OnTheFly is a web-based tool capable of annotating genes proteins and chemicals in commonly used document formats such as PDF, Microsoft Word and Excel, comma-separated values, and plain text files.
With a simple drag-and-drop motion, a set of local documents is converted to HTML files and the biomedical entities mentioned in them are being tagged.
The Reflect annotation service is performing the term tagging and the attachment of information-rich summaries to the recognized entity mentions.
Outperforming the single-document annotation model OnTheFly offers multi-format batch document processing with the extra functionality of combining entities across documents.
Such entity combination can be used to generate summaries with enriched entity descriptions, networks of known interactions (according to the STITCH database) and organized collections of relevant knowledge from public resources (via the bioCompendium service).
Although OnTheFly tries to minimize this phenomenon, the conversion of PDF and office documents may result in some format-loss, leading to slight alterations in the document appearance.
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OnTheFly Team: Evangelos Pafilis, Georgios A. Pavlopoulos, Venkata P. Satagopam, Lars Juhl Jensen, Heiko Horn, Christos Arvanitidis, Ioannis Iliopoulos, Reinhard Schneider
Funding: The project was financed by the EMBL. The research leading to these results has received funding from the European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement no 264089 (MARBIGEN project) and the European Commission FP7 programme 'Translational Potential' (TransPOT; EC contract number 285948).
