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

Morris A. Swertz; K Joeri V.D. 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 V.D. 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

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

Abstract

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. © 2010 Swertz et al.; licensee BioMed Central Ltd.

Original language	English
Journal	Genome Biology
Volume	11
Issue number	3
DOIs	https://doi.org/10.1186/gb-2010-11-3-r27
Publication status	Published - 9 Mar 2010
Externally published	Yes

Keywords

article
computer interface
computer model
software
genetic association
genotype
phenotype

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10.1186/gb-2010-11-3-r27

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Swertz, M. A., Velde, K. J. V. D., 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). https://doi.org/10.1186/gb-2010-11-3-r27

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

abstract = "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. {\textcopyright} 2010 Swertz et al.; licensee BioMed Central Ltd.",

keywords = "article, computer interface, computer model, software, genetic association, genotype, phenotype",

author = "Swertz, {Morris A.} and Velde, {K Joeri V.D.} 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",

month = mar,

day = "9",

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

language = "English",

volume = "11",

journal = "Genome Biology",

issn = "1465-6906",

publisher = "BioMed Central",

number = "3",

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Swertz, MA, Velde, KJVD, 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. https://doi.org/10.1186/gb-2010-11-3-r27

TY - JOUR

T1 - XGAP: A uniform and extensible data model and software platform for genotype and phenotype experiments

AU - Swertz, Morris A.

AU - Velde, K Joeri V.D.

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 - 2010/3/9

Y1 - 2010/3/9

N2 - 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. © 2010 Swertz et al.; licensee BioMed Central Ltd.

AB - 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. © 2010 Swertz et al.; licensee BioMed Central Ltd.

KW - article

KW - computer interface

KW - computer model

KW - software

KW - genetic association

KW - genotype

KW - phenotype

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

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

M3 - Article

SN - 1465-6906

VL - 11

JO - Genome Biology

JF - Genome Biology

IS - 3

ER -

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

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Keywords

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