has_biosource_type
type: ObjectProperty
type: FunctionalProperty
comment: property indicating that the class has a biosource type
domain: BioSourceProvider

has_host
type: ObjectProperty
comment: property indicating that the class has a host
domain: Host

has_host_part
type: ObjectProperty
comment: property indicating that the class has a host part
domain: Host

has_image_format
type: ObjectProperty
comment: property indicating that the class has an image format
domain: PhysicalBioAssay

has_initial_time_point
type: ObjectProperty
type: FunctionalProperty
comment: property indicating that the class has an individual time point
domain: Age

has_issue
type: ObjectProperty
comment: property indicating that the class has an issue
domain: BibliographicReference

has_make
type: ObjectProperty
comment: property indicating that the class has a make
domain: Hardware

has_maximum_measurement
type: ObjectProperty
comment: property indicating that the class has a maximum measurement
domain: Age

has_measurement_type
type: ObjectProperty
comment: property indicating that the class has a measurement type
domain: Measurement

has_model
type: ObjectProperty
comment: property indicating that the class has a model
domain: Hardware

has_pages
type: ObjectProperty
comment: property indicating that the class has pages
domain: BibliographicReference

has_volume
type: ObjectProperty
comment: property indicating that the class has a volume
domain: BibliographicReference

Action
type: Class
subclass of: BioMaterialPackage
subclass of: BiologicalFactorCategory
comment: Procedures used during treatment.

Age
type: Class
subclass of: BioMaterialCharacteristics
subclass of: Restriction
  on property: has_initial_time_point
  some values from: InitialTimePoint
subclass of: Restriction
  on property: has_maximum_measurement
  some values from: Measurement
subclass of: Restriction
  on property: has measurement
  some values from: Measurement
comment: The time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise the identifiable point must be specified such as planting.

Allele
type: Class
subclass of: IndividualGeneticCharacteristics
comment: One of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on phenotype or sequence. Polymorphisms are included in this definition.

ArrayDesignPackage
type: Class
subclass of: MGEDCoreOntology
comment: MAGE package that describes the array layout and design. The array may be physical or virtual.

ArrayGroup
type: Class
subclass of: ArrayPackage
subclass of: Restriction
  on property: has type
  some values from: SubstrateType
subclass of: Restriction
  on property: has fiducials
  some values from: Fiducial
comment: An array group is a physical platform that contains one or more arrays that are separately addressable or a virtual grouping of arrays.

ArrayPackage
type: Class
subclass of: MGEDCoreOntology
comment: MAGE package for describing the process by which arrays were manufactured.

Atmosphere
type: Class
subclass of: GrowthCondition
subclass of: Restriction
  on property: has atmospheric component
  some values from: Compound
comment: The atmospheric conditions used to culture or grow an organism.

AtomicAction
type: Class
subclass of: Action
comment: An atomic action is a single step process on the biomaterial, e.g mix by inversion, wait, add

AuditAndSecurityPackage
type: Class
subclass of: MGEDCoreOntology
comment: MAGE package for contacts including organizations and people.

BarrierFacility
type: Class
subclass of: GrowthCondition
comment: Rating of containment system for the protection of organisms from infectious agents.

Bedding
type: Class
subclass of: EnvironmentalHistory
comment: Refers to the bedding material present in an animals housing.

BibliographicReference
type: Class
subclass of: DescriptionPackage
subclass of: Restriction
  on property: has_issue
  some values from: Thing
subclass of: Restriction
  on property: has publisher
  some values from: Thing
subclass of: Restriction
  on property: has type
  some values from: PublicationType
subclass of: Restriction
  on property: has title
  some values from: string
subclass of: Restriction
  on property: has URI
  some values from: URI
subclass of: Restriction
  on property: has year
  some values from: Thing
subclass of: Restriction
  on property: has_volume
  some values from: Thing
subclass of: Restriction
  on property: has authors
  some values from: Thing
subclass of: Restriction
  on property: has editor
  some values from: Thing
subclass of: Restriction
  on property: has publication
  some values from: Thing
subclass of: Restriction
  on property: has_pages
  some values from: Thing
comment: A bibliographic reference is a published citation in a journal, book, other format e.g. web resource

BioAssay
type: Class
subclass of: BioAssayPackage
comment: A bioassay is an abstract class representing physical and computational groupings of biomaterials and arrays.

BioAssayData
type: Class
subclass of: BioAssayDataPackage
comment: BioAssayData refers to the data files including images generated from one or more BioAssays.

BioAssayDataCluster
type: Class
subclass of: HigherLevelAnalysisPackage
subclass of: Restriction
  on property: has nodes
  some values from: Node
comment: A grouping of bioassay data that has been organized by one or more mathematical functions into nodes.

BioAssayDataPackage
type: Class
subclass of: MGEDExtendedOntology
comment: MAGE package for BioAssayData.

BioAssayPackage
type: Class
subclass of: MGEDCoreOntology
comment: MAGE package for bioassay.

BioMaterial
type: Class
subclass of: BioMaterialPackage
subclass of: Restriction
  on property: has type
  some values from: MaterialType
subclass of: Restriction
  on property: has biomaterial characteristics
  some values from: BioMaterialCharacteristics
comment: Description of the processing state of the biomaterial for use in the microarray hybridization.

BioMaterialCharacteristicCategory
type: Class
subclass of: BiologicalFactorCategory
comment: General descriptor of a BioMaterialCharacteristic category. Such as strain or line where the name of the strain or line is encoded in the FactorValue.

BioMaterialCharacteristics
type: Class
subclass of: BioMaterialPackage
subclass of: BiologicalFactorCategory
subclass of: Restriction
  on property: is user defined
  some values from: Contact
subclass of: Restriction
  on property: is user defined
  some values from: BibliographicReference
comment: Properties of the biomaterial before treated in any manner for the purposes of the experiment.

BioMaterialPackage
type: Class
subclass of: MGEDCoreOntology
comment: Description of the source of the nucleic acid used to generate labeled material for the microarray experiment.

BioMolecularAnnotation
type: Class
subclass of: ExperimentDesignType
comment: BioMolecularAnnotation experiment design types are those which are designed to investigate functions, processes, locations and identity at the molecular level e.g. binding site identification, genotyping.

BioSample
type: Class
subclass of: BioMaterial
subclass of: Restriction
  on property: has type
  some values from: BioSampleType
subclass of: Restriction
  on property: has been treated
  some values from: Treatment
comment: The BioSource after any treatment.

BioSampleType
type: Class
subclass of: BioMaterialPackage
subclass of: Restriction
  on property: has biosample type
  some values from: Class
    one of: extract
    one of: not extract
comment: Used to tell when the BioSample is an extract or not.

BioSequence
type: Class
subclass of: BioSequencePackage
subclass of: Restriction
  on property: has species
  some values from: Organism
subclass of: Restriction
  on property: has type
  some values from: PolymerType
subclass of: Restriction
  on property: has type
  some values from: BioSequenceType
comment: A representation of a DNA, RNA, or protein sequence.

BioSequencePackage
type: Class
subclass of: MGEDCoreOntology
comment: MAGE package for biological sequences (biosequence).

BioSequenceType
type: Class
subclass of: BioSequencePackage
comment: Controlled terms for descriptors indicating the type of biosequence. Types may be physical (e.g BAC, cDNA clone), or computational (e.g unigene cluster, consensus)

BioSource
type: Class
subclass of: BioMaterial
comment: The BioSource is the original source material before any treatment events.

BioSourceProvider
type: Class
subclass of: BioMaterialCharacteristics
subclass of: Restriction
  on property: has owner
  some values from: Person
subclass of: Restriction
  on property: has donor
  some values from: Organization
comment: The resource (e.g, company, hospital, geographical location) used to obtain or purchase the biomaterial.

BioSourceType
type: Class
subclass of: BioMaterialCharacteristics
comment: The form in which the Biosource is provided, may also be used to describe biosamples e.g. agar stab.

BiologicalFactorCategory
type: Class
subclass of: ExperimentalFactorCategory
comment: Factors that relate to properties of the biomaterial, its treatment, or its growth.

BiologicalProperty
type: Class
subclass of: ExperimentDesignType
comment: A biological property experiment design type is where an intrinsic characteristic of an organism(s) or biological system is examined.

Biometrics
type: Class
subclass of: BioMaterialCharacteristics
subclass of: Restriction
  on property: has organism part
  some values from: OrganismPart
subclass of: Restriction
  on property: has individual
  some values from: Individual
subclass of: Restriction
  on property: has height
  some values from: Measurement
subclass of: Restriction
  on property: has mass
  some values from: Measurement
comment: Physical properties of the BioMaterial e. g. mass or height

CellLine
type: Class
subclass of: BioMaterialCharacteristics
subclass of: OntologyEntry
subclass of: Restriction
  on property: has database
  some values from: CellLineDatabase
comment: The identifier for the cell line if one was used as a biomaterial.

CellLineDatabase
type: Class
subclass of: Database
comment: Database of cell line information.

CellType
type: Class
subclass of: BioMaterialCharacteristics
subclass of: OntologyEntry
subclass of: Restriction
  on property: has database
  some values from: CellTypeDatabase
comment: CellType, the type of cell used in the experiment if non mixed, if mixed the TargetedCellType should be used, example of instances, epithelial, glial etc.

CellTypeDatabase
type: Class
subclass of: Database
comment: Database of cell type information.

ChromosomalAberration
type: Class
subclass of: IndividualGeneticCharacteristics
subclass of: OntologyEntry
subclass of: Restriction
  on property: has database
  some values from: ChromosomalAberrationDatabase
comment: An abnormality of a chromosome's number or structure, which excludes simple changes in sequence and is usually detectable by cytogentic and microscopic techniques such as FISH.

ChromosomalAberrationClassification
type: Class
subclass of: BioMaterialCharacteristics
comment: An irregularity in the number or structure of chromosomes, usually in the form of a gain (duplication), loss (deletion), exchange (translocation), or alteration in sequence (inversion) of genetic material. Excludes simple changes in sequence such as mutations, and is usually detectable by cytogenetic and microscopic techniques such as FISH.

ChromosomalAberrationDatabase
type: Class
subclass of: Database
comment: Database of chromosomal aberrations.

ClinicalFinding
type: Class
subclass of: OntologyEntry
subclass of: Restriction
  on property: has database
  some values from: LaboratoryTestDatabase
subclass of: Restriction
  on property: has clinical finding
  some values from: Measurement
comment: Clinical findings that are distinct from the disease state and can be referred to from an established controlled vocabulary or ontology. An example might be a test performed and/or finding.

ClinicalHistory
type: Class
subclass of: EnvironmentalHistory
subclass of: Restriction
  on property: has prior disease state
  some values from: DiseaseState
subclass of: Restriction
  on property: has clinical record
  some values from: OntologyEntry
subclass of: Restriction
  on property: has clinical treatment
  some values from: ClinicalTreatment
subclass of: Restriction
  on property: has clinical test type
  some values from: ClinicalTestType
subclass of: Restriction
  on property: has clinical finding
  some values from: ClinicalFinding
comment: The BioMaterial's (i.e., the patient's) medical record as background information relevant to the experiment.

ClinicalTest
type: Class
subclass of: BioMaterialCharacteristics
subclass of: Restriction
  on property: has measurement
  some values from: Measurement
subclass of: Restriction
  on property: has clinical test type
  some values from: ClinicalTestType

ClinicalTestType
type: Class
subclass of: BioMaterialCharacteristics
subclass of: Restriction
  on property: has database
  some values from: LaboratoryTestDatabase

ClinicalTreatment
type: Class
subclass of: BioMaterialCharacteristics
subclass of: OntologyEntry
comment: The current clinical treatment(s) of the patient from which the biosource is derived.

ComplexAction
type: Class
subclass of: Action
comment: Complex actions are composed of multiple steps (as opposed to AtomicAction) e.g. mRNA labeling, protein purification.

Compound
type: Class
subclass of: BiologicalFactorCategory
subclass of: OntologyEntry
subclass of: Restriction
  on property: has database
  some values from: CompoundDatabase
subclass of: Restriction
  on property: is solvent
  some values from: Class
    one of: yes
    one of: no
comment: A drug, solvent, chemical, etc., with a property that can be measured such as concentration.

CompoundDatabase
type: Class
subclass of: Database
comment: Database of compound information.

ConcentrationUnit
type: Class
subclass of: Unit
comment: Units used for concentration measurements.

ConcentrationUnitOther
type: Class
subclass of: ConcentrationUnit
comment: Concentration units not specified in MAGE.

Contact
type: Class
subclass of: AuditAndSecurityPackage
subclass of: Restriction
  on property: has fax
  some values from: Thing
subclass of: Restriction
  on property: has phone
  some values from: Thing
subclass of: Restriction
  on property: has email
  some values from: Thing
subclass of: Restriction
  on property: has URI
  some values from: URI
subclass of: Restriction
  on property: has type
  some values from: Roles
subclass of: Restriction
  on property: has toll free phone
  some values from: Thing
subclass of: Restriction
  on property: has address
  some values from: Thing
comment: Organizations or individuals that may be contacted.

ControlType
type: Class
subclass of: DesignElementPackage
comment: Controlled terms for descriptors for the type of control design element.

