Journal Article

OnTheFly: a tool for automated document-based text annotation, data linking and network generation

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

in Bioinformatics

Volume 25, issue 7, pages 977-978
Published in print April 2009 | ISSN: 1367-4803
Published online February 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp081

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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 pop-up 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, http://onthefly.embl.de/FAQ.html

Contact: pavlopou@embl.de

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1002 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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