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Bioinformatics Advance Access published online on February 17, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp081
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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.

OnTheFly: A Tool for automated document-based text annotation, data linking and network generation.

Georgios A. Pavlopoulos 1, Evangelos Pafilis 1, M. Kuhn 1, Sean D. Hooper 2 and Reinhard Schneider 1,*

1Structural and Computational Biology Unit, EMBL Meyerhofstrasse 1, Heidelberg, Germany.
2 Department of Energy Joint Genome Institute (DOE-JGI), Genome Biology Program, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA

*To whom correspondence should be addressed. Mr. Georgios Pavlopoulos, E-mail: pavlopou{at}embl.de


  Abstract

OnTheFly is a web-based application that applies biological named entity recognition to enrich Microsoft Office, PDF and plain text documents. The input files are converted into the HTML format and then sent to the Reflect tagging server, which highlights biological entity names like genes, proteins and chemicals, and attaches to them JavaScript code to invoke a summary popup window. The window provides an overview of relevant information about the entity, such as a protein description, the domain composition, a link to the 3D structure and links to other relevant online resources. OnTheFly is also able to extract the bioentities mentioned in a set of files and to produce a graphical representation of the networks of the known and predicted associations of these entities by retrieving the information from the STITCH database.

Availability: http://onthefly.embl.de

Supplementary material: http://onthefly.embl.de/FAQ.html

Associate Editor: Dr. Jonathan Wren

Received on November 19, 2008; revised on February 2, 2009; accepted on February 7, 2009

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