DTD Tree structure of Microarray Gene Expression Database Markup Language generated using Matra
DTD Name: Microarray Gene Expression Database Markup Language (MAGE-ML)
DTD Location:
http://www.omg.org/cgi-bin/doc?dtc/02-09-03
[cached copy]
DTD Issue Date: January 25, 2002
DTD Version: version 003 (preliminary version)
DTD Status: preliminary version
DTD-Tree [How to read it?] [Notes on the dtdtree]
StandardQuantitationType_ref (identifier, name?) PhysicalBioAssayTarget_assnref | += PhysicalBioAssay_ref (identifier, name?) ExperimentalFactor_assnref | += ExperimentalFactor_ref (identifier, name?) FeatureGroup_assnref | += FeatureGroup_ref (identifier, name?) PhysicalBioAssay_assnref | += PhysicalBioAssay_ref (identifier, name?) DerivedBioAssayDataTarget_assnref | += DerivedBioAssayData_ref (identifier, name?) MeasuredBioAssayTarget_assnref | += MeasuredBioAssay_ref (identifier, name?) PhysicalBioAssay_assnlist | +- PhysicalBioAssay+ (identifier, name?) | |- PropertySets_assnlist? | | | +- NameValueType+ (name?, value?, type?) | | | +- PropertySets_assnlist? ** | |- Descriptions_assnlist? | | | +- Description+ (text?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? ** | | | |- AuditTrail_assnlist? | | | | | +- Audit+ (date, action) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? ** | | | | | |- AuditTrail_assnlist? ** | | | | | |- Security_assnref? | | | | | | | += Security_ref (identifier, name?) | | | | | +- Performer_assnref? | | | | | |= Contact_ref (identifier, name?) | | | | | |= Person_ref (identifier, name?) | | | | | += Organization_ref (identifier, name?) | | | |- Security_assnref? --> | | | |- ExternalReference_assn? | | | | | +- ExternalReference (exportedFromServer?, exportedFromDB?, exportID?, exportName?) | | | | | +- PropertySets_assnlist? --> | | | |- Annotations_assnlist? | | | | | +- OntologyEntry+ (category, value, description?) | | | | | |- PropertySets_assnlist? --> | | | | | +- OntologyReference_assn? | | | | | +- DatabaseEntry (accession, accessionVersion?, URI?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Type_assn? | | | | | | | +- OntologyEntry (category, value, description?) ** | | | | | +- Database_assnref | | | | | += Database_ref (identifier, name?) | | | |- DatabaseReferences_assnlist? | | | | | +- DatabaseEntry+ (accession, accessionVersion?, URI?) --> | | | +- BibliographicReferences_assnlist? | | | +- BibliographicReference+ (title?, authors?, publication?, publisher?, editor?, year?, volume?, issue?, pages?, URI?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? ** | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | +- Parameters_assnlist | | | +- OntologyEntry+ (category, value, description?) --> | |- AuditTrail_assnlist? --> | |- Security_assnref? --> | |- Channels_assnreflist? | | | += Channel_ref+ (identifier, name?) | |- BioAssayFactorValues_assnreflist? | | | += FactorValue_ref+ (identifier, name?) | |- PhysicalBioAssayData_assnlist? | | | +- Image+ (identifier, name?, URI?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- Channels_assnreflist? --> | | | +- Format_assn | | | +- OntologyEntry (category, value, description?) --> | |- BioAssayCreation_assn? | | | |- BioAssayCreation (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- ProtocolApplications_assnlist? | | | | | | | +- ProtocolApplication+ (activityDate) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Descriptions_assnlist? --> | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | |- Security_assnref? --> | | | | | | | |- ParameterValues_assnlist? | | | | | | | | | +- ParameterValue+ (value?) | | | | | | | | | |- PropertySets_assnlist? --> | | | | | | | | | +- ParameterType_assnref | | | | | | | | | += Parameter_ref (identifier, name?) | | | | | | | |- HardwareApplications_assnlist? | | | | | | | | | +- HardwareApplication+ (serialNumber?) | | | | | | | | | |- PropertySets_assnlist? --> | | | | | | | | | |- Descriptions_assnlist? --> | | | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | | | |- Security_assnref? --> | | | | | | | | | |- ParameterValues_assnlist? --> | | | | | | | | | +- Hardware_assnref | | | | | | | | | += Hardware_ref (identifier, name?) | | | | | | | |- SoftwareApplications_assnlist? | | | | | | | | | +- SoftwareApplication+ (version?, releaseDate?) | | | | | | | | | |- PropertySets_assnlist? --> | | | | | | | | | |- Descriptions_assnlist? --> | | | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | | | |- Security_assnref? --> | | | | | | | | | |- ParameterValues_assnlist? --> | | | | | | | | | +- Software_assnref | | | | | | | | | += Software_ref (identifier, name?) | | | | | | | |- Performers_assnreflist? | | | | | | | | | += Person_ref+ (identifier, name?) | | | | | | | +- Protocol_assnref | | | | | | | += Protocol_ref (identifier, name?) | | | | | |- SourceBioMaterialMeasurements_assnlist? | | | | | | | +- BioMaterialMeasurement+ | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- BioMaterial_assnref | | | | | | | | | |= BioMaterial_ref (identifier, name?) | | | | | | | | | |= BioSource_ref (identifier, name?) | | | | | | | | | |= LabeledExtract_ref (identifier, name?) | | | | | | | | | += BioSample_ref (identifier, name?) | | | | | | | +- Measurement_assn? | | | | | | | +- Measurement (type="absolute", value, kindCV="other", otherKind?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | +- Unit_assn? | | | | | | | |- TimeUnit (unitName?, unitNameCV) | | | | | | | | | +- PropertySets_assnlist? --> | | | | | | | |- DistanceUnit (unitName?, unitNameCV) | | | | | | | | | +- PropertySets_assnlist? --> | | | | | | | |- TemperatureUnit (unitName?, unitNameCV) | | | | | | | | | +- PropertySets_assnlist? --> | | | | | | | |- QuantityUnit (unitName?, unitNameCV) | | | | | | | | | +- PropertySets_assnlist? --> | | | | | | | |- MassUnit (unitName?, unitNameCV) | | | | | | | | | +- PropertySets_assnlist? --> | | | | | | | |- VolumeUnit (unitName?, unitNameCV) | | | | | | | | | +- PropertySets_assnlist? --> | | | | | | | +- ConcentrationUnit (unitName?, unitNameCV) | | | | | | | +- PropertySets_assnlist? --> | | | | | +- Array_assnref | | | | | += Array_ref (identifier, name?) | | | +- Hybridization (identifier, name?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- ProtocolApplications_assnlist? --> | | | |- SourceBioMaterialMeasurements_assnlist? --> | | | +- Array_assnref --> | +- BioAssayTreatments_assnlist? | |- BioAssayTreatment (identifier, name?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- ProtocolApplications_assnlist? --> | | | +- Target_assnref | | | += PhysicalBioAssay_ref (identifier, name?) | +- ImageAcquisition (identifier, name?) | |- PropertySets_assnlist? --> | |- Descriptions_assnlist? --> | |- AuditTrail_assnlist? --> | |- Security_assnref? --> | |- ProtocolApplications_assnlist? --> | |- Target_assnref --> | +- Images_assnreflist? | += Image_ref+ (identifier, name?) MeasuredBioAssay_assnlist | +- MeasuredBioAssay+ (identifier, name?) | |- PropertySets_assnlist? | | | +- NameValueType+ (name?, value?, type?) | | | +- PropertySets_assnlist? ** | |- Descriptions_assnlist? | | | +- Description+ (text?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? ** | | | |- AuditTrail_assnlist? | | | | | +- Audit+ (date, action) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? ** | | | | | |- AuditTrail_assnlist? ** | | | | | |- Security_assnref? | | | | | | | += Security_ref (identifier, name?) | | | | | +- Performer_assnref? | | | | | |= Contact_ref (identifier, name?) | | | | | |= Person_ref (identifier, name?) | | | | | += Organization_ref (identifier, name?) | | | |- Security_assnref? --> | | | |- ExternalReference_assn? | | | | | +- ExternalReference (exportedFromServer?, exportedFromDB?, exportID?, exportName?) | | | | | +- PropertySets_assnlist? --> | | | |- Annotations_assnlist? | | | | | +- OntologyEntry+ (category, value, description?) | | | | | |- PropertySets_assnlist? --> | | | | | +- OntologyReference_assn? | | | | | +- DatabaseEntry (accession, accessionVersion?, URI?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Type_assn? | | | | | | | +- OntologyEntry (category, value, description?) ** | | | | | +- Database_assnref | | | | | += Database_ref (identifier, name?) | | | |- DatabaseReferences_assnlist? | | | | | +- DatabaseEntry+ (accession, accessionVersion?, URI?) --> | | | +- BibliographicReferences_assnlist? | | | +- BibliographicReference+ (title?, authors?, publication?, publisher?, editor?, year?, volume?, issue?, pages?, URI?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? ** | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | +- Parameters_assnlist | | | +- OntologyEntry+ (category, value, description?) --> | |- AuditTrail_assnlist? --> | |- Security_assnref? --> | |- Channels_assnreflist? | | | += Channel_ref+ (identifier, name?) | |- BioAssayFactorValues_assnreflist? | | | += FactorValue_ref+ (identifier, name?) | |- FeatureExtraction_assn? | | | +- FeatureExtraction (identifier, name?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- ProtocolApplications_assnlist? | | | | | +- ProtocolApplication+ (activityDate) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- ParameterValues_assnlist? | | | | | | | +- ParameterValue+ (value?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | +- ParameterType_assnref | | | | | | | += Parameter_ref (identifier, name?) | | | | | |- HardwareApplications_assnlist? | | | | | | | +- HardwareApplication+ (serialNumber?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Descriptions_assnlist? --> | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | |- Security_assnref? --> | | | | | | | |- ParameterValues_assnlist? --> | | | | | | | +- Hardware_assnref | | | | | | | += Hardware_ref (identifier, name?) | | | | | |- SoftwareApplications_assnlist? | | | | | | | +- SoftwareApplication+ (version?, releaseDate?