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

^*Corresponding author for this work

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

21 Citations (Scopus)

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.

Original language	English
Article number	r27
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

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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), Article r27. 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.",

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.}",

note = "Funding Information: The authors thank CASIMIR (funded by the European Commission under contract number LSHG-CT-2006-037811, [70]; Table 7), and GEN2PHEN, a FP7 project funded by the European Commission (FP7-HEALTH contract 200754, [55]; Table 7). The authors also thank NWO (Rubicon Grant 825.09.008) for financial support.",

year = "2010",

month = mar,

day = "9",

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

language = "English",

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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, r27. 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 - 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.

N1 - Funding Information: The authors thank CASIMIR (funded by the European Commission under contract number LSHG-CT-2006-037811, [70]; Table 7), and GEN2PHEN, a FP7 project funded by the European Commission (FP7-HEALTH contract 200754, [55]; Table 7). The authors also thank NWO (Rubicon Grant 825.09.008) for financial support.

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.

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.

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JF - Genome Biology

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

Abstract

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Other files and links

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High-throughput computational methods and software for quantitative trait locus (QTL) mapping

WormQTL^HD - A web database for linking human disease to natural variation data in C. Elegans

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

Cite this

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

Abstract

Access to Document

Other files and links

Fingerprint

Research output

High-throughput computational methods and software for quantitative trait locus (QTL) mapping

WormQTLHD - A web database for linking human disease to natural variation data in C. Elegans

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

Cite this

WormQTL^HD - A web database for linking human disease to natural variation data in C. Elegans