Nucleic Acids Research, 2003, Vol. 31, No. 11 2833-2838
© 2003 Oxford University Press
SPINE 2: a system for collaborative structural proteomics within a federated database framework
1 Molecular Biophysics and Biochemistry, 2 Molecular, Cellular and Developmental Biology and 3 Computer Science, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA, 4 Center for Advanced Biotechnology and Medicine, 5 Department of Molecular Biology and Biochemistry, Rutgers University and 6 Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, Piscataway, NJ 08854, USA
*To whom correspondence should be addressed. Tel: +1 203 432 6105; Fax: +1 360 838 7861; Email: mark.gerstein{at}yale.edu
Correspondence may also be addressed to Gaetano T. Montelione. Tel: +1 732 235 5321; Fax: +1 732 235 5633; Email: guy@cabm.rutgers.edu
The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors
We present version 2 of the SPINE system for structural proteomics. SPINE is available over the web at http://nesg.org. It serves as the central hub for the Northeast Structural Genomics Consortium, allowing collaborative structural proteomics to be carried out in a distributed fashion. The core of SPINE is a laboratory information management system (LIMS) for key bits of information related to the progress of the consortium in cloning, expressing and purifying proteins and then solving their structures by NMR or X-ray crystallography. Originally, SPINE focused on tracking constructs, but, in its current form, it is able to track target sample tubes and store detailed sample histories. The core database comprises a set of standard relational tables and a data dictionary that form an initial ontology for proteomic properties and provide a framework for large-scale data mining. Moreover, SPINE sits at the center of a federation of interoperable information resources. These can be divided into (i) local resources closely coupled with SPINE that enable it to handle less standardized information (e.g. integrated mailing and publication lists), (ii) other information resources in the NESG consortium that are inter-linked with SPINE (e.g. crystallization LIMS local to particular laboratories) and (iii) international archival resources that SPINE links to and passes on information to (e.g. TargetDB at the PDB).
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