Cytoscape Wiki|
← Revision 1 as of 2007-04-13 21:39:30
Size: 2344
Comment:
|
← Revision 2 as of 2007-04-13 22:11:38 →
Size: 2770
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| || '''RFC Name''' : Web Services: ID Mapping || '''Editor(s)''': Sarah, Ethan, Alex || | || '''RFC Name''' : Web Services - ID Mapping || '''Editor(s)''': Sarah, Ethan, Alex || |
| Line 14: | Line 14: |
| Line 36: | Line 37: |
|
ISB’s Current ID Service: * [description] * [example wsdl] Note that while it is implemented in SOAP, we get REST along with it so a REST api for Cytoscape is great. |
|
| Line 54: | Line 49: |
|
ISB’s Current ID Service: * attachment:ISB_SynonymService.doc - description of service/methods * attachment:ISB_Mammalian_WSDL.xml - example wsdl from our mammalian service Note that while it is implemented in SOAP, we get REST along with it. Any of the described methods can be called. ISB prototype UDDI/id mapping plugin. Our endpoints are behind a firewall, but at least it's some example type code (very alpha) * attachment:WS_IdMapping.zip - warning 7.2mb |
|
| Line 55: | Line 59: |
|
[http://biomoby.org BioMoby] (Registry/discovery tool) [http://discover.nci.nih.gov/matchminer/command.jsp NCI MatchMiner] (id mapping, do they have a web service interface?) caBig – has an id mapping service, might not be simply accessible Onco (??) Translate ( Ethan ) |
* [http://biomoby.org BioMoby] (Registry/discovery tool) * [http://discover.nci.nih.gov/matchminer/command.jsp NCI MatchMiner] (id mapping, do they have a web service interface?) * caBig – has an id mapping service, might not be simply accessible * Onco (??) Translate ( Ethan ) |
| Line 64: | Line 66: |
| * ["/Implementation Plan"] |
1. Alex, Sarah, Ethan will work together towards a common web service api for id mapping 2. Implement a discovery/use plugin prototype |
RFC Name : Web Services - ID Mapping |
Editor(s): Sarah, Ethan, Alex |
About this document
This is an official Request for Comment (RFC) for Add your text here.
For details on RFCs in general, check out the [http://www.answers.com/main/ntquery?method=4&dsid=2222&dekey=Request+for+Comments&gwp=8&curtab=2222_1&linktext=Request%20for%20Comments Wikipedia Entry: Request for Comments (RFCs)]
Status
April 13, 2007
Not yet completely written
How to Comment
To view/add comments, click on any of 'Comment' links below. By adding your ideas to the Wiki directly, we can more easily organize everyone's ideas, and keep clear records. Be sure to include today's date and your name for each comment. Here is an example to get things started: ["/Comment"].
Try to keep your comments as concrete and constructive as possible. For example, if you find a part of the RFC makes no sense, please say so, but don't stop there. Take the extra step and propose alternatives.
Proposal
Enhance Cytoscape’s data connectivity by putting together a basic API for a web service multiple groups implement as a test case for further development into web service/database connectivity for Cytoscape.
This case will deal with an id mapping/translation service.
Biological Questions / Use Cases
Biologists often need to translate one id to another to connect various pieces of data.
The mappings are available, but not easily accessible in Cytoscape currently.
General Notes
Requirements
Deferred Items
Open Issues
Backward Compatibility
Expected growth and plan for growth
References
ISB’s Current ID Service:
attachment:ISB_SynonymService.doc - description of service/methods
- attachment:ISB_Mammalian_WSDL.xml - example wsdl from our mammalian service
Note that while it is implemented in SOAP, we get REST along with it. Any of the described methods can be called.
ISB prototype UDDI/id mapping plugin. Our endpoints are behind a firewall, but at least it's some example type code (very alpha)
attachment:WS_IdMapping.zip - warning 7.2mb
Services to look at for reference points:
[http://biomoby.org BioMoby] (Registry/discovery tool)
[http://discover.nci.nih.gov/matchminer/command.jsp NCI MatchMiner] (id mapping, do they have a web service interface?)
- caBig – has an id mapping service, might not be simply accessible
- Onco (??) Translate ( Ethan )
Implementation Plan
- Alex, Sarah, Ethan will work together towards a common web service api for id mapping
- Implement a discovery/use plugin prototype