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Descriptions_assnlist? --> | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | |- Security_assnref? --> | | | | | | | |- ParameterValues_assnlist? --> | | | | | | | +- Software_assnref | | | | | | | += Software_ref (identifier, name?) | | | | | |- Performers_assnreflist? | | | | | | | += Person_ref+ (identifier, name?) | | | | | +- Protocol_assnref | | | | | += Protocol_ref (identifier, name?) | | | +- PhysicalBioAssaySource_assnref | | | += PhysicalBioAssay_ref (identifier, name?) | +- MeasuredBioAssayData_assnreflist? | += MeasuredBioAssayData_ref+ (identifier, name?) ConfidenceIndicator_assnlist | |- Error (identifier, name?, isBackground) | | | |- PropertySets_assnlist? | | | | | +- NameValueType+ (name?, value?, type?) | | | | | +- PropertySets_assnlist? ** | | | |- Descriptions_assnlist? | | | | | +- Description+ (text?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? ** | | | | | |- AuditTrail_assnlist? | | | | | | | +- Audit+ (date, action) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Descriptions_assnlist? ** | | | | | | | |- AuditTrail_assnlist? ** | | | | | | | |- Security_assnref? | | | | | | | | | += Security_ref (identifier, name?) | | | | | | | +- Performer_assnref? | | | | | | | |= Contact_ref (identifier, name?) | | | | | | | |= Person_ref (identifier, name?) | | | | | | | += Organization_ref (identifier, name?) | | | | | |- Security_assnref? --> | | | | | |- ExternalReference_assn? | | | | | | | +- ExternalReference (exportedFromServer?, exportedFromDB?, exportID?, exportName?) | | | | | | | +- PropertySets_assnlist? --> | | | | | |- Annotations_assnlist? | | | | | | | +- OntologyEntry+ (category, value, description?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | +- OntologyReference_assn? | | | | | | | +- DatabaseEntry (accession, accessionVersion?, URI?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Type_assn? | | | | | | | | | +- OntologyEntry (category, value, description?) ** | | | | | | | +- Database_assnref | | | | | | | += Database_ref (identifier, name?) | | | | | |- DatabaseReferences_assnlist? | | | | | | | +- DatabaseEntry+ (accession, accessionVersion?, URI?) --> | | | | | +- BibliographicReferences_assnlist? | | | | | +- BibliographicReference+ (title?, authors?, publication?, publisher?, editor?, year?, volume?, issue?, pages?, URI?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? ** | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | +- Parameters_assnlist | | | | | +- OntologyEntry+ (category, value, description?) --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- Channel_assnref? | | | | | += Channel_ref (identifier, name?) | | | |- Scale_assn | | | | | +- OntologyEntry (category, value, description?) --> | | | |- DataType_assn | | | | | +- OntologyEntry (category, value, description?) --> | | | |- ConfidenceIndicators_assnreflist? | | | | | |= ConfidenceIndicator_ref (identifier, name?) | | | | | |= Error_ref (identifier, name?) | | | | | |= PValue_ref (identifier, name?) | | | | | += ExpectedValue_ref (identifier, name?) | | | +- TargetQuantitationType_assnref | | | |= QuantitationType_ref (identifier, name?) | | | |= SpecializedQuantitationType_ref (identifier, name?) | | | |= DerivedSignal_ref (identifier, name?) | | | |= MeasuredSignal_ref (identifier, name?) | | | |= Error_ref (identifier, name?) | | | |= PValue_ref (identifier, name?) | | | |= ExpectedValue_ref (identifier, name?) | | | |= Ratio_ref (identifier, name?) | | | += PresentAbsent_ref (identifier, name?) | |- PValue (identifier, name?, isBackground) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- Channel_assnref? --> | | | |- Scale_assn --> | | | |- DataType_assn --> | | | |- ConfidenceIndicators_assnreflist? --> | | | +- TargetQuantitationType_assnref --> | +- ExpectedValue (identifier, name?, isBackground) | |- PropertySets_assnlist? --> | |- Descriptions_assnlist? --> | |- AuditTrail_assnlist? --> | |- Security_assnref? --> | |- Channel_assnref? --> | |- Scale_assn --> | |- DataType_assn --> | |- ConfidenceIndicators_assnreflist? --> | +- TargetQuantitationType_assnref --> DesignElement_assnlist | |- Reporter (identifier, name?) | | | |- PropertySets_assnlist? | | | | | +- NameValueType+ (name?, value?, type?) | | | | | +- PropertySets_assnlist? ** | | | |- Descriptions_assnlist? | | | | | +- Description+ (text?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? ** | | | | | |- AuditTrail_assnlist? | | | | | | | +- Audit+ (date, action) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Descriptions_assnlist? ** | | | | | | | |- AuditTrail_assnlist? ** | | | | | | | |- Security_assnref? | | | | | | | | | += Security_ref (identifier, name?) | | | | | | | +- Performer_assnref? | | | | | | | |= Contact_ref (identifier, name?) | | | | | | | |= Person_ref (identifier, name?) | | | | | | | += Organization_ref (identifier, name?) | | | | | |- Security_assnref? --> | | | | | |- ExternalReference_assn? | | | | | | | +- ExternalReference (exportedFromServer?, exportedFromDB?, exportID?, exportName?) | | | | | | | +- PropertySets_assnlist? --> | | | | | |- Annotations_assnlist? | | | | | | | +- OntologyEntry+ (category, value, description?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | +- OntologyReference_assn? | | | | | | | +- DatabaseEntry (accession, accessionVersion?, URI?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Type_assn? | | | | | | | | | +- OntologyEntry (category, value, description?) ** | | | | | | | +- Database_assnref | | | | | | | += Database_ref (identifier, name?) | | | | | |- DatabaseReferences_assnlist? | | | | | | | +- DatabaseEntry+ (accession, accessionVersion?, URI?) --> | | | | | +- BibliographicReferences_assnlist? | | | | | +- BibliographicReference+ (title?, authors?, publication?, publisher?, editor?, year?, volume?, issue?, pages?, URI?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? ** | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | +- Parameters_assnlist | | | | | +- OntologyEntry+ (category, value, description?) --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- ControlType_assn? | | | | | +- OntologyEntry (category, value, description?) --> | | | |- ImmobilizedCharacteristics_assnreflist? | | | | | += BioSequence_ref+ (identifier, name?) | | | |- WarningType_assn? | | | | | +- OntologyEntry (category, value, description?) --> | | | |- FailTypes_assnlist? | | | | | +- OntologyEntry+ (category, value, description?) --> | | | +- FeatureReporterMaps_assnreflist? | | | += FeatureReporterMap_ref+ (identifier, name?) | |- CompositeSequence (identifier, name?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- ControlType_assn? --> | | | |- BiologicalCharacteristics_assnreflist? | | | | | += BioSequence_ref+ (identifier, name?) | | | |- ReporterCompositeMaps_assnreflist? | | | | | += ReporterCompositeMap_ref+ (identifier, name?) | | | +- CompositeCompositeMaps_assnreflist? | | | += CompositeCompositeMap_ref+ (identifier, name?) | +- Feature (identifier, name?) | |- PropertySets_assnlist? --> | |- Descriptions_assnlist? --> | |- AuditTrail_assnlist? --> | |- Security_assnref? --> | |- ControlType_assn? --> | |- ControlFeatures_assnreflist? | | | += Feature_ref+ (identifier, name?) | |- ControlledFeatures_assnreflist? | | | += Feature_ref+ (identifier, name?) | |- Position_assn? | | | +- Position (x, y) | | | |- PropertySets_assnlist? --> | | | +- DistanceUnit_assn? | | | +- DistanceUnit (unitName?, unitNameCV) | | | +- PropertySets_assnlist? --> | |- Zone_assnref? | | | += Zone_ref (identifier, name?) | +- FeatureLocation_assn? | += FeatureLocation (row, column) DesignElementMap_assnlist | |- CompositeCompositeMap (identifier, name?) | | | |- PropertySets_assnlist? | | | | | +- NameValueType+ (name?, value?, type?) | | | | | +- PropertySets_assnlist? ** | | | |- Descriptions_assnlist? | | | | | +- Description+ (text?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? ** | | | | | |- AuditTrail_assnlist? | | | | | | | +- Audit+ (date, action) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Descriptions_assnlist? ** | | | | | | | |- AuditTrail_assnlist? ** | | | | | | | |- Security_assnref? | | | | | | | | | += Security_ref (identifier, name?) | | | | | | | +- Performer_assnref? | | | | | | | |= Contact_ref (identifier, name?) | | | | | | | |= Person_ref (identifier, name?) | | | | | | | += Organization_ref (identifier, name?) | | | | | |- Security_assnref? --> | | | | | |- ExternalReference_assn? | | | | | | | +- ExternalReference (exportedFromServer?, exportedFromDB?, exportID?, exportName?) | | | | | | | +- PropertySets_assnlist? --> | | | | | |- Annotations_assnlist? | | | | | | | +- OntologyEntry+ (category, value, description?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | +- OntologyReference_assn? | | | | | | | +- DatabaseEntry (accession, accessionVersion?, URI?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Type_assn? | | | | | | | | | +- OntologyEntry (category, value, description?) ** | | | | | | | +- Database_assnref | | | | | | | += Database_ref (identifier, name?) | | | | | |- DatabaseReferences_assnlist? | | | | | | | +- DatabaseEntry+ (accession, accessionVersion?, URI?) --> | | | | | +- BibliographicReferences_assnlist? | | | | | +- BibliographicReference+ (title?, authors?, publication?, publisher?, editor?, year?, volume?, issue?, pages?, URI?