Cultivar
type: Class
subclass of: StrainOrLine
subclass of: Restriction
  on property: has database
  some values from: StrainOrLineDatabase
comment: a plant variety obtained in in agriculture in horticulture

DataType
type: Class
subclass of: MGEDOntology
comment: Primitive data types found in computing languages such as float, boolean, etc.

Database
type: Class
subclass of: DescriptionPackage
subclass of: Restriction
  on property: has URI
  some values from: URI
subclass of: Restriction
  on property: has version
  some values from: Thing
comment: Identifiable resource containing data or external ontologies or controlled vocabularies which has uniquely identifiable records.

DatabaseEntryType
type: Class
subclass of: DescriptionPackage
comment: Controlled set of descriptors for the type of database record such as a protein record (in SWISS-PROT) or a gene object (in SGD).

DefectType
type: Class
subclass of: ArrayPackage
comment: Defects associated with features or zones such as those that are missing or moved.

DeliveryMethod
type: Class
subclass of: MGEDExtendedOntology
comment: Method used to deliver a compound for treatment.

DeprecatedTerms
type: Class
subclass of: MGEDOntology
comment: Class to hold deprecated instances and classes.

DerivedBioAssay
type: Class
subclass of: BioAssay
subclass of: Restriction
  on property: has type
  some values from: DerivedBioAssayType
comment: A BioAssay that is created by the transformation of measured or derived BioAssays.

DerivedBioAssayType
type: Class
subclass of: BioAssayPackage
comment: Controlled set of descriptors for the type of derivation of the BioAssay such as averaging features, taking ratios of signal QuantitationTypes, and normalizing BioAssay data.

DescriptionPackage
type: Class
subclass of: MGEDCoreOntology
comment: MAGE package for description of annotations and references to annotations.

DesignElement
type: Class
subclass of: DesignElementPackage
subclass of: Restriction
  on property: has type
  some values from: ControlType
comment: Design elements are reporters, features, and composite elements as defined by MAGE.

DesignElementGroup
type: Class
subclass of: ArrayDesignPackage
subclass of: Restriction
  on property: has type
  some values from: DesignElementGroupType
subclass of: Restriction
  on property: has species
  some values from: Organism
comment: A DesignElementGroup holds information on Features, Reporters, or CompositeSequences.

DesignElementGroupType
type: Class
subclass of: ArrayDesignPackage
comment: Controlled set of descriptors for indicating the specific type of a Feature, Reporter, or CompositeSequence.

DesignElementPackage
type: Class
subclass of: MGEDCoreOntology
comment: The MAGE package for describing the elements located on the array.

DevelopmentalStage
type: Class
subclass of: BioMaterialCharacteristics
subclass of: OntologyEntry
subclass of: Restriction
  on property: has database
  some values from: DevelopmentalStage
comment: The developmental stage of the organism's life cycle during which the biomaterial was extracted.

DevelopmentalStageDatabase
type: Class
subclass of: Database
comment: Database of developmental stage information.

DiseaseLocation
type: Class
subclass of: OrganismPart
subclass of: Restriction
  on property: has cancer site
  some values from: Class
    one of: metastatic site
    one of: primary site
comment: Anatomical location(s) of disease.

DiseaseStaging
type: Class
subclass of: BioMaterialCharacteristics
subclass of: OntologyEntry
comment: The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression.

DiseaseState
type: Class
subclass of: BioMaterialCharacteristics
subclass of: OntologyEntry
subclass of: Restriction
  on property: has disease staging
  some values from: DiseaseStaging
subclass of: Restriction
  on property: has database
  some values from: DiseaseStateDatabase
comment: The name of the pathology diagnosed in the organism from which the biomaterial was derived. The disease state is normal if no disease has been diagnosed.

DiseaseStateDatabase
type: Class
subclass of: Database
comment: Database of disease state information.

DistanceUnit
type: Class
subclass of: Unit
comment: Units used for distance measurements.

DistanceUnitOther
type: Class
subclass of: DistanceUnit
comment: Distance units not specified in MAGE.

Ecotype
type: Class
subclass of: StrainOrLine
subclass of: Restriction
  on property: has database
  some values from: StrainOrLineDatabase
comment: a biotype resulting from selection in a particular habitat, e.g. the A.thaliana Ecotype Ler

EnvironmentalFactorCategory
type: Class
subclass of: ExperimentalFactorCategory
comment: Factors that relate to properties of the environmental history of the biomaterial, its treatment, or its growth.

EnvironmentalHistory
type: Class
subclass of: BioMaterialCharacteristics
comment: A description of the conditions the organism has been exposed to that are not one of the variables under study.

EnvironmentalStress
type: Class
subclass of: MGEDExtendedOntology
subclass of: Restriction
  on property: has measurement
  some values from: Measurement
comment: Environmental stress is a treatment where some aspect of the environment is perturbed in order to stress the organism or culture, e.g. temperature shock, osmotic shock

EpidemiologicalDesign
type: Class
subclass of: ExperimentDesignType
comment: An epidemiological experiment design type is where the biosource history is studied e.g. environmental, clinical and family history.

Experiment
type: Class
subclass of: ExperimentPackage
subclass of: Restriction
  on property: has citation
  some values from: BibliographicReference
subclass of: Restriction
  on property: has bioassay data
  some values from: BioAssayData
subclass of: Restriction
  on property: has providers
  some values from: Contact
subclass of: Restriction
  on property: has bioassays
  some values from: BioAssay
subclass of: Restriction
  on property: has experiment design
  some values from: ExperimentDesign
comment: The complete set of bioassays (hybridizations) and their descriptions performed as an experiment for a common purpose. Here we take experiment to mean an observational or perturbing study. An experiment will be often equivalent to a publication.

ExperimentDesign
type: Class
subclass of: ExperimentPackage
subclass of: Restriction
  on property: has description
  some values from: string
subclass of: Restriction
  on property: has experiment design type
  some values from: ExperimentDesignType
subclass of: Restriction
  on property: has MAGE description
  some values from: NormalizationDescription
subclass of: Restriction
  on property: has experiment factors
  some values from: ExperimentalFactor
subclass of: Restriction
  on property: has bioassays
  some values from: BioAssay
subclass of: Restriction
  on property: has MAGE description
  some values from: ReplicateDescription
subclass of: Restriction
  on property: has MAGE description
  some values from: QualityControlDescription
comment: ExperimentDesign refers to both observational and experimental (perturbational) studies. The organizing principles of the study including the relationships between assays and the steps taken to interpret the data.

ExperimentDesignType
type: Class
subclass of: ExperimentPackage
comment: The ExperimentDesignType is the high level description for studies such as "time series", "dose response", etc.

ExperimentPackage
type: Class
subclass of: MGEDCoreOntology
comment: The descriptions associated with the Experiment package of MAGE

ExperimentalFactor
type: Class
subclass of: ExperimentPackage
subclass of: Restriction
  on property: has category
  some values from: BiologicalFactorCategory
subclass of: Restriction
  on property: has factor value
  some values from: FactorValue
subclass of: Restriction
  on property: has category
  some values from: MethodologicalFactorCategory
comment: The factors in the study that are experimental parameters or regarded as influencing the experimental results.

ExperimentalFactorCategory
type: Class
subclass of: ExperimentPackage
comment: A factor category describes factors which are under test in the experiment and allowable factor categories can be BioMaterialCharacteristics, Compound (names, concentrations) and Action etc. E.g. in an experiment where leukemia types are compared the factor categories are ALL and AML.

FactorValue
type: Class
subclass of: ExperimentPackage
subclass of: Restriction
  on property: has factor value ontology entry
  some values from: ExperimentalFactorCategory
subclass of: Restriction
  on property: has property set
  some values from: FactorValueDependency
subclass of: Restriction
  on property: has property set
  some values from: FactorValueSet
subclass of: Restriction
  on property: has measurement
  some values from: Measurement
comment: The value of an ExperimentFactor.

FactorValueDependency
type: Class
subclass of: ExperimentPackage
subclass of: Restriction
  on property: has value
  some values from: Thing
comment: A group of FactorValues which refer to the same condition used to treat or describe a BioMaterial, e.g. 10% glucose, 1 hour OR larval stage, age 24 hours.

FactorValueSet
type: Class
subclass of: ExperimentPackage
subclass of: Restriction
  on property: has value
  some values from: Thing
comment: A super grouping of FactorValueDependencies or FactorValues which describes combinations of conditions used to treat or describe a BioMaterial applied to a BioAssay, typically separating things on the basis of channels or the concepts of measured and reference samples e.g. 10% glucose, 1 hour AND 10mm NaCl, 2 hours in channel 1.

FailType
type: Class
subclass of: DesignElementPackage
comment: Controlled terms for descriptors of failures (as in PCR) associated with reporters.

FamilyHistory
type: Class
subclass of: EnvironmentalHistory
subclass of: Restriction
  on property: has family member
  some values from: FamilyMember
comment: Relevant aspects of genetic preconditions or family member's clinical history.

FamilyMember
type: Class
subclass of: BioMaterialPackage
subclass of: Restriction
  on property: has family relationship
  some values from: FamilyRelationship
subclass of: Restriction
  on property: has individual genetic characteristics
  some values from: IndividualGeneticCharacteristics
subclass of: Restriction
  on property: has disease state
  some values from: DiseaseState
subclass of: Restriction
  on property: has clinical record
  some values from: OntologyEntry
comment: Member of the biosource's family.

FamilyRelationship
type: Class
subclass of: BioMaterialPackage
comment: A type of relationship applicable to mammals to describe the genetic relatedness of the individual under study. E.g. brother or mother.

FeatureDefect
type: Class
subclass of: ArrayPackage
subclass of: Restriction
  on property: has type
  some values from: DefectType
comment: A technical manufacturer described defect for features.

FeatureGroup
type: Class
subclass of: ArrayDesignPackage
subclass of: Restriction
  on property: has feature shape
  some values from: FeatureShape
subclass of: Restriction
  on property: has type
  some values from: TechnologyType
comment: Technology-based grouping of features representing individual locations on the array.

FeatureShape
type: Class
subclass of: ArrayDesignPackage
comment: The expected shape of the feature on the array.

Fiducial
type: Class
subclass of: ArrayPackage
subclass of: Restriction
  on property: has type
  some values from: FiducialType
comment: A marking on the surface of the array that can be used to identify the origin of the array.

FiducialType
type: Class
subclass of: ArrayPackage
comment: A descriptor that indicates the type of the fiducial such as chrome border of an Affymetrix array or a laser ablation mark.

Generations
type: Class
subclass of: EnvironmentalHistory
comment: The number of cell passages if the organism or organism part that is cultured is unicellular or a cell culture otherwise the number of generations.

GeneticMaterial
type: Class
subclass of: MGEDExtendedOntology
comment: Genetic material may be DNA or RNA and identifiable as an entry in a public external database such as EMBL/DDBJ/GenBank or one of the model organism databases.

GeneticModification
type: Class
subclass of: BioMaterialCharacteristics
comment: The genetic modification introduced into the organism from which the biomaterial was derived. Examples of genetic variation include specification of a transgene or the gene knocked-out.

Genotype
type: Class
subclass of: IndividualGeneticCharacteristics
comment: The total sum of the genetic information of an organism that is known and relevant to the experiment being performed.

GeographicLocation
type: Class
subclass of: EnvironmentalHistory
subclass of: OntologyEntry
subclass of: Restriction
  on property: has database
  some values from: GeographicLocationDatabase
comment: A descriptor of the location from which a BioMaterial was obtained, e.g. country, region, grid reference.

GeographicLocationDatabase
type: Class
subclass of: Database
comment: Database of geographic locations.

GrowthCondition
type: Class
subclass of: EnvironmentalHistory
subclass of: Restriction
  on property: has value
  some values from: Thing
subclass of: Restriction
  on property: has_maximum_measurement
  some values from: Measurement
subclass of: Restriction
  on property: has measurement
  some values from: Measurement
comment: A description of the conditions used to grow organisms or parts of the organism. This includes isolated environments such as cultures and open environments such as field studies.

Haplotype
type: Class
subclass of: IndividualGeneticCharacteristics
comment: The genotype of a single chromosome (i.e., the haploid genotype) that is known and relevant to the experiment being performed.

Hardware
type: Class
subclass of: ProtocolPackage
subclass of: Restriction
  on property: has_model
  some values from: Thing
subclass of: Restriction
  on property: has manufacturer
  some values from: Contact
subclass of: Restriction
  on property: has software
  some values from: Software
subclass of: Restriction
  on property: has_make
  some values from: Thing
subclass of: Restriction
  on property: has type
  some values from: HardwareType
comment: The machine or instrument used.

HardwareType
type: Class
subclass of: ProtocolPackage
comment: Controlled terms for descriptors of types of hardware.

HardwareVariation
type: Class
subclass of: MethodologicalFactorCategory
comment: The effects of different hardware, types of hardware, or models of hardware on experimental results are studied.

HigherLevelAnalysisPackage
type: Class
subclass of: MGEDCoreOntology
comment: MAGE package for HigherLevelAnalysis

Histology
type: Class
subclass of: BioMaterialCharacteristics
subclass of: Restriction
  on property: has organism part
  some values from: OrganismPart
subclass of: Restriction
  on property: has database
  some values from: HistologyDatabase
comment: Microscopic morphology of tissues.

HistologyDatabase
type: Class
subclass of: Database
comment: Database of histology information.

