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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.


 Integration of genetic and medical information for health applications.

GWAS Central

Global study catalogue providing rich visualization and query tools for for comparing and contrasting multiple study datasets.

Human Genome Mutation Database (HGMD)

Genome-wide mutation database specialized in cataloguing variants of clinical utility (Stenson et al., 2008).

Human Splicing Finder (HSF).

Online tool for predicting the effect of mutation on splice signals.

Leiden Open (source) Variation Database  (LOVD)

“In-a-box” software for creating LSDBs (Fokkema, den Dunnen and Taschner, 2005).


Online tool for checking sequence variants reported according to the HGVS nomenclature guidelines (Wildeman et al., 2008).


“In-a-box” software for creating LSDBs (Riikonen and Vihinen, 1999).

SNP Effect Predictor

Extension to the Ensembl system to provide a web-based tool and API for deriving variation consequences (McLaren et al., 2010).


GEN2PHEN-sponsored data standards projects


Variation Ontology (VariO)

Systematic description of consequences and effects of variation at the DNA, RNA and protein level.

Variation data model (VarioOM) and Variation Markup Language (VarioML)

Minimal data model and XML-based format for describing LSDB content.

Phenotype Object Model (Pheno-OM)

Minimal data model to describe phenotypes and other observations.

Locus Reference Genomic (LRG)

Framework for standardized reporting of gene variants.

G2P Knowledge Centre is part of GEN2PHEN and funded by the Health Thematic Area of the Cooperation Programme of the European Commission within the VII Framework Programme for Research and Technological Development.

© GEN2PHEN 2011