Loading of Network Data

The graph editor supports loading of network data in various ways:

  1. It is possible to load GML files, a standard text format for graph files

  2. A SBML V2 import filter is available. A limited subset of the SBML standard is supported, which allows accessing the basic structure (nodes, edges) of a network, encoded in the SBML format. Certain attributes are mapped to graph element attributes. Until recently the SBML specification did not consider graph-layout information. The current layout specification proposal is not yet supported by this application. Available SBML files need to be renamed with a ".SBML" file extension (e.g. "model1.sbml") before loading is possible with the application.

  3. A KEGG importer (KGML file format) is included; these files can be loaded from disk (the KGML files need to have the file extension ".XML", e. g. "map00010.xml"). An online access to up-to-date KEGG pathway data is also possible with the KEGG Panel at the right of the application window. This tab-pane can be used as follows: First the button Select organism: needs to be clicked. This way the drop-down list beside this button is populated. By default the Reference pathways are initially selected. After selecting the desired organism the tree-list below is filled. By double-clicking an item or clicking the corresponding button at the bottom of the list, the selected pathway is loaded into a new graph-editor window.

Certain elements and specifications in the GML, SBML, Pajek .NET and KGML files may not be fully supported and cause a failure in loading a graph file. In such case it is advised to send the author of this application an E-Mail, with the problematic file attached. It is very likely, that such problems may be fixed within a short time frame.

More reference information is available for the command File/Open.

The KEGG importer needs to make certain assumptions e. g. about the connection of particular graph elements. The KGML specification does not fully define all aspects of the graphical representation. Also not all possibly defined graph elements are currently processed by the importer. Therefore it is of importance to check the validity of the loaded pathways. The Network Panel contains link-buttons which reference the corresponding KEGG pathway images. By clicking onto the corresponding command button the original KEGG pathway image is shown in an internet browser window. The purpose of this importer command is to provide a starting point for the actual work with network data.

The mapping of experimental data onto KEGG pathways is eased by two additional command buttons at the KEGG Panel:

  1. The button Analyze Pathway-Dataset Mapping makes it possible to find pathways which contain nodes which map automatically to a selected loaded experimental measurement dataset.

  2. The button Reset resets the displayed mapping count data, making it possible to analyze the possible automatic mapping of a second experimental measurement dataset.