HistoryFactor
type: Class
subclass of: MGEDExtendedOntology
comment: Factors that are measured or observed parts of the study but not induced or under the control of the experiment. These factors do not have protocols (e.g., epidemiology factors).

Host
type: Class
subclass of: EnvironmentalHistory
subclass of: Restriction
  on property: has_host_part
  some values from: OrganismPart
subclass of: Restriction
  on property: has_host
  some values from: Organism
comment: Organisms or organism parts used as a designed part of the culture (e.g., red blood cells, stromal cells).

Humidity
type: Class
subclass of: GrowthCondition
comment: The humidity that the biosource is exposed to.

ImageFormat
type: Class
subclass of: BioAssayPackage
comment: Controlled terms for descriptors of the image file format (TIFF, JPEG, GIF, etc.)

Individual
type: Class
subclass of: BioMaterialCharacteristics
subclass of: Restriction
  on property: has ID
  some values from: Thing
comment: Identifier or name of the individual organism from which the biomaterial was derived.

IndividualChromosomalAbnormality
type: Class
subclass of: IndividualGeneticCharacteristics
comment: An abnormality in the number or structure of chromosomes in the biomaterial from an individual organism, detected by karyotyping or other methods. E.g., a B-cell lymphoma from a patient has an abnormal karyotype 48,XY,t(1;2)(p22;p11),+3,+12.

IndividualGeneticCharacteristics
type: Class
subclass of: BioMaterialCharacteristics
subclass of: Restriction
  on property: has value
  some values from: Thing
comment: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes.

InitialTimePoint
type: Class
subclass of: BioMaterialPackage
comment: The point from which measurements of age were taken.

LabelCompound
type: Class
subclass of: Compound
comment: Compounds that are used for labeling extracts.

LabeledExtract
type: Class
subclass of: BioMaterial
subclass of: Restriction
  on property: has been treated
  some values from: Treatment
subclass of: Restriction
  on property: has compound
  some values from: LabelCompound
comment: The BioSample after labeling for detection of the nucleic acids.

LaboratoryTestDatabase
type: Class
subclass of: Database
comment: Database of codes for clinical findings.

Light
type: Class
subclass of: GrowthCondition
comment: The photoperiod and type (e.g., natural, restricted wavelength) of light exposure.

LightUnit
type: Class
subclass of: OtherUnit
comment: Units for measuring the intensity of light.

MGEDCoreOntology
type: Class
subclass of: MGEDOntology
subclass of: Restriction
  on property: has ID
  some values from: Thing
comment: An ontology developed by the Microarray Gene Expression Data (MGED) Society to provide descriptors required for MAGE v.1 documents.

MGEDExtendedOntology
type: Class
subclass of: MGEDOntology
comment: Location for those classes that are not in the Core ontology as they do are not containable in MAGE. It is not yet structured to work with the Core ontology

MassUnit
type: Class
subclass of: Unit
comment: Units used for mass measurements.

MassUnitOther
type: Class
subclass of: MassUnit
comment: Mass units not specified in MAGE.

MaterialType
type: Class
subclass of: BioMaterialPackage
comment: Controlled terms for the state of the BioMaterial. Each state (BioSource, different BioSamples, and LabeledExtract) have MaterialTypes. Examples are population of an organism, organism, organism part, cell, etc.

Measurement
type: Class
subclass of: MeasurementPackage
subclass of: Restriction
  on property: has units
  some values from: Unit
subclass of: Restriction
  on property: has value
  some values from: Thing
subclass of: Restriction
  on property: has_measurement_type
  some values from: Class
    one of: absolute
    one of: change biomaterial characteristics
    one of: relative
comment: Measured values and units.

MeasurementPackage
type: Class
subclass of: MGEDCoreOntology
comment: MAGE package for measurement.

Media
type: Class
subclass of: GrowthCondition
comment: The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil) .

MethodologicalDesign
type: Class
subclass of: ExperimentDesignType
comment: A methodological experiment design type investigates differences caused by application of protocols, hardware, software and bioassay relationships, e.g quality control, replicates, loop.

MethodologicalFactorCategory
type: Class
subclass of: ExperimentalFactorCategory
comment: The effects on results of changing protocols, hardware, software, or people performing the experiments are studied Examples are comparison of data across different labeling protocols, scanners, image quantification software, or laboratories.

Node
type: Class
subclass of: HigherLevelAnalysisPackage
subclass of: Restriction
  on property: has node value
  some values from: NodeValue
comment: A node is an individual component of BioAssayDataCluster that groups design elements, quantitation types, and BioAssays together. A node may contain other nodes.

NodeValue
type: Class
subclass of: HigherLevelAnalysisPackage
subclass of: Restriction
  on property: has type
  some values from: DataType
subclass of: Restriction
  on property: has scale
  some values from: Scale
subclass of: Restriction
  on property: has node value type
  some values from: NodeValueType
comment: Node values allow the organization of the nodes in relation to other nodes produced by mathematical functions such as a clustering algorithm.

NodeValueType
type: Class
subclass of: HigherLevelAnalysisPackage
comment: Controlled set of terms for describing the type of values (e.g., Euclidean distance).

NormalizationDescription
type: Class
subclass of: ExperimentPackage
subclass of: Restriction
  on property: has type
  some values from: NormalizationDescriptionType
comment: NormalizationDescription provides details of the normalization strategy for the experiment.

NormalizationDescriptionType
type: Class
subclass of: ExperimentPackage
comment: Controlled descriptors for the normalization strategy used for the experiment.

Nutrients
type: Class
subclass of: GrowthCondition
subclass of: Restriction
  on property: has nutrient component
  some values from: Compound
comment: The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.).

OntologyEntry
type: Class
subclass of: DescriptionPackage
subclass of: Restriction
  on property: has database
  some values from: Database
subclass of: Restriction
  on property: has accession
  some values from: Thing
subclass of: Restriction
  on property: has accession version
  some values from: Thing
subclass of: Restriction
  on property: has database entry type
  some values from: DatabaseEntryType
subclass of: Restriction
  on property: has description
  some values from: string
subclass of: Restriction
  on property: has value
  some values from: Thing
comment: External (to the MGED ontology) controlled vocabulary or ontology that can be referred such as ICD-9 or Gene Ontology.

OperatorVariation
type: Class
subclass of: MethodologicalFactorCategory
comment: The effects of different investigators, laboratories, or organizations on experimental results are studied.

Organism
type: Class
subclass of: BioMaterialCharacteristics
subclass of: OntologyEntry
subclass of: Restriction
  on property: has database
  some values from: OrganismDatabase
comment: The genus and species (and subspecies) of the organism from which the biomaterial is derived from.

OrganismDatabase
type: Class
subclass of: Database
comment: Database of taxonomic information.

OrganismPart
type: Class
subclass of: BioMaterialCharacteristics
subclass of: OntologyEntry
subclass of: Restriction
  on property: has database
  some values from: OrganismPartDatabase
comment: The part of the organism's anatomy from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, or body location (arm).

OrganismPartDatabase
type: Class
subclass of: Database
comment: Database of organism part information.

OrganismStatus
type: Class
subclass of: BioMaterialCharacteristics
comment: The stage premortem or postmortem at which the sample was processed for extraction of biomaterials.

Organization
type: Class
subclass of: Contact
subclass of: Restriction
  on property: has parent organization
  some values from: Organization
subclass of: Restriction
  on property: has name
  some values from: Thing
comment: The organization (e.g, company, hospital) to contact to obtain or purchase something.

OtherUnit
type: Class
subclass of: Unit
comment: Other units are those types not specified in MAGE such as lumens, radioactivity, etc.

Parameter
type: Class
subclass of: ProtocolPackage
subclass of: Restriction
  on property: has units
  some values from: Unit
subclass of: Restriction
  on property: has type
  some values from: DataType
comment: A parameter is a variable within a protocol.

PathogenTests
type: Class
subclass of: EnvironmentalHistory
subclass of: Restriction
  on property: has result summary
  some values from: Class
    one of: negative
    one of: inconclusive
    one of: positive
subclass of: Restriction
  on property: was tested for
  some values from: Organism
comment: Tests and results for pathogens infecting organism from which the biosource is derived

Person
type: Class
subclass of: Contact
subclass of: Restriction
  on property: has last name
  some values from: Thing
subclass of: Restriction
  on property: has affiliation
  some values from: Organization
subclass of: Restriction
  on property: has mid initials
  some values from: Thing
subclass of: Restriction
  on property: has first name
  some values from: Thing
comment: The individual to contact regarding something provided such as a biomaterial.

PerturbationalDesign
type: Class
subclass of: ExperimentDesignType
comment: A perturbational design type is where the organism(s) are treated or manipulated or modified, for example a genetic modification, somatic modification

Phenotype
type: Class
subclass of: BioMaterialCharacteristics
subclass of: OntologyEntry
comment: The observable form taken by some character (or group of characters) in an individual or an organism, excluding pathology and diesease. The detectable outward manifestations of a specific genotype.

PhysicalArrayDesign
type: Class
subclass of: ArrayDesignPackage
subclass of: Restriction
  on property: has type
  some values from: SurfaceType
comment: Descriptions pertaining to the array.

PhysicalBioAssay
type: Class
subclass of: BioAssay
subclass of: Restriction
  on property: has_image_format
  some values from: ImageFormat
comment: A physical bioassay is the combination of arrays and biomaterials as in a hybridization.

PhysicalBioSequenceType
type: Class
subclass of: BioSequenceType
comment: A physical biosequence type represents biological sequence that can be physically placed (spotted or synthesized) on an array e.g BAC, PAC.

Ploidy
type: Class
subclass of: IndividualGeneticCharacteristics
comment: The number of single sets of chromosomes in the cell or an organism e.g., haploid, diploid, triploid, etc.

PolymerType
type: Class
subclass of: BioSequencePackage
comment: Controlled terms for descriptors of the type of polymer (RNA, DNA, protein) of the biosequence.

PopulationDensity
type: Class
subclass of: GrowthCondition
comment: The concentration range of the organism.

Preservation
type: Class
subclass of: MGEDExtendedOntology
subclass of: Restriction
  on property: has type
  some values from: PreservationType
subclass of: Restriction
  on property: has protocol
  some values from: Protocol
comment: Method and type of preserving the organism or biosource (i.e. keeping it in stasis).

PreservationType
type: Class
subclass of: MGEDExtendedOntology
comment: The type of method used to preserve (keep in stasis) the organism or biosource.

Protocol
type: Class
subclass of: ProtocolPackage
subclass of: Restriction
  on property: has title
  some values from: string
subclass of: Restriction
  on property: has hardware
  some values from: Hardware
subclass of: Restriction
  on property: has software
  some values from: Software
subclass of: Restriction
  on property: has type
  some values from: ProtocolType
subclass of: Restriction
  on property: has text
  some values from: Thing
subclass of: Restriction
  on property: has URI
  some values from: URI
subclass of: Restriction
  on property: has citation
  some values from: BibliographicReference
subclass of: Restriction
  on property: has description
  some values from: string
comment: Documentation of the set of steps taken in a procedure.

ProtocolPackage
type: Class
subclass of: MGEDCoreOntology
comment: The MAGE package for protocols.

ProtocolParameterType
type: Class
subclass of: MGEDExtendedOntology
comment: Descriptors for protocol parameter types, e.g. compound concentration, media type.

ProtocolType
type: Class
subclass of: MethodologicalFactorCategory
subclass of: ProtocolPackage
comment: A controlled set of terms to provide a descriptor for the type of protocol.

ProtocolVariation
type: Class
subclass of: MGEDExtendedOntology
comment: The effects of different protocols or changes in protocols on experimental results are studied.

PublicationType
type: Class
subclass of: DescriptionPackage
comment: Controlled terms for descriptors of the type of publication such as those used by Medline (review, book, etc.).

QualityControlDescription
type: Class
subclass of: ExperimentPackage
subclass of: Restriction
  on property: has type
  some values from: QualityControlDescriptionType
comment: QualityControlDescription provides details of the quality control aspects of the experiment.

QualityControlDescriptionType
type: Class
subclass of: ExperimentPackage
comment: Controlled descriptors for the quality control strategy for an experiment.

QuantitationType
type: Class
subclass of: QuantitationTypePackage
subclass of: Restriction
  on property: has type
  some values from: DataType
subclass of: Restriction
  on property: has scale
  some values from: Scale
comment: The QuantitationType provides a method for calculating a single datum of the BioAssayData matrix.

QuantitationTypePackage
type: Class
subclass of: MGEDCoreOntology
comment: The MAGE package for defining classes for quantitation.

QuantityUnit
type: Class
subclass of: Unit
comment: Units used for quantity measurements.

QuantityUnitOther
type: Class
subclass of: QuantityUnit
comment: Quantity units not specified in MAGE.

RadiationUnit
type: Class
subclass of: OtherUnit
comment: Units for measuring decay of a radioactive isotope over time.

ReplicateDescription
type: Class
subclass of: ExperimentPackage
subclass of: Restriction
  on property: has type
  some values from: ReplicateDescriptionType
comment: ReplicateDescription provides details about the type of replication used in the experiment.

ReplicateDescriptionType
type: Class
subclass of: ExperimentPackage
comment: Controlled descriptors for the type of replication.

Reporter
type: Class
subclass of: DesignElement
subclass of: Restriction
  on property: has type
  some values from: WarningType
subclass of: Restriction
  on property: has type
  some values from: FailType
comment: Description of the material placed on a feature (spot).

