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Curating gene variant databases (LSDBs): toward a universal standard.

Celli, Jacopo; Dalgleish, Raymond; Vihinen, Mauno LU ; Taschner, Peter E M and den Dunnen, Johan T (2012) In Human Mutation 33(2). p.291-297
Abstract
Gene variant databases or Locus-Specific DataBases (LSDBs) are used to collect and display information on sequence variants on a gene-by-gene basis. Their most frequent use is in relation to DNA-based diagnostics, giving clinicians and scientists easy access to an up-to-date overview of all gene variants identified worldwide and whether they influence the function of the gene ("pathogenic or not"). While literature on gene variant databases is extensive, little has been published on the process of database curation itself. Based on our extensive experience as LSDB curators and our contributions to database curation courses, we discuss the subject of database curation. We describe the tasks involved, the steps to take, and the issues that... (More)
Gene variant databases or Locus-Specific DataBases (LSDBs) are used to collect and display information on sequence variants on a gene-by-gene basis. Their most frequent use is in relation to DNA-based diagnostics, giving clinicians and scientists easy access to an up-to-date overview of all gene variants identified worldwide and whether they influence the function of the gene ("pathogenic or not"). While literature on gene variant databases is extensive, little has been published on the process of database curation itself. Based on our extensive experience as LSDB curators and our contributions to database curation courses, we discuss the subject of database curation. We describe the tasks involved, the steps to take, and the issues that might occur. Our overview is a first step toward establishing overall guidelines for database curation and ultimately covers one aspect of establishing quality-assured gene variant databases. (Less)
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author
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Databases, Computational Biology: methods, Computational Biology: standards, Genetic: standards
in
Human Mutation
volume
33
issue
2
pages
291 - 297
publisher
John Wiley & Sons
external identifiers
  • pmid:21990126
  • scopus:84857772267
ISSN
1059-7794
DOI
10.1002/humu.21626
language
English
LU publication?
no
id
0fe01742-8ce8-4b1e-9f46-86d12c491ce1 (old id 3634605)
alternative location
http://www.ncbi.nlm.nih.gov/pubmed/21990126?dopt=Abstract
date added to LUP
2013-06-12 20:46:30
date last changed
2017-10-01 04:56:59
@article{0fe01742-8ce8-4b1e-9f46-86d12c491ce1,
  abstract     = {Gene variant databases or Locus-Specific DataBases (LSDBs) are used to collect and display information on sequence variants on a gene-by-gene basis. Their most frequent use is in relation to DNA-based diagnostics, giving clinicians and scientists easy access to an up-to-date overview of all gene variants identified worldwide and whether they influence the function of the gene ("pathogenic or not"). While literature on gene variant databases is extensive, little has been published on the process of database curation itself. Based on our extensive experience as LSDB curators and our contributions to database curation courses, we discuss the subject of database curation. We describe the tasks involved, the steps to take, and the issues that might occur. Our overview is a first step toward establishing overall guidelines for database curation and ultimately covers one aspect of establishing quality-assured gene variant databases.},
  author       = {Celli, Jacopo and Dalgleish, Raymond and Vihinen, Mauno and Taschner, Peter E M and den Dunnen, Johan T},
  issn         = {1059-7794},
  keyword      = {Databases,Computational Biology: methods,Computational Biology: standards,Genetic: standards},
  language     = {eng},
  number       = {2},
  pages        = {291--297},
  publisher    = {John Wiley & Sons},
  series       = {Human Mutation},
  title        = {Curating gene variant databases (LSDBs): toward a universal standard.},
  url          = {http://dx.doi.org/10.1002/humu.21626},
  volume       = {33},
  year         = {2012},
}