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  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')

Specifications

1. Overview of XGAP-OM v1.0 in UML (xgap_umldiagram_v1_0.pdf )
2. Informal description of each XGAP-OM v1.0 data entity ( generated docs)
3. Formal definition of XGAP-OM v1.2 in MOLGENIS* language(xgap_db.xml)
4. Formal definition of FuGE-OM in MOLGENIS* language (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  FuGE . When generating software from the data model one also needs the FuGE definition. See XgapCustomization.