ugurdogrusoz
commented
6 years ago @ozgunbabur has a more comprehensive issue (#121) on this, so closing this one
Closed ugurdogrusoz closed 6 years ago
ugurdogrusoz
commented
6 years ago @ozgunbabur has a more comprehensive issue (#121) on this, so closing this one
Background
BioPAX and Systems Biology Graphical Notation (SBGN) are community standards to exchange pathway data and to graphically represent pathways, respectively. Most pathway databases support download of their data in BioPAX format. However availability of such pathways in SBGN is not commonplace since some prefer other graphical notations or don't bother converting their pathways into SBGN.
Even though a converter is available within the Java library named paxtools within the Pathway Commons project from BioPAX to SBGNML (an XML based format for representing pathways in SBGN), there is no service currently available using this library to input a BioPAX .owl file and get the corresponding pathway in SBGNML. This should be especially useful for web based pathway viewers or editors.
Goal
The goal of this project is to use the paxtools library on server side and create a web service to convert pathways in BioPAX into SBGNML. If available, the service could make use of the validation services proposed here as well, before returning the file.
Difficulty Level 1
This should be a rather straightforward project for someone with background in constructing web services, Java, and web programming.
Skills
Constructing Java-based web services, JavaScript (essential) BioPAX, SBGN (nice to have)
Public Repository
A new repository is to be constructed for this.
Potential Mentors
? Ugur Dogrusoz
Contact
Ugur Dogrusoz