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Bioinformatics Advance Access published online on July 26, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl408
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received April 28, 2006
Revised May 31, 2006
Accepted July 22, 2006

Applications note

ALIBABA: PubMed as a graph

Conrad Plake 1, Torsten Schiemann 1, Marcus Pankalla 2, Jörg Hakenberg 1 *, and Ulf Leser 1

1 Knowledge Management in Bioinformatics, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
2 Dept. of Mathematics and Computer Science, Free University Berlin, Arnimallee 2-6, 14195 Berlin, Germany

* To whom correspondence should be addressed.
Jörg Hakenberg, E-mail: hakenberg{at}informatik.hu-berlin.de


  Abstract

The biomedical literature contains a wealth of information on associations between many different types of objects, such as protein-protein interactions, gene-disease associations, or subcellular locations of proteins. When searching such information using conventional search engines, e.g. PubMed, users see the data only one-abstract at a time and "hidden" in natural language text. ALIBABA is an interactive tool for graphical summarization of search results. It parses the set of abstracts that fit a PubMed query and presents extracted information on biomedical objects and their relationships as a graphical network. ALIBABA extracts associations between cells, diseases, drugs, proteins, species, and tissues. Several filter options allow for a more focused search. Thus, researchers can grasp complex networks described in various articles at a glance.

Availability: http://wbi.informatik.hu-berlin.de/alibaba/.

Associate Editor: Satoru Miyano
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