Diff for "Outdated_Cytoscape_3.0/IODiscussions"

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)