XGAP: a Uniform and Extensible Data Model and Software Platform for Genotype and Phenotype Experiments

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2010 Mar 11

PMID 20214801

Citations 13

Authors

Morris A Swertz

K Joeri van der Velde

Bruno M Tesson

Richard A Scheltema

Danny Arends

Gonzalo Vera

Rudi Alberts

Martijn Dijkstra

Paul Schofield

Klaus Schughart

John M Hancock

Damian Smedley

Katy Wolstencroft

Carole Goble

Engbert O de Brock

Andrew R Jones

Helen E Parkinson

Ritsert C Jansen

Affiliations

Soon will be listed here.

Abstract

We present an extensible software model for the genotype and phenotype community, XGAP. Readers can download a standard XGAP (http://www.xgap.org) or auto-generate a custom version using MOLGENIS with programming interfaces to R-software and web-services or user interfaces for biologists. XGAP has simple load formats for any type of genotype, epigenotype, transcript, protein, metabolite or other phenotype data. Current functionality includes tools ranging from eQTL analysis in mouse to genome-wide association studies in humans.

Citing Articles

MOLGENIS research: advanced bioinformatics data software for non-bioinformaticians.

van der Velde K, Imhann F, Charbon B, Pang C, van Enckevort D, Slofstra M Bioinformatics. 2018; 35(6):1076-1078.

PMID: 30165396 PMC: 6419911. DOI: 10.1093/bioinformatics/bty742.

Genetic variation in neurodegenerative diseases and its accessibility in the model organism Caenorhabditis elegans.

Wang Y, Kammenga J, Harvey S Hum Genomics. 2017; 11(1):12.

PMID: 28545550 PMC: 5445269. DOI: 10.1186/s40246-017-0108-4.

WormQTLHD--a web database for linking human disease to natural variation data in C. elegans.

van der Velde K, de Haan M, Zych K, Arends D, Snoek L, Kammenga J Nucleic Acids Res. 2013; 42(Database issue):D794-801.

PMID: 24217915 PMC: 3965109. DOI: 10.1093/nar/gkt1044.

WormQTL--public archive and analysis web portal for natural variation data in Caenorhabditis spp.

Snoek L, van der Velde K, Arends D, Li Y, Beyer A, Elvin M Nucleic Acids Res. 2012; 41(Database issue):D738-43.

PMID: 23180786 PMC: 3531126. DOI: 10.1093/nar/gks1124.

Systems genetics in "-omics" era: current and future development.

Li H Theory Biosci. 2012; 132(1):1-16.

PMID: 23138757 DOI: 10.1007/s12064-012-0168-x.

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