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| The file will be called "<filename>.cys" (cyc = CYtoscape Session). Basically, this is a zip file containing the following: | The file will be called "<filename>.cys" (cys = CYtoscape Session). Basically, this is a zip file containing the following: |
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=== On-demand Loader for Gene Ontology Server (tentative, 2.3 or 2.4) === It is not realistic to save entire biodataserver object to the session file. Also, loading entire Gene Ontology data into memory is not space-efficient. To avoid this problem, some sort of mechanism to load GO data only for loaded network files. This can be done with the following: 1. Prepare GO file in RDF-XML format (available [http://www.godatabase.org/dev/database/ here]). 2. Save the GO server's location in CySession.xml or cytoscape.prop 3. Create a checkbox "Load GO data for the network" in the "load network" dialog. 4. Generate query to select annotation only for nodes to be loaded. 5. Execute query and store them drectry into CyAttributes or add it to BDS object We need to refactor biodataserver class and add XQuery/SPARQL libraly to the Cytoscape. This method is universal to all data sources written in XML. I.e., if the database is available in XML format, we can query/load the data as a part of attributes in Cytoscape. |
In version 2.3, a function to save entire Cytoscape session will be added. The file will be called "<filename>.cys" (cys = CYtoscape Session). Basically, this is a zip file containing the following:
CySession.xml
- vizmap.prop
- cytoscape.prop
- Arbitrary number of network files written in ["XGMML"].
A directory named with timestamp will be created and files above will be stored in the dir.
On-demand Loader for Gene Ontology Server (tentative, 2.3 or 2.4)
It is not realistic to save entire biodataserver object to the session file. Also, loading entire Gene Ontology data into memory is not space-efficient. To avoid this problem, some sort of mechanism to load GO data only for loaded network files. This can be done with the following:
Prepare GO file in RDF-XML format (available [http://www.godatabase.org/dev/database/ here]).
Save the GO server's location in CySession.xml or cytoscape.prop
- Create a checkbox "Load GO data for the network" in the "load network" dialog.
- Generate query to select annotation only for nodes to be loaded.
Execute query and store them drectry into CyAttributes or add it to BDS object
We need to refactor biodataserver class and add XQuery/SPARQL libraly to the Cytoscape. This method is universal to all data sources written in XML. I.e., if the database is available in XML format, we can query/load the data as a part of attributes in Cytoscape.