Roles
type: Class
subclass of: AuditAndSecurityPackage
comment: Controlled terms for descriptors of the role of contact, e.g. submitter, biosource_provider.

Scale
type: Class
subclass of: MGEDOntology
comment: The scale (linear, log10, ln, etc) used to represent the value.

SeqFeatureBasis
type: Class
subclass of: BioSequencePackage
comment: Controlled terms for how the sequence features were determined (e.g., experimental, computational, etc.)

SequenceOntologyBioSequenceType
type: Class
subclass of: OntologyEntry
subclass of: PhysicalBioSequenceType
subclass of: TheoreticalBioSequenceType
subclass of: Restriction
  on property: has database
  some values from: SequenceOntologyDatabase

SequenceOntologyDatabase
type: Class
subclass of: Database
comment: Database for sequence annotation information.

Sex
type: Class
subclass of: BioMaterialCharacteristics
comment: Term applied to any organism able to undergo sexual reproduction in order to differentiate the individuals or types involved. Sexual reproduction is defined as the ability to exchange genetic material with the potential of recombinant progeny.

Software
type: Class
subclass of: ProtocolPackage
subclass of: Restriction
  on property: has manufacturer
  some values from: Contact
subclass of: Restriction
  on property: has hardware
  some values from: Hardware
subclass of: Restriction
  on property: has type
  some values from: SoftwareType
subclass of: Restriction
  on property: has software
  some values from: Software
comment: The software application used.

SoftwareType
type: Class
subclass of: ProtocolPackage
comment: Controlled terms that provide descriptors for the type of software.

SoftwareVariation
type: Class
subclass of: MethodologicalFactorCategory
comment: The effects of different software, software packages, or software versions on experimental results are studied.

SomaticModification
type: Class
subclass of: MGEDExtendedOntology
subclass of: Restriction
  on property: has part modified
  some values from: OrganismPart
comment: The organism has had non-genetic parts removed, added, or rearranged.

StrainOrLine
type: Class
subclass of: BioMaterialCharacteristics
subclass of: OntologyEntry
subclass of: Restriction
  on property: has database
  some values from: StrainOrLineDatabase
comment: Animals or plants that have a single ancestral breeding pair or parent as a result of brother x sister or parent x offspring matings.

StrainOrLineDatabase
type: Class
subclass of: Database
comment: Database of strain, line, cultivar or ecotype information.

StrandType
type: Class
subclass of: MGEDExtendedOntology
comment: A descriptor of the strand type the sequence feature belongs to. e.g. forward, reverse

SubstrateType
type: Class
subclass of: ArrayPackage
comment: Controlled terms for descriptors of types of array substrates.

SurfaceType
type: Class
subclass of: ArrayDesignPackage
comment: Controlled terms for descriptors for coating of the substrate.

TargetedCellType
type: Class
subclass of: BioMaterialCharacteristics
subclass of: OntologyEntry
comment: The target cell type is the cell of primary interest. The biomaterial may be derived from a mixed population of cells although only one cell type is of interest.

TargetedCellTypeDatabase
type: Class
subclass of: Database
comment: Database of targeted cell type information.

TechnologyType
type: Class
subclass of: ArrayDesignPackage
comment: The technology type or platform of the reporters on the array.

Temperature
type: Class
subclass of: GrowthCondition
comment: The temperature that a biosource is exposed to.

TemperatureUnit
type: Class
subclass of: Unit
comment: Units used for temperature measurements.

TheoreticalBioSequenceType
type: Class
subclass of: BioSequenceType
comment: A theoretical biosequence type is an abstraction used for annotation design of elements, e.g. gene, intron.

TimeUnit
type: Class
subclass of: Unit
comment: Units used for time measurements.

TimeUnitOther
type: Class
subclass of: TimeUnit
comment: Time units not specified in MAGE.

Transformation
type: Class
subclass of: BioAssayDataPackage
subclass of: Restriction
  on property: has protocol
  some values from: Protocol
comment: The process by which BioAssays (data, elements, quantitation types) are averaged normalized, selected, filtered, or otherwise changed into a new set of BioAssay data.

Treatment
type: Class
subclass of: BioMaterialPackage
subclass of: Restriction
  on property: has order
  some values from: integer
subclass of: Restriction
  on property: has protocol
  some values from: Protocol
subclass of: Restriction
  on property: has action
  some values from: Action
comment: A treatment is the process or action by which a biomaterial is created from an input biomaterial.

TumorGrading
type: Class
subclass of: BioMaterialCharacteristics
subclass of: OntologyEntry
comment: A descriptor used in cancer biology to describe abnormalities of tumor cells. E.g. an instance from NCI Thesaurus.

URI
type: Class
subclass of: MGEDOntology
comment: Uniform Resource Identifier

Unit
type: Class
subclass of: MeasurementPackage
comment: Units of measure.

User
type: Class
subclass of: MGEDExtendedOntology
subclass of: Restriction
  on property: has ID
  some values from: Thing
comment: User is a way to id a person in a database

VolumeUnit
type: Class
subclass of: Unit
comment: Units used for volume measurements.

VolumeUnitOther
type: Class
subclass of: VolumeUnit
comment: Volume units not specified in MAGE.

WarningType
type: Class
subclass of: DesignElementPackage
comment: Controlled terms for descriptors of the warnings associated with reporters.

Water
type: Class
subclass of: GrowthCondition
subclass of: Restriction
  on property: has additive
  some values from: Compound
subclass of: Restriction
  on property: has treatment
  some values from: Protocol
comment: Water consumed by or enveloping the organism that the biosource is derived from.

ZoneDefect
type: Class
subclass of: ArrayPackage
subclass of: Restriction
  on property: has type
  some values from: DefectType
comment: A technical manufactured described defect for zones.

http://mged.sourceforge.net/ontologies/MGEDOntology.owl#A
type: NamedIndividual
type: DistanceUnit
comment: Angstrom, unit of distance, 1 angstrom = 10 nanometers

Adult Mouse Anatomy
type: NamedIndividual
type: OrganismPartDatabase
comment: This ontology describes the anatomy of the adult mouse. It contains anatomical structures for the postnatal mouse (Theiler stage 28).
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#http___www.geneontology.org_gobo_anatomy.ontology_adult_mouse_anatomy

CABRI linenamesahc
type: NamedIndividual
type: CellLineDatabase
comment: Database entry from CABRI, a database listing sources such as cell lines, bacteria, plasmids etc.
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#http___www.cabri.org_CABRI_home_guidelines_catalogue_CPCel_linenamesahc.html

CBIL CV
type: NamedIndividual
type: CellTypeDatabase
type: OrganismPartDatabase
type: TargetedCellTypeDatabase
comment: a controlled vocabulary provided by CBIL
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#http___www.cbil.upenn.edu_anatomy.php3

CellML
type: NamedIndividual
type: OrganismPartDatabase
comment: Ontology describing anatomical and physiological relationships.
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#http___portal.bioengineering.elyt.ods.org_ontology_

ChemID
type: NamedIndividual
type: CompoundDatabase
comment: Database entry from the ChemIDplus database which stores information on the structure, identifiers etc for compounds.
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#http___chem.sis.nlm.nih.gov_chemidplus

Cy3
type: NamedIndividual
type: LabelCompound
comment: flurophore used for labeling/detection purposes

Cy5
type: NamedIndividual
type: LabelCompound
comment: flurophore used for labeling/detection purposes

DNA
type: NamedIndividual
type: MaterialType
type: PolymerType
comment: Deoxyribonucleic acid.

DNA sequencer
type: NamedIndividual
type: HardwareType
comment: An instrument that produces DNA sequences.

EMAP
type: NamedIndividual
type: DevelopmentalStageDatabase
comment: The Edinburgh Mouse Atlas Project (EMAP) ontology of mouse developmental anatomy covers the 26 developmental stages (Theiler Stages) from fertilization to birth.
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#http___genex.hgu.mrc.ac.uk

FMA
type: NamedIndividual
type: OrganismPartDatabase
comment: The Foundational Model of Anatomy (FMA) is concerned with the representation of concepts and relationships necessary for the symbolic modeling of the structure of the human body.
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#http___sig.biostr.washington.edu_projects_fm_

FlyBase
type: NamedIndividual
type: OrganismPartDatabase
comment: curated database containing information on Drosophila genes, alleles etc
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#http___cvs.sourceforge.net_cgi-bin_viewcvs.cgi_obo_obo_ontology_anatomy_gross_anatomy_animal_gross_anatomy_fly_

GALEN
type: NamedIndividual
type: DiseaseStateDatabase
comment: database entry from GALEN common reference model, a resource for medical coding and terminology
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#http___www.opengalen.org_open_crm_crm-anatomy.html

GRAMENE
type: NamedIndividual
type: StrainOrLineDatabase
comment: A Comparative Mapping Resource for Grains.
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#http___www.gramene.org_

HUMAT
type: NamedIndividual
type: DevelopmentalStageDatabase
comment: Ontology of human developmental anatomy for Carnegie stages 1-20.
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#http___obo.sourceforge.net_list.shtml

ICD-9-CM
type: NamedIndividual
type: DiseaseStateDatabase
comment: Database entry from ICD 9 2001, international classification of diseases 9, clinical modification 2001.
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ftp___ftp.cdc.gov_pub_Health_Statistics_NCHS_Publications_ICD9-CM_2002_

IUPAC Clinical Chemistry Guidelines
type: NamedIndividual
type: LaboratoryTestDatabase
comment: A resource of vocabularies for describing clinical tests, e.g. blood chemistry.
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#http___www.iupac.org_publications_pac_2000_7205_7205olesen.html

JAX mouse strains
type: NamedIndividual
type: StrainOrLineDatabase
comment: Database entry from the resource at The Jackson Laboratory which has details of approved mouse strain nomenclature.
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#http___www.informatics.jax.org_external_festing_mouse_STRAINS.shtml

JPEG
type: NamedIndividual
type: ImageFormat
comment: Joint Photographic Experts Group format, a common image data format containing grayscale or RGB data compressed with little to high data loss.

http://mged.sourceforge.net/ontologies/MGEDOntology.owl#K
type: NamedIndividual
type: TemperatureUnit
comment: Kelvin, unit of temperature

http://mged.sourceforge.net/ontologies/MGEDOntology.owl#L
type: NamedIndividual
type: VolumeUnit
comment: liter, unit of volume

LOINC
type: NamedIndividual
type: LaboratoryTestDatabase
comment: Database resource for universal identifiers for laboratory and other clinical observations
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#http___www.loinc.org_download

MAD stage
type: NamedIndividual
type: DevelopmentalStageDatabase
type: OrganismPartDatabase
type: TargetedCellTypeDatabase
comment: database entry from mouse anatomical dictionary for developmental stage term
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#http___www.informatics.jax.org_mgihome_GXD_AD_

MESH
type: NamedIndividual
type: DiseaseStateDatabase
comment: database entry from MESH, medical subject headings vocabulary resource
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#http___www.nlm.nih.gov_mesh_filelist.html

MTB Database
type: NamedIndividual
type: DiseaseStateDatabase
comment: Database entry from the mouse tumor biology database, a resource for nomenclature of mouse tumors.
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#http___tumor.informatics.jax.org

NCBI taxonomy
type: NamedIndividual
type: OrganismDatabase
type: StrainOrLineDatabase
comment: identifier for a taxon provided by the NCBI taxonomy database
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#http___www.ncbi.nlm.nih.gov_Taxonomy_taxonomyhome.html_

ORF
type: NamedIndividual
type: TheoreticalBioSequenceType
comment: sequence which represents an open reading frame, a series of codon triplets deduced from a DNA sequence, that contain a start and a stop codon.

PCR
type: NamedIndividual
type: DesignElement
comment: Polymerase chain reaction. An element generated using this procedure.

PCR amplicon
type: NamedIndividual
type: PhysicalBioSequenceType
comment: BioSequence generated by means of polymerase chain reaction

PCR amplification
type: NamedIndividual
type: ComplexAction
type: ProtocolType
comment: Amplification of nucleic acid sequence by use of the polymerase chain reaction whereby the number of templates grows geometrically with each cycle.

PCR fail
type: NamedIndividual
type: FailType
comment: PCR where no products of any kind appear in gel-separated reaction products.

PCR primer
type: NamedIndividual
type: PhysicalBioSequenceType
comment: single oligo used for polymerase chain reaction direction unspecified

PCR primer reverse
type: NamedIndividual
type: PhysicalBioSequenceType
comment: single stranded oligo used for polymerase chain reaction

PCR questionable
type: NamedIndividual
type: FailType
comment: PCR with multiple bands, or smear, in gel-separated reaction products

PNG
type: NamedIndividual
type: ImageFormat
comment: Portable Network Graphic, a lossless image data format.

RNA
type: NamedIndividual
type: PolymerType
comment: Ribonucleic acid.

RNA stability design
type: NamedIndividual
type: BioMolecularAnnotation
comment: A RNA stability experiment design type examines the stability and/or decay of RNA transcripts.

Spearmans rank correlation
type: NamedIndividual
type: NodeValueType
comment: Computed as the ordinary Pearson correlation coefficient between two groups of rankings.

