Table 1.
Packages and classes
| Logical | DesignElement | BioAssay | HigherLevelAnalysis |
| Extendable | DesignElement | BioAssay | BioAssayDataCluster |
| Describable | Feature | PhysicalBioAssay | Node |
| Identifiable | Reporter | BioAssayTreatment | NodeContents |
| NameValueType | CompositeSequence | ImageAcquisition | NodeValue |
| Position | BioAssayCreation | ||
| AuditAndSecurity | FeatureLocation | Hybridization | Measurement |
| Audit | CompositeCompositeMap | Image | Measurement |
| Contact | ReporterCompositeMap | Channel | Unit |
| Organization | FeatureReporterMap | FeatureExtraction | TemperatureUnit |
| Person | CompositePosition | MeasuredBioAssay | MassUnit |
| Security | ReporterPosition | DerivedBioAssay | VolumeUnit |
| SecurityGroup | FeatureInformation | DistanceUnit | |
| MismatchInformation | BioAssayData | TimeUnit | |
| Description | BioAssayData | QuantityUnit | |
| Description | Array | Transformation | ConcentrationUnit |
| OntologyEntry | ArrayManufacture | DerivedBioAssayData | |
| ExternalReference | Array | MeasuredBioAssayData | Protocol |
| DatabaseEntry | ArrayGroup | BioAssayDimension | Protocol |
| Database | Fiducial | QuantitationTypeDimension | Hardware |
| ArrayManufactureDeviation | DesignElementDimension | Software | |
| BioSequence | FeatureDefect | FeatureDimension | Parameterizable |
| BioSequence | ZoneDefect | ReporterDimension | Parameter |
| SeqFeature | PositionDelta | CompositeSequenceDimension | ProtocolApplication |
| SeqFeatureLocation | ManufactureLIMS | BioDataCube | HardwareApplication |
| SequencePosition | ManufactureLIMSBioMaterial | BioDataTuples | SoftwareApplication |
| CompositePosition | BioAssayDatum | ParameterizableApplication | |
| ReporterPosition | BioMaterial | QuantitationTypeMapping | ParameterValue |
| BioMaterial | QuantitationTypeMap | ||
| ArrayDesign | BioSource | DesignElementMapping | QuantitationType |
| ArrayDesign | BioSample | DesignElementMap | QuantitationType |
| CompositeGroup | LabeledExtract | BioAssayMapping | StandardQuantitationType |
| ReporterGroup | Treatment | BioAssayMap | SpecializedQuantitationType |
| DesignElementGroup | BioMaterialMeasurement | PresentAbsent | |
| FeatureGroup | CompoundMeasurement | Experiment | MeasuredSignal |
| PhysicalArrayDesign | Compound | Experiment | DerivedSignal |
| ZoneGroup | ExperimentDesign | Ratio | |
| ZoneLayout | ExperimentFactor | ConfidenceIndicator | |
| Zone | FactorValue | Pvalue | |
| Error | |||
| ExpectedValue |
Bold indicates packages and italics indicates abstract classes.