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? ** | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | +- Parameters_assnlist | | | | | +- OntologyEntry+ (category, value, description?) --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- ProtocolApplications_assnlist? | | | | | +- ProtocolApplication+ (activityDate) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- ParameterValues_assnlist? | | | | | | | +- ParameterValue+ (value?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | +- ParameterType_assnref | | | | | | | += Parameter_ref (identifier, name?) | | | | | |- HardwareApplications_assnlist? | | | | | | | +- HardwareApplication+ (serialNumber?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Descriptions_assnlist? --> | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | |- Security_assnref? --> | | | | | | | |- ParameterValues_assnlist? --> | | | | | | | +- Hardware_assnref | | | | | | | += Hardware_ref (identifier, name?) | | | | | |- SoftwareApplications_assnlist? | | | | | | | +- SoftwareApplication+ (version?, releaseDate?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Descriptions_assnlist? --> | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | |- Security_assnref? --> | | | | | | | |- ParameterValues_assnlist? --> | | | | | | | +- Software_assnref | | | | | | | += Software_ref (identifier, name?) | | | | | |- Performers_assnreflist? | | | | | | | += Person_ref+ (identifier, name?) | | | | | +- Protocol_assnref | | | | | += Protocol_ref (identifier, name?) | | | |- CompositeSequence_assnref | | | | | += CompositeSequence_ref (identifier, name?) | | | +- CompositePositionSources_assnlist | | | +- CompositePosition+ (start?, end?) | | | |- PropertySets_assnlist? --> | | | |- Composite_assnref | | | | | += CompositeSequence_ref (identifier, name?) | | | +- MismatchInformation_assnlist? | | | +- MismatchInformation+ (startCoord, newSequence?, replacedLength) | | | +- PropertySets_assnlist? --> | |- FeatureReporterMap (identifier, name?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- ProtocolApplications_assnlist? --> | | | |- Reporter_assnref | | | | | += Reporter_ref (identifier, name?) | | | +- FeatureInformationSources_assnlist | | | +- FeatureInformation+ | | | |- PropertySets_assnlist? --> | | | |- Feature_assnref | | | | | += Feature_ref (identifier, name?) | | | +- MismatchInformation_assnlist? --> | +- ReporterCompositeMap (identifier, name?) | |- PropertySets_assnlist? --> | |- Descriptions_assnlist? --> | |- AuditTrail_assnlist? --> | |- Security_assnref? --> | |- ProtocolApplications_assnlist? --> | |- CompositeSequence_assnref --> | +- ReporterPositionSources_assnlist | +- ReporterPosition+ (start?, end?) | |- PropertySets_assnlist? --> | |- Reporter_assnref --> | +- MismatchInformation_assnlist? --> MAGE-ML (identifier, name?) | |- PropertySets_assnlist? | | | +- NameValueType+ (name?, value?, type?) | | | +- PropertySets_assnlist? ** | |- Descriptions_assnlist? | | | +- Description+ (text?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? ** | | | |- AuditTrail_assnlist? | | | | | +- Audit+ (date, action) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? ** | | | | | |- AuditTrail_assnlist? ** | | | | | |- Security_assnref? | | | | | | | += Security_ref (identifier, name?) | | | | | +- Performer_assnref? | | | | | |= Contact_ref (identifier, name?) | | | | | |= Person_ref (identifier, name?) | | | | | += Organization_ref (identifier, name?) | | | |- Security_assnref? --> | | | |- ExternalReference_assn? | | | | | +- ExternalReference (exportedFromServer?, exportedFromDB?, exportID?, exportName?) | | | | | +- PropertySets_assnlist? --> | | | |- Annotations_assnlist? | | | | | +- OntologyEntry+ (category, value, description?) | | | | | |- PropertySets_assnlist? --> | | | | | +- OntologyReference_assn? | | | | | +- DatabaseEntry (accession, accessionVersion?, URI?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Type_assn? | | | | | | | +- OntologyEntry (category, value, description?) ** | | | | | +- Database_assnref | | | | | += Database_ref (identifier, name?) | | | |- DatabaseReferences_assnlist? | | | | | +- DatabaseEntry+ (accession, accessionVersion?, URI?) --> | | | +- BibliographicReferences_assnlist? | | | +- BibliographicReference+ (title?, authors?, publication?, publisher?, editor?, year?, volume?, issue?, pages?, URI?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? ** | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | +- Parameters_assnlist | | | +- OntologyEntry+ (category, value, description?) --> | |- AuditTrail_assnlist? --> | |- Security_assnref? --> | |- AuditAndSecurity_package? | | | |- Contact_assnlist? | | | | | |- Person (identifier, name?, URI?, address?, phone?, tollFreePhone?, email?, fax?, lastName?, firstName?, midInitials?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Descriptions_assnlist? --> | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | |- Security_assnref? --> | | | | | | | |- Roles_assnlist? | | | | | | | | | +- OntologyEntry+ (category, value, description?) --> | | | | | | | +- Affiliation_assnref? | | | | | | | += Organization_ref (identifier, name?) | | | | | +- Organization (identifier, name?, URI?, address?, phone?, tollFreePhone?, email?, fax?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- Roles_assnlist? --> | | | | | +- Parent_assn? | | | | | +- Organization (identifier, name?, URI?, address?, phone?, tollFreePhone?, email?, fax?) ** | | | |- SecurityGroup_assnlist? | | | | | +- SecurityGroup+ (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | +- Members_assnreflist | | | | | |= Contact_ref (identifier, name?) | | | | | |= Person_ref (identifier, name?) | | | | | += Organization_ref (identifier, name?) | | | +- Security_assnlist? | | | +- Security+ (identifier, name?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- Owner_assnref | | | | | |= Contact_ref (identifier, name?) | | | | | |= Person_ref (identifier, name?) | | | | | += Organization_ref (identifier, name?) | | | |- ReadGroups_assnreflist? | | | | | += SecurityGroup_ref+ (identifier, name?) | | | +- WriteGroups_assnreflist? | | | += SecurityGroup_ref+ (identifier, name?) | |- Description_package? | | | +- Database_assnlist? | | | +- Database+ (identifier, name?, version?, URI?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | +- Contacts_assnreflist? | | | |= Contact_ref (identifier, name?) | | | |= Person_ref (identifier, name?) | | | += Organization_ref (identifier, name?) | |= Measurement_package? | |= BQS_package? | |= BioEvent_package? | |- Protocol_package? | | | |- Hardware_assnlist? | | | | | +- Hardware+ (identifier, name?, URI?, model?, make?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- ParameterTypes_assnlist? | | | | | | | +- Parameter+ (identifier, name?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Descriptions_assnlist? --> | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | |- Security_assnref? --> | | | | | | | |- Unit_assn? | | | | | | | | | |- TimeUnit (unitName?, unitNameCV) | | | | | | | | | | | +- PropertySets_assnlist? --> | | | | | | | | | |- DistanceUnit (unitName?, unitNameCV) | | | | | | | | | | | +- PropertySets_assnlist? --> | | | | | | | | | |- TemperatureUnit (unitName?, unitNameCV) | | | | | | | | | | | +- PropertySets_assnlist? --> | | | | | | | | | |- QuantityUnit (unitName?, unitNameCV) | | | | | | | | | | | +- PropertySets_assnlist? --> | | | | | | | | | |- MassUnit (unitName?, unitNameCV) | | | | | | | | | | | +- PropertySets_assnlist? --> | | | | | | | | | |- VolumeUnit (unitName?, unitNameCV) | | | | | | | | | | | +- PropertySets_assnlist? --> | | | | | | | | | +- ConcentrationUnit (unitName?, unitNameCV) | | | | | | | | | +- PropertySets_assnlist? --> | | | | | | | +- DataType_assn? | | | | | | | +- OntologyEntry (category, value, description?) --> | | | | | |- Type_assn? --> | | | | | |- Softwares_assnreflist? | | | | | | | += Software_ref+ (identifier, name?) | | | | | +- HardwareManufacturers_assnreflist? | | | | | |= Contact_ref (identifier, name?) | | | | | |= Person_ref (identifier, name?) | | | | | += Organization_ref (identifier, name?) | | | |- Software_assnlist? | | | | | +- Software+ (identifier, name?, URI?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- ParameterTypes_assnlist? --> | | | | | |- Type_assn? --> | | | | | |- Hardware_assnref? | | | | | | | += Hardware_ref (identifier, name?) | | | | | |- Softwares_assnreflist? --> | | | | | +- SoftwareManufacturers_assnreflist? | | | | | |= Contact_ref (identifier, name?) | | | | | |= Person_ref (identifier, name?) | | | | | += Organization_ref (identifier, name?) | | | +- Protocol_assnlist? | | | +- Protocol+ (identifier, name?, URI?, text?, title?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- ParameterTypes_assnlist? --> | | | |- Type_assn? --> | | | |- Hardwares_assnreflist? | | | | | += Hardware_ref+ (identifier, name?) | | | +- Softwares_assnreflist? --> | |- BioMaterial_package? | | | |- Compound_assnlist? | | | | | +- Compound+ (identifier, name?, isSolvent="false") | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- MerckIndex_assn? | | | | | | | +- OntologyEntry (category, value, description?) --> | | | | | +- ComponentCompounds_assnlist? | | | | | +- CompoundMeasurement+ | | | | | |- PropertySets_assnlist? --> | | | | | |- Compound_assnref | | | | | | | += Compound_ref (identifier, name?) | | | | | +- Measurement_assn? | | | | | +- Measurement (type="absolute", value, kindCV="other", otherKind?) | | | | | |- PropertySets_assnlist? --> | | | | | +- Unit_assn? --> | | | +- BioMaterial_assnlist? | | | |- BioSource (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- QualityControlStatistics_assnlist? | | | | | | | +- NameValueType+ (name?, value?, type?) --> | | | | | |- Characteristics_assnlist? | | | | | | | +- OntologyEntry+ (category, value, description?) --> | | | | | |- MaterialType_assn | | | | | | | +- OntologyEntry (category, value, description?) --> | | | | | |- Treatments_assnlist? | | | | | | | +- Treatment+ (identifier, name?, order?