Improve the GPML to SIF Converter in the Cytoscape WikiPathways App

[cannin]

Background

The Cytoscape WikiPathways App (http://apps.cytoscape.org/apps/wikipathways) makes WikiPathways (wikipathways.org) networks/pathways available in Cytoscape (http://cytoscape.org/). It also allows the export of this content to other formats including the Simple Interaction Format (SIF); a tabular edgelist type format. Examples SIFs including for WikiPathways (PathwayCommons11.wp.hgnc.sif.gz) are here at (https://www.pathwaycommons.org/archives/PC2/v11/) Currently, there is a bug in the export to SIF; see screenshot (https://imgur.com/OA9CQPQ).

Goal

Goals as time allows:

• Fix this the SIF export bug
• Add additional database identifiers (e.g., HGNC, https://www.genenames.org/) as available in GPML (http://developers.pathvisio.org/wiki/EverythingGpml)
• Work on any other existing bugs (see code repository)

Difficulty Level 2

The exact problem is not known and will require the student to examine the code.

Skills

• Essential skills: Java, XML

Public Repository

• https://github.com/wikipathways/cytoscape-wikipathways-app

Potential Mentors

Augustin Luna