TAIR
type: NamedIndividual
type: StrainOrLineDatabase
comment: The Arabadopsis Information Resource.
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#http___www.arabidopsis.org_servlets_Search_action_new_search_type_ecotype

TDMS
type: NamedIndividual
type: DiseaseStateDatabase
type: HistologyDatabase
comment: Toxicology Data Management System, a database resource for systems, organs, pathology, etc.
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#http___hazel.niehs.nih.gov_user_spt_pct_terms.htm

TIFF
type: NamedIndividual
type: ImageFormat
comment: Tag Image File Format (TIFF) is a common format to describe and store raster image data from scanners and other imaging devices. TIFFs may contain one or more channels and the data may be compressed using a lossless compression algorithm.

UMLS
type: NamedIndividual
type: DiseaseState
comment: Database resource, unified medical language system, an ontology constructed by merging several disparate ontologies, available from NIH.

WebRENI
type: NamedIndividual
type: DiseaseStateDatabase
comment: database entry from WebReni A resource for rat and mouse unified nomenclature describing lesions
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#http___www.item.fraunhofer.de_reni_index.htm

YAC
type: NamedIndividual
type: PhysicalBioSequenceType
comment: sequence from yeast artificial chromosome

ad libitum
type: NamedIndividual
type: DeliveryMethod
comment: A delivery method for compounds/drugs where the compound or drug is freely available.

add
type: NamedIndividual
type: AtomicAction
comment: The procedure of placing one physical object in the same container/physical space as another.

agar
type: NamedIndividual
type: Media
comment: A type of solid media commonly used for growing organisms

agar stab
type: NamedIndividual
type: BioSourceType
comment: agar stab, a cell culture inoculated into agar for long term storage

age
type: NamedIndividual
type: BioMaterialCharacteristicCategory
comment: A descriptor for FactorValue where age is compared.

all pairs
type: NamedIndividual
type: MethodologicalDesign
comment: An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.

amino acid primary sequence record
type: NamedIndividual
type: DatabaseEntryType
comment: A record which describes and identifies an amino acid sequence which is encoded by a CDS from a primary_nucleic_acid_sequence_record

aminosilane
type: NamedIndividual
type: SurfaceType
comment: A type of surface coating.

amol
type: NamedIndividual
type: QuantityUnit
comment: attomole, quantity unit

aneuploid
type: NamedIndividual
type: Ploidy
comment: Describes a cell, nucleus or an organism whose chromosome number is not an exact multiple of the haploid number (n).

antibody
type: NamedIndividual
type: PhysicalBioSequenceType
comment: glycoprotein of the immunoglobulin family that can combine specifically non-covalently, reversibly with a corresponding antigen

array manufacturer
type: NamedIndividual
type: Roles
comment: Person or organization that manufactured the array.

array manufacturing
type: NamedIndividual
type: ProtocolType
comment: The process of manufacturing the array.

arrayer
type: NamedIndividual
type: HardwareType
comment: An instrument capable of manufacturing arrays by spotting material.

atmosphere
type: NamedIndividual
type: EnvironmentalFactorCategory
comment: The atmospheric conditions used to culture or grow an organism.

aunt
type: NamedIndividual
type: FamilyRelationship
comment: The sister of one's father or mother.

average difference
type: NamedIndividual
type: DerivedBioAssayType
comment: the method used by Affymetrix to obtain mean signal intensity from a group of related Features. This involves calculation of the overall sum of perfect match minus mismatch pairs divided by the number of pairs. (MAS 4.0 version of the Affymetrix analysis software).

averaged intensity
type: NamedIndividual
type: DerivedBioAssayType
comment: results of data reduction involving computation of the average intensity from identical Features, Reporters or CompositeSequences in different hybridizations.

barrier facility
type: NamedIndividual
type: EnvironmentalFactorCategory
comment: The rating of containment system used to protect organisms from infectious agents.

beginning of stage
type: NamedIndividual
type: InitialTimePoint
comment: time point that indicates the start of some developmental stage

behavioral stimulus
type: NamedIndividual
type: ComplexAction
type: ProtocolType
comment: The organism is forced to respond to a stimulus with some behavior (e.g., avoidance, obtaining a reward, etc.)

bioassay data transformation
type: NamedIndividual
type: ProtocolType
comment: A computational procedure used to process or transform one BioAssayDataCube into another.

bioassay replicate reduction
type: NamedIndividual
type: DerivedBioAssayType
comment: results of data reduction involving computation of a representative value, e.g. by averaging, for a group of replicated Features, Reporters or CompositeSequences from 2 or more hybridizations.

biological replicate
type: NamedIndividual
type: QualityControlDescriptionType
type: ReplicateDescriptionType
comment: A replicate that consists of independent biological replicates made from different individual BioSources.

biological resource record
type: NamedIndividual
type: DatabaseEntryType
comment: A record which describes and identifies a biological resource such as a cone or strain e.g. an ATCC record Jax strain list

biomaterial provider
type: NamedIndividual
type: BioMaterialCharacteristicCategory
type: Roles
comment: A descriptor for FactorValue where BioSource providers are compared.

biopsy
type: NamedIndividual
type: BioSourceType
comment: A biomaterial, usually tissue, cells, or fluid from a living organism

biosequence provider
type: NamedIndividual
type: Roles
comment: Provider of biosequences (clones, oligos etc) for deposition on the array.

biotin
type: NamedIndividual
type: LabelCompound
comment: a compound used for labeling/detection purposes

birth
type: NamedIndividual
type: InitialTimePoint
comment: the action of emergence and separation of offspring from the mother.

blood
type: NamedIndividual
type: BioSourceType
comment: A biomaterial obtained as fluid consisting of plasma, blood cells and platelets.

book
type: NamedIndividual
type: PublicationType
comment: A publication type which has an ISBN.

brother
type: NamedIndividual
type: FamilyRelationship
comment: A male having the same genetic parents as another, or one genetic parent in common with another.

candelas per square meter
type: NamedIndividual
type: LightUnit
comment: Unit of brightness or luminance.

cc
type: NamedIndividual
type: VolumeUnit
comment: a cubic centimeter, volume unit

cell
type: NamedIndividual
type: MaterialType
comment: One or more dissociated cell(s) possibly heterogeneous, excluding single cell organisms.

cell cycle design
type: NamedIndividual
type: BiologicalProperty
comment: A cell cycle design experiment design type is one that assays events that occurs in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells.

cell line
type: NamedIndividual
type: BioMaterialCharacteristicCategory
comment: A descriptor for FactorValue where CellLine is compared.

cell lysate
type: NamedIndividual
type: MaterialType
comment: cell lysate, a collection of cells whose membranes have been disrupted

cell type
type: NamedIndividual
type: BioMaterialCharacteristicCategory
comment: A descriptor for FactorValue where CellType is compared.

cell type comparison design
type: NamedIndividual
type: BiologicalProperty
comment: A cell type comparison design experiment design type compares cells of different type for example different cell lines.

cellular modification design
type: NamedIndividual
type: PerturbationalDesign
comment: A cellular modification design type is where a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.

change humidity
type: NamedIndividual
type: AtomicAction
comment: The action of changing the relative humidity, e.g. from 1% to 10%.

change light
type: NamedIndividual
type: AtomicAction
comment: Change in light intensity or wavelength.

change temperature
type: NamedIndividual
type: AtomicAction
comment: Change in temperature.

chromosomal deletion
type: NamedIndividual
type: ChromosomalAberrationClassification
comment: The loss of a segment of the genetic material from a chromosome.

chromosomal duplication
type: NamedIndividual
type: ChromosomalAberrationClassification
comment: An irregularity in the number of chromosomes, usually in the form of a gain of genetic material.

chromosomal insertion
type: NamedIndividual
type: ChromosomalAberrationClassification
comment: The gain of a segment of the genetic material in a chromosome by fragmentation of a chromosome and transfer of the broken-off portion of another chromosome or other sources.

chromosomal inversion
type: NamedIndividual
type: ChromosomalAberrationClassification
comment: Chromosome segments that have been turned through 180 degrees with the result that the gene sequence for the segment is reversed with respect to the rest of the chromosome.

chromosomal translocation
type: NamedIndividual
type: ChromosomalAberrationClassification
comment: A type of aberration characterized by fragmentation of a chromosome and transfer of the broken-off portion to another chromosome, often of a different pair.

chromosome
type: NamedIndividual
type: PhysicalBioSequenceType
type: TheoreticalBioSequenceType
comment: Physical or theoretical sequence of, or representing a chromosome, one of the DNA molecules that comprises the genome.

circadian rhythm design
type: NamedIndividual
type: BiologicalProperty
comment: A circadian rhythm experiment design type assays the events associated with the circadian rhythm which is a biological activity that exhibits an endogenous periodicity independently of any daily variation in the environment.

clinical history design
type: NamedIndividual
type: EpidemiologicalDesign
comment: A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied.

clinical information
type: NamedIndividual
type: BioMaterialCharacteristicCategory
comment: A descriptor for FactorValue where ClinicalInformation is compared.

clinical record
type: NamedIndividual
type: DatabaseEntryType
comment: ecord which describes and identifies clinical information about an organism

clinical treatment
type: NamedIndividual
type: BioMaterialCharacteristicCategory
comment: A descriptor for a clinical treatment for a patient.

clone
type: NamedIndividual
type: PhysicalBioSequenceType
comment: Sequence from some nucleic acid copy and the associated vector

clustered data
type: NamedIndividual
type: DerivedBioAssayType
comment: results of an analysis method that groups data based on some measure of similarity, e.g. Pearson correlation coeficient, Euclidean distance.

clustering software
type: NamedIndividual
type: SoftwareType
comment: Software used to cluster the data.

cm
type: NamedIndividual
type: DistanceUnit
comment: centimeter, a unit of distance

coitus
type: NamedIndividual
type: InitialTimePoint
comment: sexual intercourse or copulation

collapsed spot replicate
type: NamedIndividual
type: DerivedBioAssayType
comment: results of data reduction involving computation of a representative value, e.g. by averaging, for a group of replicated Features, Reporters or CompositeSequences from a single hybridization.

compound based treatment
type: NamedIndividual
type: ComplexAction
type: ProtocolType
comment: The treatment is effected by a defined chemical, biological or compound. The compound may be a drug, solvent, chemical, etc., with a property that can be measured such as concentration.

compound record
type: NamedIndividual
type: DatabaseEntryType
comment: a record which describes and identifies a compound e.g. drug record part of NCI thesaurus

compound treatment design
type: NamedIndividual
type: PerturbationalDesign
comment: A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.

computational feature
type: NamedIndividual
type: SeqFeatureBasis
comment: Computationally derived sequence feature.

computed amino acid sequence feature record
type: NamedIndividual
type: DatabaseEntryType
comment: a record which describes and identifies an amino acid feature which is computationally derived e.g. PFAM

computed nucleic acid sequence feature record
type: NamedIndividual
type: DatabaseEntryType
comment: A record which identifies and describes a nucleic sequence feature which has been computationally determined or predeicted E.g. and Ensembl record

computed protein structure record
type: NamedIndividual
type: DatabaseEntryType
comment: a record which describes and identifies a protein structure e.g. PDB

concentrate
type: NamedIndividual
type: AtomicAction
comment: Increasing the concentration of solutes in a solution or suspension.

consensus mRNA
type: NamedIndividual
type: TheoreticalBioSequenceType
comment: mRNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple sequences as input.

consortium member
type: NamedIndividual
type: Roles
comment: A member of a consortium of institutions.

consultant
type: NamedIndividual
type: Roles
comment: A contact who provides some service related to some aspect of the experiment which is not data coding or analysis. E.g. help with an experimental design.

control biosequence
type: NamedIndividual
type: ControlType
comment: A Reporter associated with a BioSequence that has a context dependent predicted signal. e.g. a yeast reporter on a human array is a control_biosequence expected to be of low signal if no spikes are used. If spikes are used, the signal is expected to be high.

control buffer
type: NamedIndividual
type: ControlType
comment: A Reporter where only buffer was deposited on the array

control design element group type
type: NamedIndividual
type: DesignElementGroupType
comment: A grouping of DesignElements features/Reporters/Composites which are not designed to detect a signal in the biomaterial and which are on the array for control purposes e.g a grouping of controls used for spiking.

control empty
type: NamedIndividual
type: ControlType
comment: A Reporter where no material or buffer was deposited on the array

control genomic DNA
type: NamedIndividual
type: ControlType
comment: A Reporter where genomic DNA has been deposited, the genomic DNA may be fragmented, e.g. salmon sperm DNA, Cot1DNA.

control reporter size
type: NamedIndividual
type: ControlType
comment: A Reporter of whose BioSequence is of known length used as a methodological control for hybridization efficiency.

control unknown type
type: NamedIndividual
type: ControlType
comment: A Reporter indicated as being a control of unknown type.

cosmid
type: NamedIndividual
type: PhysicalBioSequenceType
comment: sequence from cosmid, a hybrid cloning vector containing cos sites, usually of ~40kB size

count
type: NamedIndividual
type: QuantityUnitOther
comment: Unit for a simple count of things

cpm
type: NamedIndividual
type: RadiationUnit
comment: counts per minute, unit of light emissions produced by ionizing radiation.

curated amino acid sequence record
type: NamedIndividual
type: DatabaseEntryType
comment: A record which describes and identifies an amino acid sequence which has been curated

curated nucleic acid sequence feature record
type: NamedIndividual
type: DatabaseEntryType
comment: A record which identifies a nucleic acid sequence feature(s) and which has been curated.

