RFC Name : Cytoscape Data Integration

Editor(s): Sarah Killcoyne, Alex Pico

Status: Open for Comments

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Improve Cytoscape's data integration by creating a set of API's for some generic services that would be useful to the users and plugin developers. Create a registry and associated service taxonomy to allow users to search for and choose the service they are interested in using. Add a description of the services and API's to the wiki or manual for others to use when creating a new service.

Propsed Services

Synonym mapping


Network creation




Implementation Plan

These steps would be required for each service, the steps outlined below are specific to the Synonym Service because it is the first one we would like to implement. All time estimates are for 1 FTE. Time estimates will vary for the other services, though with experience implementing one any others should be simpler.

  1. Create WSDL for each service (start with id mapping as ISB and UCSF/Gladstone have working ones already)
    1. WSDL basically defines the API of a service
    2. Time: 2 weeks
    3. Deliverable - WSDL
  2. Create taxonomy to describe synonym services
    1. Time: 1 week
    2. Deliverable - Service taxonomy
  3. Create at least one service that implements the WSDL and taxonomy.
    1. ISB has a prototype in place that could be made public
    2. UCSF/Gladstone has ID mapping services it would like to reimplement as a web service
    3. Time: 2 weeks if we adopt our or another service, 16 weeks to create otherwise
    4. Deliverable - Usable services
  4. Choose and implement registry to locate services (see ISB’s UDDI browser plugin screenshots)
    1. There is already 3rd party software available for this used in the ISB browser
    2. Time: 2 weeks
    3. Deliverable - registry search backend
  5. Implement UI
    1. Time: 1 week
    2. Deliverable - UI
  6. Document WSDL, taxonomy and registry for other servers, unit tests
    1. Contact others who might be interested in implementing the service?
    2. Time: 3 weeks
    3. Deliverable - documentation and unit tests


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DataIntegration (last edited 2009-02-12 01:04:12 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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