Exploring biomedical databases with BioNav

ABSTRACT

We demonstrate the BioNav system, a novel search interface for biomedical databases, such as PubMed. BioNav enables users to navigate large number of query results by categorizing them using MeSH; a comprehensive concept hierarchy used by PubMed. Once the query results are organized into a navigation tree, BioNav reveals only a small subset of the concept nodes at each step, selected such that the expected user navigation cost is minimized. In contrast, previous works expand the hierarchy in a predefined static manner, without navigation cost modeling. BioNav is available at http://db.cse.buffalo.edu/bionav.

REFERENCES

• 1: Abhijith Kashyap , Vagelis Hristidis , Michalis Petropoulos , Sotiria Tavoulari, BioNav: Effective Navigation on Query Results of Biomedical Databases, Proceedings of the 2009 IEEE International Conference on Data Engineering, p.1287-1290, March 29-April 02, 2009 [doi>10.1109/ICDE.2009.222]
• 2: Kaushik Chakrabarti , Surajit Chaudhuri , Seung-won Hwang, Automatic categorization of query results, Proceedings of the 2004 ACM SIGMOD international conference on Management of data, June 13-18, 2004, Paris, France [doi>10.1145/1007568.1007653]
• 3: Zhiyuan Chen , Tao Li, Addressing diverse user preferences in SQL-query-result navigation, Proceedings of the 2007 ACM SIGMOD international conference on Management of data, June 11-14, 2007, Beijing, China [doi>10.1145/1247480.1247551]
• 4: Entrez Programming Utilities. http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html
• 5: Medical Subject Headings(MeSH). http://nlm.nih.gov/mesh/
• 6: Transinsight GmbH GoPubMed. http://gopubmed.org
• 7: J.A. Mitchell, A.R. Aronson and J.G. Mork: Gene Indexing: Characterization and Analysis of NLM's GeneRIFs. In Proceedings of the AMIA Symposium, 8th-12th November, Washington, DC, pp. 460--464, 2003.

INDEX TERMS

Primary Classification:
  H. Information Systems
  H.3 INFORMATION STORAGE AND RETRIEVAL
      H.3.3 Information Search and Retrieval
          Subjects: Selection process

Additional Classification:
  H. Information Systems
  H.3 INFORMATION STORAGE AND RETRIEVAL
      H.3.3 Information Search and Retrieval
          Subjects: Information filtering; Search process
      H.3.7 Digital Libraries
          Subjects: Dissemination; User issues

  J. Computer Applications
  J.3 LIFE AND MEDICAL SCIENCES
      Subjects: Medical information systems

General Terms:
Algorithms, Design, Human Factors

Keywords:
query results navigation, taxonomy, user interfaces