The MGED Ontology
type: Ontology
subject: An ontology for microarray experiments in support of MAGE v.1.
date: February 9, 2007
imports: http://purl.org/dc/elements/1.1/
imports: protege
creator: Chris Stoeckert, Helen Parkinson, Trish Whetzel, Paul Spellman, Catherine A. Ball, Joseph White, John Matese, Liju Fan, Gilberto Fragoso, Mervi Heiskanen, Susanna Sansone, Helen Causton, Laurence Game, Chris Taylor
description: Concepts, definitions, terms, and resources for standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1
version info: 1.3.1.1

CancerSite
type: Class
subclass of: MGEDCoreOntology
class source: ontology
unique identifier: MO_26
class role: concrete
comment: class to hold instances used as the filler for the property has_cancer_site

MGEDCoreOntology
type: Class
class source: ontology
unique identifier: MO_57
class role: abstract
subclass of: MGEDOntology
subclass of: Restriction
  some values from: string
  on property: has ID
comment: An ontology developed by the Microarray Gene Expression Data (MGED) Society to provide descriptors required for MAGE v.1 documents.

BioMaterialPackage
type: Class
comment: Description of the source of the nucleic acid used to generate labeled material for the microarray experiment.
unique identifier: MO_182
subclass of: MGEDCoreOntology
class source: mage
class role: abstract

StrainOrLine
type: Class
class source: ontology
class role: abstract
subclass of: OntologyEntry
subclass of: BioMaterialCharacteristics
subclass of: Restriction
  on property: has database
  some values from: StrainOrLineDatabase
subclass of: Restriction
  some values from: Organism
  on property: has species
unique identifier: MO_9
comment: A strain or line is an animal or plant offspring that has a single ancestral breeding pair or parent as a result of brother x sister or parent x offspring matings. This class is extended to include F1 offspring and established breeding lines. For microbes, these are isolates derived from nature or in the laboratory.

OntologyEntry
type: Class
class role: abstract
subclass of: DescriptionPackage
subclass of: Restriction
  some values from: string
  on property: has value
subclass of: Restriction
  some values from: Database
  on property: has database
comment: External (to the MGED ontology) controlled vocabulary or ontology that can be referred such as ICD-9 or Gene Ontology.
subclass of: Restriction
  on property: has accession version
  some values from: string
subclass of: Restriction
  on property: has accession
  some values from: string
subclass of: Restriction
  on property: has database entry type
  some values from: DatabaseEntryType
unique identifier: MO_87
subclass of: Restriction
  on property: has description
  some values from: string
class source: ontology

BioMaterialCharacteristics
type: Class
unique identifier: MO_5
comment: Properties of the biomaterial before treated in any manner for the purposes of the experiment.
class role: abstract
subclass of: BioMaterialPackage
subclass of: BiologicalFactorCategory
class source: ontology

has database
type: ObjectProperty
comment: property indicating that the class has a database
unique identifier: MO_233

StrainOrLineDatabase
type: Class
class role: concrete
unique identifier: MO_30
subclass of: Database
comment: Database of strain, line, cultivar or ecotype information.
class source: ontology

Organism
type: Class
subclass of: BioMaterialCharacteristics
subclass of: OntologyEntry
subclass of: Restriction
  some values from: OrganismDatabase
  on property: has database
comment: The genus and species (and subspecies) of the organism from which the biomaterial is derived from.
class role: abstract
class source: ontology
unique identifier: MO_229

has species
type: ObjectProperty
unique identifier: MO_320
comment: property indicating that the class has species

Water
type: Class
comment: Water consumed by or enveloping the organism that the biosource is derived from.
class source: ontology
subclass of: Restriction
  some values from: Protocol
  on property: has treatment
subclass of: GrowthCondition
subclass of: Restriction
  on property: has additive
  some values from: Compound
class role: abstract
unique identifier: MO_153

Protocol
type: Class
subclass of: Restriction
  on property: has citation
  some values from: BibliographicReference
unique identifier: MO_214
subclass of: Restriction
  on property: has software
  some values from: Software
class source: mage
subclass of: Restriction
  on property: has title
  some values from: string
class role: concrete
comment: Documentation of the set of steps taken in a procedure.
subclass of: ProtocolPackage
subclass of: Restriction
  some values from: string
  on property: has description
subclass of: Restriction
  on property: has text
  some values from: string
subclass of: Restriction
  on property: has hardware
  some values from: Hardware
subclass of: Restriction
  on property: has type
  some values from: ProtocolType
subclass of: Restriction
  some values from: URI
  on property: has URI

has treatment
type: ObjectProperty
unique identifier: MO_262
comment: property indicating that the class has a treatment

GrowthCondition
type: Class
subclass of: Restriction
  some values from: Measurement
  on property: has maximum measurement
subclass of: Restriction
  on property: has value
  some values from: string
subclass of: EnvironmentalHistory
subclass of: Restriction
  some values from: Measurement
  on property: has 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.
class source: ontology
unique identifier: MO_183
class role: abstract

has additive
type: ObjectProperty
unique identifier: MO_314
comment: property indicating that the class has an additive

Compound
type: Class
subclass of: Restriction
  some values from: Compound
  on property: has measurement
class source: ontology
subclass of: OntologyEntry
class role: abstract
comment: A drug, solvent, chemical, etc., with a property that can be measured such as concentration.
subclass of: Restriction
  on property: is solvent
  some values from: boolean
unique identifier: MO_70
subclass of: Restriction
  on property: has database
  some values from: CompoundDatabase
subclass of: BiologicalFactorCategory

QuantitationTypePackage
type: Class
comment: The MAGE package for defining classes for quantitation.
class role: abstract
class source: mage
unique identifier: MO_130
subclass of: MGEDCoreOntology

DevelopmentalStage
type: Class
comment: The developmental stage of the organism's life cycle during which the biomaterial was extracted.
class role: abstract
unique identifier: MO_120
subclass of: OntologyEntry
subclass of: Restriction
  some values from: DevelopmentalStageDatabase
  on property: has database
subclass of: BioMaterialCharacteristics
class source: ontology

DevelopmentalStageDatabase
type: Class
class role: concrete
subclass of: Database
class source: ontology
comment: Database of developmental stage information.
unique identifier: MO_215

Bedding
type: Class
comment: Refers to the bedding material present in an animals housing.
class role: place_holder
unique identifier: MO_154
class source: ontology
subclass of: EnvironmentalHistory

EnvironmentalHistory
type: Class
subclass of: BioMaterialCharacteristics
unique identifier: MO_55
class source: ontology
class role: abstract
comment: A description of the conditions the organism has been exposed to that are not one of the variables under study.

Parameter
type: Class
class role: concrete
class source: mage
comment: A parameter is a variable within a protocol.
subclass of: Restriction
  on property: has units
  some values from: Unit
subclass of: ProtocolPackage
subclass of: Restriction
  on property: has type
  some values from: DataType
unique identifier: MO_110

has units
type: ObjectProperty
unique identifier: MO_269
comment: property indicating that the class has units

Unit
type: Class
comment: Units of measure.
class source: ontology
subclass of: MeasurementPackage
class role: abstract
unique identifier: MO_3

ProtocolPackage
type: Class
class source: mage
comment: The MAGE package for protocols.
unique identifier: MO_63
class role: abstract
subclass of: MGEDCoreOntology

has type
type: ObjectProperty
unique identifier: MO_319
comment: property indicating that the class has a type

DataType
type: Class
class source: ontology
subclass of: MGEDCoreOntology
comment: Primitive data types found in computing languages such as float, boolean, etc.
unique identifier: MO_125
class role: concrete

SequenceOntologyDatabase
type: Class
class source: ontology
class role: concrete
comment: Database for sequence annotation information.
unique identifier: MO_83
subclass of: Database

Database
type: Class
comment: Identifiable resource containing data or external ontologies or controlled vocabularies which has uniquely identifiable records.
class source: ontology
unique identifier: MO_118
subclass of: DescriptionPackage
subclass of: Restriction
  on property: has version
  some values from: string
subclass of: Restriction
  on property: has URI
  some values from: URI
class role: abstract

MeasurementPackage
type: Class
class role: abstract
comment: MAGE package for measurement.
subclass of: MGEDCoreOntology
unique identifier: MO_89
class source: mage

TumorGradingDatabase
type: Class
subclass of: Database
comment: Database of tumor grading information
class source: ontology
class role: concrete
unique identifier: MO_187

Measurement
type: Class
comment: Measured values and units.
subclass of: Restriction
  some values from: string
  on property: has value
subclass of: Restriction
  on property: has measurement type
  some values from: MeasurementType
subclass of: Restriction
  on property: has units
  some values from: Unit
subclass of: MeasurementPackage
class source: mage
class role: concrete
unique identifier: MO_144

has value
type: DatatypeProperty
comment: property indicating that the class has a value
unique identifier: MO_326

has measurement type
type: ObjectProperty
comment: property indicating that the class has a measurement type
unique identifier: MO_242
domain: Measurement

MeasurementType
type: Class
comment: class to hold instances used as the filler for the property has_measurement_type
class role: concrete
unique identifier: MO_72
class source: ontology
subclass of: MGEDCoreOntology

SurfaceType
type: Class
unique identifier: MO_198
comment: Controlled terms for descriptors for coating of the substrate.
class source: ontology
subclass of: ArrayDesignPackage
class role: concrete

ArrayDesignPackage
type: Class
subclass of: MGEDCoreOntology
comment: MAGE package that describes the array layout and design. The array may be physical or virtual.
class role: abstract
unique identifier: MO_33
class source: mage

Result
type: Class
class source: ontology
comment: class to hold instances used as the filler for the property has_result
unique identifier: MO_65
class role: concrete
subclass of: MGEDCoreOntology

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.
class role: concrete
unique identifier: MO_213
class source: ontology

ExperimentDesignType
type: Class
unique identifier: MO_158
class source: ontology
class role: abstract
comment: The ExperimentDesignType is the high level description for studies such as "time series", "dose response", etc.
subclass of: ExperimentPackage

FeatureShape
type: Class
subclass of: ArrayDesignPackage
comment: The expected shape of the feature on the array.
class role: concrete
class source: ontology
unique identifier: MO_8

ClinicalHistory
type: Class
class role: abstract
subclass of: Restriction
  on property: has clinical treatment
  some values from: ClinicalTreatment
subclass of: Restriction
  some values from: OntologyEntry
  on property: has clinical record
subclass of: Restriction
  some values from: TestResult
  on property: has clinical finding
subclass of: Restriction
  some values from: DiseaseState
  on property: has prior disease state
subclass of: Restriction
  on property: has test type
  some values from: TestType
class source: ontology
comment: The BioMaterial's (i.e., the patient's) medical record as background information relevant to the experiment.
subclass of: EnvironmentalHistory
unique identifier: MO_189

has clinical treatment
type: ObjectProperty
comment: property indicating that the class has a clinical treatment
unique identifier: MO_282

ClinicalTreatment
type: Class
class source: ontology
unique identifier: MO_69
class role: abstract
comment: The current clinical treatment(s) of the patient from which the biosource is derived.
subclass of: BioMaterialCharacteristics
subclass of: Restriction
  on property: has database
  some values from: ClinicalTreatmentDatabase
subclass of: OntologyEntry

has clinical record
type: ObjectProperty
unique identifier: MO_247
comment: property indicating that the class has a clinical record

TestResult
type: Class
comment: TestResult is the recorded value of the test outcome.
subclass of: Restriction
  on property: has measurement
  some values from: Measurement
subclass of: BioMaterialCharacteristics
class source: ontology
unique identifier: MO_96
class role: abstract

has clinical finding
type: ObjectProperty
comment: property indicating that the class has a clinical finding
unique identifier: MO_316

DiseaseState
type: Class
subclass of: OntologyEntry
subclass of: Restriction
  on property: has disease location
  some values from: DiseaseLocation
class role: abstract
subclass of: Restriction
  on property: has disease staging
  some values from: DiseaseStaging
unique identifier: MO_126
class source: ontology
subclass of: Restriction
  on property: has database
  some values from: DiseaseStateDatabase
subclass of: BioMaterialCharacteristics
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.