curator
type: NamedIndividual
type: Roles
comment: Person who curates data.

cytoplasmic RNA
type: NamedIndividual
type: MaterialType
comment: RNA obtained from the cytoplasm.

data analyst
type: NamedIndividual
type: Roles
comment: A contact who performs data analysis, e.g. statistician.

data coder
type: NamedIndividual
type: Roles
comment: Person who codes data.

date
type: NamedIndividual
type: DataType
comment: Time stated in terms of the day, month, and year.

daughter
type: NamedIndividual
type: FamilyRelationship
comment: The female offspring of the patient or individual under study.

days
type: NamedIndividual
type: TimeUnit
comment: 24 hours, time unit

degrees C
type: NamedIndividual
type: TemperatureUnit
comment: degrees celsius, unit of temperature

degrees F
type: NamedIndividual
type: TemperatureUnit
comment: degrees Fahrenheit, unit of temperature

development or differentiation design
type: NamedIndividual
type: BiologicalProperty
comment: A development or differentiation experiment design type assays events associated with development or differentiation or moving through a life cycle. Development applies to organism(s) acquiring a mature state, and differentiation applies to cells acquiring specialized functions.

developmental stage
type: NamedIndividual
type: BioMaterialCharacteristicCategory
comment: A descriptor for FactorValue where DevelopmentalStage is compared.

diameter aberration
type: NamedIndividual
type: DefectType
comment: The diameter of the Feature is much smaller or much larger than expected based on the spotting pin diameter.

dilute
type: NamedIndividual
type: AtomicAction
comment: Decreasing the concentration of solutes in a solution or suspension.

diploid
type: NamedIndividual
type: Ploidy
comment: Describes a cell, nucleus or an organism with two copies of each chromosome.

disease staging
type: NamedIndividual
type: BioMaterialCharacteristicCategory
comment: The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression.

disease state
type: NamedIndividual
type: BioMaterialCharacteristicCategory
comment: A descriptor for FactorValue where DiseaseState is compared.

disease state design
type: NamedIndividual
type: EpidemiologicalDesign
type: PerturbationalDesign
comment: A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied.

displaced feature or zone
type: NamedIndividual
type: DefectType
comment: The Feature or Zone is displaced from its expected position, due to e.g. a bent spotting pin(s).

dissect
type: NamedIndividual
type: ComplexAction
type: ProtocolType
comment: The action of removing one or more OrganismParts.

dl
type: NamedIndividual
type: VolumeUnit
comment: deciliter, unit of volume

dose response design
type: NamedIndividual
type: PerturbationalDesign
comment: A dose response design type examines the relationship between the size of the administered dose and the extent of the response of the organism(s).

double stranded
type: NamedIndividual
type: StrandType
comment: a nucleic acid consiting of two polynucleotide chains having antiparallel orientation and being bound together by hydrogen bonding between the chains. This would apply to DNA and some RNA genomes, but not to rRNA or tRNA, etc.

dpm
type: NamedIndividual
type: RadiationUnit
comment: disintegrations per minute, unit of atom disintegrations per minute. dpm = (cpm - measured background)/efficiency. Efficiency is dependent on the radioisotope used and the instrument.

ds oligo
type: NamedIndividual
type: PhysicalBioSequenceType
comment: a double stranded oligonucleotide

dye swap quality control
type: NamedIndividual
type: QualityControlDescriptionType
comment: Indicates that a dye swap was performed for some or all hybridizations within an experiment

dye swap replicate reduction
type: NamedIndividual
type: DerivedBioAssayType
comment: results of data reduction involving computation of a representative value, e.g. by averaging, for identical Features, Reporters or CompositeSequences from 2 hybridizations utilizing dye-swapped LabeledExtracts.

eVOC
type: NamedIndividual
type: CellTypeDatabase
type: DevelopmentalStageDatabase
type: DiseaseStateDatabase
type: OrganismPartDatabase
comment: Ontology of human terms that describe the sample source of human cDNA and SAGE libraries.
has URI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#http___www.sanbi.ac.za_evoc_ontologies.html

eclosion
type: NamedIndividual
type: InitialTimePoint
comment: Emergence of an adult insect from its pupa or cocoon.

ellipsoid feature
type: NamedIndividual
type: FeatureShape
comment: The shape of the feature on the array is circular or oval.

environmental history design
type: NamedIndividual
type: EnvironmentalHistory
comment: An environmental history design type is where some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc.

exon
type: NamedIndividual
type: TheoreticalBioSequenceType
comment: sequence which represents regions of a transcript that are joined to another exon during splicing

experimental and computational feature
type: NamedIndividual
type: SeqFeatureBasis
comment: Sequence features derived by both computational and experimental methods.

experimental design element group type
type: NamedIndividual
type: DesignElementGroupType
comment: A grouping of DesignElements, Features/Reporters/Composite Sequences which are expected to detect a signal in the biomaterial.

experimental feature
type: NamedIndividual
type: SeqFeatureBasis
comment: An experimentally defined sequence feature.

extract
type: Thing
type: BioSampleType
type: NamedIndividual
comment: The BioSample immediately before labeling.

fM
type: NamedIndividual
type: ConcentrationUnit
comment: femtomolar, concentration unit

family history design
type: NamedIndividual
type: EpidemiologicalDesign
comment: A family history design type is where the family history such as traits, characteristics, susceptibility to disease is studied

father
type: NamedIndividual
type: FamilyRelationship
comment: A male parent.

feces
type: NamedIndividual
type: BioSourceType
comment: A biosource obtained as fecal matter.

feeding
type: NamedIndividual
type: DeliveryMethod
comment: Delivery method where a compound/drug is administered in food or water.

fg
type: NamedIndividual
type: MassUnit
comment: femtogram, unit of mass

filtered data
type: NamedIndividual
type: DerivedBioAssayType
comment: data from which a subset has been removed based on some criteria, e.g. data below an intensity threshhold

fl
type: NamedIndividual
type: VolumeUnit
comment: femtoliter, unit of volume

flip-dye consistency
type: NamedIndividual
type: NormalizationDescriptionType
comment: A method of checking the consistency of expression levels between a pair of features from flip-dye hybridizations by studying the distribution of the logarithm of ratios of intensity ratios from the two spots.

fractionate
type: NamedIndividual
type: ComplexAction
type: ProtocolType
comment: The action of separating a BioMaterial into one or more fractions e.g. differential centrifugation or FACS when used for cell sorting (see purify).

frozen sample
type: NamedIndividual
type: BioSourceType
comment: A biomaterial obtained frozen

frozen storage
type: NamedIndividual
type: PreservationType
comment: Storage where the thing stored is stored below 0 degrees celsius.

function record
type: NamedIndividual
type: DatabaseEntryType
comment: a record which identifies and describes the function of a gene product, e.g. E.C. record

funder
type: NamedIndividual
type: Roles
comment: Contact which provides funding for experiments.

http://mged.sourceforge.net/ontologies/MGEDOntology.owl#g
type: NamedIndividual
type: MassUnit
comment: gram, unit of mass

gene
type: NamedIndividual
type: TheoreticalBioSequenceType
comment: genomic sequence which corresponds to the primary transcript and uses the furthest 5' and 3' UTR's, doesn't include non transcribed regulatory regions. Can be experimentally or computationally determined

gene fragment
type: NamedIndividual
type: TheoreticalBioSequenceType
comment: sequence of part of a gene, which is missing one or both ends

gene knock in
type: NamedIndividual
type: GeneticModification
comment: The modification of an organism that inserts a functional gene at the site of a nonfunctional locus for that gene using recombinant methods.

gene knock out
type: NamedIndividual
type: GeneticModification
comment: The modification of an organism that renders a gene non-functional e.g. due to the removal of all, or part of, the gene using recombinant methods.

genetic modification
type: NamedIndividual
type: ComplexAction
type: ProtocolType
comment: An action whereby an organism(s) has had genetic material removed, added, or rearranged.

genetic modification design
type: NamedIndividual
type: PerturbationalDesign
comment: A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out

genetic variation
type: NamedIndividual
type: BioMaterialCharacteristicCategory
comment: A descriptor for FactorValue where GeneticVariation is compared.

genomic DNA
type: NamedIndividual
type: MaterialType
type: PhysicalBioSequenceType
comment: high molecular weight DNA

genotyping design
type: NamedIndividual
type: BioMolecularAnnotation
comment: A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's.

glass
type: NamedIndividual
type: SubstrateType
comment: The array is made on a glass slide.

gram percent
type: NamedIndividual
type: ConcentrationUnit
comment: grams per deciliter, concentration unit

granddaughter
type: NamedIndividual
type: FamilyRelationship
comment: A daughter of one's son or daughter.

grandfather
type: NamedIndividual
type: FamilyRelationship
comment: The father of one's father or mother.

grandmother
type: NamedIndividual
type: FamilyRelationship
comment: The mother of one's father or mother.

grandson
type: NamedIndividual
type: FamilyRelationship
comment: A son of one's son or daughter.

grow
type: NamedIndividual
type: ComplexAction
type: ProtocolType
comment: A ComplexAction or ProtocolType describing growth of an organism or cell culture.

growth condition design
type: NamedIndividual
type: PerturbationalDesign
comment: A growth condition experiment design type is where some part of the growth condition is changed for the purposes of the experiment, examples of growth conditions changed are media, temperature, humidity, light, nutrients.

hardware manufacturer
type: NamedIndividual
type: Roles
comment: Person or organization that manufactured the hardware.

hardware variation design
type: NamedIndividual
type: MethodologicalDesign
comment: A hardware variation experiment design type compares different types of hardware for performance, reproducibility, accuracy and precision.

hatching
type: NamedIndividual
type: InitialTimePoint
comment: The point at which an organism emerges from an egg.

heating block
type: NamedIndividual
type: HardwareType
comment: A device for controlling temperature.

heavy background
type: NamedIndividual
type: DefectType
comment: The Zone is excluded due to smearing, streaking, or dense background in the Zone.

hermaphrodite
type: NamedIndividual
type: Sex
comment: an organism with both male and female sexual organs in one individual

homogenizer
type: NamedIndividual
type: HardwareType
comment: An instrument which fragments tissues or other biomaterials.

hours
type: NamedIndividual
type: TimeUnit
comment: 60 minutes, time unit

hybridization
type: NamedIndividual
type: ComplexAction
type: ProtocolType
comment: The process of incubating one or more labeled extracts with an array.

hybridization chamber
type: NamedIndividual
type: HardwareType
comment: A chamber in which the hybridization is performed which maintains constant conditions.

hybridization station
type: NamedIndividual
type: HardwareType
comment: An instrument which controls hybridization conditions, into which a hybridization chamber may fit.

image acquisition
type: NamedIndividual
type: ComplexAction
type: ProtocolType
comment: The process of generating an image from the array.

image record
type: NamedIndividual
type: DatabaseEntryType
comment: A record which describes and identifies an image, e.g. an image from the mouse atlas

in situ oligo features
type: NamedIndividual
type: TechnologyType
comment: The TechnologyType of the FeatureGroup is manufactured using in situ methods such as photolithography (e.g. Affymetrix) or chemical synthesis (e.g. Agilent)

incubate
type: NamedIndividual
type: ComplexAction
type: ProtocolType
comment: The procedure of placing a physical object under specified conditions e.g. time, temperature, humidity for the purposes of obtaining a different product.

individual
type: NamedIndividual
type: BioMaterialCharacteristicCategory
comment: A descriptor for FactorValue where BioSources are compared.

individual genetic characteristic
type: NamedIndividual
type: BioMaterialCharacteristicCategory
comment: A descriptor for FactorValue where IndividualGeneticCharacteristic is compared.

individual genetic characteristics design
type: NamedIndividual
type: BiologicalProperty
comment: An experiment design type where genotype, haplotype, or other individual genetic characteristics are compared.

induced mutation
type: NamedIndividual
type: GeneticModification
comment: The modification of the genetic material (either coding or non-coding) of an organism by mutagenic compounds or irradiation.

infect
type: NamedIndividual
type: ComplexAction
type: ProtocolType
comment: The organism (or organism part) has been exposed to a virus or pathogen.

injury design
type: NamedIndividual
type: PerturbationalDesign
comment: An injury experiment design type is where the response of an organism(s) to injury or damage is studied.

institution
type: NamedIndividual
type: Roles
comment: A contact's affiliation, e.g. university, research institute or business.

integer
type: NamedIndividual
type: DataType
comment: A value which is a whole number (e.g. 10).

intramuscular injection
type: NamedIndividual
type: DeliveryMethod
comment: Delivery method for a compound or drug where the substance is administered via an injection into the muscle.

intraperitoneal injection
type: NamedIndividual
type: DeliveryMethod
comment: A delivery method for compound or drug whereby the substance is administered via the peritoneum.

intravenous
type: NamedIndividual
type: DeliveryMethod
comment: delivery method whereby a compound or drug is administered via a vein

investigator
type: NamedIndividual
type: Roles
comment: Person who contributed to the study.

irradiate
type: NamedIndividual
type: ComplexAction
type: ProtocolType
comment: treatment of a biomaterial with radiation e.g. electromagnetic radiation

irregular shape
type: NamedIndividual
type: DefectType
comment: The perimeter of the spotted DNA on the slide is irregular.

