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. 2003 Jun 1;31(11):2833-8.
doi: 10.1093/nar/gkg397.

SPINE 2: a system for collaborative structural proteomics within a federated database framework

Chern-Sing Goh  1 , Ning Lan, Nathaniel Echols, Shawn M Douglas, Duncan Milburn, Paul Bertone, Rong Xiao, Li-Chung Ma, Deyou Zheng, Zeba Wunderlich, Tom Acton, Gaetano T Montelione, Mark Gerstein
Affiliations

SPINE 2: a system for collaborative structural proteomics within a federated database framework

Chern-Sing Goh et al. Nucleic Acids Res. .

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).

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Figures

Figure 1
Figure 1
Schema of the SPINE database, showing evolution of tables and data flow. (A) The original version of SPINE, in which the construct was the primary object tracked. Table records typically had one-to-one relationships. Each target could be associated with a single expression and purification. (B) Current schema. Experimental records (outlined in blue) all have one-to-many relationships branching from target entries. User and tracking information and, most recently, detailed sample tube data can now be tracked in SPINE. The newest additions to the database are highlighted in red.
Figure 2
Figure 2
Overview of the SPINE federation. Tier 1 (white) resources are the local resources integrated in SPINE. Tier 2 (orange) resources are other web resources of the NESG project that are linked to SPINE. Tier 3 (yellow) resources are external archival resources that SPINE is connected to.
Figure 3
Figure 3
Assorted screenshots from the NESG/SPINE web server. (A) The NESG home page, providing links to all the institutions involved and to the gallery of structures produced by them. (B) The SPINE target summary page showing the data recorded in SPINE at each stage of the protein production and structure determination process (blue shading indicates data are present) for every target in the project. (C) One of the new additions in version 2 of SPINE is the ability to track in detail a given sample tube down to a well, plate and physical location. Any changes can be made by clicking on the desired sample entry (blue circle). (D) The NESG structure gallery showing all the structures that have been determined by the NESG consortium. The structure gallery also contains links to the PDB, the BMRB, the Structure Validation Website and the Structure/Functional Annotation Website.
Figure 3
Figure 3
Assorted screenshots from the NESG/SPINE web server. (A) The NESG home page, providing links to all the institutions involved and to the gallery of structures produced by them. (B) The SPINE target summary page showing the data recorded in SPINE at each stage of the protein production and structure determination process (blue shading indicates data are present) for every target in the project. (C) One of the new additions in version 2 of SPINE is the ability to track in detail a given sample tube down to a well, plate and physical location. Any changes can be made by clicking on the desired sample entry (blue circle). (D) The NESG structure gallery showing all the structures that have been determined by the NESG consortium. The structure gallery also contains links to the PDB, the BMRB, the Structure Validation Website and the Structure/Functional Annotation Website.
Figure 3
Figure 3
Assorted screenshots from the NESG/SPINE web server. (A) The NESG home page, providing links to all the institutions involved and to the gallery of structures produced by them. (B) The SPINE target summary page showing the data recorded in SPINE at each stage of the protein production and structure determination process (blue shading indicates data are present) for every target in the project. (C) One of the new additions in version 2 of SPINE is the ability to track in detail a given sample tube down to a well, plate and physical location. Any changes can be made by clicking on the desired sample entry (blue circle). (D) The NESG structure gallery showing all the structures that have been determined by the NESG consortium. The structure gallery also contains links to the PDB, the BMRB, the Structure Validation Website and the Structure/Functional Annotation Website.
Figure 3
Figure 3
Assorted screenshots from the NESG/SPINE web server. (A) The NESG home page, providing links to all the institutions involved and to the gallery of structures produced by them. (B) The SPINE target summary page showing the data recorded in SPINE at each stage of the protein production and structure determination process (blue shading indicates data are present) for every target in the project. (C) One of the new additions in version 2 of SPINE is the ability to track in detail a given sample tube down to a well, plate and physical location. Any changes can be made by clicking on the desired sample entry (blue circle). (D) The NESG structure gallery showing all the structures that have been determined by the NESG consortium. The structure gallery also contains links to the PDB, the BMRB, the Structure Validation Website and the Structure/Functional Annotation Website.
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References

    1. Burley S.K. (2000) An overview of structural genomics. Nature Struct. Biol., 7 (Suppl.), 932–934. - PubMed
    1. Berman H.M., Bhat,T.N., Bourne,P.E., Feng,Z., Gilliland,G., Weissig,H. and Westbrook,J. (2000) The Protein Data Bank and the challenge of structural genomics. Nature Struct. Biol., 7 (Suppl.), 957–959. - PubMed
    1. Christendat D., Yee,A., Dharamsi,A., Kluger,Y., Savchenko,A., Cort,J.R., Booth,V., Mackereth,C.D., Saridakis,V., Ekiel,I. et al. (2000) Structural proteomics of an archaeon. Nature Struct. Biol., 7, 903–909. - PubMed
    1. Brenner S.E., Barken,D. and Levitt,M. (1999) The PRESAGE database for structural genomics. Nucleic Acids Res., 27, 251–253. - PMC - PubMed
    1. Bertone P., Kluger,Y., Lan,N., Zheng,D., Christendat,D., Yee,A., Edwards,A.M., Arrowsmith,C.H., Montelione,G.T. and Gerstein,M. (2001) SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics. Nucleic Acids Res., 29, 2884–2898. - PMC - PubMed