Memo on ID mapping and bridgedb (skyped with Martijn 04/30/09)

• ID mapper API needs to be redesigned, using bridgedb Xref.
  
• ID mapper API should be generic, or independent of Cytoscape.
• ID mapper API design V3 on the project wiki is preferred.
• IDMapperRDB in ID mapping API would be a wrapped-up interface of GDB in bridgedb.
  
• ID mapper makes use of bridgedb, but not the other way.
  
• bridgedb can be adapted to the need to ID mapping.
• Integrate web service in bridgedb.
• Many people are thinking about ID mapping, so it's important to start coordinating.
• I will focus on the following two things before May 23:
  1. Refine ID mapper API with the team.
     
  2. Design GUI according to bridgedb spec V & VI: make some GUI mockup and discuss with others.
     
  
  
  
  

GSoC, I'm back!

After a long (2-week) anxious wait, I got accepted by GenMAPP as a GSoC student again this year. My project is to develop ID mapping plugin for Cytoscape. Dr. David States is my mentor for this project.

During the last summer, I developed the Advanced Network Merge plugin (mentored by Kei Ono). ID mapping based network merge was one of the features of that plugin. As a result, some preliminary work has been done in ANM. For instance, the ID mapping APIs have been designed, the file-based ID mapping has been implemented, and the ID mapping GUI has been designed.

In the following summer, I will work closely with my mentor Dr. States and the BridgeDb team. Our project aim is to provide the community with a set of ID mapping APIs and a ID mapping plugin for Cytoscape, using different ID mapping sources such as local/remote files, databases and web services. 

More project progress will be blogged here...