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Descriptions_assnlist? --> | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | |- Security_assnref? --> | | | | | | | |- ProtocolApplications_assnlist? | | | | | | | | | +- ProtocolApplication+ (activityDate) | | | | | | | | | |- PropertySets_assnlist? --> | | | | | | | | | |- Descriptions_assnlist? --> | | | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | | | |- Security_assnref? --> | | | | | | | | | |- ParameterValues_assnlist? | | | | | | | | | | | +- ParameterValue+ (value?) | | | | | | | | | | | |- PropertySets_assnlist? --> | | | | | | | | | | | +- ParameterType_assnref | | | | | | | | | | | += Parameter_ref (identifier, name?) | | | | | | | | | |- HardwareApplications_assnlist? | | | | | | | | | | | +- HardwareApplication+ (serialNumber?) | | | | | | | | | | | |- PropertySets_assnlist? --> | | | | | | | | | | | |- Descriptions_assnlist? --> | | | | | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | | | | | |- Security_assnref? --> | | | | | | | | | | | |- ParameterValues_assnlist? --> | | | | | | | | | | | +- Hardware_assnref --> | | | | | | | | | |- SoftwareApplications_assnlist? | | | | | | | | | | | +- SoftwareApplication+ (version?, releaseDate?) | | | | | | | | | | | |- PropertySets_assnlist? --> | | | | | | | | | | | |- Descriptions_assnlist? --> | | | | | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | | | | | |- Security_assnref? --> | | | | | | | | | | | |- ParameterValues_assnlist? --> | | | | | | | | | | | +- Software_assnref | | | | | | | | | | | += Software_ref (identifier, name?) | | | | | | | | | |- Performers_assnreflist? | | | | | | | | | | | += Person_ref+ (identifier, name?) | | | | | | | | | +- Protocol_assnref | | | | | | | | | += Protocol_ref (identifier, name?) | | | | | | | |- Action_assn | | | | | | | | | +- OntologyEntry (category, value, description?) --> | | | | | | | |- ActionMeasurement_assn? | | | | | | | | | +- Measurement (type="absolute", value, kindCV="other", otherKind?) --> | | | | | | | |- CompoundMeasurements_assnlist? | | | | | | | | | +- CompoundMeasurement+ --> | | | | | | | +- SourceBioMaterialMeasurements_assnlist? | | | | | | | +- BioMaterialMeasurement+ | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- BioMaterial_assnref | | | | | | | | | |= BioMaterial_ref (identifier, name?) | | | | | | | | | |= BioSource_ref (identifier, name?) | | | | | | | | | |= LabeledExtract_ref (identifier, name?) | | | | | | | | | += BioSample_ref (identifier, name?) | | | | | | | +- Measurement_assn? --> | | | | | +- SourceContact_assnref? | | | | | |= Contact_ref (identifier, name?) | | | | | |= Person_ref (identifier, name?) | | | | | += Organization_ref (identifier, name?) | | | |- LabeledExtract (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- QualityControlStatistics_assnlist? --> | | | | | |- Characteristics_assnlist? --> | | | | | |- MaterialType_assn --> | | | | | |- Treatments_assnlist? --> | | | | | +- Labels_assnreflist | | | | | += Compound_ref+ (identifier, name?) | | | +- BioSample (identifier, name?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- QualityControlStatistics_assnlist? --> | | | |- Characteristics_assnlist? --> | | | |- MaterialType_assn --> | | | |- Treatments_assnlist? --> | | | +- Type_assn --> | |- BioSequence_package? | | | +- BioSequence_assnlist? | | | +- BioSequence+ (identifier, name?, length?, isApproximateLength?, isCircular?, sequence?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- SequenceDatabases_assnlist? | | | | | +- DatabaseEntry+ (accession, accessionVersion?, URI?) --> | | | |- OntologyEntries_assnlist? | | | | | +- OntologyEntry+ (category, value, description?) --> | | | |- PolymerType_assn | | | | | +- OntologyEntry (category, value, description?) --> | | | |- Type_assn --> | | | |- Species_assn? | | | | | +- OntologyEntry (category, value, description?) --> | | | +- SeqFeatures_assnlist? | | | +- SeqFeature+ (basis) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | +- Regions_assnlist? | | | +- SeqFeatureLocation+ (strandType) | | | |- PropertySets_assnlist? --> | | | |- Subregions_assnlist? | | | | | +- SeqFeatureLocation+ (strandType) ** | | | +- Coordinate_assn | | | |- SequencePosition (start?, end?) | | | | | +- PropertySets_assnlist? --> | | | |- ReporterPosition (start?, end?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Reporter_assnref | | | | | | | += Reporter_ref (identifier, name?) | | | | | +- MismatchInformation_assnlist? | | | | | +- MismatchInformation+ (startCoord, newSequence?, replacedLength) | | | | | +- PropertySets_assnlist? --> | | | +- CompositePosition (start?, end?) | | | |- PropertySets_assnlist? --> | | | |- Composite_assnref | | | | | += CompositeSequence_ref (identifier, name?) | | | +- MismatchInformation_assnlist? --> | |- DesignElement_package? | | | |- CompositeSequence_assnlist? | | | | | +- CompositeSequence+ (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- ControlType_assn? | | | | | | | +- OntologyEntry (category, value, description?) --> | | | | | |- BiologicalCharacteristics_assnreflist? | | | | | | | += BioSequence_ref+ (identifier, name?) | | | | | |- ReporterCompositeMaps_assnreflist? | | | | | | | += ReporterCompositeMap_ref+ (identifier, name?) | | | | | +- CompositeCompositeMaps_assnreflist? | | | | | += CompositeCompositeMap_ref+ (identifier, name?) | | | |- Reporter_assnlist? | | | | | +- Reporter+ (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- ControlType_assn? --> | | | | | |- ImmobilizedCharacteristics_assnreflist? | | | | | | | += BioSequence_ref+ (identifier, name?) | | | | | |- WarningType_assn? | | | | | | | +- OntologyEntry (category, value, description?) --> | | | | | |- FailTypes_assnlist? | | | | | | | +- OntologyEntry+ (category, value, description?) --> | | | | | +- FeatureReporterMaps_assnreflist? | | | | | += FeatureReporterMap_ref+ (identifier, name?) | | | |- CompositeCompositeMap_assnlist? | | | | | +- CompositeCompositeMap+ (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- ProtocolApplications_assnlist? --> | | | | | |- CompositeSequence_assnref | | | | | | | += CompositeSequence_ref (identifier, name?) | | | | | +- CompositePositionSources_assnlist | | | | | +- CompositePosition+ (start?, end?) --> | | | |- ReporterCompositeMap_assnlist? | | | | | +- ReporterCompositeMap+ (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- ProtocolApplications_assnlist? --> | | | | | |- CompositeSequence_assnref --> | | | | | +- ReporterPositionSources_assnlist | | | | | +- ReporterPosition+ (start?, end?) --> | | | +- FeatureReporterMap_assnlist? | | | +- FeatureReporterMap+ (identifier, name?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- ProtocolApplications_assnlist? --> | | | |- Reporter_assnref --> | | | +- FeatureInformationSources_assnlist | | | +- FeatureInformation+ | | | |- PropertySets_assnlist? --> | | | |- Feature_assnref | | | | | += Feature_ref (identifier, name?) | | | +- MismatchInformation_assnlist? --> | |- ArrayDesign_package? | | | |- ReporterGroup_assnlist? | | | | | +- ReporterGroup+ (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- Types_assnlist? | | | | | | | +- OntologyEntry+ (category, value, description?) --> | | | | | |- Species_assn? --> | | | | | +- Reporters_assnreflist | | | | | += Reporter_ref+ (identifier, name?) | | | |- CompositeGroup_assnlist? | | | | | +- CompositeGroup+ (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- Types_assnlist? --> | | | | | |- Species_assn? --> | | | | | +- CompositeSequences_assnreflist | | | | | += CompositeSequence_ref+ (identifier, name?) | | | +- ArrayDesign_assnlist? | | | |- ArrayDesign (identifier, name?, version?, numberOfFeatures?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- ProtocolApplications_assnlist? --> | | | | | |- FeatureGroups_assnlist? | | | | | | | +- FeatureGroup+ (identifier, name?, featureWidth?, featureLength?, featureHeight?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Descriptions_assnlist? --> | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | |- Security_assnref? --> | | | | | | | |- Types_assnlist? --> | | | | | | | |- Species_assn? --> | | | | | | | |- TechnologyType_assn? | | | | | | | | | +- OntologyEntry (category, value, description?) --> | | | | | | | |- FeatureShape_assn? | | | | | | | | | +- OntologyEntry (category, value, description?) --> | | | | | | | |- DistanceUnit_assn? | | | | | | | | | +- DistanceUnit (unitName?, unitNameCV) --> | | | | | | | +- Features_assnlist | | | | | | | +- Feature+ (identifier, name?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Descriptions_assnlist? --> | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | |- Security_assnref? --> | | | | | | | |- ControlType_assn? --> | | | | | | | |- ControlFeatures_assnreflist? | | | | | | | | | += Feature_ref+ (identifier, name?) | | | | | | | |- ControlledFeatures_assnreflist? | | | | | | | | | += Feature_ref+ (identifier, name?) | | | | | | | |- Position_assn? | | | | | | | | | +- Position (x, y) | | | | | | | | | |- PropertySets_assnlist? --> | | | | | | | | | +- DistanceUnit_assn? --> | | | | | | | |- Zone_assnref? | | | | | | | | | += Zone_ref (identifier, name?) | | | | | | | +- FeatureLocation_assn? | | | | | | | += FeatureLocation (row, column) | | | | | |- ReporterGroups_assnreflist? | | | | | | | += ReporterGroup_ref+ (identifier, name?) | | | | | |- CompositeGroups_assnreflist? | | | | | | | += CompositeGroup_ref+ (identifier, name?) | | | | | +- DesignProviders_assnreflist? | | | | | |= Contact_ref (identifier, name?) | | | | | |= Person_ref (identifier, name?) | | | | | += Organization_ref (identifier, name?) | | | +- PhysicalArrayDesign (identifier, name?, version?, numberOfFeatures?