Poster (Scientific congresses, symposiums and conference proceedings)
OnTheFly 2.0: a tool for automatic annotation of files and biological information extraction.
Pafilis, Evangelos; Pavlopoulos, Georgios; Satagopam, Venkata et al.
201313th IEEE International Conference on Bioinformatics and Bioengineering (BIBE13)
 

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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 center :
The European Commission FP7 programme 'Translational Potential' (TransPOT; ECcontract number 285948)
Disciplines :
Life sciences: Multidisciplinary, general & others
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
External co-authors :
yes
Language :
English
Title :
OnTheFly 2.0: a tool for automatic annotation of files and biological information extraction.
Publication date :
2013
Event name :
13th IEEE International Conference on Bioinformatics and Bioengineering (BIBE13)
Event place :
Chania, Greece
Event date :
from 10-11-2013 to 13-11-2013
European Projects :
FP7 - 264089 - MARBIGEN - Supporting research potential for MARine BIodiversity and GENomics in the Eastern Mediterranean
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
CE - Commission Européenne [BE]
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