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Nucleic Acids Research, 2002, Vol. 30, No. 1 354-360
© 2002 Oxford University Press

Olfactory Receptor Database: a metadata-driven automated population from sources of gene and protein sequences

Chiquito Crasto1,2,*, Luis Marenco1, Perry Miller1,3 and Gordon Shepherd2

1Center for Medical Informatics, 2Section for Neurobiology and 3Department of Molecular, Cellular and Developmental Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 05611, USA

The Olfactory Receptor Database (ORDB; http://senselab.med.yale.edu/senselab/ordb) is a central repository of olfactory receptor (OR) and olfactory receptor-like gene and protein sequences. To deal with the very large OR gene family, we have constructed an algorithm that automatically downloads sequences from web sources such as GenBank and SWISS-PROT into the database. The algorithm uses hypertext markup language (HTML) parsing techniques that extract information relevant to ORDB. The information is then correlated with the metadata in the ORDB knowledge base to encode the unstructured text extracted into the structured format compliant with the database architecture, entity attribute value with classes and relationship (EAV/CR), which supports the SenseLab project as a whole. Three population methods: batch, automatic and semi-automatic population are discussed. The data is imported into the database using extensible markup language (XML).

* To whom correspondence should be addressed at: Center for Medical Informatics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 05611, USA. Tel: +1 203 764 9136; Fax: +1 203 764 6717; Email: chiquito.crasto{at}yale.edu


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