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| || '''RFC Name''' : ....... || '''Editor(s)''': Keiichiro Ono || '''Status''': ....... || | || '''RFC Name''' : BioWebServiceConnectivity || '''Editor(s)''': KeiichiroOno || '''Status''': Planning || |
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| 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. | |
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* 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.'' |
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This component consists of 3 parts: 1. Core web service connectivity module 1. Core mapping module - Mapping fetched annotations onto !CyAttributes. 1. Support module for individual web services 1. GUI for each web services By keeping these as modular as possible, we can easily add new UI for other web services. |
RFC Name : BioWebServiceConnectivity |
Editor(s): KeiichiroOno |
Status: Planning |
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:
- Core web service connectivity module
Core mapping module - Mapping fetched annotations onto CyAttributes.
- Support module for individual web services
- 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
How to Comment
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