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- ProtocolApplications_assnlist? --> | | | |- FeatureGroups_assnlist? --> | | | |- ReporterGroups_assnreflist? --> | | | |- CompositeGroups_assnreflist? --> | | | |- DesignProviders_assnreflist? --> | | | |- SurfaceType_assn? | | | | | +- OntologyEntry (category, value, description?) --> | | | +- ZoneGroups_assnlist? | | | +- ZoneGroup+ (spacingsBetweenZonesX?, spacingsBetweenZonesY?, zonesPerX?, zonesPerY?) | | | |- PropertySets_assnlist? --> | | | |- DistanceUnit_assn? --> | | | |- ZoneLayout_assn? | | | | | +- ZoneLayout (numFeaturesPerRow?, numFeaturesPerCol?, spacingBetweenRows?, spacingBetweenCols?) | | | | | |- PropertySets_assnlist? --> | | | | | +- DistanceUnit_assn? --> | | | +- ZoneLocations_assnlist? | | | +- Zone+ (identifier, name?, row?, column?, upperLeftX?, upperLeftY?, lowerRightX?, lowerRightY?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | +- DistanceUnit_assn? --> | |- Array_package? | | | |- ArrayGroup_assnlist? | | | | | +- ArrayGroup+ (identifier, name?, barcode?, arraySpacingX?, arraySpacingY?, numArrays?, orientationMark?, orientationMarkPosition?, width?, length?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- Fiducials_assnlist? | | | | | | | +- Fiducial+ | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Descriptions_assnlist? --> | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | |- Security_assnref? --> | | | | | | | |- FiducialType_assn? | | | | | | | | | +- OntologyEntry (category, value, description?) --> | | | | | | | |- DistanceUnit_assn? --> | | | | | | | +- Position_assn --> | | | | | |- Arrays_assnreflist | | | | | | | += Array_ref+ (identifier, name?) | | | | | |- SubstrateType_assn? | | | | | | | +- OntologyEntry (category, value, description?) --> | | | | | +- DistanceUnit_assn? --> | | | |- Array_assnlist? | | | | | +- Array+ (identifier, name?, arrayIdentifier?, arrayXOrigin?, arrayYOrigin?, originRelativeTo?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- ArrayDesign_assnref | | | | | | | |= ArrayDesign_ref (identifier, name?) | | | | | | | |= ArrayDesign_ref (identifier, name?) | | | | | | | += PhysicalArrayDesign_ref (identifier, name?) | | | | | |- Information_assnref | | | | | | | += ArrayManufacture_ref (identifier, name?) | | | | | |- ArrayGroup_assnref? | | | | | | | += ArrayGroup_ref (identifier, name?) | | | | | +- ArrayManufactureDeviations_assnlist? | | | | | +- ArrayManufactureDeviation+ | | | | | |- PropertySets_assnlist? --> | | | | | |- Adjustments_assnlist? | | | | | | | +- ZoneDefect+ | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- DefectType_assn | | | | | | | | | +- OntologyEntry (category, value, description?) --> | | | | | | | |- PositionDelta_assn? | | | | | | | | | +- PositionDelta (deltaX, deltaY) | | | | | | | | | |- PropertySets_assnlist? --> | | | | | | | | | +- DistanceUnit_assn? --> | | | | | | | +- Zone_assnref --> | | | | | +- FeatureDefects_assnlist? | | | | | +- FeatureDefect+ | | | | | |- PropertySets_assnlist? --> | | | | | |- DefectType_assn --> | | | | | |- PositionDelta_assn? --> | | | | | +- Feature_assnref --> | | | +- ArrayManufacture_assnlist? | | | +- ArrayManufacture+ (identifier, name?, manufacturingDate?, tolerance?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- Arrays_assnreflist --> | | | |- ArrayManufacturers_assnreflist? | | | | | |= Contact_ref (identifier, name?) | | | | | |= Person_ref (identifier, name?) | | | | | += Organization_ref (identifier, name?) | | | |- QualityControlStatistics_assnlist? --> | | | |- FeatureLIMSs_assnlist? | | | | | |- ManufactureLIMS (quality?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Descriptions_assnlist? --> | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | |- Security_assnref? --> | | | | | | | |- Feature_assnref --> | | | | | | | |- BioMaterial_assnref? --> | | | | | | | +- IdentifierLIMS_assn? | | | | | | | +- DatabaseEntry (accession, accessionVersion?, URI?) --> | | | | | +- ManufactureLIMSBiomaterial (quality?, bioMaterialPlateIdentifier?, bioMaterialPlateRow?, bioMaterialPlateCol?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- Feature_assnref --> | | | | | |- BioMaterial_assnref? --> | | | | | +- IdentifierLIMS_assn? --> | | | +- ProtocolApplications_assnlist? --> | |- BioAssay_package? | | | |- Channel_assnlist? | | | | | +- Channel+ (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | +- Labels_assnreflist? --> | | | +- BioAssay_assnlist? | | | |- PhysicalBioAssay (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- Channels_assnreflist? | | | | | | | += Channel_ref+ (identifier, name?) | | | | | |- BioAssayFactorValues_assnreflist? | | | | | | | += FactorValue_ref+ (identifier, name?) | | | | | |- PhysicalBioAssayData_assnlist? | | | | | | | +- Image+ (identifier, name?, URI?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Descriptions_assnlist? --> | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | |- Security_assnref? --> | | | | | | | |- Channels_assnreflist? --> | | | | | | | +- Format_assn | | | | | | | +- OntologyEntry (category, value, description?) --> | | | | | |- BioAssayCreation_assn? | | | | | | | |- BioAssayCreation (identifier, name?) | | | | | | | | | |- PropertySets_assnlist? --> | | | | | | | | | |- Descriptions_assnlist? --> | | | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | | | |- Security_assnref? --> | | | | | | | | | |- ProtocolApplications_assnlist? --> | | | | | | | | | |- SourceBioMaterialMeasurements_assnlist? --> | | | | | | | | | +- Array_assnref | | | | | | | | | += Array_ref (identifier, name?) | | | | | | | +- Hybridization (identifier, name?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Descriptions_assnlist? --> | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | |- Security_assnref? --> | | | | | | | |- ProtocolApplications_assnlist? --> | | | | | | | |- SourceBioMaterialMeasurements_assnlist? --> | | | | | | | +- Array_assnref --> | | | | | +- BioAssayTreatments_assnlist? | | | | | |- BioAssayTreatment (identifier, name?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Descriptions_assnlist? --> | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | |- Security_assnref? --> | | | | | | | |- ProtocolApplications_assnlist? --> | | | | | | | +- Target_assnref | | | | | | | += PhysicalBioAssay_ref (identifier, name?) | | | | | +- ImageAcquisition (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- ProtocolApplications_assnlist? --> | | | | | |- Target_assnref --> | | | | | +- Images_assnreflist? | | | | | += Image_ref+ (identifier, name?) | | | |- DerivedBioAssay (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- Channels_assnreflist? --> | | | | | |- BioAssayFactorValues_assnreflist? --> | | | | | |- Type_assn? --> | | | | | +- DerivedBioAssayData_assnreflist? | | | | | += DerivedBioAssayData_ref+ (identifier, name?) | | | +- MeasuredBioAssay (identifier, name?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- Channels_assnreflist? --> | | | |- BioAssayFactorValues_assnreflist? --> | | | |- FeatureExtraction_assn? | | | | | +- FeatureExtraction (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- ProtocolApplications_assnlist? --> | | | | | +- PhysicalBioAssaySource_assnref | | | | | += PhysicalBioAssay_ref (identifier, name?) | | | +- MeasuredBioAssayData_assnreflist? | | | += MeasuredBioAssayData_ref+ (identifier, name?) | |- QuantitationType_package? | | | +- QuantitationType_assnlist? | | | |- SpecializedQuantitationType (identifier, name?, isBackground) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- Channel_assnref? | | | | | | | += Channel_ref (identifier, name?) | | | | | |- Scale_assn | | | | | | | +- OntologyEntry (category, value, description?) --> | | | | | |- DataType_assn --> | | | | | +- ConfidenceIndicators_assnreflist? | | | | | |= ConfidenceIndicator_ref (identifier, name?) | | | | | |= Error_ref (identifier, name?) | | | | | |= PValue_ref (identifier, name?) | | | | | += ExpectedValue_ref (identifier, name?) | | | |- DerivedSignal (identifier, name?, isBackground) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- Channel_assnref? --> | | | | | |- Scale_assn --> | | | | | |- DataType_assn --> | | | | | +- ConfidenceIndicators_assnreflist? --> | | | |- MeasuredSignal (identifier, name?, isBackground) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- Channel_assnref? --> | | | | | |- Scale_assn --> | | | | | |- DataType_assn --> | | | | | +- ConfidenceIndicators_assnreflist? --> | | | |- Error (identifier, name?, isBackground) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- Channel_assnref? --> | | | | | |- Scale_assn --> | | | | | |- DataType_assn --> | | | | | |- ConfidenceIndicators_assnreflist? --> | | | | | +- TargetQuantitationType_assnref | | | | | |= QuantitationType_ref (identifier, name?) | | | | | |= SpecializedQuantitationType_ref (identifier, name?) | | | | | |= DerivedSignal_ref (identifier, name?) | | | | | |= MeasuredSignal_ref (identifier, name?) | | | | | |= Error_ref (identifier, name?) | | | | | |= PValue_ref (identifier, name?) | | | | | |= ExpectedValue_ref (identifier, name?) | | | | | |= Ratio_ref (identifier, name?) | | | | | += PresentAbsent_ref (identifier, name?) | | | |- PValue (identifier, name?, isBackground) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- Channel_assnref? --> | | | | | |- Scale_assn --> | | | | | |- DataType_assn --> | | | | | |- ConfidenceIndicators_assnreflist? --> | | | | | +- TargetQuantitationType_assnref --> | | | |- ExpectedValue (identifier, name?, isBackground) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- Channel_assnref? --> | | | | | |- Scale_assn --> | | | | | |- DataType_assn --> | | | | | |- ConfidenceIndicators_assnreflist? --> | | | | | +- TargetQuantitationType_assnref --> | | | |- Ratio (identifier, name?, isBackground) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- Channel_assnref? --> | | | | | |- Scale_assn --> | | | | | |- DataType_assn --> | | | | | +- ConfidenceIndicators_assnreflist? --> | | | +- PresentAbsent (identifier, name?, isBackground) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- Channel_assnref? --> | | | |- Scale_assn --> | | | |- DataType_assn --> | | | +- ConfidenceIndicators_assnreflist? --> | |- BioAssayData_package? | | | |- BioAssayDimension_assnlist? | | | | | +- BioAssayDimension+ (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | +- BioAssays_assnreflist? | | | | | |= BioAssay_ref (identifier, name?) | | | | | |= PhysicalBioAssay_ref (identifier, name?) | | | | | |= DerivedBioAssay_ref (identifier, name?) | | | | | += MeasuredBioAssay_ref (identifier, name?) | | | |- DesignElementDimension_assnlist? | | | | | |- CompositeSequenceDimension (identifier, name?