SPINE 2: a system for collaborative structural proteomics within a federated database framework
- 1 June 2003
- journal article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 31 (11), 2833-2838
- https://doi.org/10.1093/nar/gkg397
Abstract
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).Keywords
This publication has 16 references indexed in Scilit:
- WormBase: a cross-species database for comparative genomicsNucleic Acids Research, 2003
- The Protein Information ResourceNucleic Acids Research, 2003
- The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003Nucleic Acids Research, 2003
- Target space for structural genomics revisitedBioinformatics, 2002
- SPINS: Standardized ProteIn NMR Storage. A data dictionary and object-oriented relational database for archiving protein NMR spectraJournal of Biomolecular NMR, 2002
- SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomicsNucleic Acids Research, 2001
- PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction informationNucleic Acids Research, 2001
- The Protein Data Bank and the challenge of structural genomics.Nature Structural & Molecular Biology, 2000
- Structural proteomics of an archaeon.Nature Structural & Molecular Biology, 2000
- The PRESAGE database for structural genomicsNucleic Acids Research, 1999