has prior disease state
type: ObjectProperty
comment: property indicating that the class has a prior disease state
unique identifier: MO_276

has test type
type: ObjectProperty
comment: property indicating that the class has a clinical test
unique identifier: MO_311

TestType
type: Class
comment: Descriptor of the Test performed e.g. Leukocyte count
class source: ontology
class role: abstract
subclass of: Restriction
  some values from: TestTypeDatabase
  on property: has database
subclass of: BioMaterialCharacteristics
subclass of: OntologyEntry
unique identifier: MO_218

FamilyMember
type: Class
subclass of: Restriction
  some values from: DiseaseState
  on property: has disease state
class source: ontology
subclass of: Restriction
  on property: has individual genetic characteristics
  some values from: IndividualGeneticCharacteristics
unique identifier: MO_188
comment: Member of the biosource's family.
class role: abstract
subclass of: BioMaterialPackage
subclass of: Restriction
  some values from: OntologyEntry
  on property: has clinical record
subclass of: Restriction
  some values from: FamilyRelationship
  on property: has family relationship

has disease state
type: ObjectProperty
comment: property indicating that the class has a disease state
unique identifier: MO_305

has individual genetic characteristics
type: ObjectProperty
comment: property indicating that the class has individual genetic characteristics
unique identifier: MO_254

IndividualGeneticCharacteristics
type: Class
class role: abstract
unique identifier: MO_66
subclass of: Restriction
  some values from: string
  on property: has value
subclass of: BioMaterialCharacteristics
comment: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes.
class source: ontology

FamilyRelationship
type: Class
class source: ontology
unique identifier: MO_36
comment: A type of relationship applicable to mammals to describe the genetic relatedness of the individual under study. E.g. brother or mother.
subclass of: BioMaterialPackage
class role: concrete

has family relationship
type: ObjectProperty
comment: property indicating that the class has a family relationship
unique identifier: MO_250

SeqFeatureBasis
type: Class
comment: Controlled terms for how the sequence features were determined (e.g., experimental, computational, etc.)
unique identifier: MO_207
class source: ontology
class role: concrete
subclass of: BioSequencePackage

BioSequencePackage
type: Class
subclass of: MGEDCoreOntology
class source: mage
unique identifier: MO_191
class role: abstract
comment: MAGE package for biological sequences (biosequence).

BioAssayData
type: Class
subclass of: BioAssayDataPackage
unique identifier: MO_40
comment: BioAssayData refers to the data files including images generated from one or more BioAssays.

BioAssayDataPackage
type: Class
comment: MAGE package for BioAssayData.
subclass of: MGEDExtendedOntology
unique identifier: MO_186

Roles
type: Class
comment: Controlled terms for descriptors of the role of contact, e.g. submitter, biosource_provider.
unique identifier: MO_180
subclass of: AuditAndSecurityPackage
class role: concrete
class source: ontology

AuditAndSecurityPackage
type: Class
class source: mage
unique identifier: MO_172
comment: MAGE package for contacts including organizations and people.
class role: abstract
subclass of: MGEDCoreOntology

HardwareType
type: Class
unique identifier: MO_113
class role: concrete
comment: Controlled terms for descriptors of types of hardware.
class source: ontology
subclass of: ProtocolPackage

BioMaterial
type: Class
unique identifier: MO_226
class source: mage
comment: Description of the processing state of the biomaterial for use in the microarray hybridization.
class role: abstract
subclass of: Restriction
  on property: has type
  some values from: MaterialType
subclass of: Restriction
  on property: has biomaterial characteristics
  some values from: BioMaterialCharacteristics
subclass of: BioMaterialPackage

MaterialType
type: Class
subclass of: BioMaterialPackage
class role: concrete
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.
class source: ontology
unique identifier: MO_32

has biomaterial characteristics
type: ObjectProperty
unique identifier: MO_272
comment: property indicating that the class has biomaterial characteristics

QuantityUnitOther
type: Class
class role: concrete
subclass of: QuantityUnit
class source: ontology
unique identifier: MO_156
comment: Quantity units not specified in MAGE.

QuantityUnit
type: Class
class role: concrete
subclass of: Unit
class source: ontology
comment: Units used for quantity measurements.
unique identifier: MO_210

Transformation
type: Class
unique identifier: MO_216
subclass of: Restriction
  on property: has protocol
  some values from: Protocol
subclass of: BioAssayDataPackage
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.

has protocol
type: ObjectProperty
comment: property indicating that the class has a protocol
unique identifier: MO_300

Host
type: Class
class role: abstract
unique identifier: MO_101
comment: Organisms or organism parts used as a designed part of the culture (e.g., red blood cells, stromal cells).
subclass of: Restriction
  on property: has host part
  some values from: OrganismPart
subclass of: Restriction
  on property: has host
  some values from: Organism
subclass of: EnvironmentalHistory
class source: ontology

has host part
type: ObjectProperty
domain: Host
unique identifier: MO_283
comment: property indicating that the class has a host part

OrganismPart
type: Class
class role: abstract
class source: ontology
subclass of: Restriction
  on property: has database
  some values from: OrganismPartDatabase
subclass of: BioMaterialCharacteristics
subclass of: OntologyEntry
comment: The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm).
unique identifier: MO_1

has host
type: ObjectProperty
domain: Host
comment: property indicating that the class has a host
unique identifier: MO_313

GeographicLocation
type: Class
class source: ontology
subclass of: OntologyEntry
subclass of: EnvironmentalHistory
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.
class role: abstract
unique identifier: MO_132

GeographicLocationDatabase
type: Class
subclass of: Database
class source: ontology
comment: Database of geographic locations.
unique identifier: MO_35
class role: concrete

DataTransformationProtocolType
type: Class
unique identifier: MO_165
comment: The process by which derived BioAssays are created from measured BioAssays and/or derived BioAssays.
subclass of: ProtocolType
class role: concrete
class source: ontology

ProtocolType
type: Class
comment: A controlled set of terms to provide a descriptor for the type of protocol.
class source: ontology
subclass of: ProtocolPackage
subclass of: MethodologicalFactorCategory
class role: abstract
unique identifier: MO_150

MethodologicalDesign
type: Class
comment: A methodological experiment design type investigates differences caused by application of protocols, hardware, software and bioassay relationships, e.g. quality control, replicates, loop.
class source: ontology
unique identifier: MO_2
class role: concrete
subclass of: ExperimentDesignType

Age
type: Class
class source: ontology
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 (e.g. 3 days post planting).
class role: abstract
subclass of: BioMaterialCharacteristics
subclass of: Restriction
  on property: has measurement
  some values from: Measurement
subclass of: Restriction
  on property: has maximum measurement
  some values from: Measurement
subclass of: Restriction
  on property: has initial time point
  some values from: InitialTimePoint
unique identifier: MO_178

has measurement
type: ObjectProperty
unique identifier: MO_325
comment: property indicating that the class has a measurement

has maximum measurement
type: ObjectProperty
unique identifier: MO_297
comment: property indicating that the class has a maximum measurement
domain: Age

has initial time point
type: FunctionalProperty
domain: Age
comment: property indicating that the class has an individual time point
type: ObjectProperty
unique identifier: MO_292

InitialTimePoint
type: Class
comment: The point from which measurements of age were taken.
subclass of: BioMaterialPackage
class source: ontology
unique identifier: MO_80
class role: concrete

OperatorVariation
type: Class
class role: place_holder
unique identifier: MO_38
class source: ontology
subclass of: MethodologicalFactorCategory
comment: The effects of different investigators, laboratories, or organizations on experimental results are studied.

MethodologicalFactorCategory
type: Class
class role: abstract
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.
subclass of: ExperimentalFactorCategory
unique identifier: MO_85
class source: ontology

ReplicateDescription
type: Class
subclass of: Restriction
  on property: has type
  some values from: ReplicateDescriptionType
subclass of: ExperimentPackage
class source: ontology
class role: abstract
unique identifier: MO_162
comment: ReplicateDescription provides details about the type of replication used in the experiment.

ReplicateDescriptionType
type: Class
class role: concrete
subclass of: ExperimentPackage
unique identifier: MO_52
class source: ontology
comment: Controlled descriptors for the type of replication.

ExperimentPackage
type: Class
unique identifier: MO_31
comment: The descriptions associated with the Experiment package of MAGE
class role: abstract
class source: mage
subclass of: MGEDCoreOntology

Biometrics
type: Class
class source: ontology
subclass of: Restriction
  some values from: Measurement
  on property: has cubic volume
comment: Physical properties of the BioMaterial e. g. mass or height
subclass of: Restriction
  on property: has mass
  some values from: Measurement
subclass of: Restriction
  on property: has diameter
  some values from: Measurement
subclass of: Restriction
  some values from: Measurement
  on property: has length
subclass of: BioMaterialCharacteristics
subclass of: Restriction
  on property: has height
  some values from: Measurement
class role: abstract
subclass of: Restriction
  on property: has individual
  some values from: Individual
subclass of: Restriction
  some values from: OrganismPart
  on property: has organism part
unique identifier: MO_129

has cubic volume
type: ObjectProperty
comment: property indicating that the class contains a cubic volume measurement
unique identifier: MO_245

has mass
type: ObjectProperty
comment: property indicating that the class has a mass
unique identifier: MO_280

has diameter
type: ObjectProperty
unique identifier: MO_301
comment: property indicating that the class has a diameter

has height
type: ObjectProperty
comment: property indicating that the class has a height
unique identifier: MO_317

has individual
type: ObjectProperty
comment: property indicating that the class has an individual
unique identifier: MO_327

Individual
type: Class
subclass of: BioMaterialCharacteristics
class role: place_holder
unique identifier: MO_169
class source: ontology
comment: Identifier or name of the individual organism from which the biomaterial was derived.

has organism part
type: ObjectProperty
unique identifier: MO_285
comment: property indicating that the class has an organism part

WarningType
type: Class
class source: ontology
unique identifier: MO_41
comment: Controlled terms for descriptors of the warnings associated with reporters.
subclass of: DesignElementPackage
class role: concrete

DesignElementPackage
type: Class
class role: abstract
unique identifier: MO_15
subclass of: MGEDCoreOntology
comment: The MAGE package for describing the elements located on the array.
class source: mage

ChromosomalAberrationClassification
type: Class
class role: concrete
subclass of: BioMaterialCharacteristics
unique identifier: MO_6
class source: ontology
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.

EnvironmentalFactorCategory
type: Class
class role: concrete
class source: ontology
unique identifier: MO_117
subclass of: ExperimentalFactorCategory
comment: Factors that relate to properties of the environmental history of the biomaterial, its treatment, or its growth.

ExperimentalFactorCategory
type: Class
unique identifier: MO_205
subclass of: ExperimentPackage
class source: ontology
comment: A factor category describes factors which are examined in the experiment, e.g. disease_state, where the factor values are ALL and AML.
class role: abstract

OrganismDatabase
type: Class
unique identifier: MO_64
class role: concrete
class source: ontology
subclass of: Database
comment: Database of taxonomic information.

