title: SPINE 2: a system for collaborative structural proteomics within a federated database framework.
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).
authors.affiliation: Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA.
authors.forename: Chern-Sing
authors.initials: CS
authors.lastname: Goh
authors.forename: Ning
authors.initials: N
authors.lastname: Lan
authors.forename: Nathaniel
authors.initials: N
authors.lastname: Echols
authors.forename: Shawn M
authors.initials: SM
authors.lastname: Douglas
authors.forename: Duncan
authors.initials: D
authors.lastname: Milburn
authors.forename: Paul
authors.initials: P
authors.lastname: Bertone
authors.forename: Rong
authors.initials: R
authors.lastname: Xiao
authors.forename: Li-Chung
authors.initials: LC
authors.lastname: Ma
authors.forename: Deyou
authors.initials: D
authors.lastname: Zheng
authors.forename: Zeba
authors.initials: Z
authors.lastname: Wunderlich
authors.forename: Tom
authors.initials: T
authors.lastname: Acton
authors.forename: Gaetano T
authors.initials: GT
authors.lastname: Montelione
authors.forename: Mark
authors.initials: M
authors.lastname: Gerstein
mesh_terms: D003299:Cooperative Behavior; D003628:Database Management Systems; D030562:Databases, Protein; D020407:Internet; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D040901:Proteomics; D012984:Software; D018511:Systems Integration
chemical_list: D011506:Proteins