BioWebServiceConnectivity

TableOfContents([2])

Proposal

These days, there are several public biological database web wervices such as Biomart, NCBI, or KEGG. It is very useful for many users if Cytoscape have an access to those huge data resources through simple user interface. By using this function, users can access virtually all kinds of annotations for the nodes, including variety of ID's, sequences, descriptions, orthologs, pathway names which contains the nodes, etc. Also, this is a general solution for all types of node ID mapping problems Cytoscape currently have. In addition, users can access network database web services thirough the same mechanism. The goal of this project is the following:

• Implement a mechanism to manage web service clients in the Cytoscape core.
• Design an interface which wraps each web service client.
• Design mechanism how web service clients communicate with the core (Event handling).
• Implement an simple UI for importing annotations and networks from the web services.

Biological Questions / Use Cases

• User loaded network with EntrezGene ID as node identifier into Cytoscape. He/she needs to import annotation files with Gene Symbol as the key.

• I need to add sequence data to each nodes in my network.

General Notes

Requirements

This component consists of 3 parts:

1. Core web service manager class
   • - Web Service Client Manager is just maintain list of web service clients.

     - Each web service client implements an interface Web Service Client

2. Core mapping module - Mapping fetched annotations onto CyAttributes.

3. Support module for individual web services
4. GUI for each web services

By keeping these as modular as possible, we can easily add new UI for other web services.

Deferred Items