MGEDOntology
type: Class
comment: The MGED Ontology is a top level container for the MGEDCoreOntology and the MGEDExtendedOntology. The MGED ontology describes microarray experiments and is split into the MGEDCoreOntology, which supports MAGE-OM v1.0 and is organized consistently with MAGE, and the MGEDExtendedOntology, which expands MAGE v1.0 and contains concepts and relationships which are not included in MAGE.
class source: ontology
unique identifier: MO_174
class role: abstract
subclass of: Restriction
  on property: is user defined
  some values from: Contact
subclass of: Thing
subclass of: Restriction
  some values from: BibliographicReference
  on property: is user defined

is user defined
type: ObjectProperty
unique identifier: MO_279
comment: property indicating that the class is user defined

Contact
type: Class
subclass of: Restriction
  on property: has address
  some values from: string
class role: abstract
subclass of: Restriction
  some values from: string
  on property: has phone
subclass of: Restriction
  some values from: URI
  on property: has URI
comment: Organizations or individuals that may be contacted.
subclass of: Restriction
  on property: has email
  some values from: string
subclass of: AuditAndSecurityPackage
unique identifier: MO_147
subclass of: Restriction
  some values from: string
  on property: has fax
subclass of: Restriction
  some values from: string
  on property: has toll free phone
class source: mage
subclass of: Restriction
  some values from: Roles
  on property: has type

BibliographicReference
type: Class
subclass of: Restriction
  on property: has pages
  some values from: string
class role: concrete
unique identifier: MO_201
subclass of: Restriction
  on property: has issue
  some values from: string
subclass of: Restriction
  some values from: string
  on property: has editor
comment: A bibliographic reference is a published citation in a journal, book, other format e.g. web resource
subclass of: DescriptionPackage
subclass of: Restriction
  some values from: URI
  on property: has URI
subclass of: Restriction
  on property: has volume
  some values from: string
class source: mage
subclass of: Restriction
  some values from: string
  on property: has authors
subclass of: Restriction
  some values from: PublicationType
  on property: has type
subclass of: Restriction
  on property: has year
  some values from: date
subclass of: Restriction
  on property: has publication
  some values from: string
subclass of: Restriction
  on property: has publisher
  some values from: string
subclass of: Restriction
  on property: has title
  some values from: string

Fiducial
type: Class
subclass of: Restriction
  on property: has type
  some values from: FiducialType
subclass of: ArrayPackage
unique identifier: MO_136
class source: mage
comment: A marking on the surface of the array that can be used to identify the origin of the array.
class role: concrete

FiducialType
type: Class
comment: A descriptor that indicates the type of the fiducial such as chrome border of an Affymetrix array or a laser ablation mark.
class source: ontology
subclass of: ArrayPackage
unique identifier: MO_17
class role: concrete

ArrayPackage
type: Class
unique identifier: MO_107
subclass of: MGEDCoreOntology
class source: mage
comment: MAGE package for describing the process by which arrays were manufactured.
class role: abstract

FactorValue
type: Class
subclass of: Restriction
  some values from: Measurement
  on property: has measurement
comment: The value of an ExperimentFactor.
class source: mage
subclass of: ExperimentPackage
subclass of: Restriction
  on property: has property set
  some values from: FactorValueSet
class role: concrete
unique identifier: MO_203
subclass of: Restriction
  on property: has property set
  some values from: FactorValueDependency
subclass of: Restriction
  on property: has factor value ontology entry
  some values from: ExperimentalFactorCategory

has property set
type: ObjectProperty
comment: property indicating that the class has a property set
unique identifier: MO_266

FactorValueSet
type: Class
deprecation reason: deleted_term
subclass of: Restriction
  has value: deleted term
  on property: has reason for deprecation
class role: place_holder
subclass of: Restriction
  on property: deprecated from version
  has value: version 1.1.9
subclass of: DeprecatedTerms
unique identifier: MO_217
deprecation old parent: ExperimentPackage
subclass of: Restriction
  on property: has value
  some values from: string
deprecation in version: 1.1.9
deprecation old restriction: some|has_value|string
class source: ontology
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.
subclass of: ExperimentPackage

FactorValueDependency
type: Class
unique identifier: MO_148
deprecation old parent: ExperimentPackage
subclass of: Restriction
  some values from: string
  on property: has value
subclass of: Restriction
  on property: deprecated from version
  has value: version 1.1.9
deprecation reason: deleted_term
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.
class role: place_holder
subclass of: DeprecatedTerms
subclass of: Restriction
  has value: deleted term
  on property: has reason for deprecation
class source: ontology
subclass of: ExperimentPackage
deprecation in version: 1.1.9
deprecation old restriction: some|has_value|string

has factor value ontology entry
type: ObjectProperty
comment: property indicating that the class has an ontology entry
unique identifier: MO_263

LabeledExtract
type: Class
unique identifier: MO_221
class role: concrete
subclass of: Restriction
  some values from: LabelCompound
  on property: has compound
subclass of: Restriction
  on property: has been treated
  some values from: Treatment
subclass of: BioMaterial
comment: The BioSample after labeling for detection of the nucleic acids.
class source: mage

LabelCompound
type: Class
unique identifier: MO_13
class role: concrete
subclass of: Compound
class source: ontology
comment: Compounds that are used for labeling extracts.

has compound
type: ObjectProperty
comment: property indicating that the class has a compound
unique identifier: MO_302

has been treated
type: FunctionalProperty
unique identifier: MO_341
comment: property indicating that the class has been treated
type: ObjectProperty

Treatment
type: Class
subclass of: BioMaterialPackage
subclass of: Restriction
  on property: has action
  some values from: Action
subclass of: Restriction
  some values from: int
  on property: has order
subclass of: Restriction
  on property: has protocol
  some values from: Protocol
class source: mage
comment: A treatment is the process or action by which a biomaterial is created from an input biomaterial.
unique identifier: MO_23
class role: concrete

Software
type: Class
subclass of: Restriction
  some values from: Hardware
  on property: has hardware
unique identifier: MO_109
class role: concrete
subclass of: Restriction
  on property: has type
  some values from: SoftwareType
comment: The software application used.
subclass of: ProtocolPackage
class source: mage
subclass of: Restriction
  on property: has manufacturer
  some values from: Contact
subclass of: Restriction
  on property: has software
  some values from: Software

Hardware
type: Class
comment: The machine or instrument used.
subclass of: ProtocolPackage
subclass of: Restriction
  on property: has type
  some values from: HardwareType
subclass of: Restriction
  some values from: Software
  on property: has software
subclass of: Restriction
  on property: has model
  some values from: string
subclass of: Restriction
  on property: has make
  some values from: string
class role: concrete
class source: mage
unique identifier: MO_134
subclass of: Restriction
  some values from: Contact
  on property: has manufacturer

has hardware
type: ObjectProperty
unique identifier: MO_286
comment: property indicating that the class has hardware

SoftwareType
type: Class
subclass of: ProtocolPackage
class role: concrete
unique identifier: MO_202
class source: ontology
comment: Controlled terms that provide descriptors for the type of software.

has manufacturer
type: ObjectProperty
unique identifier: MO_232
comment: property indicating that the class has a manufacturer

has software
type: ObjectProperty
comment: property indicating that the class has software
unique identifier: MO_284

ExperimentDesign
type: Class
subclass of: Restriction
  on property: has MAGE description
  some values from: ReplicateDescription
subclass of: Restriction
  some values from: QualityControlDescription
  on property: has MAGE description
unique identifier: MO_170
subclass of: Restriction
  some values from: BioAssay
  on property: has bioassays
subclass of: ExperimentPackage
subclass of: Restriction
  on property: has experiment factors
  some values from: ExperimentalFactor
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.
class source: mage
subclass of: Restriction
  some values from: NormalizationDescription
  on property: has MAGE description
subclass of: Restriction
  some values from: ExperimentDesignType
  on property: has experiment design type
subclass of: Restriction
  on property: has description
  some values from: string
class role: concrete

has MAGE description
type: ObjectProperty
comment: property indicating that the class has an association to a MAGE description
unique identifier: MO_260

QualityControlDescription
type: Class
subclass of: Restriction
  on property: has type
  some values from: QualityControlDescriptionType
subclass of: ExperimentPackage
unique identifier: MO_88
class role: abstract
comment: QualityControlDescription provides details of the quality control aspects of the experiment.
class source: ontology

BioAssay
type: Class
comment: A bioassay is an abstract class representing physical and computational groupings of biomaterials and arrays.
unique identifier: MO_56
class role: abstract
class source: mage
subclass of: BioAssayPackage

has bioassays
type: ObjectProperty
unique identifier: MO_238
comment: property indicating that the class has bioassays

has experiment factors
type: ObjectProperty
unique identifier: MO_328
comment: property indicating that the class has experiment factors

ExperimentalFactor
type: Class
unique identifier: MO_10
comment: The factors in the study that are experimental parameters or regarded as influencing the experimental results.
subclass of: Restriction
  on property: has category
  some values from: BiologicalFactorCategory
subclass of: ExperimentPackage
subclass of: Restriction
  some values from: MethodologicalFactorCategory
  on property: has category
subclass of: Restriction
  some values from: FactorValue
  on property: has factor value
class source: mage
class role: concrete

NormalizationDescription
type: Class
class source: ontology
comment: NormalizationDescription provides details of the normalization strategy for the experiment.
unique identifier: MO_131
class role: abstract
subclass of: Restriction
  on property: has type
  some values from: NormalizationDescriptionType
subclass of: ExperimentPackage

has experiment design type
type: ObjectProperty
comment: property indicating that the class has an experiment design type
unique identifier: MO_288

has description
type: DatatypeProperty
unique identifier: MO_334
comment: property indicating that the class has a description

MGEDExtendedOntology
type: Class
subclass of: MGEDOntology
unique identifier: MO_196
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

ArrayGroup
type: Class
comment: An array group is a physical platform that contains one or more arrays that are separately addressable or a virtual grouping of arrays.
unique identifier: MO_34
class role: concrete
class source: mage
subclass of: Restriction
  some values from: Fiducial
  on property: has fiducials
subclass of: ArrayPackage
subclass of: Restriction
  some values from: SubstrateType
  on property: has type

has fiducials
type: ObjectProperty
unique identifier: MO_267
comment: property indicating that the class has fiducials

SubstrateType
type: Class
subclass of: ArrayPackage
comment: Controlled terms for descriptors of types of array substrates.
unique identifier: MO_79
class source: ontology
class role: concrete

BiologicalFactorCategory
type: Class
subclass of: ExperimentalFactorCategory
comment: Factors that relate to properties of the biomaterial, its treatment, or its growth.
class source: ontology
class role: abstract
unique identifier: MO_190

BioSequenceType
type: Class
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).
subclass of: BioSequencePackage
class role: abstract
unique identifier: MO_152
class source: ontology

Generation
type: Class
class role: place_holder
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.
class source: ontology
subclass of: EnvironmentalHistory
unique identifier: MO_43

PreservationType
type: Class
unique identifier: MO_195
comment: The type of method used to preserve (keep in stasis) the organism or biosource.
subclass of: MGEDExtendedOntology

Histology
type: Class
subclass of: Restriction
  on property: has performer
  some values from: Contact
subclass of: OntologyEntry
subclass of: BioMaterialCharacteristics
class source: ontology
subclass of: Restriction
  some values from: OrganismPart
  on property: has organism part
comment: Microscopic morphology of tissues.
subclass of: Restriction
  some values from: HistologyDatabase
  on property: has database
class role: abstract
unique identifier: MO_194

has performer
type: ObjectProperty
unique identifier: MO_273
comment: property indicating that the protocol has a performer or contact person

HistologyDatabase
type: Class
class role: concrete
unique identifier: MO_175
comment: Database of histology information.
class source: ontology
subclass of: Database

StrandType
type: Class
subclass of: MGEDExtendedOntology
comment: A descriptor of the strand type the sequence feature belongs to. e.g. forward, reverse
unique identifier: MO_7

Experiment
type: Class
subclass of: Restriction
  on property: has experiment design
  some values from: ExperimentDesign
class source: mage
class role: concrete
subclass of: Restriction
  some values from: BibliographicReference
  on property: has citation
subclass of: Restriction
  some values from: BioAssay
  on property: has bioassays
subclass of: Restriction
  on property: has providers
  some values from: Contact
subclass of: Restriction
  on property: has bioassay data
  some values from: BioAssayData
subclass of: ExperimentPackage
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.
unique identifier: MO_112

has experiment design
type: ObjectProperty
unique identifier: MO_291
comment: property indicating that the class has an experiment design

has citation
type: ObjectProperty
comment: property indicating that the class has a citation
unique identifier: MO_274

has providers
type: ObjectProperty
unique identifier: MO_303
comment: property indicating that the class has providers

has bioassay data
type: ObjectProperty
unique identifier: MO_252
comment: property indicating that the class has bioassaydata

ImageFormat
type: Class
comment: Controlled terms for descriptors of the image file format (TIFF, JPEG, GIF, etc.)
class role: concrete
subclass of: BioAssayPackage
class source: ontology
unique identifier: MO_211

BioAssayPackage
type: Class
class role: abstract
unique identifier: MO_0
class source: mage
comment: MAGE package for bioassay.
subclass of: MGEDCoreOntology

FeatureDefect
type: Class
class source: mage
comment: A technical manufacturer described defect for features.
class role: concrete
subclass of: Restriction
  some values from: DefectType
  on property: has type
subclass of: ArrayPackage
unique identifier: MO_138

DefectType
type: Class
class source: ontology
unique identifier: MO_16
class role: concrete
subclass of: ArrayPackage
comment: Defects associated with features or zones such as those that are missing or moved.

