"The MGED Ontology" Sept 3, 2004 Chris Stoeckert, Helen Parkinson, Trish Whetzel, Paul Spellman, Catherine A. Ball, Joseph White, John Matese, Liju Fan, Gilberto Fragoso, Mervi Heiskanen, Susanna Sansone, Helen Causton, Laurence Game, Chris Taylor Concepts, definitions, terms, and resources for standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1 An ontology for microarray experiments in support of MAGE v.1. "1.1.9" TargetedCellTypeDatabase SubstrateType Temperature DesignElementPackage ClinicalTreatment BioMaterialCharacteristicCategory NodeValue OrganismPartDatabase Organism Software HistologyDatabase AtomicAction BioAssayDataPackage LightUnit DeprecatedTerms Bedding CellTypeDatabase Preservation BioMaterialCharacteristics HigherLevelAnalysisProtocolType DiseaseStateDatabase PhysicalBioSequenceType DiseaseLocation FamilyHistory EnvironmentalHistory ExperimentPackage MGEDExtendedOntology SoftwareVariation OntologyEntry ExperimentalFactor ProtocolType DescriptionPackage DatabaseEntryType HigherLevelAnalysisPackage DataType Database SeqFeatureBasis Genotype ExperimentalFactorCategory PerturbationalDesign TargetedCellType GeneticModification ReplicateDescriptionType CompoundDatabase ProtocolPackage DiseaseState Action TimeUnit Allele MethodologicalFactorCategory TestResult QuantitationTypePackage ProtocolParameterType Light Media Roles Scale Water BioSequencePackage CancerSite BarrierFacility Histology OrganismPart DevelopmentalStage ConcentrationUnitOther QuantityUnitOther MethodologicalDesign DiseaseStagingDatabase PhysicalArrayDesign ConcentrationUnit Person Ploidy ImageFormat Result OperatorVariation Contact Organization FeatureGroup Parameter FeatureShape QuantityUnit ClinicalHistory Haplotype PreservationType TumorGradingDatabase HardwareVariation PublicationType MGEDCoreOntology ChromosomalAberration BioMaterialPackage Biometrics HardwareType OrganismStatus BiologicalFactorCategory QuantitationType TestType BiologicalProperty BioAssayDataCluster OtherUnit MeasurementType MeasurementPackage EpidemiologicalDesign MGEDOntology BioMaterial VolumeUnit Protocol ArrayDesignPackage Measurement Fiducial QualityControlDescriptionType CellLine CellType RadiationUnit ProtocolVariation DesignElementGroupType DerivedBioAssayType PopulationDensity ControlType PhenotypeDatabase OrganismDatabase ObservationDatabase BioSourceType ZoneDefect GeographicLocation Atmosphere TemperatureUnit ArrayGroup ArrayPackage Compound BioAssayPackage BioSourceProvider IndividualGeneticCharacteristics DiseaseStaging SurfaceType ChromosomalAberrationClassification MaterialType ReplicateDescription Phenotype NormalizationDescriptionType IndividualChromosomalAbnormality Reporter CellLineDatabase TumorGrading LabelCompound ClinicalTreatmentDatabase FamilyRelationship MGEDOntologyVersion TimeUnitOther SomaticModification TheoreticalBioSequenceType FactorValueSet Ecotype VolumeUnitOther TestTypeDatabase DefectType DataTransformationProtocolType BioSequence FactorValueDependency SoftwareType InitialTimePoint DistanceUnitOther DeprecationReason Hardware ExperimentDesignType BioSequenceType MassUnitOther FamilyMember BioAssayData SequenceOntologyDatabase GrowthCondition BioMolecularAnnotation QualityControlDescription DeliveryMethod Age Sex URI MassUnit BioSample BioSource DevelopmentalStageDatabase LabeledExtract WarningType AuditAndSecurityPackage DerivedBioAssay Cultivar PathogenTest BioSampleType StrandType Experiment NormalizationDescription GeographicLocationDatabase Individual Humidity Nutrients Transformation PolymerType FeatureDefect DistanceUnit StrainOrLine FailType TechnologyType DesignElement Treatment SequenceOntologyBioSequenceType ExperimentDesign Generation Host Node Test Unit User FactorValue EnvironmentalStress DesignElementGroup EnvironmentalFactorCategory BioAssay ComplexAction GeneticMaterial ExperimentalProtocolType Observation FiducialType BibliographicReference PhysicalBioAssay NodeValueType StrainOrLineDatabase HistoryFactor has_accession has_description has_test_protocol has_clinical_finding has_citation has_factor_value has_laboratory_test has_cancer_site has_additive has_atmospheric_component was_tested_for has_family_member has_toll_free_phone has_protocol has_disease_staging has_publication has_biosource_type has_machine_readable_URI has_manufacturer has_accession_version has_test_type has_compound has_database_entry_type has_bioassay_data has_feature_shape is_solvent has_species has_first_name has_maximum_measurement has_diameter has_individual has_host_part has_experiment_design_type has_test_result has_providers has_category has_hardware has_property_set has_bioassays has_chromosomal_aberration_classification has_donor has_email has_issue has_model has_treatment has_nodes has_order has_owner has_pages has_phone has_scale has_title has_units has_value has_address has_disease_state has_ID has_mid_initials has_initial_time_point has_parent_organization has_clinical_record has_authors has_performer has_MAGE_description deprecated_from_version has_measurement_type has_factor_value_ontology_entry has_fiducials has_reason_for_deprecation has_experiment_factors has_human_readable_URI has_prior_disease_state has_biomaterial_characteristics has_nutrient_component has_organism_part has_part_modified has_software has_clinical_treatment has_node_value has_been_treated has_disease_location has_image_format has_host has_make has_mass has_name has_text has_type has_year was_replaced_by has_database has_action has_editor has_publisher has_version has_height has_experiment_design has_family_relationship has_length is_user_defined has_affiliation has_result has_URI has_fax has_volume has_node_value_type has_last_name has_individual_genetic_characteristics has_measurement = 0.]]> 0.]]> 0.]]>