Skip to main content
Article thumbnail
Location of Repository

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

By Georgios A. Pavlopoulos, Evangelos Pafilis, M. Kuhn, Sean D. Hooper and Reinhard Schneider


OnTheFly is a web-based application that applies biological named entity recognition to enrich Microsoft Office, PDF and plain text documents. The input files are converted into the HTML format and then sent to the Reflect tagging server, which highlights biological entity names like genes, proteins and chemicals, and attaches to them JavaScript code to invoke a summary pop-up window. The window provides an overview of relevant information about the entity, such as a protein description, the domain composition, a link to the 3D structure and links to other relevant online resources. OnTheFly is also able to extract the bioentities mentioned in a set of files and to produce a graphical representation of the networks of the known and predicted associations of these entities by retrieving the information from the STITCH database

Topics: Applications Note
Publisher: Oxford University Press
OAI identifier:
Provided by: PubMed Central

Suggested articles


  1. (2008). PDF to HTML v2.0. Available at
  2. (2006). PIPE: a protein–protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs.
  3. (2008). Text processing through Web services: calling Whatizit.

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.