NodeValueType
type: Class
class source: ontology
subclass of: HigherLevelAnalysisPackage
class role: concrete
unique identifier: MO_160
comment: Controlled set of terms for describing the type of values (e.g., Euclidean distance).

HigherLevelAnalysisPackage
type: Class
class source: mage
subclass of: MGEDCoreOntology
unique identifier: MO_228
class role: abstract
comment: MAGE package for HigherLevelAnalysis

SomaticModification
type: Class
comment: The organism has had non-genetic parts removed, added, or rearranged.
unique identifier: MO_44
subclass of: Restriction
  some values from: OrganismPart
  on property: has part modified
subclass of: MGEDExtendedOntology

has part modified
type: ObjectProperty
comment: property indicating that the class has a modified part
unique identifier: MO_241

Haplotype
type: Class
class role: place_holder
comment: The genotype of a single chromosome (i.e., the haploid genotype) that is known and relevant to the experiment being performed.
class source: ontology
unique identifier: MO_146
subclass of: IndividualGeneticCharacteristics

ConcentrationUnitOther
type: Class
comment: Concentration units not specified in MAGE.
class source: ontology
class role: concrete
unique identifier: MO_86
subclass of: ConcentrationUnit

ConcentrationUnit
type: Class
unique identifier: MO_61
subclass of: Unit
comment: Units used for concentration measurements.
class role: concrete
class source: ontology

CellType
type: Class
class role: abstract
subclass of: BioMaterialCharacteristics
subclass of: Restriction
  on property: has database
  some values from: CellTypeDatabase
subclass of: OntologyEntry
class source: ontology
unique identifier: MO_135
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
unique identifier: MO_141
comment: Database of cell type information.
class role: concrete
class source: ontology

URI
type: Class
comment: Uniform Resource Identifier
unique identifier: MO_12
subclass of: MGEDCoreOntology
class source: ontology
class role: abstract

DatabaseEntryType
type: Class
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).
class role: concrete
class source: ontology
subclass of: DescriptionPackage
unique identifier: MO_157

DescriptionPackage
type: Class
comment: MAGE package for description of annotations and references to annotations.
subclass of: MGEDCoreOntology
class source: mage
class role: abstract
unique identifier: MO_167

VolumeUnit
type: Class
comment: Units used for volume measurements.
class role: concrete
class source: ontology
subclass of: Unit
unique identifier: MO_179

PublicationType
type: Class
comment: Controlled terms for descriptors of the type of publication such as those used by Medline (review, book, etc.).
class role: concrete
subclass of: DescriptionPackage
unique identifier: MO_208
class source: ontology

Reporter
type: Class
class source: mage
subclass of: Restriction
  some values from: WarningType
  on property: has type
subclass of: Restriction
  on property: has type
  some values from: FailType
subclass of: DesignElement
comment: Description of the material placed on a feature (spot).
unique identifier: MO_74
class role: concrete

FailType
type: Class
class source: ontology
subclass of: DesignElementPackage
unique identifier: MO_98
class role: concrete
comment: Controlled terms for descriptors of failures (as in PCR) associated with reporters.

DesignElement
type: Class
subclass of: Restriction
  some values from: ControlType
  on property: has type
subclass of: DesignElementPackage
comment: Design elements are reporters, features, and composite elements as defined by MAGE.
class source: ontology
class role: concrete
unique identifier: MO_173

has pages
type: DatatypeProperty
domain: BibliographicReference
unique identifier: MO_246
comment: property indicating that the class has pages

has issue
type: DatatypeProperty
comment: property indicating that the class has an issue
domain: BibliographicReference
unique identifier: MO_294

has editor
type: DatatypeProperty
comment: property indicating that the class has an editor
unique identifier: MO_256

has URI
type: FunctionalProperty
comment: property indicating that the class has a URI
unique identifier: MO_340
type: ObjectProperty

has volume
type: DatatypeProperty
unique identifier: MO_308
domain: BibliographicReference
comment: property indicating that the class has a volume

has authors
type: DatatypeProperty
unique identifier: MO_318
comment: property indicating that the class has authors

has year
type: DatatypeProperty
comment: property indicating that the class has a year
unique identifier: MO_322

has publication
type: DatatypeProperty
unique identifier: MO_251
comment: property indicating that the class has a publication

has publisher
type: DatatypeProperty
unique identifier: MO_295
comment: property indicating that the class has a publisher

has title
type: DatatypeProperty
comment: property indicating that the class has a title
unique identifier: MO_337

TestTypeDatabase
type: Class
class source: ontology
subclass of: Database
unique identifier: MO_76
class role: concrete
comment: Database of codes for clinical findings.

CellularComponent
type: Class
comment: A structure within a cell, such as an anatomical structure (e.g. rough endoplasmic reticulum or nucleus) or a gene product group (e.g. ribosome, proteasome or a protein dimer).
class role: abstract
unique identifier: MO_1020
subclass of: Restriction
  on property: has database
  some values from: CellularComponentDatabase
subclass of: OntologyEntry
subclass of: BioMaterialCharacteristics
class source: ontology

CellularComponentDatabase
type: Class
class source: ontology
comment: A resource for terms to describe cellular components, e.g. GO Cellular Component ontology.
unique identifier: MO_1021
subclass of: Database
class role: concrete

IndividualChromosomalAbnormality
type: Class
unique identifier: MO_185
subclass of: Restriction
  has value: version 1.2.0
  on property: deprecated from version
class source: ontology
deprecation reason: deleted_term
subclass of: Restriction
  on property: has reason for deprecation
  has value: deleted term
subclass of: DeprecatedTerms
deprecation in version: 1.2.0
subclass of: IndividualGeneticCharacteristics
deprecation old parent: 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.
class role: place_holder

version 1.2.0
type: MGEDOntologyVersion
unique identifier: MO_1033
comment: Version of the MGEDOntology.

deprecated from version
type: ObjectProperty
comment: property indicating the version of the MGED Ontology that the term was deprecated from
unique identifier: MO_299

has reason for deprecation
type: ObjectProperty
comment: property to indicate the reason for deprecating a term
unique identifier: MO_306

deleted term
type: DeprecationReason
comment: The term was deleted from the MGED CoreOntology.
unique identifier: MO_1023

DeprecatedTerms
type: Class
class role: concrete
class source: ontology
comment: Class to hold deprecated instances and classes.
subclass of: Restriction
  some values from: DeprecationReason
  on property: has reason for deprecation
subclass of: MGEDCoreOntology
unique identifier: MO_206

DeprecationReason
type: Class
class role: concrete
unique identifier: MO_94
class source: ontology
comment: class to hold instances used as the filler for the property has_reason_for_deprecation
subclass of: MGEDCoreOntology

has version
type: DatatypeProperty
comment: property indicating that the class has a version
unique identifier: MO_239

Sex
type: Class
unique identifier: MO_168
class source: ontology
class role: concrete
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.
subclass of: BioMaterialCharacteristics

BioSourceType
type: Class
class role: concrete
unique identifier: MO_95
comment: The form in which the BioMaterial was obtained/maintained e.g. frozen, fresh etc. Note can be used to describe BioSamples as well as BioSources.
subclass of: BioMaterialCharacteristics
class source: ontology

PathogenTest
type: Class
class role: abstract
class source: ontology
subclass of: EnvironmentalHistory
subclass of: Restriction
  on property: was tested for
  some values from: Organism
subclass of: Restriction
  on property: has result
  some values from: Result
unique identifier: MO_184
comment: Tests and results for pathogens infecting organism from which the biosource is derived

was tested for
type: ObjectProperty
unique identifier: MO_265
comment: property indicating that the class was tested for

has result
type: ObjectProperty
unique identifier: MO_324
comment: property indicating the class has a result

ObservationDatabase
type: Class
class role: concrete
unique identifier: MO_91
comment: Database of terms for observations such as 'abnormal coat', 'skin pigment abnormality' describing macroscopic examinations.
subclass of: Database
class source: ontology

CellLine
type: Class
comment: The identifier for the established culture of a metazoan cell if one was used as a biomaterial.
class source: ontology
class role: abstract
subclass of: OntologyEntry
subclass of: BioMaterialCharacteristics
subclass of: Restriction
  some values from: CellLineDatabase
  on property: has database
unique identifier: MO_49

CellLineDatabase
type: Class
subclass of: Database
class source: ontology
class role: concrete
comment: Database of cell line information.
unique identifier: MO_145

ComplexAction
type: Class
unique identifier: MO_90
subclass of: Action
class source: ontology
comment: Complex actions are composed of multiple steps (as opposed to AtomicAction) e.g. mRNA labeling, protein purification.
class role: concrete

Action
type: Class
class role: abstract
unique identifier: MO_193
class source: ontology
comment: Procedures used during treatment.
subclass of: BioMaterialPackage
subclass of: BiologicalFactorCategory

version 1.1.9
type: MGEDOntologyVersion
comment: Version of the MGEDOntology.
unique identifier: MO_1032

TargetedCellTypeDatabase
type: Class
unique identifier: MO_45
class source: ontology
subclass of: Database
class role: concrete
comment: Database of targeted cell type information.

MassUnit
type: Class
comment: Units used for mass measurements.
class role: concrete
class source: ontology
unique identifier: MO_149
subclass of: Unit

BioSourceProvider
type: Class
class role: abstract
comment: The resource (e.g. company, hospital, geographical location) used to obtain or purchase the biomaterial.
unique identifier: MO_230
class source: ontology
subclass of: Restriction
  on property: has owner
  some values from: Person
subclass of: BioMaterialCharacteristics
subclass of: Restriction
  on property: has donor
  some values from: Organization

has owner
type: FunctionalProperty
type: ObjectProperty
comment: property indicating that the class has an owner
unique identifier: MO_278

Person
type: Class
subclass of: Restriction
  on property: has first name
  some values from: string
class role: concrete
unique identifier: MO_24
subclass of: Restriction
  on property: has last name
  some values from: string
subclass of: Restriction
  some values from: Organization
  on property: has affiliation
class source: mage
comment: The individual to contact regarding something provided such as a biomaterial.
subclass of: Contact
subclass of: Restriction
  on property: has mid initials
  some values from: string

has donor
type: FunctionalProperty
unique identifier: MO_342
type: ObjectProperty
comment: property indicating that the class has a donor

Organization
type: Class
class source: mage
class role: concrete
comment: The organization (e.g. company, hospital) to contact to obtain or purchase something.
subclass of: Restriction
  on property: has name
  some values from: string
subclass of: Contact
subclass of: Restriction
  some values from: Organization
  on property: has parent organization
unique identifier: MO_177

has disease location
type: ObjectProperty
unique identifier: MO_290
comment: property indicating the location of the disease.

