XGAP: A uniform and extensible data model and software platform for genotype and phenotype experiments

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

doi:10.1186/gb-2010-11-3-r27

XGAP: A uniform and extensible data model and software platform for genotype and phenotype experiments

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

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

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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.

Original language	English
Article number	27
Number of pages	15
Journal	Genome Biology
Volume	11
Issue number	3
DOIs	https://doi.org/10.1186/gb-2010-11-3-r27
Publication status	Published - 2010

Keywords

QUANTITATIVE TRAIT LOCI
GENE-EXPRESSION
FUNCTIONAL GENOMICS
DATA INTEGRATION
SYSTEMS BIOLOGY
BIOINFORMATICS
IDENTIFICATION
BIOCONDUCTOR
ARABIDOPSIS
CHALLENGES

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Swertz, M. A., van der Velde, K. J., Tesson, B. M., Scheltema, R. A., Arends, D., Vera, G., Alberts, R., Dijkstra, M., Schofield, P., Schughart, K., Hancock, J. M., Smedley, D., Wolstencroft, K., Goble, C., de Brock, E. O., Jones, A. R., Parkinson, H. E., & Jansen, R. C. (2010). XGAP: A uniform and extensible data model and software platform for genotype and phenotype experiments. Genome Biology, 11(3), Article 27. https://doi.org/10.1186/gb-2010-11-3-r27

@article{2222b97e4e0a471191b46b283c5760fd,

title = "XGAP: A uniform and extensible data model and software platform for genotype and phenotype experiments",

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.",

keywords = "QUANTITATIVE TRAIT LOCI, GENE-EXPRESSION, FUNCTIONAL GENOMICS, DATA INTEGRATION, SYSTEMS BIOLOGY, BIOINFORMATICS, IDENTIFICATION, BIOCONDUCTOR, ARABIDOPSIS, CHALLENGES",

author = "Swertz, {Morris A.} and {van der Velde}, {K. Joeri} and Tesson, {Bruno M.} and Scheltema, {Richard A.} and Danny Arends and Gonzalo Vera and Rudi Alberts and Martijn Dijkstra and Paul Schofield and Klaus Schughart and Hancock, {John M.} and Damian Smedley and Katy Wolstencroft and Carole Goble and {de Brock}, {Engbert O.} and Jones, {Andrew R.} and Parkinson, {Helen E.} and Jansen, {Ritsert C.}",

year = "2010",

doi = "10.1186/gb-2010-11-3-r27",

language = "English",

volume = "11",

journal = "Genome Biology",

issn = "1474-760X",

publisher = "BMC",

number = "3",

}

Swertz, MA , van der Velde, KJ, Tesson, BM, Scheltema, RA, Arends, D, Vera, G, Alberts, R, Dijkstra, M, Schofield, P, Schughart, K, Hancock, JM, Smedley, D, Wolstencroft, K, Goble, C, de Brock, EO, Jones, AR, Parkinson, HE & Jansen, RC 2010, 'XGAP: A uniform and extensible data model and software platform for genotype and phenotype experiments', Genome Biology, vol. 11, no. 3, 27. https://doi.org/10.1186/gb-2010-11-3-r27

TY - JOUR

T1 - XGAP

T2 - A uniform and extensible data model and software platform for genotype and phenotype experiments

AU - Swertz, Morris A.

AU - van der Velde, K. Joeri

AU - Tesson, Bruno M.

AU - Scheltema, Richard A.

AU - Arends, Danny

AU - Vera, Gonzalo

AU - Alberts, Rudi

AU - Dijkstra, Martijn

AU - Schofield, Paul

AU - Schughart, Klaus

AU - Hancock, John M.

AU - Smedley, Damian

AU - Wolstencroft, Katy

AU - Goble, Carole

AU - de Brock, Engbert O.

AU - Jones, Andrew R.

AU - Parkinson, Helen E.

AU - Jansen, Ritsert C.

PY - 2010

Y1 - 2010

N2 - 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.

AB - 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.

KW - QUANTITATIVE TRAIT LOCI

KW - GENE-EXPRESSION

KW - FUNCTIONAL GENOMICS

KW - DATA INTEGRATION

KW - SYSTEMS BIOLOGY

KW - BIOINFORMATICS

KW - IDENTIFICATION

KW - BIOCONDUCTOR

KW - ARABIDOPSIS

KW - CHALLENGES

U2 - 10.1186/gb-2010-11-3-r27

DO - 10.1186/gb-2010-11-3-r27

M3 - Article

SN - 1474-760X

VL - 11

JO - Genome Biology

JF - Genome Biology

IS - 3

M1 - 27

ER -

XGAP: A uniform and extensible data model and software platform for genotype and phenotype experiments

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