is contaminated
type: NamedIndividual
type: WarningType
comment: The clone used to originate the BioSequence which corresponds to the reporter was found to be contaminated (e.g. well-well contamination) on examination.

is expressed design
type: NamedIndividual
type: BiologicalProperty
comment: A design aimed at identifying genes expressed in biomaterials of interest.

iterative mean log centering
type: NamedIndividual
type: NormalizationDescriptionType
comment: A method of re-scaling ratio data by subtracting the mean log base 2 ratio from each log2(ratio). This adjusts the mean log2(ratio) to zero.

journal article
type: NamedIndividual
type: PublicationType
comment: A article published in a print or online journal having an ISSN.

kg
type: NamedIndividual
type: MassUnit
comment: kilogram, 1000 grams, unit of mass

labeling
type: NamedIndividual
type: ComplexAction
type: ProtocolType
comment: The procedure of labeling a biosample.

linear regression normalization
type: NamedIndividual
type: NormalizationDescriptionType
comment: A method of re-scaling intensity data from one channel relative to another based on regression of the intensities in one channel on those of the other. The slope of the regression line is used to re-scale the intensities in one channel for each Feature. This single parameter method assumes that there is a linear relationship between the intensities in one channel relative to the other.

linlog normalization
type: NamedIndividual
type: NormalizationDescriptionType
comment: A transformation method in which low intensities are linearly scaled while high intensities are logarithmically scaled. The transition point is determined by minimizing the absolute deviation of the variance of log ratios.

liquid
type: NamedIndividual
type: Media
comment: media type, usually some sort of broth

liquid handler
type: NamedIndividual
type: HardwareType
comment: Hardware for automated liquid transfer and handling.

liquid handler software
type: NamedIndividual
type: SoftwareType
comment: Software used to control automated liquid handler.

list of boolean
type: NamedIndividual
type: DataType
comment: An ordered, finite set of booleans.

list of float
type: NamedIndividual
type: DataType
comment: An ordered, finite set of floats.

list of integer
type: NamedIndividual
type: DataType
comment: An ordered, finite set of integers.

list of negative float
type: NamedIndividual
type: DataType
comment: An ordered, finite set of negative floats.

list of negative integer
type: NamedIndividual
type: DataType
comment: An ordered, finite set of negative integers.

list of nonpositive float
type: NamedIndividual
type: DataType
comment: An ordered, finite set of nonpositive floats.

list of positive integer
type: NamedIndividual
type: DataType
comment: An ordered, finite set of positive integers.

list of string
type: NamedIndividual
type: DataType
comment: An ordered, finite set of strings.

log base 10
type: NamedIndividual
type: Scale
comment: The values presented are logarithm, base 10.

log base 2
type: NamedIndividual
type: Scale
comment: The values presented are logarithm, base 2.

log base e
type: NamedIndividual
type: Scale
comment: The values presented are logarithm, base e.

long oligo
type: NamedIndividual
type: DesignElement
comment: An element that is an oligonucleotide of at least 50 nucleotides in length.

low intensity filter
type: NamedIndividual
type: NormalizationDescriptionType
comment: A transformation method that involves removal of Features with low intensities in one or both channels from the data set. The threshold for exclusion is usually based on some estimation of local background intensity.

lumen
type: NamedIndividual
type: LightUnit
comment: The unit of total light output from a light source.

lux
type: NamedIndividual
type: LightUnit
comment: A metric unit equal to one lumen per square meter. This unit is the modern equivalent of foot-candles where one footcandle is 10.76 lux.

mM
type: NamedIndividual
type: ConcentrationUnit
comment: milimolar, concentration unit

mRNA
type: NamedIndividual
type: TheoreticalBioSequenceType
comment: sequence of a processed transcript capable of directing protein synthesis

male
type: NamedIndividual
type: Sex
comment: individual whose sex organs contain only male gametes

mating type a
type: NamedIndividual
type: Sex
comment: Mating type of S. cerevisiae.

mating type alpha
type: NamedIndividual
type: Sex
comment: Mating type of S. cerevisiae.

mean and coefficient of variation
type: NamedIndividual
type: DerivedBioAssayType
comment: the mean and coefficient of variation values resulting from computationally combining 2 or more sets of BioAssayData

mean and confidence indicators
type: NamedIndividual
type: DerivedBioAssayType
comment: the mean and associated confidence values resulting from combining the data from 2 or more sets of BioAssayData. Confidence indicators include, but are not limited to:confidence interval, standard deviation, coefficient of variation, and p-value.

mean and p values
type: NamedIndividual
type: DerivedBioAssayType
comment: the mean and associated p-values resulting from computationally combining 2 or more sets of BioAssayData

mean and standard deviation
type: NamedIndividual
type: DerivedBioAssayType
comment: the mean and standard deviation values resulting from computationally combining 2 or more sets of BioAssayData

mean and variance
type: NamedIndividual
type: DerivedBioAssayType
comment: the mean and variance values resulting from computationally combining 2 or more sets of BioAssayData

media
type: NamedIndividual
type: EnvironmentalFactorCategory
comment: The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil)

microarray experiment record
type: NamedIndividual
type: DatabaseEntryType
comment: A record which describes and identifies a microarray experiment e.g. GEO

minutes
type: NamedIndividual
type: TimeUnit
comment: 60 seconds, unit of time

missing feature or zone
type: NamedIndividual
type: DefectType
comment: The source DNA was not printed for a Feature or Zone on the slide, possibly due to lack of sample, broken or clogged spotting pin.

mix by inversion
type: NamedIndividual
type: AtomicAction
comment: Mix through the process of inverting.

mix by pipette
type: NamedIndividual
type: AtomicAction
comment: Mix by drawing up and down with a pipette.

mix by vortex
type: NamedIndividual
type: AtomicAction
comment: Mix through the use of a vortexer.

mix general
type: NamedIndividual
type: AtomicAction
comment: The procedure of agitating 2 or more materials in order to combine them. The materials may be of any state solid/liquid/gas.

mixed design element group type
type: NamedIndividual
type: DesignElementGroupType
comment: a designelement group consisting of multiple types

mixed sex
type: NamedIndividual
type: Sex
comment: A population of multiple sexes, e.g. a mixture of females and males, or males and hermaphrodites.

ml
type: NamedIndividual
type: VolumeUnit
comment: milliliter, volume unit

mm
type: NamedIndividual
type: DistanceUnit
comment: millimeter, unit of distance

mol
type: NamedIndividual
type: QuantityUnit
comment: mole, unit of quantity

molecular mixture
type: NamedIndividual
type: MaterialType
comment: an unspecified collection of heterogeneous molecules, e.g. lipids, carbohydrate , nucleic acids and proteins

molecules
type: NamedIndividual
type: QuantityUnit
comment: number of molecules, quantity unit

monosomy
type: NamedIndividual
type: ChromosomalAberrationClassification
comment: Absence of one chromosome of a pair of homologous chromosomes. In a normally diploid cell it is represented symbolically as 2N-1.

months
type: NamedIndividual
type: TimeUnit
comment: Unit of time corresponding to approx. one cycle of the moon's phases.

mother
type: NamedIndividual
type: FamilyRelationship
comment: A female parent.

ms
type: NamedIndividual
type: TimeUnit
comment: millisecond, time unit

negative float
type: NamedIndividual
type: DataType
comment: A float that is < 0.

negative integer
type: NamedIndividual
type: DataType
comment: An integer < 0.

nitrocellulose
type: NamedIndividual
type: SubstrateType
comment: The array is made on a nitrocellulose filter.

nl
type: NamedIndividual
type: VolumeUnit
comment: nanoliter unit of volume

nmol
type: NamedIndividual
type: QuantityUnit
comment: nanomoles, quantity unit

non-targeted transgenic variation design
type: NamedIndividual
type: PerturbationalDesign
comment: The modification of an organism due to the presence of DNA from another individual, e.g. of a different strain, species or breed. These do not include targeted transgenics such as knock-ins and knock-outs.

nonnegative float
type: NamedIndividual
type: DataType
comment: A float greater than or equal to 0.

nonnegative integer
type: NamedIndividual
type: DataType
comment: An integer >= 0.

nonpositive float
type: NamedIndividual
type: DataType
comment: A float less than or equal to zero.

nonpositive integer
type: NamedIndividual
type: DataType
comment: An integer less than or equal to zero.

normalization testing design
type: NamedIndividual
type: MethodologicalDesign
comment: A normalization testing experiment design tests different normalization procedures.

normalized intensities
type: NamedIndividual
type: DerivedBioAssayType
comment: intensities from one or both channels resulting from normalization of MeasuredBioAssayData.

normalized ratios
type: NamedIndividual
type: DerivedBioAssayType
comment: ratios resulting from normalization of MeasuredBioAssayData

not extract
type: Thing
type: BioSampleType
type: NamedIndividual
comment: The BioSample at any stage other than immediately before labeling.

not sequence verified
type: NamedIndividual
type: WarningType
comment: The sequence of the BioSequence that relates to this reporter has not been sequence verified by the experimenter.

not uniform
type: NamedIndividual
type: DefectType
comment: The source DNA for a Feature was not uniformly deposited.

nuclear RNA
type: NamedIndividual
type: MaterialType
comment: RNA obtained from the nucleus.

nucleic acid extraction
type: NamedIndividual
type: ComplexAction
type: ProtocolType
comment: The procedure of extracting nucleic acid from the biomaterial.

nucleic acid primary sequence record
type: NamedIndividual
type: DatabaseEntryType
comment: A record which describes and identifies a primary sequence record e.g. DDBJ/EMBL/Genbank

nutrients
type: NamedIndividual
type: EnvironmentalFactorCategory
comment: The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.).

nylon
type: NamedIndividual
type: SubstrateType
comment: The array is made on a nylon membrane.

oligo synthesizer
type: NamedIndividual
type: HardwareType
comment: Hardware for synthesizing oligos.

online resource
type: NamedIndividual
type: PublicationType
comment: A publication type which is available online and which is not an online journal article, e.g. a web site or service.

ontology record
type: NamedIndividual
type: DatabaseEntryType
comment: A record which describes and identifies a term, class or instance in an ontology or controlled vocabulary e.g. ICD

operating system
type: NamedIndividual
type: SoftwareType
comment: Software upon which other software runs.

operator variation design
type: NamedIndividual
type: MethodologicalDesign
comment: An operator variation experiment design type assesses the operator performance and relation to data consistency and quality.

operon identification design
type: NamedIndividual
type: BioMolecularAnnotation
comment: An operon identification experiment type is designed to identify locations and members of operons in a genome.

optimization design
type: NamedIndividual
type: MethodologicalDesign
comment: An optimization experiment design type is where different protocols or protocol parameters are compared.

oral gavage
type: NamedIndividual
type: DeliveryMethod
comment: delivery method for drug or compound whereby the drug is administered via the mouth

organellar DNA
type: NamedIndividual
type: MaterialType
comment: DNA from organelles such as the mitochondria or chloroplast.

organellar RNA
type: NamedIndividual
type: MaterialType
comment: RNA obtained from an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus.

organism
type: NamedIndividual
type: BioMaterialCharacteristicCategory
comment: one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria

organism part
type: NamedIndividual
type: BioMaterialCharacteristicCategory
type: MaterialType
comment: The part of the organism's anatomy from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, or body location (arm).

organism part comparison design
type: NamedIndividual
type: BiologicalProperty
comment: An organism part comparison experiment design type compares tissues, regions, organs within or between organisms

organism status
type: NamedIndividual
type: BioMaterialCharacteristicCategory
comment: The stage premortem or postmortem at which the sample was processed for extraction of biomaterials.

pH
type: NamedIndividual
type: ConcentrationUnitOther
comment: potential of hydrogen

pM
type: NamedIndividual
type: ConcentrationUnit
comment: picomolar, concentration unit

paraffin sample
type: NamedIndividual
type: BioSourceType
comment: A biomaterial obtained embedded in paraffin (wax).

pathogenicity design
type: NamedIndividual
type: PerturbationalDesign
comment: A pathogenicity experiment design type is where an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed.

pathway record
type: NamedIndividual
type: DatabaseEntryType
comment: a record which identifies and describes biological pathways, e.g. a KEGG record

pedigree record
type: NamedIndividual
type: DatabaseEntryType
comment: A record which descibes and identifies a pedigree or lineage for a strain, line,individal or cell whose lineage traceable e.g. a wormbase cell lineage record, or a pedigree record for a mouse

peer review quality control
type: NamedIndividual
type: QualityControlDescriptionType
comment: An experiment which has a peer reviewed publication attached.

pg
type: NamedIndividual
type: MassUnit
comment: picogram, mass unit

physical characteristics
type: NamedIndividual
type: BioMaterialCharacteristicCategory
comment: A descriptor for FactorValue where PhysicalCharacteristics are compared.

pl
type: NamedIndividual
type: VolumeUnit
comment: picoliter, volume unit

place
type: NamedIndividual
type: AtomicAction
comment: The procedure of putting a physical object in a container/physical space.

planting
type: NamedIndividual
type: InitialTimePoint
comment: time point at which a seed was planted

plasmid
type: NamedIndividual
type: PhysicalBioSequenceType
comment: sequence from a plasmid, an extrachromosomal autonomously replicating piece of DNA excluding mitochondria and chloroplasts

ploidy
type: NamedIndividual
type: ChromosomalAberrationClassification
comment: A chromosomal abnormality in which there are extra complete multiples.

