Evading the annotation bottleneck: using sequence similarity to search non-sequence gene data

Background: Non-sequence gene data (images, literature, etc.) can be found in many different public databases. Access to these data is mostly by text based methods using gene names; however, gene annotation is neither complete, nor fully systematic between organisms, and is also not generally stable over time. This provides some challenges for text based access, especially for cross-species searches. We propose a method for non-sequence data retrieval based on sequence similarity, which removes dependence on annotation and text searches. This work was motivated by the need to provide better access to large numbers of in situ images, and the observation that such image data were usually associated with a specific gene sequence. Sequence similarity searches are found in existing gene oriented databases, but mostly give indirect access to non-sequence data via navigational links. Results: Three applications were built to explore the proposed method: accessing image data, literature and g...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Michael J. Gilchrist, Mikkel B. Christensen, Richard Harland, Nicolas Pollet, James C. Smith, Naoto Ueno, Nancy Papalopulu
• Keywords: BMCBI 2008, Gene, Image, Image Data