14 votes

Reflect: Augmented Browsing for the Life Scientist

Evangelos Pafilis¹, Seán I. O’Donoghue¹, Lars J. Jensen², Heiko Horn¹, Michael Kuhn¹, Nigel P. Brown¹ & Reinhard Schneider¹

Correspondence: (Login to view email address)

1. European Molecular Biology Laboratory, Germany
2. NNF Center for Protein Research, University of Copenhagen, Denmark

PDF (5.6 MB)

Document Type:

Manuscript

Date:

Received 02 May 2009 01:44 UTC; Posted 04 May 2009

Subjects:

Biotechnology, Chemistry, Genetics & Genomics, Molecular Cell Biology, Bioinformatics

Tags:

• text mining
• entity recognition
• small molecules
• curation
• plug-in
• bioinformatics
• browser
• proteins
• chemicals
• drugs
• semantic markup
• PubChem
• STITCH
• SMART
• PDB

Abstract:

Anyone who regularly reads life science literature often comes across names of genes, proteins, or small molecules that they would like to know more about. To make this process easier, we have developed a new, free service called Reflect (http://reflect.ws) that can be installed as a plug-in to Firefox or Internet Explorer. Reflect tags gene, protein, and small molecule names in any web page, typically within a few seconds, and without affecting document layout. Clicking on a tagged gene or protein name opens a popup showing a concise summary that includes synonyms, database identifiers, sequence, domains, 3D structure, interaction partners, subcellular location, and related literature. Clicking on a tagged small molecule name opens a popup showing 2D structure and interaction partners. The popups also allow navigation to commonly used databases. In the future we plan to add further entity types to Reflect, including outside the life sciences.

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Additional information

License:

This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Pafilis, Evangelos, O’Donoghue, Seán, Jensen, Lars, Horn, Heiko, Kuhn, Michael, Brown, Nigel, and Schneider, Reinhard. Reflect: Augmented Browsing for the Life Scientist. Available from Nature Precedings <http://hdl.handle.net/10101/npre.2009.3212.1> (2009)

Version info:

Published version:

10.1038/nbt0609-508 (Peer Reviewed) Published in Nature Biotechnology 27, 508 - 510 (2009).

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