SimpleTextTableImport

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About this document

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

For details on RFCs in general, check out the Wikipedia Entry: Request for Comments (RFCs)

Status

• This RFC is incomplete. Will be opened for public comments shortly.

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Proposal

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

• There are many biological data files saved in table/spreadsheet form. This new format enable biologists to import those files directly into Cytoscape.
• Although XML (XGMML) file already supports this type of network and attributes, most biologists are not familiar with XML documents. Simple table format enable users to edit data files in Excel or other spredsheet software.

General Notes

• Table format (under construction...)

Requirements

• Support for the text table format consists of the following parts:
  • Table file reader
  • GUI (possibly Wizard) for importing table
  • Optional: file writer for exporting table
• To import network, node/edge attributes, we need 2 files. One is for network and edge attributes, and the other one is for node attributes.
• Node attribute file is optional. Example Entry in the text file:

  • Network & edge attribute file: node1, node2, attribue1, attribute2, ...

    • In this file, one of the attributes will be used as interaction

    • By default, the third column will be used for interaction.

    • Just like attribute text table import, users can select arbitrary column as node1, node2, and interaction.
  • Node attribute file (optional): node, attribute1, attribute2, ...

Deferred Items

Open Issues

Backward Compatibility

Expected growth and plan for growth

References

Implementation Plan

• /Implementation Plan

Comments

• Add your comments here.