The Nuclear Protein Database
Why was the NPD created?
The NPD is an initiative undertaken by the Bickmore Group of the MRC-Human Genetics Unit (HGU) to organise, and make available data on novel nuclear proteins isolated using
gene-trap and other technologies (see Publications). It quickly became apparent that such a
database would be a valuable resource to the entire community, and so data from nuclear
proteins reported in the literature has also been added. Thus, this database provides a
comprehensive overview of the diversity of many sub-nuclear compartments (see Statistics).
In future, we would like to include data from other groups interested in nuclear compartmentalisation and function. We are also eager to develop strategic partnerships with other database projects devoted to various aspects of functional genomics, including gene-expression and protein-protein interaction data.
The database was first prototyped in MSAccess as the MyGene DB, and was made possible by funding from the Medical Research Council (UK) and the James S. McDonnell Foundation. The NPD was later adapted to provide online access to the content, by:
- Graham Dellaire, Ph.D
- Rachel Farrall, B.Sc. (MCSE)
and content for the website was provided by:
- Wendy Bickmore, Ph.D.
- Francois-Michel Boisvert, M.Sc.
- Stephanie, Cliff, B.Sc.
- Jonathan Chubb, Ph.D.
- Graham Dellaire, Ph.D.
- Nick Gilbert, Ph.D.
- Jeremy Sanford, Ph.D.
- Heidi G.E. Sutherland, Ph.D.
The NPD remained in that state until 2009, when it was upgraded to version 2.0 by Mark MacGillivray as an MSc research project. Much of the website content
was adapted from the original, but the underlying structure was completely redeveloped. The current NPD now operates solely as a web service, with online access
to curation functionality negating the need for a further Access database. Additionally, access methods to the NPD were updated to take advantage of modern practices
in Service Oriented Architecture, leading to access onto NPD content via both RESTful protocols and via a SOAP WSDL. Further details of this functionality is available
on the Web Services page.
For further information or comments on the NPD please contact: Professor Wendy Bickmore
- Bickmore, WA and HGE Sutherland (2002) Addressing protein localization within the nucleus EMBO J. 21(6):1248-1254.
- Sutherland HG, Mumford GK, Newton K, Ford LV, Farrall R, Dellaire G, Caceres JF, Bickmore WA. (2001) Large-scale identification of mammalian proteins localized to nuclear sub-compartments. Hum Mol Genet. 10(18):1995-2011.
- Tate P, Lee M, Tweedie S, Skarnes WC, Bickmore WA.
(1998) Capturing novel mouse genes encoding chromosomal and other nuclear proteins. J Cell Sci. 111 (17):2575-85.