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

Chiquito Crasto, Luis Marenco, Perry Miller, Gordon Shepherd

Research output: Contribution to journalArticle

55 Scopus citations

Abstract

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 down-loads 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).

Original languageEnglish
Pages (from-to)354-360
Number of pages7
JournalNucleic Acids Research
Volume30
Issue number1
DOIs
StatePublished - Jan 1 2002

Fingerprint Dive into the research topics of 'Olfactory Receptor Database: A metadata-driven automated population from sources of gene and protein sequences'. Together they form a unique fingerprint.

Cite this