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 typs of node ID mapping problems Cytoscape currently have.

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 connectivity module

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

Open Issues

Backward Compatibility

Expected growth and plan for growth

References

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.