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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.

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Extensible genotype and phenotype object model. Experimental genotype and (molecular) phenotype data can be described using Subject, Trait, Data and DataElement; the experimental procedures can be described using Investigation, Protocol and ProtocolApplication (B). Specific attributes and relationships can be added by extending core data types, for example, Sample and Gene (A, C). See Table 2, 3 and 4 for uses of this model. The model is visualized in the Unified Modeling Language (UML): arrows denote relationships (Data has a field Investigation that refers to Investigation ID); triangle terminated lines denote inheritance (Metabolite inherits all properties ID, Name, Type from Trait, next to its own attributes Mass, Formula and Structure); triangle terminated dotted lines denote use of interfaces (Probe 'implements' properties of Locus); relationships are shown both as arrows and as properties ('xref' for one-to-many, 'mref' for many-to-many relationships). Asterisks mark FuGE-derived types (for example, Protocol*).
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Figure 1: Extensible genotype and phenotype object model. Experimental genotype and (molecular) phenotype data can be described using Subject, Trait, Data and DataElement; the experimental procedures can be described using Investigation, Protocol and ProtocolApplication (B). Specific attributes and relationships can be added by extending core data types, for example, Sample and Gene (A, C). See Table 2, 3 and 4 for uses of this model. The model is visualized in the Unified Modeling Language (UML): arrows denote relationships (Data has a field Investigation that refers to Investigation ID); triangle terminated lines denote inheritance (Metabolite inherits all properties ID, Name, Type from Trait, next to its own attributes Mass, Formula and Structure); triangle terminated dotted lines denote use of interfaces (Probe 'implements' properties of Locus); relationships are shown both as arrows and as properties ('xref' for one-to-many, 'mref' for many-to-many relationships). Asterisks mark FuGE-derived types (for example, Protocol*).

Mentions: Figure 1b shows the core components of a genotype-to-phenotype investigation: the biological subjects studied (for example, human individuals, mouse strains, plant tissue samples), the biomolecular protocols used (for example, Affymetrix, Illumina, Qiagen, liquid chromatography-mass spectrometry (LC/MS), Orbitrap, NMR), the trait data generated (usually data matrices with, for example, phenotype or transcript abundance data), the additional information on these traits (for example, genome location of a transcript, masses of LC/MS peaks), the wet-lab or computational protocols used (for example, MetaNetwork [22] in the case of QTL and network analysis) and the derived data (for example, QTL likelihood curves).


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)

Extensible genotype and phenotype object model. Experimental genotype and (molecular) phenotype data can be described using Subject, Trait, Data and DataElement; the experimental procedures can be described using Investigation, Protocol and ProtocolApplication (B). Specific attributes and relationships can be added by extending core data types, for example, Sample and Gene (A, C). See Table 2, 3 and 4 for uses of this model. The model is visualized in the Unified Modeling Language (UML): arrows denote relationships (Data has a field Investigation that refers to Investigation ID); triangle terminated lines denote inheritance (Metabolite inherits all properties ID, Name, Type from Trait, next to its own attributes Mass, Formula and Structure); triangle terminated dotted lines denote use of interfaces (Probe 'implements' properties of Locus); relationships are shown both as arrows and as properties ('xref' for one-to-many, 'mref' for many-to-many relationships). Asterisks mark FuGE-derived types (for example, Protocol*).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Extensible genotype and phenotype object model. Experimental genotype and (molecular) phenotype data can be described using Subject, Trait, Data and DataElement; the experimental procedures can be described using Investigation, Protocol and ProtocolApplication (B). Specific attributes and relationships can be added by extending core data types, for example, Sample and Gene (A, C). See Table 2, 3 and 4 for uses of this model. The model is visualized in the Unified Modeling Language (UML): arrows denote relationships (Data has a field Investigation that refers to Investigation ID); triangle terminated lines denote inheritance (Metabolite inherits all properties ID, Name, Type from Trait, next to its own attributes Mass, Formula and Structure); triangle terminated dotted lines denote use of interfaces (Probe 'implements' properties of Locus); relationships are shown both as arrows and as properties ('xref' for one-to-many, 'mref' for many-to-many relationships). Asterisks mark FuGE-derived types (for example, Protocol*).
Mentions: Figure 1b shows the core components of a genotype-to-phenotype investigation: the biological subjects studied (for example, human individuals, mouse strains, plant tissue samples), the biomolecular protocols used (for example, Affymetrix, Illumina, Qiagen, liquid chromatography-mass spectrometry (LC/MS), Orbitrap, NMR), the trait data generated (usually data matrices with, for example, phenotype or transcript abundance data), the additional information on these traits (for example, genome location of a transcript, masses of LC/MS peaks), the wet-lab or computational protocols used (for example, MetaNetwork [22] in the case of QTL and network analysis) and the derived data (for example, QTL likelihood curves).

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
Related in: MedlinePlus