Changes between Initial Version and Version 1 of VisualizationInteraction

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Timestamp:
2010/02/09 18:51:45 (13 years ago)
Author:
andrea
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  • VisualizationInteraction

    v1 v1  
     1A relevant amount of interaction data is available in RDF. 
     2Most notably the whole collection of PathwayCommons (represented in BioPAX). 
     3 
     4Bruno Aranda is working on PSIQIQ (mispelled?) and has the intention to realize an RDF export for this resource. This will comprise most of interaction data available. In particular interaction data from this initiative are varied (protein-protein, genetic...), the export will likely be based on ontologies coming from PSI-MI. 
     5 
     6Note: Bind is not public anymore! 
     7 
     8In general an export of Kegg in RDF seems to be missing (can somebody correct here ?) 
     9 
     10As for the usage of interaction data: 
     11 
     12It seems there is a "common usage" where users search one or more "proteins" of interest, expand these via a network of interacting proteins, analyze the network (e.g.: clustering) and visualize it. 
     13 
     14There are no hints for better way to handle these data, except too much data is no data. Some 3D system is on the way, but it's not clear what this can add.  
     15 
     16Overall Cytoscape seems to be the main platform for visualization of interaction data, which will be largely in RDF. A simple disciplines on URIs (suggested: Uniprot) would make intergation very easy. 
     17 
     18Automatic layout of pathways remains problematic. 
     19 
     20Should we open a googe group about visualization of/and interaction on the (bio) semantic web ?