GEN2PHEN Resources
GEN2PHEN-sponsored software development projects
Café Variome
A central data 'clearinghouse' for streamlining the flow of single-locus variation data from clinical diagnostic laboratories to LSDBs. Can be redeployed to support the safe advertising of many types of data. http://www.cafevariome.org
DiseaseCard
Integration of genetic and medical information for health applications. http://www.diseasecard.org
GWAS Central
Global study catalogue providing rich visualization and query tools for for comparing and contrasting multiple study datasets. http://www.gwascentral.org
Human Genome Mutation Database (HGMD)
Genome-wide mutation database specialized in cataloguing variants of clinical utility (Stenson et al., 2008). http://www.hgmd.org
Human Splicing Finder (HSF).
Online tool for predicting the effect of mutation on splice signals. http://www.umd.be/HSF/
Leiden Open (source) Variation Database (LOVD)
“In-a-box” software for creating LSDBs (Fokkema, den Dunnen and Taschner, 2005). http://www.lovd.nl
Mutalyzer
Online tool for checking sequence variants reported according to the HGVS nomenclature guidelines (Wildeman et al., 2008). https://mutalyzer.nl
MUTbase
“In-a-box” software for creating LSDBs (Riikonen and Vihinen, 1999). http://bioinf.uta.fi/MUTbase/
SNP Effect Predictor
Extension to the Ensembl system to provide a web-based tool and API for deriving variation consequences (McLaren et al., 2010). http://www.ensembl.org
GEN2PHEN-sponsored data standards projects
Variation Ontology (VariO)
Systematic description of consequences and effects of variation at the DNA, RNA and protein level. http://www.variationontology.org
Variation data model (VarioOM) and Variation Markup Language (VarioML)
Minimal data model and XML-based format for describing LSDB content. http://www.varioml.org
Phenotype Object Model (Pheno-OM)
Minimal data model to describe phenotypes and other observations. https://gen2phen.org/document/pheno-om-2010-03-10
Locus Reference Genomic (LRG)
Framework for standardized reporting of gene variants. http://www.lrg-sequence.org