Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities

BMC Bioinformatics. 2006 Feb 15:7:71. doi: 10.1186/1471-2105-7-71.


Background: Existing biological databases support a variety of queries such as keyword or definition search. However, they do not provide any measure of relevance for the instances reported, and result sets are usually sorted arbitrarily.

Results: We describe a system that builds upon the complex infrastructure of the Biozon database and applies methods similar to those of Google to rank documents that match queries. We explore different prominence models and study the spectral properties of the corresponding data graphs. We evaluate the information content of principal and non-principal eigenspaces, and test various scoring functions which combine contributions from multiple eigenspaces. We also test the effect of similarity data and other variations which are unique to the biological knowledge domain on the quality of the results. Query result sets are assessed using a probabilistic approach that measures the significance of coherence between directly connected nodes in the data graph. This model allows us, for the first time, to compare different prominence models quantitatively and effectively and to observe unique trends.

Conclusion: Our tests show that the ranked query results outperform unsorted results with respect to our significance measure and the top ranked entities are typically linked to many other biological entities. Our study resulted in a working ranking system of biological entities that was integrated into Biozon at

Publication types

  • Evaluation Study
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Abstracting and Indexing / methods
  • Database Management Systems*
  • Databases, Genetic*
  • Information Storage and Retrieval / methods*
  • Natural Language Processing*
  • Online Systems
  • User-Computer Interface*
  • Vocabulary, Controlled