Cytoscape Wiki|
← Revision 1 as of 2008-02-07 21:57:28 →
Size: 517
Comment:
|
Size: 1315
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 17: | Line 17: |
|
1. '''''File-->Import-->Import network from web services...''''' 1. Select '''NCBI''' as datasource and type ''human muscular dystrophy'' as search keyword 1. Press '''Search'''. Number of candidates will be displayed. Then press OK. This process takes a long time. 1. '''''File-->Import-->Import Attributes from NCBI Entrez Gene...''''' 1. Select '''ID''' as key attribute and check all available annotations 1. Press '''''Import'''''. Again, this process takes a long time depends on network connection. 1. 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.) attachment:workflow1_1.png |
Sample Workflows Using Web Service Clients
This is a simple example workflow with web service clients.
Prerequisites
- Cytoscape version 2.6.0 or later
- High-Speed Network Connection
- Plugins
- NCBIClient
- NCBIEntrezGeneUserInterface
BiomartClient
BiomartUserInterface
IntActClient
EnhancedSearch (optional)
Workflow 1: Start from Keyword
File-->Import-->Import network from web services...
Select NCBI as datasource and type human muscular dystrophy as search keyword
Press Search. Number of candidates will be displayed. Then press OK. This process takes a long time.
File-->Import-->Import Attributes from NCBI Entrez Gene...
Select ID as key attribute and check all available annotations
Press Import. Again, this process takes a long time depends on network connection.
- 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.)
- attachment:workflow1_1.png
Workflow 2: Start from List of IDs