iRefScape paper published

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ian.donaldson

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Oct 18, 2011, 11:55:55 AM10/18/11
to irefindex
We are pleased to announce that the iRefScape paper has been
published.

http://www.biomedcentral.com/1471-2105/12/388/abstract

iRefScape is a Cytoscape plugin providing access to protein
interaction data from 10 databases consolidated by the iRefIndex
process.

The latest version installed using the Cytoscape plugin manager.

More information on the iRefIndex site: http://irefindex.uio.no

Best regards

The iRefIndex team


Abstract
Background
The iRefIndex consolidates protein interaction data from ten databases
in a rigorous manner using sequence-based hash keys. Working with
consolidated interaction data comes with distinct challenges: data are
redundant, overlapping, highly interconnected and may be collected and
represented using different curation practices. These phenomena were
quantified in our previous studies.

Results
The iRefScape plug-in for the Cytoscape graphical viewer addresses
these challenges. We show how these factors impact on data-mining
tasks and how our solutions resolve them in a simple and efficient
manner. A uniform accession space is used to limit redundancy and
support search expansion and searching on multiple accession types.
Multiple node and edge features support data filtering and mining.
Node colours and features supply information about search result
provenance. Overlapping evidence is presented using a multi-graph and
a bi-partite representation is used to distinguish binary and n-ary
source data. Searching for interactions between sets of proteins is
supported and specifically includes searches on disease-related genes
found in OMIM. Finally, a synchronized adjacency-matrix view
facilitates visualization of relationships between sets of user
defined groups.

Conclusions
The iRefScape plug-in will be of interest to advanced users of
interaction data. The plug-in provides access to a consolidated data
set in a uniform accession space while remaining faithful to the
underlying source data. Tools are provided to facilitate a range of
tasks from a simple search to knowledge discovery. The plug-in uses a
number of strategies that will be of interest to other plug-in
developers.

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