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

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2012

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Junker, Astrid
Rohn, Hendrik
Czauderna, Tobias
Klukas, Christian
Hartmann, Anja

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https://doi.org/10.1038/nprot.2012.002
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Published

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Nature Protocols. 2012, 7(3), pp. 579-593. ISSN 1754-2189. eISSN 1750-2799. Available under: doi: 10.1038/nprot.2012.002

Zusammenfassung

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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ISO 690JUNKER, Astrid, Hendrik ROHN, Tobias CZAUDERNA, Christian KLUKAS, Anja HARTMANN, Falk SCHREIBER, 2012. Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation. In: Nature Protocols. 2012, 7(3), pp. 579-593. ISSN 1754-2189. eISSN 1750-2799. Available under: doi: 10.1038/nprot.2012.002
BibTex
@article{Junker2012-03-01Creat-38265,
  year={2012},
  doi={10.1038/nprot.2012.002},
  title={Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation},
  number={3},
  volume={7},
  issn={1754-2189},
  journal={Nature Protocols},
  pages={579--593},
  author={Junker, Astrid and Rohn, Hendrik and Czauderna, Tobias and Klukas, Christian and Hartmann, Anja and Schreiber, Falk}
}
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