DiseaseLocation
type: Class
class role: concrete
class source: ontology
unique identifier: MO_37
comment: Anatomical location(s) of disease.
subclass of: Restriction
  on property: has cancer site
  some values from: CancerSite
subclass of: OrganismPart

has disease staging
type: ObjectProperty
comment: property indicating that the class has disease staging
unique identifier: MO_275

DiseaseStaging
type: Class
class source: ontology
unique identifier: MO_133
subclass of: BioMaterialCharacteristics
subclass of: Restriction
  some values from: DiseaseStagingDatabase
  on property: has database
subclass of: OntologyEntry
comment: The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression.
class role: abstract

DiseaseStateDatabase
type: Class
unique identifier: MO_181
subclass of: Database
class role: concrete
comment: Database of disease state information.
class source: ontology

PopulationDensity
type: Class
unique identifier: MO_46
subclass of: GrowthCondition
class source: ontology
comment: The concentration range of the organism.
class role: abstract

TimeUnit
type: Class
comment: Units used for time measurements.
unique identifier: MO_166
class role: concrete
class source: ontology
subclass of: Unit

HigherLevelAnalysisProtocolType
type: Class
subclass of: ProtocolType
comment: A protocol which yields a dataset(s) from which biological conclusions can be derived. E.g. clustering (not normalization or averaging).
class role: concrete
class source: ontology
unique identifier: MO_47

Test
type: Class
class source: ontology
comment: An assay performed on a biomaterial for the purposes of determining one or more biomaterial characteristics e.g. clinical chemistry.
unique identifier: MO_197
class role: abstract
subclass of: Restriction
  some values from: Contact
  on property: has performer
subclass of: BioMaterialCharacteristics
subclass of: Restriction
  some values from: TestType
  on property: has test type
subclass of: Restriction
  some values from: TestResult
  on property: has test result

has test result
type: ObjectProperty
comment: property indicating that the test has a test result
unique identifier: MO_261

Image
type: Class
class role: concrete
unique identifier: MO_22
class source: mage
subclass of: DescriptionPackage
subclass of: Restriction
  on property: has URI
  some values from: URI
subclass of: Restriction
  some values from: ImageFormat
  on property: has image format
subclass of: Restriction
  on property: has database
  some values from: Database

has image format
type: ObjectProperty
comment: property indicating that the class has an image format
domain: PhysicalBioAssay
unique identifier: MO_234

VolumeUnitOther
type: Class
class role: place_holder
unique identifier: MO_155
subclass of: VolumeUnit
class source: ontology
comment: Volume units not specified in MAGE.

TumorGrading
type: Class
comment: A descriptor used in cancer biology to describe abnormalities of tumor cells. E.g. an instance from NCI Thesaurus.
subclass of: Restriction
  on property: has database
  some values from: TumorGradingDatabase
subclass of: BioMaterialCharacteristics
subclass of: OntologyEntry
unique identifier: MO_28
class role: abstract
class source: ontology

Allele
type: Class
class source: ontology
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.
class role: concrete
unique identifier: MO_58

has text
type: DatatypeProperty
comment: property indicating that the class has text
unique identifier: MO_298

GeneticMaterial
type: Class
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.
unique identifier: MO_137
subclass of: MGEDExtendedOntology

Media
type: Class
unique identifier: MO_19
comment: The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil) .
class source: ontology
class role: concrete
subclass of: GrowthCondition

Node
type: Class
unique identifier: MO_73
class source: mage
subclass of: Restriction
  on property: has node value
  some values from: NodeValue
subclass of: HigherLevelAnalysisPackage
class role: concrete
comment: A node is an individual component of BioAssayDataCluster that groups design elements, quantitation types, and BioAssays together. A node may contain other nodes.

has node value
type: ObjectProperty
comment: property indicating that the class has a node value
unique identifier: MO_310

NodeValue
type: Class
class role: concrete
comment: Node values allow the organization of the nodes in relation to other nodes produced by mathematical functions such as a clustering algorithm.
subclass of: Restriction
  on property: has node value type
  some values from: NodeValueType
subclass of: Restriction
  some values from: Scale
  on property: has scale
subclass of: HigherLevelAnalysisPackage
subclass of: Restriction
  on property: has type
  some values from: DataType
class source: mage
unique identifier: MO_104

BioSource
type: Class
unique identifier: MO_77
class role: concrete
class source: mage
subclass of: BioMaterial
comment: The BioSource is the original source material before any treatment events.

LightUnit
type: Class
unique identifier: MO_119
class source: ontology
comment: Units for measuring the intensity of light.
subclass of: OtherUnit
class role: concrete

OtherUnit
type: Class
class source: ontology
comment: Other units are those types not specified in MAGE such as lumens, radioactivity, etc.
unique identifier: MO_199
class role: concrete
subclass of: Unit

BarrierFacility
type: Class
class role: abstract
comment: Rating of containment system for the protection of organisms from infectious agents.
class source: ontology
subclass of: GrowthCondition
unique identifier: MO_97

BioMaterialPurity
type: Class
class role: abstract
class source: ontology
unique identifier: MO_20
subclass of: BioMaterialCharacteristics
comment: A measure of homogeneity of a biomaterial. For example, an expression of the percentage of a tumor biopsy that is tumor cells.

has accession version
type: DatatypeProperty
comment: property indicating that the class has an accession number version
unique identifier: MO_339

has accession
type: DatatypeProperty
comment: property indicating that the class has an accession number
unique identifier: MO_231

has database entry type
type: ObjectProperty
unique identifier: MO_240
comment: property indicating that the class has a database entry type

DistanceUnit
type: Class
comment: Units used for distance measurements.
class role: concrete
unique identifier: MO_4
class source: ontology
subclass of: Unit

DistanceUnitOther
type: Class
subclass of: DistanceUnit
comment: Distance units not specified in MAGE.
unique identifier: MO_143
class role: place_holder
class source: ontology

HardwareVariation
type: Class
class source: ontology
comment: The effects of different hardware, types of hardware, or models of hardware on experimental results are studied.
unique identifier: MO_81
subclass of: MethodologicalFactorCategory
class role: place_holder

BioAssayDataCluster
type: Class
class source: mage
unique identifier: MO_116
comment: A grouping of bioassay data that has been organized by one or more mathematical functions into nodes.
class role: concrete
subclass of: Restriction
  some values from: Node
  on property: has nodes
subclass of: HigherLevelAnalysisPackage

has nodes
type: ObjectProperty
unique identifier: MO_307
comment: property indicating that the class has a node

Preservation
type: Class
subclass of: Restriction
  some values from: Protocol
  on property: has protocol
subclass of: Restriction
  on property: has type
  some values from: PreservationType
subclass of: MGEDExtendedOntology
unique identifier: MO_176
comment: Method and type of preserving the organism or biosource (i.e. keeping it in stasis).

Genotype
type: Class
class source: ontology
class role: concrete
subclass of: IndividualGeneticCharacteristics
comment: The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.
unique identifier: MO_51

MGEDOntologyVersion
type: Class
class role: concrete
comment: The version of the MGED Ontology.
unique identifier: MO_115
subclass of: MGEDCoreOntology
class source: ontology

BioMaterialCharacteristicCategory
type: Class
unique identifier: MO_100
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.
subclass of: BiologicalFactorCategory

has address
type: DatatypeProperty
comment: property indicating that the class has an address
unique identifier: MO_277

has phone
type: DatatypeProperty
comment: property indicating that the class has a phone
unique identifier: MO_235

has email
type: DatatypeProperty
comment: property indicating that the class has an email address
unique identifier: MO_293

has fax
type: DatatypeProperty
unique identifier: MO_289
comment: property indicating that the class has a fax

has toll free phone
type: DatatypeProperty
comment: property indicating that the class has a toll free phone
unique identifier: MO_329

Humidity
type: Class
subclass of: GrowthCondition
class source: ontology
class role: abstract
comment: The humidity that the biosource is exposed to.
unique identifier: MO_29

BioSequence
type: Class
unique identifier: MO_163
class source: mage
comment: A representation of a DNA, RNA, or protein sequence.
subclass of: Restriction
  on property: has species
  some values from: Organism
subclass of: Restriction
  some values from: PolymerType
  on property: has type
subclass of: Restriction
  some values from: BioSequenceType
  on property: has type
subclass of: BioSequencePackage
class role: concrete

PolymerType
type: Class
class source: ontology
comment: Controlled terms for descriptors of the type of polymer (RNA, DNA, protein) of the biosequence.
unique identifier: MO_102
subclass of: BioSequencePackage
class role: concrete

TemperatureUnit
type: Class
unique identifier: MO_48
subclass of: Unit
class source: ontology
class role: concrete
comment: Units used for temperature measurements.

ControlType
type: Class
class role: concrete
comment: Controlled terms for descriptors for the type of control design element.
subclass of: DesignElementPackage
unique identifier: MO_50
class source: ontology

BioSampleType
type: Class
subclass of: BioMaterialPackage
class source: ontology
class role: concrete
comment: Used to tell when the BioSample is an extract or not.
unique identifier: MO_161

QualityControlDescriptionType
type: Class
class source: ontology
class role: concrete
unique identifier: MO_121
subclass of: ExperimentPackage
comment: Controlled descriptors for the quality control strategy for an experiment.

BiologicalProperty
type: Class
class source: ontology
unique identifier: MO_224
comment: A biological property experiment design type is where an intrinsic characteristic of an organism(s) or biological system is examined.
subclass of: ExperimentDesignType
class role: concrete

DiseaseStagingDatabase
type: Class
class source: ontology
subclass of: Database
class role: concrete
comment: Database of disease staging information
unique identifier: MO_225

Ploidy
type: Class
comment: The number of single sets of chromosomes in the cell or an organism e.g., haploid, diploid, triploid, etc.
class role: concrete
subclass of: IndividualGeneticCharacteristics
unique identifier: MO_220
class source: ontology

ExperimentalProtocolType
type: Class
unique identifier: MO_75
subclass of: ProtocolType
comment: All protocols which involve treatment of a biomaterial or an array during the course of a microarray experiment.
class role: concrete
class source: ontology

has action
type: ObjectProperty
comment: property indicating that the class has an action
unique identifier: MO_312

has order
type: DatatypeProperty
unique identifier: MO_335
comment: property indicating that the class has an order

AtomicAction
type: Class
unique identifier: MO_68
class source: ontology
subclass of: Action
comment: An atomic action is a single step process on the biomaterial, e.g. mix by inversion, wait, add
class role: concrete

EpidemiologicalDesign
type: Class
class role: concrete
class source: ontology
subclass of: ExperimentDesignType
unique identifier: MO_142
comment: An epidemiological experiment design type is where the biosource history is studied e.g. environmental, clinical and family history.

PhysicalBioSequenceType
type: Class
subclass of: BioSequenceType
class source: ontology
unique identifier: MO_92
comment: A physical biosequence type represents biological sequence that can be physically placed (spotted or synthesized) on an array e.g. BAC, PAC.
class role: concrete

SamplingTimePoint
type: Class
class role: abstract
subclass of: EnvironmentalHistory
class source: ontology
comment: A descriptor of the time point that a sample was taken. Not to be used where the sample is part of a time course. SamplingTimePoint is not related to age. An instance could be summer, a date, a time, or a range value.
unique identifier: MO_139

Observation
type: Class
comment: Observation will record the macroscopic examination of the biomaterial.
class role: abstract
unique identifier: MO_53
subclass of: Restriction
  some values from: Contact
  on property: has performer
subclass of: Restriction
  on property: has database
  some values from: ObservationDatabase
subclass of: BioMaterialCharacteristics
class source: ontology

has category
type: ObjectProperty
unique identifier: MO_249
comment: property indicating that the class has a category

has factor value
type: ObjectProperty
comment: property indicating that the class has a factor value
unique identifier: MO_236

has model
type: DatatypeProperty
comment: property indicating that the class has a model
unique identifier: MO_270
domain: Hardware

has make
type: DatatypeProperty
domain: Hardware
unique identifier: MO_271
comment: property indicating that the class has a make

OrganismStatus
type: Class
unique identifier: MO_84
subclass of: BioMaterialCharacteristics
class source: ontology
comment: The stage premortem or postmortem at which the sample was processed for extraction of biomaterials.
class role: concrete

has cancer site
type: ObjectProperty
unique identifier: MO_248
comment: property indicating that the class has a cancer site

Light
type: Class
comment: The photoperiod and type (e.g., natural, restricted wavelength) of light exposure.
unique identifier: MO_60
class role: abstract
subclass of: GrowthCondition
class source: ontology

ClinicalTreatmentDatabase
type: Class
unique identifier: MO_114
comment: Database of clinical treatment information
class role: concrete
subclass of: Database
class source: ontology

has node value type
type: ObjectProperty
comment: property indicating that the class has a node value type
unique identifier: MO_264

Scale
type: Class
subclass of: MGEDCoreOntology
unique identifier: MO_108
class source: ontology
comment: The scale (linear, log10, ln, etc) used to represent the value.
class role: concrete

has scale
type: ObjectProperty
comment: property indicating that the class has a scale
unique identifier: MO_287

