"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.]]>
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