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 interlinked 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).
| Original language | English (US) |
|---|---|
| Pages (from-to) | 2833-2838 |
| Number of pages | 6 |
| Journal | Nucleic Acids Research |
| Volume | 31 |
| Issue number | 11 |
| DOIs | |
| State | Published - Jun 1 2003 |
| Externally published | Yes |
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ASJC Scopus subject areas
- Genetics
Cite this
SPINE 2 : A system for collaborative structural proteomics within a federated database framework. / Goh, Chern Sing; Lan, Ning; Echols, Nathaniel; Douglas, Shawn M.; Milburn, Duncan; Bertone, Paul; Xiao, Rong; Ma, Li Chung; Zheng, Deyou; Wunderlich, Zeba; Acton, Tom; Montelione, Gaetano T.; Gerstein, Mark.
In: Nucleic Acids Research, Vol. 31, No. 11, 01.06.2003, p. 2833-2838.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - SPINE 2
T2 - A system for collaborative structural proteomics within a federated database framework
AU - Goh, Chern Sing
AU - Lan, Ning
AU - Echols, Nathaniel
AU - Douglas, Shawn M.
AU - Milburn, Duncan
AU - Bertone, Paul
AU - Xiao, Rong
AU - Ma, Li Chung
AU - Zheng, Deyou
AU - Wunderlich, Zeba
AU - Acton, Tom
AU - Montelione, Gaetano T.
AU - Gerstein, Mark
PY - 2003/6/1
Y1 - 2003/6/1
N2 - 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 interlinked 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).
AB - 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 interlinked 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).
UR - http://www.scopus.com/inward/record.url?scp=0038268061&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0038268061&partnerID=8YFLogxK
U2 - 10.1093/nar/gkg397
DO - 10.1093/nar/gkg397
M3 - Article
C2 - 12771210
AN - SCOPUS:0038268061
VL - 31
SP - 2833
EP - 2838
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - 11
ER -