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Related Experiment Video

Updated: Jun 25, 2026

A Single-fly Assay for Foraging Behavior in Drosophila

A Single-fly Assay for Foraging Behavior in Drosophila

Published on: November 4, 2013

OnTheFly: a tool for automated document-based text annotation, data linking and network generation.

Georgios A Pavlopoulos¹, Evangelos Pafilis, M Kuhn

¹Structural and Computational Biology Unit, EMBL Meyerhofstrasse 1, Heidelberg, . pavlopou@embl.de

Bioinformatics (Oxford, England)

|February 19, 2009

Summary

This summary is machine-generated.

OnTheFly is a web tool that uses biological named entity recognition to enrich documents. It highlights genes, proteins, and chemicals, providing linked summaries and network visualizations for biological research.

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Area of Science:

Bioinformatics
Computational Biology
Text Mining

Background:

Biological research generates vast amounts of unstructured text data.
Extracting and organizing information on biological entities (genes, proteins, chemicals) is crucial for scientific discovery.
Existing tools may lack integrated approaches for document enrichment and network analysis.

Purpose of the Study:

To introduce OnTheFly, a web-based application for biological named entity recognition.
To enhance scientific documents by identifying and annotating biological entities.
To facilitate the visualization of biological networks based on extracted entities.

Main Methods:

Web-based application utilizing biological named entity recognition.
Conversion of input documents (Office, PDF, plain text) to HTML.
Integration with the Reflect tagging server for entity highlighting and pop-up summaries.
Data retrieval from the STITCH database for network visualization.

Main Results:

OnTheFly successfully identifies and highlights biological entities within various document formats.
Pop-up windows provide comprehensive information, including descriptions, domain composition, and external links.
Graphical representations of biological association networks can be generated from extracted entities.

Conclusions:

OnTheFly offers a valuable tool for enriching scientific documents with biological information.
The application streamlines the process of accessing entity-specific data and understanding biological relationships.
OnTheFly supports researchers in navigating and analyzing complex biological information from textual sources.