pmol
type: NamedIndividual
type: QuantityUnit
comment: picomoles, quantity unit

polylysine
type: NamedIndividual
type: SurfaceType
comment: A type of surface coating.

polypeptide
type: NamedIndividual
type: PhysicalBioSequenceType
type: TheoreticalBioSequenceType
comment: sequence of a protein, a linear amino acid polymer

polyploid
type: NamedIndividual
type: Ploidy
comment: Describes a cell, nucleus or organism with three or more copies of each chromosome.

population density
type: NamedIndividual
type: EnvironmentalFactorCategory
comment: The concentration range of the organism.

positive float
type: NamedIndividual
type: DataType
comment: A float > 0.

positive integer
type: NamedIndividual
type: DataType
comment: An integer > 0.

postmortem
type: NamedIndividual
type: OrganismStatus
comment: biomaterial removed after the death of the organism

predicted gene
type: NamedIndividual
type: TheoreticalBioSequenceType
comment: gene sequence which has been computationally predicted

premortem
type: NamedIndividual
type: OrganismStatus
comment: sample which has been removed prior to the death of an organism

preservation
type: NamedIndividual
type: ComplexAction
type: ProtocolType
comment: The type of protocol used to preserve (including storage or keep in statis) the biomaterial.

promoter
type: NamedIndividual
type: TheoreticalBioSequenceType
comment: genomic sequence 5' to a gene where the transcription initiation complex forms.

protein
type: NamedIndividual
type: MaterialType
type: PolymerType
comment: Polymer of amino acids.

purify
type: NamedIndividual
type: ComplexAction
type: ProtocolType
comment: The action of enriching a BioMaterial (organism, cell, nucleic acid etc) or Compound e.g. for FACS for positive selection or RNA cleanup the Action or ProtocolType is purify (see fractionate).

quality control testing design
type: NamedIndividual
type: MethodologicalDesign
comment: A quality control testing experiment design type is where some aspect of the experiment is quality controlled for the purposes of quality assurance

ratio
type: NamedIndividual
type: DerivedBioAssayType
comment: results of data reduction involving computation of the ratio of signal intensities obtained from hybridization of two, or more, labelled extracts to one, or more arrays

reciprocal translocation
type: NamedIndividual
type: ChromosomalAberrationClassification
comment: Interchanges of genetic material among different chromosomes such that the total chromosome complement may still contain all of the genetic material.

rectangular feature
type: NamedIndividual
type: FeatureShape
comment: The shape of the feature on the array is rectangular.

reference design
type: NamedIndividual
type: MethodologicalDesign
comment: A reference experiment design type is where all samples are compared to a common reference.

remove
type: NamedIndividual
type: AtomicAction
comment: The procedure of extracting/taking out a part of a reaction/contents of a container.

replicate design
type: NamedIndividual
type: MethodologicalDesign
comment: A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.

resuspend
type: NamedIndividual
type: AtomicAction
comment: The procedure in which solid material is dispensed or dissolved in a liquid.

reverse transcription
type: NamedIndividual
type: ComplexAction
type: ProtocolType
comment: Generation of a DNA strand from an RNA strand using reverse transcriptase.

robertsonian translocation
type: NamedIndividual
type: ChromosomalAberrationClassification
comment: Translocation in which the centromeres of two acrocentric chromosomes appear to have fused, forming an abnormal chromosome consisting of the long arms of two different chromosomes with loss of the short arms.

sacrifice
type: NamedIndividual
type: ComplexAction
type: ProtocolType
comment: The procedure of euthanizing an organism.

seconds
type: NamedIndividual
type: TimeUnit
comment: time unit

secreted protein identification design
type: NamedIndividual
type: BioMolecularAnnotation
comment: A secreted protein identification design type identifies transcripts associated with a secretory pathway during translation and is used to infer which proteins are secreted or membrane bound.

seed dormancy
type: NamedIndividual
type: PreservationType
comment: preservation type whereby the seed is maintained in a dormant state

self vs self design
type: NamedIndividual
type: MethodologicalDesign
comment: A self vs. self experiment design investigates variance and error estimates in the experimental system, and is where the same extract is compared.

semisolid
type: NamedIndividual
type: Media
comment: semisolid media type

set temperature
type: NamedIndividual
type: AtomicAction
comment: An action where the temperature is specified.

sex
type: NamedIndividual
type: BioMaterialCharacteristicCategory
comment: A descriptor for FactorValue where Sex is compared.

sex design
type: NamedIndividual
type: BiologicalProperty
comment: A sex experiment design type assays differences associated with an organism's sex, gender or mating type.

short oligo
type: NamedIndividual
type: DesignElement
comment: An element that is an oligonucleotide of less than 50 nucleotides in length (usually 20 to 25 nt as in Affymetrix probes).

signal
type: NamedIndividual
type: DerivedBioAssayType
comment: A quantitative measure of the relative abundance of a transcript (MAS 4.0 version of the Affymetrix analysis software).

silicon
type: NamedIndividual
type: SubstrateType
comment: the array is made on silicon

single stranded
type: NamedIndividual
type: StrandType
comment: a nucleic acid consiting of a single polynucleotide chain.

slice analysis
type: NamedIndividual
type: NormalizationDescriptionType
comment: A method of analyzing the significant expression level of a Feature by calculating the intensity-dependent Z distribution value for the logarithm of the intensity ratios from the two channels.

software manufacturer
type: NamedIndividual
type: Roles
comment: Person or organization that manufactured the software.

soil
type: NamedIndividual
type: Media
comment: soil, growth media for plants and other soil living organisms

son
type: NamedIndividual
type: FamilyRelationship
comment: The male offspring of the patient or individual under study.

sonicator
type: NamedIndividual
type: HardwareType
comment: An instrument for sonicating biomaterials.

species design
type: NamedIndividual
type: BiologicalProperty
comment: A species experiment design type assays differences between distinct species.

species specific design element group type
type: NamedIndividual
type: DesignElementGroupType
comment: A grouping of DesignElements, Features, Reporters, Composite Sequences on the basis of a common species.

specified biomaterial action
type: NamedIndividual
type: AtomicAction
type: ComplexAction
type: ProtocolType
comment: Conceptual action for specified protocol applied in treatment.

spectrophotometer
type: NamedIndividual
type: HardwareType
comment: Hardware for measuring light at different wavelengths.

spike quality control
type: NamedIndividual
type: QualityControlDescriptionType
comment: An experiment in which spikes were introduced into some or all of the hybridizations for quality control or data transformation purposes.

spotted antibody features
type: NamedIndividual
type: TechnologyType
comment: TechnologyType of FeatureGroup where antibodies are spotted directly.

spotted colony features
type: NamedIndividual
type: TechnologyType
comment: TechnologyType of FeatureGroup where bacterial or other colonies are spotted directly.

spotted ds DNA features
type: NamedIndividual
type: TechnologyType
comment: A descriptor for the TechnologyType for a group of features where double stranded DNA is spotted on the array e.g. a PCR of a cDNA clone.

spotted protein features
type: NamedIndividual
type: TechnologyType
comment: TechnologyType of FeatureGroup where protein (other than antibody) is spotted directly.

spotted ss oligo features
type: NamedIndividual
type: TechnologyType
comment: The TechnologyType of the FeatureGroup is spotted single stranded oligonucleotides (of any length) on the substrate.

square feature
type: NamedIndividual
type: FeatureShape
comment: The shape of the feature on the array is square.

ss oligo
type: NamedIndividual
type: PhysicalBioSequenceType
comment: sequence of a single stranded synthesized oligonucleotide

starvation
type: NamedIndividual
type: ComplexAction
type: ProtocolType
comment: Depriving an organism of food or nutrients

stimulus or stress design
type: NamedIndividual
type: PerturbationalDesign
comment: A stimulus or stress experiment design type is where the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc.

store
type: NamedIndividual
type: ComplexAction
type: ProtocolType
comment: The procedure of placing a physical object under specified conditions e.g. time, temperature, humidity, for the purposes of keeping it in the same state.

strain or line
type: NamedIndividual
type: BioMaterialCharacteristicCategory
comment: A descriptor of FactorValue where comparisons of strains or lines are made.

strain or line design
type: NamedIndividual
type: BiologicalProperty
comment: A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.

string datatype
type: NamedIndividual
type: DataType
comment: The values are a sequence of one or more characters.

subcutaneous
type: NamedIndividual
type: DeliveryMethod
comment: Delivery method whereby a drug or compound is administered under the skin of the organism.

submitter
type: NamedIndividual
type: Roles
comment: Person who is the primary contact for data submitted to a database.

technical replicate
type: NamedIndividual
type: QualityControlDescriptionType
type: ReplicateDescriptionType
comment: A replicate where the same BioSample is use e.g. the same pool of RNA used to assess technical (as opposed to biological) variation within an experiment.

time series design
type: NamedIndividual
type: MethodologicalDesign
comment: Groups of assays that are related as part of a time series.

total RNA
type: NamedIndividual
type: MaterialType
comment: Total cellular and nuclear RNA.

transcript
type: NamedIndividual
type: TheoreticalBioSequenceType
comment: sequence that represents the product of an RNA polymerase engaged in transcription

transcript identification design
type: NamedIndividual
type: BioMolecularAnnotation
comment: A transcript identification design type characterizes the length and position of transcripts and allows identification of all forms of transcripts in the genome.

transfect
type: NamedIndividual
type: ComplexAction
type: ProtocolType
comment: The process of bringing about genetic alteration of any cell or organism by a variety of means including recombinant DNA technology, viruses, chemical mutagens, and X-rays.

translational bias design
type: NamedIndividual
type: BioMolecularAnnotation
comment: A translational bias is an experiment design which characterizes the association of transcripts and translation machinery.

trisomy
type: NamedIndividual
type: ChromosomalAberrationClassification
comment: The possession of a third chromosome of any one type in an otherwise diploid cell.

tumor grading
type: NamedIndividual
type: BioMaterialCharacteristicCategory
comment: A descriptor used in cancer biology to describe abnormalities of tumor cells.

uM
type: NamedIndividual
type: ConcentrationUnit
comment: micromolar, concentration unit

ug
type: NamedIndividual
type: MassUnit
comment: microgram, unit of mass

ul
type: NamedIndividual
type: VolumeUnit
comment: microliter, unit of volume

um
type: NamedIndividual
type: DistanceUnit
comment: micrometer, unit of distance

umol
type: NamedIndividual
type: QuantityUnit
comment: micromoles, quantity unit

uncle
type: NamedIndividual
type: FamilyRelationship
comment: The brother of one's father or mother.

unknown basis feature
type: NamedIndividual
type: SeqFeatureBasis
comment: Sequence feature whose derivation is unknown.

unknown experiment design type
type: NamedIndividual
type: BioMolecularAnnotation
type: BiologicalProperty
type: EpidemiologicalDesign
type: MethodologicalDesign
type: PerturbationalDesign
comment: ExperimentDesignType of unknown type.

unknown protocol type
type: NamedIndividual
type: ProtocolType
comment: ProtocolType of unknown type.

unknown sequence
type: NamedIndividual
type: PhysicalBioSequenceType
type: TheoreticalBioSequenceType
comment: BioSequence of unknown type

unknown sex
type: NamedIndividual
type: Sex
comment: organism(s) whose sex is unknown

unknown substrate type
type: NamedIndividual
type: SubstrateType
comment: SubstrateType of unknown type.

unknown surface type
type: NamedIndividual
type: SurfaceType
comment: A SurfaceType of unknown type.

unscaled
type: NamedIndividual
type: Scale
comment: The values are unordered and have no scale.

us
type: NamedIndividual
type: TimeUnit
comment: microsecond, unit of time

vector
type: NamedIndividual
type: PhysicalBioSequenceType
comment: Sequence from a vector, DNA of any transmissible agent e.g. plasmid or virus into which a segment of foreign DNA can be spliced, does not include insert sequence. These terms should be used when other terms such as plasmid, YAC, BAC are used.

virus
type: NamedIndividual
type: MaterialType
comment: one or more DNA or RNA based non cellular infective agent, including bacteriophage

vortexer
type: NamedIndividual
type: HardwareType
comment: An instrument that mixes by rapid oscillation.

wait
type: NamedIndividual
type: AtomicAction
comment: Allow time to pass. It's measurement should be a unit of time.

wash
type: NamedIndividual
type: ComplexAction
type: ProtocolType
comment: The process of applying a solvent (e.g. water) or a solution (e.g. SSC/SDS) to a BioMaterial or an array to remove impurities or unwanted compounds.

water
type: NamedIndividual
type: EnvironmentalFactorCategory
comment: Water consumed by or enveloping the organism that the biosource is derived from.

waterbath
type: NamedIndividual
type: HardwareType
comment: A device for controlling temperature by immersion in water.

weeks
type: NamedIndividual
type: TimeUnit
comment: 7 days, unit of time

whole organism
type: NamedIndividual
type: MaterialType
comment: one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria

wild type
type: NamedIndividual
type: Allele
type: Genotype
comment: The genotype or phenotype that is found in nature or in standard laboratory stocks for a given organism. For a single locus, the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism.

years
type: NamedIndividual
type: TimeUnit
comment: 365 days, time unit