Table 1 Features of XGAP database for genotype and phenotype experiments
Store | Store genotype and phenotype experimental data using only four 'core' data types: Trait, Subject, Data, and DataElement. For example: a single-channel microarray reports raw gene expression Data for each microarray probe Trait and each individual Subject. Add information on data provenance by giving details in Investigation, Protocols and ProtocolApplications |
Customize | Customize 'my' XGAP database with extended variants of Trait and Subject. In the online XGAP demonstrator, Probe traits have a sequence and genome location and Strain subjects have parent strains and (in)breeding method. Describe extensions using MOLGENIS language and the generator automatically changes XGAP database software to your research |
Upload | Upload data from measurement devices, public databases, collaborating XGAP databases, or a public XGAP repository with community data. Simply download trait information as tab-delimited files from one XGAP and upload it into another; this works because of the uniformity of the core data types (and extensions thereof) |
Search | Search genetical genomics data using the graphical user interface with advanced query tools. The uniformity of the 'code generated' interfaces make it easy to learn and use interfaces for both 'core' data types as well as customized extensions |
Analyze | Analyze data by connecting tools using simple methods in Java, R, Web Services or Internet hyperlinks. For example, map and plot quantitative trait loci in R using XGAP data retrieved via the R interface |
Plug-in | Plug-in the best analysis tools into the user interface so biologists can use them. Bioinformaticians are provided with simple mechanisms to seamlessly add such tools to XGAP, building on the automatically generated GUI and API building blocks |
Share | Share data, customizations, connected analysis tools and user interface plug-ins with the genetical genomics community, using XGAP as exchange platform. For example, the MetaNetwork R package can talk to data in XGAP. This makes it easy for other XGAP owners to also use it |