Ecotype
type: Class
class source: ontology
class role: abstract
unique identifier: MO_71
subclass of: Restriction
  on property: has database
  some values from: StrainOrLineDatabase
subclass of: StrainOrLine
comment: a biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler

TargetedCellType
type: Class
class role: abstract
subclass of: OntologyEntry
subclass of: BioMaterialCharacteristics
class source: ontology
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.
unique identifier: MO_123

FeatureGroup
type: Class
class source: mage
unique identifier: MO_54
comment: Technology-based grouping of features representing individual locations on the array.
class role: concrete
subclass of: DesignElementGroup
subclass of: Restriction
  on property: has feature shape
  some values from: FeatureShape
subclass of: Restriction
  on property: has type
  some values from: TechnologyType

DesignElementGroup
type: Class
class source: mage
unique identifier: MO_128
comment: A DesignElementGroup holds information on Features, Reporters, or CompositeSequences.
class role: abstract
subclass of: Restriction
  on property: has species
  some values from: Organism
subclass of: Restriction
  some values from: DesignElementGroupType
  on property: has type
subclass of: ArrayDesignPackage

has feature shape
type: ObjectProperty
comment: property indicating that the class has a feature shape
unique identifier: MO_268

TechnologyType
type: Class
class source: ontology
class role: concrete
subclass of: ArrayDesignPackage
comment: The technology type or platform of the reporters on the array.
unique identifier: MO_18

is solvent
type: DatatypeProperty
comment: property indicating that the class is a solvent
unique identifier: MO_332

CompoundDatabase
type: Class
subclass of: Database
comment: Database of compound information.
class role: concrete
unique identifier: MO_151
class source: ontology

ChromosomalAberration
type: Class
subclass of: Restriction
  has value: deleted term
  on property: has reason for deprecation
deprecation in version: 1.1.7
comment: An abnormality of a chromosome's number or structure, which excludes simple changes in sequence and is usually detectable by cytogenetic and microscopic techniques such as FISH.
subclass of: Restriction
  on property: has chromosomal aberration classification
  some values from: ChromosomalAberrationClassification
deprecation reason: deleted_term
class role: abstract
subclass of: DeprecatedTerms
unique identifier: MO_78
subclass of: Restriction
  on property: deprecated from version
  has value: version 1.1.7
deprecation old restriction: some|has_chromosomal_aberration_classification|ChromosomalAberrationClassification
class source: ontology

has chromosomal aberration classification
type: ObjectProperty
comment: property indicating that the class has a chromosomal aberration classification
unique identifier: MO_253

version 1.1.7
type: MGEDOntologyVersion
unique identifier: MO_1031
comment: Version of the MGED Ontology.

PhysicalBioAssay
type: Class
subclass of: Restriction
  on property: has image format
  some values from: ImageFormat
subclass of: BioAssay
unique identifier: MO_99
comment: A physical bioassay is the combination of arrays and biomaterials as in a hybridization.
class role: concrete
class source: mage

RadiationUnit
type: Class
comment: Units for measuring decay of a radioactive isotope over time.
class source: ontology
unique identifier: MO_204
subclass of: OtherUnit
class role: concrete

ProtocolParameterType
type: Class
subclass of: MGEDExtendedOntology
unique identifier: MO_164
comment: Descriptors for protocol parameter types, e.g. compound concentration, media type.

OrganismPartDatabase
type: Class
comment: Database of organism part information.
class source: ontology
class role: concrete
unique identifier: MO_200
subclass of: Database

has first name
type: DatatypeProperty
comment: property indicating that the class has a first name
unique identifier: MO_258

has last name
type: DatatypeProperty
comment: property indicating that the class has a last name
unique identifier: MO_255

has affiliation
type: ObjectProperty
comment: property indicating that the class has an affiliation to an institution
unique identifier: MO_309

has mid initials
type: DatatypeProperty
comment: property indicating that the class has a middle initials
unique identifier: MO_237

GeneticModification
type: Class
unique identifier: MO_122
subclass of: BioMaterialCharacteristics
comment: The genetic modification introduced into the organism from which the biomaterial was derived. Examples of genetic modification include specification of a transgene or the gene knocked-out or details of transient transfection.
class role: concrete
class source: ontology

Serotype
type: Class
unique identifier: MO_159
comment: An antigenic property of a cell (e.g. bacteria, RBC) or virus identified by serological methods
class role: place_holder
subclass of: BioMaterialCharacteristics
class source: ontology

SoftwareVariation
type: Class
class source: ontology
comment: The effects of different software, software packages, or software versions on experimental results are studied.
class role: place_holder
subclass of: MethodologicalFactorCategory
unique identifier: MO_222

TechnologicalDesign
type: Class
comment: The purpose(s) for which the array is used within an experiment, e.g. to assess the transcriptome, the genomic content, or to identify transcription factor binding sites.
class role: concrete
unique identifier: MO_21
subclass of: ExperimentDesignType
class source: ontology

TimeUnitOther
type: Class
class role: concrete
comment: Time units not specified in MAGE.
class source: ontology
unique identifier: MO_103
subclass of: TimeUnit

HistoryFactor
type: Class
unique identifier: MO_82
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).

ProtocolVariation
type: Class
unique identifier: MO_140
comment: The effects of different protocols or changes in protocols on experimental results are studied.
subclass of: MGEDExtendedOntology

NormalizationDescriptionType
type: Class
comment: Controlled descriptors for the normalization strategy used for the experiment.
class source: ontology
unique identifier: MO_27
subclass of: ExperimentPackage
class role: concrete

DesignElementGroupType
type: Class
comment: Controlled set of descriptors for indicating the specific type of a Feature, Reporter, or CompositeSequence.
class source: ontology
class role: concrete
subclass of: ArrayDesignPackage
unique identifier: MO_14

TheoreticalBioSequenceType
type: Class
class role: concrete
subclass of: BioSequenceType
unique identifier: MO_42
class source: ontology
comment: A theoretical biosequence type is an abstraction used for annotation design of elements, e.g. gene, intron.

Temperature
type: Class
subclass of: GrowthCondition
unique identifier: MO_171
comment: The temperature that a biosource is exposed to.
class source: ontology
class role: abstract

Atmosphere
type: Class
class role: abstract
unique identifier: MO_219
comment: The atmospheric conditions used to culture or grow an organism.
subclass of: GrowthCondition
subclass of: Restriction
  on property: has atmospheric component
  some values from: Compound
class source: ontology

has atmospheric component
type: ObjectProperty
unique identifier: MO_259
comment: property indicating that the class has an atmospheric component

PerturbationalDesign
type: Class
comment: A perturbational design type is where the organism(s) are treated or manipulated or modified, for example a genetic modification, somatic modification
class source: ontology
class role: concrete
subclass of: ExperimentDesignType
unique identifier: MO_106

BioSample
type: Class
class role: concrete
class source: mage
comment: The BioSource after any treatment.
unique identifier: MO_93
subclass of: Restriction
  on property: has type
  some values from: BioSampleType
subclass of: Restriction
  some values from: Treatment
  on property: has been treated
subclass of: BioMaterial

MassUnitOther
type: Class
class role: place_holder
comment: Mass units not specified in MAGE.
subclass of: MassUnit
unique identifier: MO_11
class source: ontology

User
type: Class
subclass of: Restriction
  on property: has ID
  some values from: string
subclass of: MGEDExtendedOntology
comment: User is a way to id a person in a database
unique identifier: MO_62

has ID
type: DatatypeProperty
unique identifier: MO_323
comment: property indicating that the class has an identifier

PhenotypeDatabase
type: Class
subclass of: Database
class role: concrete
class source: ontology
comment: Database of phenotype information
unique identifier: MO_39

DeliveryMethod
type: Class
subclass of: MGEDExtendedOntology
unique identifier: MO_223
comment: Method used to deliver a compound for treatment.

FamilyHistory
type: Class
class role: abstract
unique identifier: MO_59
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.
class source: ontology

has family member
type: ObjectProperty
comment: property indicating that the class has a family member
unique identifier: MO_243

Nutrients
type: Class
subclass of: Restriction
  on property: has nutrient component
  some values from: Compound
subclass of: GrowthCondition
unique identifier: MO_127
comment: The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.).
class role: abstract
class source: ontology

has nutrient component
type: ObjectProperty
comment: property indicating that the class has a nutrient component
unique identifier: MO_321

QuantitationType
type: Class
class role: abstract
unique identifier: MO_67
subclass of: Restriction
  on property: has scale
  some values from: Scale
subclass of: Restriction
  some values from: DataType
  on property: has type
subclass of: QuantitationTypePackage
class source: mage
comment: The QuantitationType provides a method for calculating a single datum of the BioAssayData matrix.

PhysicalArrayDesign
type: Class
unique identifier: MO_212
subclass of: Restriction
  on property: has type
  some values from: SurfaceType
subclass of: ArrayDesignPackage
class source: mage
comment: Descriptions pertaining to the array.
class role: concrete

Phenotype
type: Class
class source: ontology
subclass of: Restriction
  some values from: PhenotypeDatabase
  on property: has database
subclass of: OntologyEntry
subclass of: BioMaterialCharacteristics
unique identifier: MO_192
comment: The observable form taken by some character (or group of characters) in an individual or an organism, excluding pathology and disease. The detectable outward manifestations of a specific genotype.
class role: abstract

ZoneDefect
type: Class
comment: A technical manufactured described defect for zones.
class role: concrete
subclass of: ArrayPackage
subclass of: Restriction
  on property: has type
  some values from: DefectType
unique identifier: MO_105
class source: mage

has name
type: DatatypeProperty
unique identifier: MO_296
comment: property indicating that the class has a name

has parent organization
type: ObjectProperty
unique identifier: MO_257
comment: property indicating that the class has a parent organization

Cultivar
type: Class
comment: a plant variety obtained in agriculture in horticulture
class role: abstract
subclass of: StrainOrLine
subclass of: Restriction
  some values from: StrainOrLineDatabase
  on property: has database
class source: ontology
unique identifier: MO_124

EnvironmentalStress
type: Class
unique identifier: MO_227
subclass of: Restriction
  on property: has measurement
  some values from: Measurement
subclass of: MGEDExtendedOntology
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

SequenceOntologyBioSequenceType
type: Class
unique identifier: MO_25
class source: ontology
subclass of: Restriction
  on property: has database
  some values from: SequenceOntologyDatabase
subclass of: OntologyEntry
subclass of: PhysicalBioSequenceType
subclass of: TheoreticalBioSequenceType
class role: abstract
comment: Descriptors of biosequence based on the Sequence Ontology (SO) project.

DerivedBioAssayType
type: Class
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.
class source: ontology
class role: concrete
unique identifier: MO_111
subclass of: BioAssayPackage

DerivedBioAssay
type: Class
comment: A BioAssay that is created by the transformation of measured or derived BioAssays.
subclass of: BioAssay
subclass of: Restriction
  some values from: DerivedBioAssayType
  on property: has type
unique identifier: MO_209
class source: mage
class role: concrete

was replaced by
type: ObjectProperty
unique identifier: MO_304
comment: instance property to indicate what the term was replaced by

has test protocol
type: ObjectProperty
unique identifier: MO_244
comment: property indicating that the test has a test protocol

has laboratory test
type: ObjectProperty
comment: property indicating that the class has a laboratory test
unique identifier: MO_281

has human readable URI
type: DatatypeProperty
unique identifier: MO_330
comment: property indicating that the contents found at this uri are human readable

has machine readable URI
type: DatatypeProperty
comment: property indicating that the contents found at this uri are machine readable (i.e. in a standard format)
unique identifier: MO_336

has biosource type
type: FunctionalProperty
domain: BioSourceProvider
comment: property indicating that the class has a biosource type
type: ObjectProperty
unique identifier: MO_315

GIF
type: ImageFormat
comment: Graphics Interchange Format , a common image data format containing RGB data compressed with fairly high data loss.
unique identifier: MO_963

deprecation replacement term
type: AnnotationProperty
type: ObjectProperty
comment: The value of the property indicates the replacement term for the deprecated term. If the term is deprecated without replacement, the value of the property will be the same as the deprecated term itself.
unique identifier: MO_1012

egg laying
type: InitialTimePoint
unique identifier: MO_767
comment: The point at which the egg(s) is laid by an organism.

hybridization chamber
type: HardwareType
comment: A chamber in which the hybridization is performed which maintains constant conditions.
unique identifier: MO_563

nl
type: VolumeUnit
comment: nanoliter unit of volume
unique identifier: MO_754

population density
type: EnvironmentalFactorCategory
unique identifier: MO_650
comment: The concentration range of the organism.

pl
type: VolumeUnit
unique identifier: MO_905
comment: picoliter, volume unit

vacuum dryer
type: HardwareType
unique identifier: MO_696
comment: An instrument designed to remove excess liquid by vacuum and heating.

