retrieving interaction data from biotapestry file

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Kueh

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Aug 27, 2010, 2:45:47 AM8/27/10
to BioTapestry-users
Hi Bill,

Nice work on the latest version of bio-tapestry! I found that the
navigation between the different hierarchies works really well.

I'm wondering if we can retrieve interaction data from a biotapestry
format? I am planning to draw a network diagram interactively, and
would like to get the resultant interaction data out from the
biotapestry. If there is a quick and easy way to do this, please let
me know. Thanks!

Best,
Kueh

William Longabaugh

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Aug 27, 2010, 8:00:48 PM8/27/10
to biotapes...@googlegroups.com
Kueh:

Thanks!

The current way to get interaction data out is to navigate to
a particular model and then select the option:

File->Export->Export to SIF...

This will create a Cytoscape-compatible SIF file with
a line for each interaction. This is an old function,
and the node names used in the file can get pretty
obtuse. Here is a previous posting that discusses how
to parse out the node names that show up in this file:

http://groups.google.com/group/biotapestry-users/browse_thread/thread/f770cf9daef327b6#

While this approach does not describe how to extract the info
from the .btp file directly, I hope this does what you need.

-- Bill

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