Diff for "SimpleTextTableImport"

TableOfContents([2])

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 [http://www.answers.com/main/ntquery?method=4&dsid=2222&dekey=Request+for+Comments&gwp=8&curtab=2222_1&linktext=Request%20for%20Comments Wikipedia Entry: Request for Comments (RFCs)]

Status

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

How to Comment

To view/add comments, click on any of 'Comment' links below. By adding your ideas to the Wiki directly, we can more easily organize everyone's ideas, and keep clear records. Be sure to include today's date and your name for each comment. Here is an example to get things started: ["/Comment"].

Try to keep your comments as concrete and constructive as possible. For example, if you find a part of the RFC makes no sense, please say so, but don't stop there. Take the extra step and propose alternatives.

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/spredsheet 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

Deferred Items

Open Issues

Backward Compatibility

Expected growth and plan for growth

References

Implementation Plan

• ["/Implementation Plan"]

Comments

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