Limits...
XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments.

Swertz MA, 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, Coordination of Mouse Informatics Resources (CASIMIR)Genotype-To-Phenotype (GEN2PHEN) ConsortiumsJansen RC - Genome Biol. (2010)

Bottom Line: We present an extensible software model for the genotype and phenotype community, XGAP.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genomics Coordination Center, Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands. m.a.swertz@rug.nl

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.

Show MeSH
Application programming interfaces. APIs enable bioinformaticians to integrate data and tools with XGAP using web services, R-project language, Java, or simple HTTP hyperlinks. The figure shows how scientists can use the R/API to upload raw investigation data (Scientist A) so another researcher can download these data and immediately use it for the calculation of QTL profiles and upload the results thereof back to the XGAP database for use by another collaborator (Scientist B). Note how 'add.datamatrix' enables flexible upload of matrices for any Subject or Trait combination; this function adds one row to Data for each matrix, and as many rows to DataElement as the matrix has cells. See Table 6 for uses of these APIs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2864567&req=5

Figure 4: Application programming interfaces. APIs enable bioinformaticians to integrate data and tools with XGAP using web services, R-project language, Java, or simple HTTP hyperlinks. The figure shows how scientists can use the R/API to upload raw investigation data (Scientist A) so another researcher can download these data and immediately use it for the calculation of QTL profiles and upload the results thereof back to the XGAP database for use by another collaborator (Scientist B). Note how 'add.datamatrix' enables flexible upload of matrices for any Subject or Trait combination; this function adds one row to Data for each matrix, and as many rows to DataElement as the matrix has cells. See Table 6 for uses of these APIs.

Mentions: Figure 4 demonstrates how researchers can use the R/API to download (or upload) all trait/subject/data involved in their investigation from (or to) their XGAP database for (after) analysis in R. When XGAP is customized with additional data type variants, the APIs are automatically extended in the XGAP database instances by re-running the MOLGENIS generator, thus also allowing interaction with new data types in a uniform way. These new types can then be used as standard parameters for new analysis software written in R and Java. Table 6 summarizes use of the application programming interface.


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

Swertz MA, 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, Coordination of Mouse Informatics Resources (CASIMIR)Genotype-To-Phenotype (GEN2PHEN) ConsortiumsJansen RC - Genome Biol. (2010)

Application programming interfaces. APIs enable bioinformaticians to integrate data and tools with XGAP using web services, R-project language, Java, or simple HTTP hyperlinks. The figure shows how scientists can use the R/API to upload raw investigation data (Scientist A) so another researcher can download these data and immediately use it for the calculation of QTL profiles and upload the results thereof back to the XGAP database for use by another collaborator (Scientist B). Note how 'add.datamatrix' enables flexible upload of matrices for any Subject or Trait combination; this function adds one row to Data for each matrix, and as many rows to DataElement as the matrix has cells. See Table 6 for uses of these APIs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2864567&req=5

Figure 4: Application programming interfaces. APIs enable bioinformaticians to integrate data and tools with XGAP using web services, R-project language, Java, or simple HTTP hyperlinks. The figure shows how scientists can use the R/API to upload raw investigation data (Scientist A) so another researcher can download these data and immediately use it for the calculation of QTL profiles and upload the results thereof back to the XGAP database for use by another collaborator (Scientist B). Note how 'add.datamatrix' enables flexible upload of matrices for any Subject or Trait combination; this function adds one row to Data for each matrix, and as many rows to DataElement as the matrix has cells. See Table 6 for uses of these APIs.
Mentions: Figure 4 demonstrates how researchers can use the R/API to download (or upload) all trait/subject/data involved in their investigation from (or to) their XGAP database for (after) analysis in R. When XGAP is customized with additional data type variants, the APIs are automatically extended in the XGAP database instances by re-running the MOLGENIS generator, thus also allowing interaction with new data types in a uniform way. These new types can then be used as standard parameters for new analysis software written in R and Java. Table 6 summarizes use of the application programming interface.

Bottom Line: We present an extensible software model for the genotype and phenotype community, XGAP.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genomics Coordination Center, Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands. m.a.swertz@rug.nl

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.

Show MeSH