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Bioinformatics 2009 25(10):1321-1328; doi:10.1093/bioinformatics/btp142
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

DASMI: exchanging, annotating and assessing molecular interaction data

Hagen Blankenburg 1, Robert D. Finn 2, Andreas Prlic 2, Andrew M. Jenkinson 3, Fidel Ramírez 1, Dorothea Emig 1, Sven-Eric Schelhorn 1, Joachim Büch 1, Thomas Lengauer 1 and Mario Albrecht 1,*

1Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken, Germany, 2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA and 3European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

*To whom correspondence should be addressed.


  Abstract

Motivation: Ever increasing amounts of biological interaction data are being accumulated worldwide, but they are currently not readily accessible to the biologist at a single site. New techniques are required for retrieving, sharing and presenting data spread over the Internet.

Results: We introduce the DASMI system for the dynamic exchange, annotation and assessment of molecular interaction data. DASMI is based on the widely used Distributed Annotation System (DAS) and consists of a data exchange specification, web servers for providing the interaction data and clients for data integration and visualization. The decentralized architecture of DASMI affords the online retrieval of the most recent data from distributed sources and databases. DASMI can also be extended easily by adding new data sources and clients. We describe all DASMI components and demonstrate their use for protein and domain interactions.

Availability: The DASMI tools are available at http://www.dasmi.de/ and http://ipfam.sanger.ac.uk/graph. The DAS registry and the DAS 1.53E specification is found at http://www.dasregistry.org/.

Contact: mario.albrecht{at}mpi-inf.mpg.de

Supplementary information: Supplementary data and all figures in color are available at Bioinformatics online.

Associate Editor: Jonathan D. Wren

Received on August 14, 2008; revised on January 27, 2009; accepted on March 9, 2009

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