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

Authors: Pafilis, Evangelos; Pavlopoulos, Georgios; Satagopam, Venkata; Papanikolaou, Nikolas; Horn, Heiko; Arvanitidis, Christos; Jensen, Lars Juhl; +2 Authors

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

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.

Country
Luxembourg
Keywords

: Multidisciplinaire, généralités & autres [F99] [Sciences du vivant], : Multidisciplinary, general & others [F99] [Life sciences]

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    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Average
  • citations
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    0
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Average
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Average
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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average
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
Related to Research communities
European Marine Science
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