping. (ZIP 8 kb)

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Junker, A., Rohn, H., Czauderna, T. et al. Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation. Nat Protoc 7, 579–593 (2012). https://doi.org/10.1038/nprot.2012.002

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