Cytoscape Wiki
Cytoscape 3 Data I/O Layer
(Under Construction)
Data Sources
- Files
- Should be URI-based.
- Web Services
All wrapped services (in 2.6, they are called CyWebServiceClient) will be registered to OSGi Service Registory
WebServiceManager will be an intermediate service broker for other bundles (i.e., plugins).
- Database
- Should support roundtrip between Network/Attribute Model (Objects) and major RDB (MySQL/Derby/PostgreSQL)
- O/R Mapper will be used (Hibernate?)
Cytoscape as a Data Source (Server Version)
- Use the Cytoscape Data Model as its backend
- Publish as web services
Use Cases
- Read and write networks as XGMML/SIF/GML/PSI-MI (TAB/XML)/SBML.
- Read and write attributes as part of XGMML.
- Design general interfaces that support exporting different aspects of the Cytoscape system.
- Export just network topology.
- Export network topology AND graphical information.
- Export attribute data.
- Export images of networks.
- Export Cytoscape session files.
Open Issues
- Support for other popular network file formats
- GraphML
- Binary Matrix (sometimes called
DOT (used by [http://www.graphviz.org/ Graphviz])
NET (used by [http://vlado.fmf.uni-lj.si/pub/networks/pajek/ Pajek])
Edge List (simple 2-column text file supported by [http://cneurocvs.rmki.kfki.hu/igraph/ igraph] and many other applicaitons)
[http://www.gupro.de/GXL/ GXL]
[http://www.w3.org/RDF/ RDF] (we should have a general RDF parser)