COMMON:Phenotype
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Contents |
Description
- Phenotype model developed at 1st phenotype data workshop in Geneva (09).
- Phenotype models
- Gen2phen data model and standards group
Class diagram (Latest version - 12.6.2009)
Change log
- Cardinality between Inferred value and Observed_value changed to many-to-many
- Many-to-many relation was added between Protocol and Observable_feature
- Association between Observed_value and Observable_feature changed to many-to-one
- New class called Variable_definition was added. The class is specialisation of Observable_feature and it provides detailed definitions like unit used.
- Recursive self association added into Protocol. This allows to handle sub-protocols.
Description
Note most of the attributes are missing
- Individual - Individual. Subject of study
- Inferred_value - Inferred conclusion, derived from zero or many observed values
- Observable_feature - Is something we can measure in relation to individual. For example blood pressure
- Observation_target - Super class of all observation targets like Individual or Panel
- Ontology_term - Term defined in specific name space (ontology source). All names and terms will be defined using ontology terms
- Observed_value - Measured value
- Panel - Collection of individuals
- Protocol - Description how measurement is planned to be done
- Protocol_application - Description of how an actual measurement was done (optional different from protocol)
- Variable definition - Extends the Observable_feature class to enable precise definition of the feature in used applications (for example has unit). Another suggested name for the class: Observable_feature_specific
Object instance diagram
Notes
Value is not in normal form in the multivalue case (Observation targets exists multiple times). Should the Observation_target be moved into Protocol_application ?
Object instance diagram - Inferred value
Mapping to PaGE-OM
| Model | PaGE-OM |
|---|---|
| Individual | Individual |
| Inferred_value | Observed_value (self association) |
| Observable_feature | Observable_feature |
| Observation_target | Abstract_observation_target |
| Observed_value | Observed_value |
| Panel | Panel |
| Protocol | |
| Protocol_application | Observation_method |
| Observable_feature_category |
Notably structural difference is that in PaGE-OM Protocol_application (Observation_method) is between Observable_feature and Observed_value. In this model Protocol_application is independent on Observable_feature.
Mapping to XGAPOM
| Model | XGAP |
|---|---|
| Individual | Individual |
| Inferred_value | via ProtocolApplication.inputData |
| Observable_feature | Phenotype |
| Observation_target | Subject |
| Data | |
| Observed_value | DataElement |
| Panel | Panel |
| Protocol | Protocol |
| Protocol_application | ProtocolApplication |
Note that in XGAP observations are groups into 'Data' sets that can contain many Observed_Value (DataElement) objects. An ProtocolApplication can have multiple input/outputData.
Class diagram (Original Geneve version)