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Descriptions_assnlist? --> | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | |- Security_assnref? --> | | | | | | | +- CompositeSequences_assnreflist? --> | | | | | |- ReporterDimension (identifier, name?) | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- Descriptions_assnlist? --> | | | | | | | |- AuditTrail_assnlist? --> | | | | | | | |- Security_assnref? --> | | | | | | | +- Reporters_assnreflist? --> | | | | | +- FeatureDimension (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | +- ContainedFeatures_assnreflist? | | | | | += Feature_ref+ (identifier, name?) | | | |- QuantitationTypeDimension_assnlist? | | | | | +- QuantitationTypeDimension+ (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | +- QuantitationTypes_assnreflist? | | | | | |= QuantitationType_ref (identifier, name?) | | | | | |= SpecializedQuantitationType_ref (identifier, name?) | | | | | |= DerivedSignal_ref (identifier, name?) | | | | | |= MeasuredSignal_ref (identifier, name?) | | | | | |= Error_ref (identifier, name?) | | | | | |= PValue_ref (identifier, name?) | | | | | |= ExpectedValue_ref (identifier, name?) | | | | | |= Ratio_ref (identifier, name?) | | | | | += PresentAbsent_ref (identifier, name?) | | | |- BioAssayMap_assnlist? | | | | | +- BioAssayMap+ (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- ProtocolApplications_assnlist? --> | | | | | |- BioAssayMapTarget_assnref | | | | | | | += DerivedBioAssay_ref (identifier, name?) | | | | | +- SourceBioAssays_assnreflist? | | | | | |= BioAssay_ref (identifier, name?) | | | | | |= PhysicalBioAssay_ref (identifier, name?) | | | | | |= DerivedBioAssay_ref (identifier, name?) | | | | | += MeasuredBioAssay_ref (identifier, name?) | | | |- QuantitationTypeMap_assnlist? | | | | | +- QuantitationTypeMap+ (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- ProtocolApplications_assnlist? --> | | | | | |- TargetQuantitationType_assnref --> | | | | | +- SourcesQuantitationType_assnreflist? | | | | | |= QuantitationType_ref (identifier, name?) | | | | | |= SpecializedQuantitationType_ref (identifier, name?) | | | | | |= DerivedSignal_ref (identifier, name?) | | | | | |= MeasuredSignal_ref (identifier, name?) | | | | | |= Error_ref (identifier, name?) | | | | | |= PValue_ref (identifier, name?) | | | | | |= ExpectedValue_ref (identifier, name?) | | | | | |= Ratio_ref (identifier, name?) | | | | | += PresentAbsent_ref (identifier, name?) | | | +- BioAssayData_assnlist? | | | |- DerivedBioAssayData (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- SummaryStatistics_assnlist? | | | | | | | +- NameValueType+ (name?, value?, type?) --> | | | | | |- BioDataValues_assn? | | | | | | | |- BioDataCube | | | | | | | | | |- PropertySets_assnlist? --> | | | | | | | | | |- BioAssayDimension_assnref | | | | | | | | | | | += BioAssayDimension_ref (identifier, name?) | | | | | | | | | |- DesignElementDimension_assnref | | | | | | | | | | | |= DesignElementDimension_ref (identifier, name?) | | | | | | | | | | | |= CompositeSequenceDimension_ref (identifier, name?) | | | | | | | | | | | |= ReporterDimension_ref (identifier, name?) | | | | | | | | | | | += FeatureDimension_ref (identifier, name?) | | | | | | | | | |- QuantitationTypeDimension_assnref | | | | | | | | | | | += QuantitationTypeDimension_ref (identifier, name?) | | | | | | | | | |- QuantitationTypeDimension_assnref --> | | | | | | | | | |- DesignElementDimension_assnref --> | | | | | | | | | |- DesignElementDimension_assnref --> | | | | | | | | | |- QuantitationTypeDimension_assnref --> | | | | | | | | | |- BioAssayDimension_assnref --> | | | | | | | | | |- BioAssayDimension_assnref --> | | | | | | | | | |- QuantitationTypeDimension_assnref --> | | | | | | | | | |- QuantitationTypeDimension_assnref --> | | | | | | | | | |- BioAssayDimension_assnref --> | | | | | | | | | |- DesignElementDimension_assnref --> | | | | | | | | | |- DesignElementDimension_assnref --> | | | | | | | | | |- BioAssayDimension_assnref --> | | | | | | | | | |- DataInternal_assn | | | | | | | | | | | +- DataInternal | | | | | | | | | +- DataExternal_assn | | | | | | | | | += DataExternal (dataFormat="whitespace", dataFormatInfoURI?, filenameURI) | | | | | | | +- BioDataTuples | | | | | | | |- PropertySets_assnlist? --> | | | | | | | |- BioAssayDimension_assnref? --> | | | | | | | |- DesignElementDimension_assnref? --> | | | | | | | |- QuantitationTypeDimension_assnref? --> | | | | | | | +- BioAssayTuples_assnlist? | | | | | | | +- BioAssayTuple+ | | | | | | | |- BioAssay_assnref | | | | | | | | | |= BioAssay_ref (identifier, name?) | | | | | | | | | |= PhysicalBioAssay_ref (identifier, name?) | | | | | | | | | |= DerivedBioAssay_ref (identifier, name?) | | | | | | | | | += MeasuredBioAssay_ref (identifier, name?) | | | | | | | +- DesignElementTuples_assnlist | | | | | | | +- DesignElementTuple+ | | | | | | | |- DesignElement_assnref | | | | | | | | | |= DesignElement_ref (identifier, name?) | | | | | | | | | |= Reporter_ref (identifier, name?) | | | | | | | | | |= CompositeSequence_ref (identifier, name?) | | | | | | | | | += Feature_ref (identifier, name?) | | | | | | | +- QuantitationTypeTuples_assnlist | | | | | | | +- QuantitationTypeTuple+ | | | | | | | |- QuantitationType_assnref | | | | | | | | | |= QuantitationType_ref (identifier, name?) | | | | | | | | | |= SpecializedQuantitationType_ref (identifier, name?) | | | | | | | | | |= DerivedSignal_ref (identifier, name?) | | | | | | | | | |= MeasuredSignal_ref (identifier, name?) | | | | | | | | | |= Error_ref (identifier, name?) | | | | | | | | | |= PValue_ref (identifier, name?) | | | | | | | | | |= ExpectedValue_ref (identifier, name?) | | | | | | | | | |= Ratio_ref (identifier, name?) | | | | | | | | | += PresentAbsent_ref (identifier, name?) | | | | | | | +- Datum_assn | | | | | | | += Datum (value) | | | | | +- ProducerTransformation_assn? | | | | | +- Transformation (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- ProtocolApplications_assnlist? --> | | | | | |- BioAssayDataSources_assnreflist? | | | | | | | |= BioAssayData_ref (identifier, name?) | | | | | | | |= DerivedBioAssayData_ref (identifier, name?) | | | | | | | += MeasuredBioAssayData_ref (identifier, name?) | | | | | |- QuantitationTypeMapping_assn? | | | | | | | +- QuantitationTypeMapping | | | | | | | |- PropertySets_assnlist? --> | | | | | | | +- QuantitationTypeMaps_assnreflist | | | | | | | += QuantitationTypeMap_ref+ (identifier, name?) | | | | | |- DesignElementMapping_assn? | | | | | | | +- DesignElementMapping | | | | | | | |- PropertySets_assnlist? --> | | | | | | | +- DesignElementMaps_assnreflist | | | | | | | |= DesignElementMap_ref (identifier, name?) | | | | | | | |= CompositeCompositeMap_ref (identifier, name?) | | | | | | | |= FeatureReporterMap_ref (identifier, name?) | | | | | | | += ReporterCompositeMap_ref (identifier, name?) | | | | | +- BioAssayMapping_assn? | | | | | +- BioAssayMapping | | | | | |- PropertySets_assnlist? --> | | | | | +- BioAssayMaps_assnreflist | | | | | += BioAssayMap_ref+ (identifier, name?) | | | +- MeasuredBioAssayData (identifier, name?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- SummaryStatistics_assnlist? --> | | | +- BioDataValues_assn? --> | |- Experiment_package? | | | +- Experiment_assnlist? | | | +- Experiment+ (identifier, name?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- Providers_assnreflist? | | | | | |= Contact_ref (identifier, name?) | | | | | |= Person_ref (identifier, name?) | | | | | += Organization_ref (identifier, name?) | | | |- AnalysisResults_assnreflist? | | | | | += BioAssayDataCluster_ref+ (identifier, name?) | | | |- BioAssayData_assnreflist? | | | | | |= BioAssayData_ref (identifier, name?) | | | | | |= DerivedBioAssayData_ref (identifier, name?) | | | | | += MeasuredBioAssayData_ref (identifier, name?) | | | |- BioAssays_assnreflist? --> | | | +- ExperimentDesign_assn | | | +- ExperimentDesign | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- Types_assnlist? --> | | | |- TopLevelBioAssays_assnreflist? | | | | | |= BioAssay_ref (identifier, name?) | | | | | |= PhysicalBioAssay_ref (identifier, name?) | | | | | |= DerivedBioAssay_ref (identifier, name?) | | | | | += MeasuredBioAssay_ref (identifier, name?) | | | |- ExperimentalFactors_assnlist? | | | | | +- ExperimentalFactor+ (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- Category_assn? | | | | | | | +- OntologyEntry (category, value, description?) --> | | | | | +- FactorValues_assnlist? | | | | | +- FactorValue+ (identifier, name?