LUpsb_logo1

Protein Structure and
Bioinformatics Group

Prof. Mauno Vihinen

Lund University

Standards and guidelines


VariO_logo

VariO
(Variation Ontology) is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations.
http://variationontology.org

 

MIASM
Minumum Information About Somatic Mutation
http://structure.bmc.lu.se/MIASM/miasm.html


HVP_logo

HVP Guidelines
Gene/Disease Specific Variant Database Quality Parameters
http://www.humanvariomeproject.org/finish/19/255.html

Disclaimer Statements for Gene/Disease Specific Databases
http://www.humanvariomeproject.org/finish/19/273.html

Variant Terminology and Exon Numbering
http://www.humanvariomeproject.org/finish/19/352.html

 

Human Variome Project quality assessment criteria for variation databases.
Vihinen M, Hancock JM, Maglott DR, Landrum MJ, Schaafsma GCP, Taschner P, 2016. Hum Mutat. 37:549-558 PubMed

 

Guidelines for reporting and using prediction tools for genetic variation analysis.
Vihinen M, 2013. Hum Mutat. 34:275-282 PubMed

 

Guidelines for establishing locus specific databases.
Vihinen M, den Dunnen JT, Dalgleish R, Cotton RG, 2012. Hum Mutat 33:298-305 PubMed

 

Curating gene variant databases (LSDBs): toward a universal standard.
Celli J, Dalgleish R, Vihinen M, Taschner PEM, den Dunnen JT, 2012. Hum Mutat 33:291-297 PubMed

 

Human Variome Project country nodes: documenting genetic information within a country.
Patrinos GP, Smith TD, Howard H, Al-Mulla F, Chouchane L, Hadjisavvas A, Hamed SA, Li XT, Marafie M, Ramesar RS, Ramos FJ, de Ravel T, El-Ruby MO, Shrestha TR, Sobrido MJ, Tadmouri G, Witsch-Baumgartner M, Zilfalil BA, Auerbach AD, Carpenter K, Cutting GR, Dung VC, Grody W, Hasler J, Jorde L, Kaput J, Macek M, Matsubara Y, Padilla C, Robinson H, Rojas-Martinez A, Taylor GR, Vihinen M, Weber T, Burn J, Qi M, Cotton RG, Rimoin D; International Confederation of Countries Advisory Council, 2012. Hum Mutat 33:1513-1519 PubMed

 

Recommendations for locus-specific databases and their curation.
Cotton RG, Auerbach AD, Beckmann JS, Blumenfeld OO, Brookes AJ, Brown AF, Carrera P, Cox DW, Gottlieb B, Greenblatt MS, Hilbert P, Lehvaslaiho H, Liang P, Marsh S, Nebert DW, Povey S, Rossetti S, Scriver CR, Summar M, Tolan DR, Verma IC, Vihinen M, den Dunnen JT, 2008. Hum Mutat 29:2-5 PubMed

Updated 2015-08-19 by Gerard Schaafsma

Home

Databases:
IDbases
KinMutBase
SH2base
ImmunoDeficiency Resource (IDR)
Immunome Knowledge Base (IKB)
GOme

Bioinformatics services:
B-Cell Proteome
Bioinformatics benchmarks
MultiDisp
PID classification
PON-BTK
PON-P2
PON-PS
PON-MMR2
PON-mt-tRNA
PON-Diso
PON-Sol
ProCon
PPSC
VariBench
VariSNP

Standards and guidelines:
VariO
MIASM
HVP Guidelines
Guidelines for prediction tools
Curating gene variant databases
HVP Country Nodes
Recommendations for LSDBs

Research:
Group members
Publications

News from PSB:
News

Links:
Lund University
Medical Faculty
Department of Experimental Medical Science


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