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SBGN ML_Example_Files

Vasundra edited this page Jun 11, 2016 · 12 revisions

This page provides some SBGN-ML example files created with LibSBGN.

Examples 1 to 5 are based on the examples in the SBGN Process Description specification [1].

Glycolysis

This example illustrates how SBGN can be used to describe metabolic pathways. [1]

Download glycolysis.sbgn

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Insulin-like Growth Factor (IGF) signalling

This example shows the use of compartments and how details can be hidden by using a submap. The submap is shown in the next example. [1]

Download insulin-like_growth_factor_signaling.sbgn

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MAPK cascade

A submap of the previous map showing the MAPK cascade. [1]

Download mapk_cascade.sbgn

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Neuronal/Muscle signalling

A description of inter-cellular signalling using SBGN. [1]

Download neuronal_muscle_signalling.sbgn

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Activated STAT1alpha induction of the IRF1 gene

An example of gene regulation using logical operators. [1]

Download activated_stat1alpha_induction_of_the_irf1_gene.sbgn

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Central plant metabolism

This is the representation of major parts of the central metabolism in monocotyledon plants. The information has been derived from the MetaCrop [2] database, a manually curated repository of high quality information concerning the metabolism of crop plants. This includes pathways, reactions, locations, transport processes, and more.

Download central_plant_metabolism.sbgn

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Full resolution‎ (5,891 × 3,791 pixels, file size: 1.46 MB)

References

[1] S. Moodie, N. Le Novere, E. Demir, H. Mi, and F. Schreiber. Systems Biology Graphical Notation: Process Description language Level 1. Available from Nature Precedings http://precedings.nature.com/documents/3721/version/2 (2010).

[2] E. Grafahrend-Belau, S. Weise, D. Koschützki, U. Scholz, B. H. Junker, and F. Schreiber. MetaCrop: a detailed database of crop plant metabolism. Nucleic Acids Research, 36(Database issue):D954-D958 (2008).

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