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | +- Measurement_assn --> | | | |- QualityControlDescription_assn? | | | | | +- Description (text?) --> | | | |- NormalizationDescription_assn? | | | | | +- Description (text?) --> | | | +- ReplicateDescription_assn? | | | +- Description (text?) --> | +- HigherLevelAnalysis_package? | +- BioAssayDataCluster_assnlist? | +- BioAssayDataCluster+ (identifier, name?) | |- PropertySets_assnlist? --> | |- Descriptions_assnlist? --> | |- AuditTrail_assnlist? --> | |- Security_assnref? --> | |- ClusterBioAssayData_assnref? | | | |= BioAssayData_ref (identifier, name?) | | | |= DerivedBioAssayData_ref (identifier, name?) | | | += MeasuredBioAssayData_ref (identifier, name?) | +- Nodes_assnlist | +- Node+ | |- PropertySets_assnlist? --> | |- Descriptions_assnlist? --> | |- AuditTrail_assnlist? --> | |- Security_assnref? --> | |- Nodes_assnlist? ** | |- NodeContents_assnlist? | | | +- NodeContents+ | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- BioAssayDimension_assnref? --> | | | |- DesignElementDimension_assnref? --> | | | +- QuantitationDimension_assnref? | | | += QuantitationTypeDimension_ref (identifier, name?) | +- NodeValue_assnlist? | +- NodeValue+ (name?, value) | |- PropertySets_assnlist? --> | |- Type_assn --> | |- Scale_assn? --> | +- DataType_assn? --> Person_assnlist | +- Person+ (identifier, name?, URI?, address?, phone?, tollFreePhone?, email?, fax?, lastName?, firstName?, midInitials?) | |- PropertySets_assnlist? | | | +- NameValueType+ (name?, value?, type?) | | | +- PropertySets_assnlist? ** | |- Descriptions_assnlist? | | | +- Description+ (text?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? ** | | | |- AuditTrail_assnlist? | | | | | +- Audit+ (date, action) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? ** | | | | | |- AuditTrail_assnlist? ** | | | | | |- Security_assnref? | | | | | | | += Security_ref (identifier, name?) | | | | | +- Performer_assnref? | | | | | |= Contact_ref (identifier, name?) | | | | | |= Person_ref (identifier, name?) | | | | | += Organization_ref (identifier, name?) | | | |- Security_assnref? --> | | | |- ExternalReference_assn? | | | | | +- ExternalReference (exportedFromServer?, exportedFromDB?, exportID?, exportName?) | | | | | +- PropertySets_assnlist? --> | | | |- Annotations_assnlist? | | | | | +- OntologyEntry+ (category, value, description?) | | | | | |- PropertySets_assnlist? --> | | | | | +- OntologyReference_assn? | | | | | +- DatabaseEntry (accession, accessionVersion?, URI?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Type_assn? | | | | | | | +- OntologyEntry (category, value, description?) ** | | | | | +- Database_assnref | | | | | += Database_ref (identifier, name?) | | | |- DatabaseReferences_assnlist? | | | | | +- DatabaseEntry+ (accession, accessionVersion?, URI?) --> | | | +- BibliographicReferences_assnlist? | | | +- BibliographicReference+ (title?, authors?, publication?, publisher?, editor?, year?, volume?, issue?, pages?, URI?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? ** | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | +- Parameters_assnlist | | | +- OntologyEntry+ (category, value, description?) --> | |- AuditTrail_assnlist? --> | |- Security_assnref? --> | |- Roles_assnlist? | | | +- OntologyEntry+ (category, value, description?) --> | +- Affiliation_assnref? | += Organization_ref (identifier, name?) DerivedBioAssay_assnlist | +- DerivedBioAssay+ (identifier, name?) | |- PropertySets_assnlist? | | | +- NameValueType+ (name?, value?, type?) | | | +- PropertySets_assnlist? ** | |- Descriptions_assnlist? | | | +- Description+ (text?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? ** | | | |- AuditTrail_assnlist? | | | | | +- Audit+ (date, action) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? ** | | | | | |- AuditTrail_assnlist? ** | | | | | |- Security_assnref? | | | | | | | += Security_ref (identifier, name?) | | | | | +- Performer_assnref? | | | | | |= Contact_ref (identifier, name?) | | | | | |= Person_ref (identifier, name?) | | | | | += Organization_ref (identifier, name?) | | | |- Security_assnref? --> | | | |- ExternalReference_assn? | | | | | +- ExternalReference (exportedFromServer?, exportedFromDB?, exportID?, exportName?) | | | | | +- PropertySets_assnlist? --> | | | |- Annotations_assnlist? | | | | | +- OntologyEntry+ (category, value, description?) | | | | | |- PropertySets_assnlist? --> | | | | | +- OntologyReference_assn? | | | | | +- DatabaseEntry (accession, accessionVersion?, URI?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Type_assn? | | | | | | | +- OntologyEntry (category, value, description?) ** | | | | | +- Database_assnref | | | | | += Database_ref (identifier, name?) | | | |- DatabaseReferences_assnlist? | | | | | +- DatabaseEntry+ (accession, accessionVersion?, URI?) --> | | | +- BibliographicReferences_assnlist? | | | +- BibliographicReference+ (title?, authors?, publication?, publisher?, editor?, year?, volume?, issue?, pages?, URI?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? ** | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | +- Parameters_assnlist | | | +- OntologyEntry+ (category, value, description?) --> | |- AuditTrail_assnlist? --> | |- Security_assnref? --> | |- Channels_assnreflist? | | | += Channel_ref+ (identifier, name?) | |- BioAssayFactorValues_assnreflist? | | | += FactorValue_ref+ (identifier, name?) | |- Type_assn? --> | +- DerivedBioAssayData_assnreflist? | += DerivedBioAssayData_ref+ (identifier, name?) MeasuredBioAssayData_assnlist | +- MeasuredBioAssayData+ (identifier, name?) | |- PropertySets_assnlist? | | | +- NameValueType+ (name?, value?, type?) | | | +- PropertySets_assnlist? ** | |- Descriptions_assnlist? | | | +- Description+ (text?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? ** | | | |- AuditTrail_assnlist? | | | | | +- Audit+ (date, action) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? ** | | | | | |- AuditTrail_assnlist? ** | | | | | |- Security_assnref? | | | | | | | += Security_ref (identifier, name?) | | | | | +- Performer_assnref? | | | | | |= Contact_ref (identifier, name?) | | | | | |= Person_ref (identifier, name?) | | | | | += Organization_ref (identifier, name?) | | | |- Security_assnref? --> | | | |- ExternalReference_assn? | | | | | +- ExternalReference (exportedFromServer?, exportedFromDB?, exportID?, exportName?) | | | | | +- PropertySets_assnlist? --> | | | |- Annotations_assnlist? | | | | | +- OntologyEntry+ (category, value, description?) | | | | | |- PropertySets_assnlist? --> | | | | | +- OntologyReference_assn? | | | | | +- DatabaseEntry (accession, accessionVersion?, URI?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Type_assn? | | | | | | | +- OntologyEntry (category, value, description?) ** | | | | | +- Database_assnref | | | | | += Database_ref (identifier, name?) | | | |- DatabaseReferences_assnlist? | | | | | +- DatabaseEntry+ (accession, accessionVersion?, URI?) --> | | | +- BibliographicReferences_assnlist? | | | +- BibliographicReference+ (title?, authors?, publication?, publisher?, editor?, year?, volume?, issue?, pages?, URI?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? ** | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | +- Parameters_assnlist | | | +- OntologyEntry+ (category, value, description?) --> | |- AuditTrail_assnlist? --> | |- Security_assnref? --> | |- SummaryStatistics_assnlist? | | | +- NameValueType+ (name?, value?, type?) --> | +- BioDataValues_assn? | |- BioDataCube | | | |- PropertySets_assnlist? --> | | | |- BioAssayDimension_assnref | | | | | += BioAssayDimension_ref (identifier, name?) | | | |- DesignElementDimension_assnref | | | | | |= DesignElementDimension_ref (identifier, name?) | | | | | |= CompositeSequenceDimension_ref (identifier, name?) | | | | | |= ReporterDimension_ref (identifier, name?) | | | | | += FeatureDimension_ref (identifier, name?) | | | |- QuantitationTypeDimension_assnref | | | | | += QuantitationTypeDimension_ref (identifier, name?) | | | |- QuantitationTypeDimension_assnref --> | | | |- DesignElementDimension_assnref --> | | | |- DesignElementDimension_assnref --> | | | |- QuantitationTypeDimension_assnref --> | | | |- BioAssayDimension_assnref --> | | | |- BioAssayDimension_assnref --> | | | |- QuantitationTypeDimension_assnref --> | | | |- QuantitationTypeDimension_assnref --> | | | |- BioAssayDimension_assnref --> | | | |- DesignElementDimension_assnref --> | | | |- DesignElementDimension_assnref --> | | | |- BioAssayDimension_assnref --> | | | |- DataInternal_assn | | | | | +- DataInternal | | | +- DataExternal_assn | | | += DataExternal (dataFormat="whitespace", dataFormatInfoURI?, filenameURI) | +- BioDataTuples | |- PropertySets_assnlist? --> | |- BioAssayDimension_assnref? --> | |- DesignElementDimension_assnref? --> | |- QuantitationTypeDimension_assnref? --> | +- BioAssayTuples_assnlist? | +- BioAssayTuple+ | |- BioAssay_assnref | | | |= BioAssay_ref (identifier, name?) | | | |= PhysicalBioAssay_ref (identifier, name?) | | | |= DerivedBioAssay_ref (identifier, name?) | | | += MeasuredBioAssay_ref (identifier, name?) | +- DesignElementTuples_assnlist | +- DesignElementTuple+ | |- DesignElement_assnref | | | |= DesignElement_ref (identifier, name?) | | | |= Reporter_ref (identifier, name?) | | | |= CompositeSequence_ref (identifier, name?) | | | += Feature_ref (identifier, name?) | +- QuantitationTypeTuples_assnlist | +- QuantitationTypeTuple+ | |- QuantitationType_assnref | | | |= QuantitationType_ref (identifier, name?) | | | |= SpecializedQuantitationType_ref (identifier, name?) | | | |= DerivedSignal_ref (identifier, name?) | | | |= MeasuredSignal_ref (identifier, name?) | | | |= Error_ref (identifier, name?) | | | |= PValue_ref (identifier, name?) | | | |= ExpectedValue_ref (identifier, name?) | | | |= Ratio_ref (identifier, name?) | | | += PresentAbsent_ref (identifier, name?) | +- Datum_assn | += Datum (value) DerivedBioAssayData_assnlist | +- DerivedBioAssayData+ (identifier, name?) | |- PropertySets_assnlist? | | | +- NameValueType+ (name?, value?, type?) | | | +- PropertySets_assnlist? ** | |- Descriptions_assnlist? | | | +- Description+ (text?