RFC Name : ...

Editor(s): ...

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About this document

This is an official Request for Comment (RFC) for Simple text table import function.

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Currently Cytoscape supports three main formats: sif, GML and XGMML. Although XGMML is a flexible file format, it is a bit hard to edit by hand. To solve this problem, Cytoscape should be able to import nodes, edges as well as their properties (attributes) from a common, simple file format. I suggest that Cytoscape reads tab-delimited or CSV text files, which essentially represent tables. This format is easy to create as output from other programs, especially using spreadsheets. Basically, this is an extended version of sif file. Potentially, this format could also be used as an export format for Cytoscape.

Biological Questions / Use Cases

General Notes


Deferred Items

Open Issues

Backward Compatibility

Expected growth and plan for growth


Implementation Plan


SimpleTextTableImport (last edited 2009-02-12 01:03:33 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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