MBEI
type: DerivedBioAssayType
comment: Multiarray-Based Expression Index (MBEI). A quantitative measure of the relative abundance of a transcript. MBEI is used in the dChip software to obtain a signal intensity from a group of related Features on an Affymetrix array.
unique identifier: MO_756

individual genetic characteristics design
type: BiologicalProperty
unique identifier: MO_527
comment: An experiment design type where genotype, haplotype, or other individual genetic characteristics are compared.

disease state design
type: PerturbationalDesign
type: EpidemiologicalDesign
comment: An experiment design type in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress.
unique identifier: MO_902

version 1.1.8
type: MGEDOntologyVersion
unique identifier: MO_469
comment: Version of the MGED Ontology.

mtDNA
type: DeprecatedTerms
unique identifier: MO_581
deprecation reason: deleted_term
deprecation in version: 1.3.1.1
deprecation replacement term: PhysicalBioSequenceType
deprecation old parent: PhysicalBioSequenceType
comment: sequence from the mitochondrial genome

absolute
type: MeasurementType
comment: a measurement where the value is independent of other measurements
unique identifier: MO_741

days
type: TimeUnit
synonym: d
comment: 24 hours, time unit
unique identifier: MO_513

K
type: TemperatureUnit
unique identifier: MO_614
comment: Kelvin, unit of temperature

g
type: MassUnit
unique identifier: MO_825
comment: gram, unit of mass

intergenic
type: DeprecatedTerms
deprecation replacement term: TheoreticalBioSequenceType
deprecation reason: deleted_term
unique identifier: MO_463
comment: sequence from the region between genes
deprecation in version: 1.2.0
has reason for deprecation: deleted term
deprecated from version: version 1.2.0
deprecation old parent: TheoreticalBioSequenceType

incubate
type: ExperimentalProtocolType
type: ComplexAction
unique identifier: MO_965
comment: The procedure of placing a physical object under specified conditions e.g. time, temperature, humidity for the purposes of obtaining a different product.

oligosomy
type: ChromosomalAberrationClassification
unique identifier: MO_1028
comment: A state or condition describing a cell or organism that has fewer copies of a single chromosome than the usual complement.

behavioral stimulus
type: ExperimentalProtocolType
unique identifier: MO_674
type: ComplexAction
comment: The organism is forced to respond to a stimulus with some behavior (e.g., avoidance, obtaining a reward, etc.)

bioassay replicate reduction
type: DerivedBioAssayType
unique identifier: MO_976
comment: Results of data reduction involving computation of a representative value, e.g. averaging across a group of identical Features, Reporters or CompositeSequences from 2 or more hybridizations, matched replicate spots on 2D gels run from the same or an equivalent sample, or repeat measurements of the same metabolite in replicate cell cultures.

book
type: PublicationType
unique identifier: MO_627
comment: A publication type which has an ISBN.

atmosphere
type: EnvironmentalFactorCategory
unique identifier: MO_498
comment: The atmospheric conditions used to culture or grow an organism.

operon identification design
type: BioMolecularAnnotation
comment: An operon identification experiment type is designed to identify locations and members of operons in a genome.
unique identifier: MO_772

secreted protein identification design
type: BioMolecularAnnotation
unique identifier: MO_694
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.

irregular shape
type: DefectType
unique identifier: MO_669
comment: The perimeter of the spotted DNA on the slide is irregular.

array platform variation design
type: MethodologicalDesign
comment: An experiment in which the array platform is compared, e.g. Agilent versus Affy.
unique identifier: MO_899

intraperitoneal injection
type: DeliveryMethod
comment: A delivery method for compound or drug whereby the substance is administered via the peritoneum.
unique identifier: MO_473

PCR amplification
type: ComplexAction
comment: Amplification of nucleic acid sequence by use of the polymerase chain reaction whereby the number of templates grows geometrically with each cycle.
unique identifier: MO_358
type: ExperimentalProtocolType

split to term
type: AnnotationProperty
comment: The value of the property indicates a replacement term since the term was split.
unique identifier: MO_1017
type: ObjectProperty

condition specificity
type: HigherLevelAnalysisProtocolType
comment: An analysis aimed at ranking genes or transcripts according to the uniformity of expression across a set of conditions. For example, the analysis can be used to rank genes according to the degree of tissue or developmental stage specificity.
unique identifier: MO_417

consultant
type: Roles
unique identifier: MO_984
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.

date
type: DataType
comment: Time stated in terms of the day, month, and year.
unique identifier: MO_587

FlyBase developmental stage database
type: DevelopmentalStageDatabase
unique identifier: MO_865
comment: uri for FlyBase developmental stage terms
has machine readable URI: http://cvs.sourceforge.net/viewcvs.py/*checkout*/obo/obo/ontology/developmental/animal_development/fly/fly_development.ontology

multiple testing correction
type: HigherLevelAnalysisProtocolType
unique identifier: MO_561
comment: Multiple testing correction uses individual p-values derived from multiple statistical tests to control either the family-wise error rate or the false discovery rate.

starvation
type: ComplexAction
comment: Depriving an organism of food or nutrients
unique identifier: MO_370
type: ExperimentalProtocolType

premortem
type: OrganismStatus
comment: sample which has been removed prior to the death of an organism
unique identifier: MO_705

deprecation old restriction
type: AnnotationProperty
comment: The value of the property indicates the restriction that was applied to the class at the time it was deprecated. The value is in the form of: some|property|filler, e.g. some|has_species|Organism.
type: DatatypeProperty
unique identifier: MO_1015

positive integer
type: DataType
unique identifier: MO_629
comment: An integer > 0.

biological replicate
type: QualityControlDescriptionType
unique identifier: MO_952
type: ReplicateDescriptionType
comment: A replicate that consists of independent biological replicates made from different individual BioSources.

uM
type: ConcentrationUnit
unique identifier: MO_740
comment: Micromole per liter or micromolar, concentration unit

experimental and computational feature
type: SeqFeatureBasis
unique identifier: MO_516
comment: Sequence features derived by both computational and experimental methods.

alexa 660
type: LabelCompound
unique identifier: MO_547
comment: Absorbs at 663 nm, emission maxima at 690 nm (far-red). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble.

LOINC
type: TestTypeDatabase
comment: Database resource for universal identifiers for laboratory and other clinical observations
unique identifier: MO_731
has machine readable URI: http://www.loinc.org/download

computed amino acid sequence feature record
type: DatabaseEntryType
unique identifier: MO_797
comment: a record which describes and identifies an amino acid feature which is computationally derived e.g. PFAM

lux
type: LightUnit
unique identifier: MO_573
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.

chromosomal insertion
type: ChromosomalAberrationClassification
unique identifier: MO_518
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.

hybridization
type: ExperimentalProtocolType
type: ComplexAction
comment: The process of incubating one or more labeled extracts with an array.
unique identifier: MO_884

unscaled
type: Scale
unique identifier: MO_542
comment: The values are unordered and have no scale.

journal article
type: PublicationType
unique identifier: MO_430
comment: A article published in a print or online journal having an ISSN.

control label
type: ControlType
comment: Reporter used as a control where some label has been deposited. This includes fluor and radioactively labeled oligos and fluors alone.
unique identifier: MO_708

ChemID
type: CompoundDatabase
comment: Database entry from the ChemIDplus database which stores information on the structure, identifiers etc for compounds.
has human readable URI: http://chem.sis.nlm.nih.gov/chemidplus
unique identifier: MO_426

operating system
type: SoftwareType
unique identifier: MO_847
comment: Software upon which other software runs.

translational bias design
type: BioMolecularAnnotation
comment: A translational bias is an experiment design which characterizes the association of transcripts and translation machinery.
unique identifier: MO_939

aneuploid
type: Ploidy
unique identifier: MO_918
comment: Describes a cell, nucleus or an organism whose chromosome number is not an exact multiple of the haploid number (n).

technical replicate
type: QualityControlDescriptionType
unique identifier: MO_641
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.
type: ReplicateDescriptionType

strain or line design
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.
unique identifier: MO_462

family history design
type: EpidemiologicalDesign
unique identifier: MO_544
comment: A family history design type is where the family history such as traits, characteristics, susceptibility to disease is studied

RNA stability design
type: BioMolecularAnnotation
comment: A RNA stability experiment design type examines the stability and/or decay of RNA transcripts.
unique identifier: MO_553

ul
type: VolumeUnit
unique identifier: MO_926
comment: microliter, unit of volume

deprecation in version
type: AnnotationProperty
comment: The value of the property indicates what version of the ontology the term was deprecated from.
type: DatatypeProperty
range: DataRange
  one of: 1.1.7
  one of: 1.1.9
  one of: 1.2.0
  one of: 1.1.8
  one of: 1.3.0
  one of: 1.3.1.1
unique identifier: MO_1014

count
type: QuantityUnitOther
unique identifier: MO_500
comment: Unit for a simple count of things

investigator
type: Roles
comment: Person who contributed to the study.
unique identifier: MO_769

online resource
type: PublicationType
unique identifier: MO_991
comment: A publication type which is available online and which is not an online journal article, e.g. a web site or service.

slice analysis
type: DeprecatedTerms
has reason for deprecation: deleted term
deprecation replacement term: NormalizationDescriptionType
deprecation old parent: NormalizationDescriptionType
deprecation reason: deleted_term
deprecated from version: version 1.2.0
deprecation in version: 1.2.0
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.
unique identifier: MO_531

spotted ds DNA features
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.
unique identifier: MO_499

curated amino acid sequence record
type: DatabaseEntryType
unique identifier: MO_451
comment: A record which describes and identifies an amino acid sequence which has been curated

injury design
type: PerturbationalDesign
unique identifier: MO_726
comment: An injury experiment design type is where the response of an organism(s) to injury or damage is studied.

string datatype
type: DataType
comment: The values are a sequence of one or more characters.
unique identifier: MO_352

is contaminated
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.
unique identifier: MO_489

image acquisition
type: ExperimentalProtocolType
unique identifier: MO_929
comment: The process of generating an image from the array.

mixed sex
type: Sex
comment: A population of multiple sexes, e.g. a mixture of females and males, or males and hermaphrodites.
unique identifier: MO_436

L
type: VolumeUnit
comment: liter, unit of volume
unique identifier: MO_444

ng
type: MassUnit
unique identifier: MO_796
comment: nanogram, a mass unit

months
type: TimeUnit
unique identifier: MO_631
comment: Unit of time corresponding to approx. one cycle of the moon's phases.

alexa 430
type: LabelCompound
comment: Absorbs at 433 nm, emission maxima at 539 nm (yellow-green), Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble.
unique identifier: MO_401

peer review quality control
type: QualityControlDescriptionType
unique identifier: MO_365
comment: An experiment which has a peer reviewed publication attached.

NASC
type: StrainOrLineDatabase
unique identifier: MO_379
comment: The Nottingham Arabidopsis Stock Centre (NASC). Provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.
has human readable URI: http://arabidopsis.info/catalogue.html

NCI tumor grading database
type: TumorGradingDatabase
unique identifier: MO_819
has human readable URI: http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp
comment: a controlled vocabulary of tumor grading terms

comparative genome hybridization design
type: TechnologicalDesign
unique identifier: MO_856
comment: Experiment design type in which genomic content is studied using an array based assay.
type: BioMolecularAnnotation
synonym: array_CGH
synonym: array CGH
synonym: CGH

clinical history design
type: EpidemiologicalDesign
comment: A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied.
unique identifier: MO_832

spectrophotometer
type: HardwareType
synonym: thermocycler
unique identifier: MO_716
comment: Hardware for measuring light at different wavelengths.

