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Varisnp, A Benchmark Database For Variations from dbSNP.

Schaafsma, Gerard LU and Vihinen, Mauno LU (2015) In Human Mutation 36(2). p.161-166
Abstract
For development and evaluation of methods for predicting the effects of variations, benchmark datasets are needed. Some previously developed datasets are available for this purpose, but newer and larger benchmark sets for benign variants have largely been missing. VariSNP datasets are selected from dbSNP. These subsets were filtered against disease-related variants in the ClinVar, UniProtKB/Swiss-Prot and PhenCode databases, to identify neutral or non-pathogenic cases. All variant descriptions include mapping to reference sequences on chromosomal, genomic, coding DNA and protein levels. The datasets will be updated with automated scripts on a regular basis and are freely available at https://structure.bmc.lu.se/VariSNP. This article is... (More)
For development and evaluation of methods for predicting the effects of variations, benchmark datasets are needed. Some previously developed datasets are available for this purpose, but newer and larger benchmark sets for benign variants have largely been missing. VariSNP datasets are selected from dbSNP. These subsets were filtered against disease-related variants in the ClinVar, UniProtKB/Swiss-Prot and PhenCode databases, to identify neutral or non-pathogenic cases. All variant descriptions include mapping to reference sequences on chromosomal, genomic, coding DNA and protein levels. The datasets will be updated with automated scripts on a regular basis and are freely available at https://structure.bmc.lu.se/VariSNP. This article is protected by copyright. All rights reserved. (Less)
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author
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type
Contribution to journal
publication status
published
subject
in
Human Mutation
volume
36
issue
2
pages
161 - 166
publisher
John Wiley and Sons
external identifiers
  • pmid:25385275
  • wos:000349397300002
  • scopus:84922011086
  • pmid:25385275
ISSN
1059-7794
DOI
10.1002/humu.22727
language
English
LU publication?
yes
id
90d20837-a7b0-4d7d-a2cc-da84b0e52338 (old id 4817033)
alternative location
http://www.ncbi.nlm.nih.gov/pubmed/25385275?dopt=Abstract
date added to LUP
2016-04-01 10:15:12
date last changed
2021-01-06 05:59:23
@article{90d20837-a7b0-4d7d-a2cc-da84b0e52338,
  abstract     = {For development and evaluation of methods for predicting the effects of variations, benchmark datasets are needed. Some previously developed datasets are available for this purpose, but newer and larger benchmark sets for benign variants have largely been missing. VariSNP datasets are selected from dbSNP. These subsets were filtered against disease-related variants in the ClinVar, UniProtKB/Swiss-Prot and PhenCode databases, to identify neutral or non-pathogenic cases. All variant descriptions include mapping to reference sequences on chromosomal, genomic, coding DNA and protein levels. The datasets will be updated with automated scripts on a regular basis and are freely available at https://structure.bmc.lu.se/VariSNP. This article is protected by copyright. All rights reserved.},
  author       = {Schaafsma, Gerard and Vihinen, Mauno},
  issn         = {1059-7794},
  language     = {eng},
  number       = {2},
  pages        = {161--166},
  publisher    = {John Wiley and Sons},
  series       = {Human Mutation},
  title        = {Varisnp, A Benchmark Database For Variations from dbSNP.},
  url          = {http://dx.doi.org/10.1002/humu.22727},
  doi          = {10.1002/humu.22727},
  volume       = {36},
  year         = {2015},
}