| | 1 | = XGAP Object Model = |
| | 2 | 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: |
| | 3 | |
| | 4 | * '''A core for the raw, in process and result data''' using only four core data types Trait, Subject, Data and !DataElement. |
| | 5 | * '''A core to for experimental design annotations''' reusing [http://fuge.sourceforge.net/ FuGE] data types Investigation, Protocols and !ProtocolApplications, !OntologyTerms, etc. |
| | 6 | * '''Consistently annotate Traits and Subjects''' using standardized extensions of Trait (e.g. Probe, Marker) and Subject (e.g. Individual, Strain). |
| | 7 | * '''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') |
| | 8 | |
| | 9 | [[Image(xgap-om.gif)]] |
| | 10 | |
| | 11 | == Specifications == |
| | 12 | 1. Overview of XGAP-OM v1.0 in UML ([attachment:xgap_umldiagram_v1_0.pdf]) |
| | 13 | 1. Informal description of each XGAP-OM v1.0 data entity ([http://gbicserver1.biol.rug.nl:8080/xgap4exampledatasets/doc/objectmodel.html generated docs]) |
| | 14 | 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]) |
| | 15 | 1. Formal definition of FuGE-OM** in MOLGENIS* language ([http://www.xgap.org/browser/xgap_1_2_distro/fuge_db.xml fuge_db.xml]) |
| | 16 | |
| | 17 | *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. |
