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 check the orthologs for the genes in my network.

• I want to expand existing network with known interaction data in [http://www.ebi.ac.uk/intact/site/index.jsf IntAct]

• Mapping known pathways onto network data in Cytoscape.
• Executing an analysis program running on remote server which is implemented as a web service.

General Notes

Each web service is a building block to make higher-level functions. This means plugin writers should be able to use registered web services as if they are local Java APIs. To achive this, we should be careful to separate UI from the core web service clients.

Requirements

This component consists of 5 parts:

1. Web Service Client Manager in the core
   • - Maintaining list of web service clients.

     - Each web service client implements an interface WebServiceClient

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

3. Event Handlers - Implementing custom event and its listeners only for WebServiceClients

4. Web Service Clients - these are jar files which contains properties and classes created from WSDL. They will be loaded as normal cytoscape plugins.
5. GUI for each web services

Deferred Items

Open Issues

• Taxonomy of the services

Backward Compatibility

Expected growth and plan for growth

References

• [http://taverna.sourceforge.net/index.php?doc=services.html Biological Web Services] by myGrid/Taverna Project

Implementation Plan

Comments

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SarahKillcoyne August 16, 2007

This RFC would seem to be very related to the [:DataIntegration: Data Integration] one. Might be useful to discuss this as part of a larger web services integration if we decide a larger, more general solution would be useful.