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? ** | | | |- AuditTrail_assnlist? | | | | | +- Audit+ (date, action) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? ** | | | | | |- AuditTrail_assnlist? ** | | | | | |- Security_assnref? | | | | | | | += Security_ref (identifier, name?) | | | | | +- Performer_assnref? | | | | | |= Contact_ref (identifier, name?) | | | | | |= Person_ref (identifier, name?) | | | | | += Organization_ref (identifier, name?) | | | |- Security_assnref? --> | | | |- ExternalReference_assn? | | | | | +- ExternalReference (exportedFromServer?, exportedFromDB?, exportID?, exportName?) | | | | | +- PropertySets_assnlist? --> | | | |- Annotations_assnlist? | | | | | +- OntologyEntry+ (category, value, description?) | | | | | |- PropertySets_assnlist? --> | | | | | +- OntologyReference_assn? | | | | | +- DatabaseEntry (accession, accessionVersion?, URI?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Type_assn? | | | | | | | +- OntologyEntry (category, value, description?) ** | | | | | +- Database_assnref | | | | | += Database_ref (identifier, name?) | | | |- DatabaseReferences_assnlist? | | | | | +- DatabaseEntry+ (accession, accessionVersion?, URI?) --> | | | +- BibliographicReferences_assnlist? | | | +- BibliographicReference+ (title?, authors?, publication?, publisher?, editor?, year?, volume?, issue?, pages?, URI?) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? ** | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | +- Parameters_assnlist | | | +- OntologyEntry+ (category, value, description?) --> | |- AuditTrail_assnlist? --> | |- Security_assnref? --> | |- SummaryStatistics_assnlist? | | | +- NameValueType+ (name?, value?, type?) --> | |- BioDataValues_assn? | | | |- BioDataCube | | | | | |- PropertySets_assnlist? --> | | | | | |- BioAssayDimension_assnref | | | | | | | += BioAssayDimension_ref (identifier, name?) | | | | | |- DesignElementDimension_assnref | | | | | | | |= DesignElementDimension_ref (identifier, name?) | | | | | | | |= CompositeSequenceDimension_ref (identifier, name?) | | | | | | | |= ReporterDimension_ref (identifier, name?) | | | | | | | += FeatureDimension_ref (identifier, name?) | | | | | |- QuantitationTypeDimension_assnref | | | | | | | += QuantitationTypeDimension_ref (identifier, name?) | | | | | |- QuantitationTypeDimension_assnref --> | | | | | |- DesignElementDimension_assnref --> | | | | | |- DesignElementDimension_assnref --> | | | | | |- QuantitationTypeDimension_assnref --> | | | | | |- BioAssayDimension_assnref --> | | | | | |- BioAssayDimension_assnref --> | | | | | |- QuantitationTypeDimension_assnref --> | | | | | |- QuantitationTypeDimension_assnref --> | | | | | |- BioAssayDimension_assnref --> | | | | | |- DesignElementDimension_assnref --> | | | | | |- DesignElementDimension_assnref --> | | | | | |- BioAssayDimension_assnref --> | | | | | |- DataInternal_assn | | | | | | | +- DataInternal | | | | | +- DataExternal_assn | | | | | += DataExternal (dataFormat="whitespace", dataFormatInfoURI?, filenameURI) | | | +- BioDataTuples | | | |- PropertySets_assnlist? --> | | | |- BioAssayDimension_assnref? --> | | | |- DesignElementDimension_assnref? --> | | | |- QuantitationTypeDimension_assnref? --> | | | +- BioAssayTuples_assnlist? | | | +- BioAssayTuple+ | | | |- BioAssay_assnref | | | | | |= BioAssay_ref (identifier, name?) | | | | | |= PhysicalBioAssay_ref (identifier, name?) | | | | | |= DerivedBioAssay_ref (identifier, name?) | | | | | += MeasuredBioAssay_ref (identifier, name?) | | | +- DesignElementTuples_assnlist | | | +- DesignElementTuple+ | | | |- DesignElement_assnref | | | | | |= DesignElement_ref (identifier, name?) | | | | | |= Reporter_ref (identifier, name?) | | | | | |= CompositeSequence_ref (identifier, name?) | | | | | += Feature_ref (identifier, name?) | | | +- QuantitationTypeTuples_assnlist | | | +- QuantitationTypeTuple+ | | | |- QuantitationType_assnref | | | | | |= QuantitationType_ref (identifier, name?) | | | | | |= SpecializedQuantitationType_ref (identifier, name?) | | | | | |= DerivedSignal_ref (identifier, name?) | | | | | |= MeasuredSignal_ref (identifier, name?) | | | | | |= Error_ref (identifier, name?) | | | | | |= PValue_ref (identifier, name?) | | | | | |= ExpectedValue_ref (identifier, name?) | | | | | |= Ratio_ref (identifier, name?) | | | | | += PresentAbsent_ref (identifier, name?) | | | +- Datum_assn | | | += Datum (value) | +- ProducerTransformation_assn? | +- Transformation (identifier, name?) | |- PropertySets_assnlist? --> | |- Descriptions_assnlist? --> | |- AuditTrail_assnlist? --> | |- Security_assnref? --> | |- ProtocolApplications_assnlist? | | | +- ProtocolApplication+ (activityDate) | | | |- PropertySets_assnlist? --> | | | |- Descriptions_assnlist? --> | | | |- AuditTrail_assnlist? --> | | | |- Security_assnref? --> | | | |- ParameterValues_assnlist? | | | | | +- ParameterValue+ (value?) | | | | | |- PropertySets_assnlist? --> | | | | | +- ParameterType_assnref | | | | | += Parameter_ref (identifier, name?) | | | |- HardwareApplications_assnlist? | | | | | +- HardwareApplication+ (serialNumber?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- ParameterValues_assnlist? --> | | | | | +- Hardware_assnref | | | | | += Hardware_ref (identifier, name?) | | | |- SoftwareApplications_assnlist? | | | | | +- SoftwareApplication+ (version?, releaseDate?) | | | | | |- PropertySets_assnlist? --> | | | | | |- Descriptions_assnlist? --> | | | | | |- AuditTrail_assnlist? --> | | | | | |- Security_assnref? --> | | | | | |- ParameterValues_assnlist? --> | | | | | +- Software_assnref | | | | | += Software_ref (identifier, name?) | | | |- Performers_assnreflist? | | | | | += Person_ref+ (identifier, name?) | | | +- Protocol_assnref | | | += Protocol_ref (identifier, name?) | |- BioAssayDataSources_assnreflist? | | | |= BioAssayData_ref (identifier, name?) | | | |= DerivedBioAssayData_ref (identifier, name?) | | | += MeasuredBioAssayData_ref (identifier, name?) | |- QuantitationTypeMapping_assn? | | | +- QuantitationTypeMapping | | | |- PropertySets_assnlist? --> | | | +- QuantitationTypeMaps_assnreflist | | | += QuantitationTypeMap_ref+ (identifier, name?) | |- DesignElementMapping_assn? | | | +- DesignElementMapping | | | |- PropertySets_assnlist? --> | | | +- DesignElementMaps_assnreflist | | | |= DesignElementMap_ref (identifier, name?) | | | |= CompositeCompositeMap_ref (identifier, name?) | | | |= FeatureReporterMap_ref (identifier, name?) | | | += ReporterCompositeMap_ref (identifier, name?) | +- BioAssayMapping_assn? | +- BioAssayMapping | |- PropertySets_assnlist? --> | +- BioAssayMaps_assnreflist | += BioAssayMap_ref+ (identifier, name?) Tree representation of the Protein Sequence Database Markup Language DTD - generated using Matra 0.8.2b (http://matra.sourceforge.net/)
How to read the above tree?
Please check the article How to read the DTD Tree to learn how to read the above dtd tree generated by the Matra DTD Parser.
Notes on the above tree
This dtd uses the Multi Root Document Types design pattern.
This is apparent from the dtdtree generated - as we find ten potential root elements -
MAGE-ML
PhysicalBioAssay_assnlist
MeasuredBioAssay_assnlist
ConfidenceIndicator_assnlist
DesignElement_assnlist
DesignElementMap_assnlist
Person_assnlist
DerivedBioAssay_assnlist
MeasuredBioAssayData_assnlist
DerivedBioAssayData_assnlist
On examining the above tree, we find a few orphan trees and one orphan-element.
StandardQuantitationType_ref (identifier, name?) PhysicalBioAssayTarget_assnref | += PhysicalBioAssay_ref (identifier, name?) ExperimentalFactor_assnref | += ExperimentalFactor_ref (identifier, name?) FeatureGroup_assnref | += FeatureGroup_ref (identifier, name?) PhysicalBioAssay_assnref | += PhysicalBioAssay_ref (identifier, name?) DerivedBioAssayDataTarget_assnref | += DerivedBioAssayData_ref (identifier, name?) MeasuredBioAssayTarget_assnref | += MeasuredBioAssay_ref (identifier, name?)The orphan-element
StandardQuantitationType_ref does not have any content model and is not included in
the content model of any other element-types. In other words, This element type does not have any parent element types
and nor does it have any child element types. The obvious conclusion is that StandardQuantitationType_ref
was missed out (which is not very uncommon in large dtds). It should either be removed from the dtd or it should be
added to the content model of another element type.
The other orphan-trees have too short a structure. Though xml documents could potentially be formed with two element types, typically xml documents tend to be more structured and have more than two element types. Due to this, I find the above structures suspicious and I feel that they should fit into one of the other dtdtrees.
About Microarray Gene Expression Markup Language
Microarray Gene Expression Markup Language (MAGE-ML) is a language designed to describe and communicate information about microarray based experiments.
You can find more information on MAGE-ML at the MAGE Home Page.
About Matra
Matra is a java based XML DTD parser utility. It is available from http://matra.sourceforge.net. It is freely available under the open-source MPL 1.1 license.
