Sample Workflows Using Web Service Clients

This is a simple example workflow with web service clients.


Workflow 1: Start from Keyword

  1. File-->Import-->Import network from web services...

  2. Select NCBI as datasource and type human muscular dystrophy as search keyword

  3. Press Search. Number of candidates will be displayed. Then press OK. This process takes a long time.

  4. File-->Import-->Import Attributes from NCBI Entrez Gene...

  5. Select ID as key attribute and check all available annotations

  6. Press Import. Again, this process takes a long time depends on network connection.

  7. Based on the attributes imported, visualize the network. (Example below: edge color is mapped to data source of the interaction, and phynotype is mapped to node color. Red border shows the node is on a known KEGG/Reactome pathway.)
    • workflow1_1.png

  8. 'File-->Import-->Import attributes from BioMart...

  9. Set ID as key attribute, and select the type to Entrez Gene ID

  10. Select ENSEMBL 48 GENES (SANGER) - Homo sapiense genes (NCBI36) as data source

  11. Check several attributes you want to import and then press Import

  12. New attributes will be imported. Once you get new annotations, you can go to the datasource web page by Linkout feature.

    • workflow2.png

Workflow 2: Start from List of IDs

Workflow 3: Start from User's Network

Workflow 4: Start from Other Species Network

  • workflow4_1.png

WebServiceWorkflow (last edited 2009-02-12 01:03:08 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.

MoinMoin Appliance - Powered by TurnKey Linux