The aim is to provide the most accurate translation for metabolic networks between GraphML (yEd) and SBGN-ML file formats. Translation in both direction is possible. This project should ultimately be integrated into SBFC.
Compatible formats:
- SBGN-ML 0.2 (Process Description)
- yEd 3.17.1
To find more information, please check the Wiki. The javadoc documentation for the source files is available here and the full application can be directly donwloaded from here.
Known issues are shown in the issues group and the limitations of the tool are listed on the Limitations page.
- Java 8 (with JavaFX if you want to use the GUI)
- Maven (tested with Maven 3.5)
After cloning the repository and getting into its directory:
mvn clean
mvn install
A small GUI is also provided as the main class of the package. It can be launched by double clicking on the jar or by
directly calling the package with java -jar. Be sure to have JavaFX working in your Java distribution.
With the scripts, all log messages will go to System.out. With the GUI, everything will be written in the selected log file.
If you have any suggestions or want to report a bug, don't hesitate to create an issue. Pull requests and all forms of contribution will be warmly welcomed.
- More details about the SBGN-ML format
- SBFC doc
- The yEd Graph Editor framework
- A useful tool for translation between CellDesigner to SBGN-ML (bidirectional conversion) is CD2SBGMML
- More details about the eTRIKS Project and the Disease Maps Project
This work has been initiated at EISBM in collaboration with Dr. Alexander Mazein and Ludovic Roy, with Vasundra Toure from NTNU, and with the Disease Maps community.
This work has been supported by the Innovative Medicines Initiative Joint Undertaking under grant agreement no. IMI 115446 (eTRIKS), resources of which are composed of financial contribution from the European Union’s Seventh Framework Programme (FP7/2007-2013) and EFPIA companies.