= XGAP Object Model =
XGAP-OM is the conceptual model behind the XGAP platform. It is designed to provide uniform model for a wide variety of organisms, experimental designs, and biomolecular profiling technologies:

 * '''A core for the raw, in process and result data'''                                 using only four core data types Trait, Subject, Data and                                 !DataElement.
 * '''A core to for experimental design annotations'''                                 reusing [http://fuge.sourceforge.net/ FuGE]                                 data types Investigation, Protocols and !ProtocolApplications,                                 !OntologyTerms, etc.
 * '''Consistently annotate Traits and Subjects'''                                 using standardized extensions of Trait (e.g. Probe, Marker) and                                 Subject (e.g. Individual, Strain).
 * '''Consistently extend XGAP for new types of annotations                                 '''                                 by adding more types of Strain and Subject (e.g. add '!MassPeak' as a                                 new Trait to annotate 'retentiontime' and 'mz')

[[Image(xgap-om.gif)]]

== Specifications ==
 1. Overview of XGAP-OM v1.0 in UML ([attachment:xgap_umldiagram_v1_0.pdf])
 1. Informal description of each XGAP-OM v1.0 data entity ([http://gbicserver1.biol.rug.nl:8080/xgap4exampledatasets/doc/objectmodel.html generated docs])
 1. Formal definition of XGAP-OM v1.2 in MOLGENIS* language([http://www.xgap.org/browser/xgap_1_2_distro/xgap_db.xml xgap_db.xml])
 1. Formal definition of FuGE-OM** in MOLGENIS* language ([http://www.xgap.org/browser/xgap_1_2_distro/fuge_db.xml fuge_db.xml])

*We use MOLGENIS to auto-generate software from the XGAP-OM. **To                         ease integration with other research domain,                       XGAP                         has been structured as full extension of functional genomics standard                         [http://fuge.sourceforge.net/ FuGE]                         . When generating software from the data model one also needs the                         FuGE definition. See XgapCustomization.