Abstract
SPINE (Structural Proteomics In Europe) was established in 2002 as an integrated research project to develop new methods and technologies for high‐throughput structural biology. Development areas were broken down into workpackages and this article gives an overview of ongoing activity in the bioinformatics workpackage. Developments cover target selection, target registration, wet and dry laboratory data management and structure annotation as they pertain to high‐throughput studies. Some individual projects and developments are discussed in detail, while those that are covered elsewhere in this issue are treated more briefly. In particular, this overview focuses on the infrastructure of the software that allows the experimentalist to move projects through different areas that are crucial to high‐throughput studies, leading to the collation of large data sets which are managed and eventually archived and/or deposited.
Highlights
Bioinformatics as originally defined is the application of informatics techniques to biological systems and this general data-management and analysis problem is commonly regarded as being of central importance to large-scale genomic projects such as structural genomics (Burley et al, 1999; Stevens et al, 2001)
Not strictly a structural genomics project itself, the remit of Structural Proteomics In Europe (SPINE) in developing high-throughput methods for structural biology and the distributed nature of the project suggests that its data-management issues will be critical
While it is generally accepted that the current principal bottlenecks in structural biology are the production of soluble protein and its crystallization, bioinformatics and data management are much more than a necessary housekeeping exercise
Summary
Bioinformatics as originally defined is the application of informatics techniques to biological systems and this general data-management and analysis problem is commonly regarded as being of central importance to large-scale genomic projects such as structural genomics (Burley et al, 1999; Stevens et al, 2001). SPINE has played a central role in European efforts to provide an effective data-management solution covering experiments It has supported the creation of a universal dictionary for describing experiments associated with protein production (the Protein Production Data Model curated by the EBI partner; Pajon et al, 2005) and is working to extend the scope of this system to cover other aspects of structural proteomics. SPINE has played a leading role in bringing together groups developing piecemeal solutions to datamanagement problems, brokering an agreement to develop a common framework for LIMS across Europe These efforts are beginning to bear fruit in the PIMS project (http:// www.pims-lims.org) that is being developed by several SPINE partners in collaboration with others.
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