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

	Document type :	Scientific congresses, symposiums and conference proceedings : Poster
	Discipline(s) :	Life sciences : Multidisciplinary, general & others
	To cite this reference:	http://hdl.handle.net/10993/26854

Title :	OnTheFly 2.0: a tool for automatic annotation of files and biological information extraction.
Language :	English
Author, co-author :	Pafilis, Evangelos [Institute of Marine Biology, Biotechnology and Aquacultures (IMBBC) > Hellenic Center for Marine Research (HCMR)]
	Pavlopoulos, Georgios [University of Crete > Medical School]
	Satagopam, Venkata [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
	Papanikolaou, Nikolas [University of Crete > Medical School]
	Horn, Heiko [University of Copenhagen > The Novo Nordisk Foundation Center for Protein Research]
	Arvanitidis, Christos [Institute of Marine Biology, Biotechnology and Aquacultures (IMBBC) > Hellenic Center for Marine Research (HCMR)]
	Jensen, Lars Juhl [University of Copenhagen > The Novo Nordisk Foundation Center for Protein Research]
	Schneider, Reinhard [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
	Iliopoulos, Ioannis [University of Crete > Medical School]
Publication date :	2013
Peer reviewed :	Yes
Event name :	13th IEEE International Conference on Bioinformatics and Bioengineering (BIBE13)
Event date :	from 10-11-2013 to 13-11-2013
Event place (city) :	Chania
Event country :	Greece
Abstract :	[en] 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.
Research centres :	The European Commission FP7 programme 'Translational Potential' (TransPOT; ECcontract number 285948)
Funders :	European Molecular biology Laboratory (EMBL-Heidelberg), Heidelberg, Germany ; European Union’s Seventh Framework Programme (FP7/2007-2013) under grant agreement no 264089 (MARBIGEN project) ; he Novo
Permalink :	http://hdl.handle.net/10993/26854
DOI :	10.1109/BIBE.2013.6701679
Framework Programme / European Project :	FP7 ; 264089 - MARBIGEN - Supporting research potential for MARine BIodiversity and GENomics in the Eastern Mediterranean

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