The KEGG PATHWAY database continues to enjoy great popularity and is frequently being used as the initial source of information for creating models of biological processes. KEGG represents its pathways using its own XML-based format call KGML (KEGG Markup Language), whose main purpose is the visual representation of pathways in a textbook like form, i.e., the focus is more on identifying general mechanisms rather than organism- or tissue-specific processes. The software KEGGtranslator turns KGML files into several much better documented community formats, including BioPAX, SBGN-ML, and SBML, thereby pulling a lot of additional information from KEGG that is not encoded within the original KGML files. The resulting models are much better reusable.
Goal
SBML is one of the most popular modeling and data exchange languages in systems biology. The SBML format has evolved and provides now several new packages and features that allow for better translations of the content of the KEGG PATHWAY database. In particular, this includes support for hierarchical models, i.e., models that are composed of submodels (such as individual pathways) as well as composite reactive species. One main feature of KEGG are the manually drawn pathway maps. KEGGtranslator can already preserve the position and sizes of map components using the SBML layout extension, but it does not yet store rendering information, such as color or shapes. This can be done using the SBML render package. The aim of this project is to incorporate support for these new technologies into the popular stand-alone desktop tool KEGGtranslator.
Background
The KEGG PATHWAY database continues to enjoy great popularity and is frequently being used as the initial source of information for creating models of biological processes. KEGG represents its pathways using its own XML-based format call KGML (KEGG Markup Language), whose main purpose is the visual representation of pathways in a textbook like form, i.e., the focus is more on identifying general mechanisms rather than organism- or tissue-specific processes. The software KEGGtranslator turns KGML files into several much better documented community formats, including BioPAX, SBGN-ML, and SBML, thereby pulling a lot of additional information from KEGG that is not encoded within the original KGML files. The resulting models are much better reusable.
Goal
SBML is one of the most popular modeling and data exchange languages in systems biology. The SBML format has evolved and provides now several new packages and features that allow for better translations of the content of the KEGG PATHWAY database. In particular, this includes support for hierarchical models, i.e., models that are composed of submodels (such as individual pathways) as well as composite reactive species. One main feature of KEGG are the manually drawn pathway maps. KEGGtranslator can already preserve the position and sizes of map components using the SBML layout extension, but it does not yet store rendering information, such as color or shapes. This can be done using the SBML render package. The aim of this project is to incorporate support for these new technologies into the popular stand-alone desktop tool KEGGtranslator.
Technologies
A starting point would be the existing KEGGtranslator repository on GitHub. For the display of biological networks yFiles is used.
Potential mentors
Andreas Dräger Nicolas Rodriguez
Contact
SBML Team
Useful pointers to documentation related to GSOC for student on the main NRNB web site :