research product . 2013

OnTheFly 2.0: a tool for automatic annotation of files and biological information extraction.

Pafilis, Evangelos; Pavlopoulos, Georgios; Satagopam, Venkata; Papanikolaou, Nikolas; Horn, Heiko; Arvanitidis, Christos; Jensen, Lars Juhl; Schneider, Reinhard; Iliopoulos, Ioannis;
Restricted English
  • Published: 01 Jan 2013
  • Country: Luxembourg
Abstract
Retrieving all of the necessary information from databases about bioentities mentioned in an article is not a trivial or an easy task. Following the daily literature about a specific biological topic and collecting all the necessary information about the bioentities mentioned in the literature manually is tedious and time consuming. OnTheFly 2.0 is a web application mainly designed for non-computer experts which aims to automate data collection and knowledge extraction from biological literature in a user friendly and efficient way. OnTheFly 2.0 is able to extract bioentities from individual articles such as text, Microsoft Word, Excel and PDF files. With a simple drag-and-drop motion, the text of a document is extensively parsed for bioentities such as protein/gene names and chemical compound names. Utilizing high quality data integration platforms, OnTheFly allows the generation of informative summaries, interaction networks and at-a-glance popup windows containing knowledge related to the bioentities found in documents. OnTheFly 2.0 provides a concise application to automate the extraction of bioentities hidden in various documents and is offered as a web based application.
Subjects
free text keywords: : Multidisciplinary, general & others [F99] [Life sciences], : Multidisciplinaire, généralités & autres [F99] [Sciences du vivant]
Communities
  • European Marine Science
Funded by
EC| MARBIGEN
Project
MARBIGEN
Supporting research potential for MARine BIodiversity and GENomics in the Eastern Mediterranean
  • Funder: European Commission (EC)
  • Project Code: 264089
  • Funding stream: FP7 | SP4 | REGPOT
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