A search engine and information extraction tool for biological research

David Corney, David Jones and Bernard Buxton A large and growing amount of information is published every year in scientific journals. In the biomedical field, there are thousands of journals, each publishing many issues annually, any one of which could contain information that is relevant to a researcher. However, no one has time to read every paper. One solution is to use a software tool to search through publications to identify important results in response to the users' queries. BioRAT is such a tool. It was initially developed as part of a three-year research project (2001-2004), in collaboration with a major pharmaceutical company; the ongoing project is now funded by the BBSRC (2004-2007). The software is available for academic research purposes only.

Download the software

Read the documentation

Example templates and results

For queries regarding BioRAT:

For details, please see the following references:

  • Corney, D. P. A., Buxton, B. F., Langdon W.B. and Jones, D. T. (2004) "BioRAT: Extracting Biological Information from Full-length Papers", Bioinformatics (Nov 22 2004; vol. 20(17); pp.3206-13). PubMed 15231534Journal pre-print (local PDF)
  • Corney, D. P. A., Buxton, B. F., Langdon W.B., Charlwood, J., Woollard, P.M. and Jones, D. T. (2003) Extracting Biological Information from Full-length Papers. UCL-CS Technical Report: RN/03/17 PDF Note: This report is less up-to-date than the above Bioinformatics paper, but contains some extra details.
  • Corney, D. P. A., Byrne, E.L., Buxton, B. F. and Jones, D. T. (2005) "A Logical Framework for Template Creation and Information Extraction", Foundations of Semantic Oriented Data and Web Mining workshop, part of ICDM2005 (the Fifth IEEE International Conference on Data Mining). PDF


  • Dec 2003: New site online. First public release of software.
  • July 2004: Link to Bioinformatics paper added.
  • January 2005: Software updated.
  • August 2005: Software updated (version 1.8).
  • July 2006: Software updated (version 2.0).