NCI compound database
type: CompoundDatabase
comment: a controlled vocabulary for compounds
unique identifier: MO_376
has human readable URI: http://nciterm.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp

alexa 633
type: LabelCompound
comment: Absorbs at 632 nm, emission maxima at 647 nm (red). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble.
unique identifier: MO_345

mg
type: MassUnit
unique identifier: MO_949
comment: milligram, mass unit

normalized intensities
type: DerivedBioAssayType
comment: Results of normalization, by some method, of a bioassay data set such as; intensities from one or both channels of a microarray-based assay; orthologous spot sets on 2D gels; or repeat measurements of the same metabolite in replicate cell cultures.
unique identifier: MO_994

genetic variation
type: DeprecatedTerms
deprecation old parent: BioMaterialCharacteristicCategory
comment: A descriptor for FactorValue where GeneticVariation is compared.
deprecation replacement term: BioMaterialCharacteristicCategory
deprecation in version: 1.1.8
deprecation reason: deleted_term
has reason for deprecation: deleted term
unique identifier: MO_557
deprecated from version: version 1.1.8

curated nucleic acid sequence feature record
type: DatabaseEntryType
comment: A record which identifies a nucleic acid sequence feature(s) and which has been curated.
unique identifier: MO_644

nucleic acid primary sequence record
type: DatabaseEntryType
unique identifier: MO_757
comment: A record which describes and identifies a primary sequence record e.g. DDBJ/EMBL/Genbank

CABRI Human and Animal Cell lines
type: CellLineDatabase
comment: Database entry from CABRI, a database listing sources such as cell lines, bacteria, plasmids etc.
has human readable URI: http://www.cabri.org/HyperCat/cells/all.htm
unique identifier: MO_536

wash station
type: HardwareType
unique identifier: MO_626
comment: An instrument designed to mechanically wash or stain arrays.

MTB Database
type: DiseaseStateDatabase
has human readable URI: http://tumor.informatics.jax.org
unique identifier: MO_942
comment: Database entry from the mouse tumor biology database, a resource for nomenclature of mouse tumors.

hybridization station
type: HardwareType
comment: An instrument which controls hybridization conditions, into which a hybridization chamber may fit.
unique identifier: MO_497

mean and variance
type: DerivedBioAssayType
comment: the mean and variance values resulting from computationally combining 2 or more sets of BioAssayData
unique identifier: MO_458

spike quality control
type: QualityControlDescriptionType
comment: An experiment in which spikes were introduced into some or all of the hybridizations for quality control or data transformation purposes.
unique identifier: MO_937

NCI targeted cell type database
type: TargetedCellTypeDatabase
has human readable URI: http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp
comment: a controlled vocabulary of targeted cell types
unique identifier: MO_351

induced mutation
type: GeneticModification
unique identifier: MO_564
comment: The modification of the genetic material (either coding or non-coding) of an organism by mutagenic compounds or irradiation.

unknown substrate type
type: SubstrateType
unique identifier: MO_484
comment: SubstrateType of unknown type.

ml per kg
type: ConcentrationUnitOther
unique identifier: MO_403
comment: milliliter per kilogram

clinical treatment
type: BioMaterialCharacteristicCategory
unique identifier: MO_384
comment: A descriptor for a clinical treatment for a patient.

CABRI Yeasts Strains
type: StrainOrLineDatabase
has human readable URI: http://www.cabri.org/HyperCat/yeast/all_A.htm
comment: List of CABRI yeasts strains sorted by genus and species. It includes more than 30,000 resources that are available from four European collections participating in the CABRI (Common Access to Biological Resources and Information) initiative (see http://www.cabri.org/ ). Detailed descriptions can be reached from the list and strains of interest can be requested.
unique identifier: MO_1010

CellML
type: OrganismPartDatabase
unique identifier: MO_967
has human readable URI: http://portal.bioengineering.elyt.ods.org/ontology/
comment: Ontology describing anatomical and physiological relationships.

lowess group normalization
type: DataTransformationProtocolType
comment: Application of a normalization of type lowess_normalization where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed.
unique identifier: MO_861

Ci
type: RadiationUnit
comment: Curie. Unit of the rate of radioactive decay, i.e., the activity of that quantity of radioactive material in which the number of disintegrations per second is 3.7E10. 1 Ci = 3.75 x1010 atom disintegrations per second (dps).
unique identifier: MO_642

umol
type: QuantityUnit
comment: micromoles, quantity unit
unique identifier: MO_752

split term
type: DeprecationReason
comment: the term has been decomposed into more specific terms
unique identifier: MO_1027

TAIR arabidopsis anatomy ontology
type: OrganismPartDatabase
unique identifier: MO_809
comment: A structured controlled vocabulary for the anatomy of Arabidopsis.
has machine readable URI: http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/anatomy/gross_anatomy/plant_gross_anatomy/Arabidopsis/Attic/arabidopsis_anatomy.ontology

UMLS
type: DiseaseStateDatabase
comment: Database resource, unified medical language system, an ontology constructed by merging several disparate ontologies, available from NIH.
has human readable URI: http://www.nlm.nih.gov/research/umls/
unique identifier: MO_947

alexa 532
type: LabelCompound
unique identifier: MO_375
comment: Absorbs at 532 nm, emission maxima at 554 nm (yellow). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble.

intramuscular injection
type: DeliveryMethod
comment: Delivery method for a compound or drug where the substance is administered via an injection into the muscle.
unique identifier: MO_617

control spike calibration
type: ControlType
comment: A Reporter that could be hybridized to an exogenously added nucleic acid or protein (spike) before or during hybridization and is used as a control for data processing. It may be deposited at one or more known concentrations (calibration). A reporter may be a spike, a calibration control or both.
unique identifier: MO_364

unknown basis feature
type: SeqFeatureBasis
comment: Sequence feature whose derivation is unknown.
unique identifier: MO_525

hermaphrodite
type: Sex
synonym: intersex
unique identifier: MO_356
comment: an organism with both male and female sexual organs in one individual synonym: intersex

CBIL CV
type: OrganismPartDatabase
type: TargetedCellTypeDatabase
type: CellTypeDatabase
has human readable URI: http://www.cbil.upenn.edu/anatomy.php3
comment: a controlled vocabulary provided by CBIL
unique identifier: MO_886

consensus DNA
type: DeprecatedTerms
deprecation reason: deleted_term
deprecation in version: 1.3.1.1
unique identifier: MO_361
deprecation replacement term: TheoreticalBioSequenceType
comment: DNA sequence produced from some base calling or alignment algorithm which uses multiple sequence as input
deprecation old parent: TheoreticalBioSequenceType

species specific design element group type
type: DesignElementGroupType
comment: A grouping of DesignElements, Features, Reporters, Composite Sequences on the basis of a common species.
unique identifier: MO_395

kg per m2
type: OtherUnit
unique identifier: MO_658
synonym: kg/m2
comment: The mass of an object in kilograms divided by the surface area in meters squared. Also known as the Body Mass Index (when applied to a person) which is a measure of leaness/obesity. Exact synonym:kg/m2

pH
type: ConcentrationUnitOther
comment: potential of hydrogen
unique identifier: MO_814

barrier facility
type: EnvironmentalFactorCategory
comment: The rating of containment system used to protect organisms from infectious agents.
unique identifier: MO_511

sex design
type: BiologicalProperty
unique identifier: MO_575
comment: A sex experiment design type assays differences associated with an organism's sex, gender or mating type.

change humidity
type: AtomicAction
comment: The action of changing the relative humidity, e.g. from 1% to 10%.
unique identifier: MO_917

molecular mixture
type: MaterialType
comment: an unspecified collection of heterogeneous molecules, e.g. lipids, carbohydrate , nucleic acids and proteins
unique identifier: MO_889

control genomic DNA
type: ControlType
unique identifier: MO_449
comment: A Reporter where genomic DNA has been deposited, the genomic DNA may be fragmented, e.g. salmon sperm DNA, Cot1DNA.

uncle
type: FamilyRelationship
unique identifier: MO_950
comment: The brother of one's father or mother.

percent purity
type: ConcentrationUnitOther
unique identifier: MO_482
comment: A relative measurement of homogeneity of a biomaterial e.g. tumor biopsy.

image record
type: DatabaseEntryType
unique identifier: MO_691
comment: A record which describes and identifies an image, e.g. an image from the mouse atlas

function record
type: DatabaseEntryType
unique identifier: MO_538
comment: a record which identifies and describes the function of a gene product, e.g. E.C. record

replaced with term
type: AnnotationProperty
comment: The value of the property indicates the replacement term.
unique identifier: MO_1018
type: ObjectProperty

vector
type: DeprecatedTerms
deprecation replacement term: PhysicalBioSequenceType
deprecated from version: version 1.2.0
deprecation in version: 1.2.0
has reason for deprecation: deleted term
deprecation reason: deleted_term
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.
unique identifier: MO_551
deprecation old parent: PhysicalBioSequenceType

F
type: Sex
unique identifier: MO_717
comment: mating type indicating the presence of F plasmid in a bacterial cell

GeneOntology
type: CellularComponentDatabase
has machine readable URI: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo
unique identifier: MO_1022
comment: The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.

chromosomal inversion
type: ChromosomalAberrationClassification
unique identifier: MO_622
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.

infect
type: DeprecatedTerms
deprecation in version: 1.3.0
comment: The organism (or organism part) has been exposed to a virus or pathogen.
replaced with term: inoculate
deprecation old parent: ComplexAction
deprecated from version: version 1.3.0
deprecation reason: replaced_term
was replaced by: inoculate
has reason for deprecation: replaced term
unique identifier: MO_616
deprecation old parent: ExperimentalProtocolType

inoculate
type: ComplexAction
unique identifier: MO_559
comment: The process of introducing a foreign agent such as serum, vaccine, antigenic substance or organism.
type: ExperimentalProtocolType
synonym: infect

version 1.3.0
type: MGEDOntologyVersion
unique identifier: MO_440
comment: Version of the MGEDOntology.

replaced term
type: DeprecationReason
comment: The term name was changed to one more appropriate to the intent of the definition.
unique identifier: MO_1026

mRNA
type: DeprecatedTerms
deprecation old parent: TheoreticalBioSequenceType
deprecated from version: version 1.2.0
deprecation replacement term: TheoreticalBioSequenceType
unique identifier: MO_803
comment: sequence of a processed transcript capable of directing protein synthesis
deprecation reason: deleted_term
deprecation in version: 1.2.0
has reason for deprecation: deleted term

nylon
type: SubstrateType
unique identifier: MO_492
comment: The array is made on a nylon membrane.

chromosomal duplication
type: ChromosomalAberrationClassification
comment: An irregularity in the number of chromosomes, usually in the form of a gain of genetic material.
unique identifier: MO_1002

sister
type: FamilyRelationship
unique identifier: MO_723
comment: A female having the same genetic parents as another, or one genetic parent in common with another.

in vitro design
type: MethodologicalDesign
comment: An experiment done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture.
unique identifier: MO_347

percent weight per vol
type: ConcentrationUnit
comment: percent weight per volume, concentration unit
unique identifier: MO_420

curator
type: Roles
unique identifier: MO_893
comment: person who checks the consistency of the data and MAGE-ML file

spotted protein features
type: TechnologyType
comment: TechnologyType of FeatureGroup where protein (other than antibody) is spotted directly.
unique identifier: MO_996

experimental feature
type: SeqFeatureBasis
comment: An experimentally defined sequence feature.
unique identifier: MO_452

control reporter size
type: ControlType
comment: A Reporter of whose BioSequence is of known length used as a methodological control for hybridization efficiency.
unique identifier: MO_431

not extract
type: BioSampleType
unique identifier: MO_894
comment: The BioSample at any stage other than immediately before labeling.

negative integer
type: DataType
unique identifier: MO_864
comment: An integer < 0.

NCI disease state database
type: DiseaseStateDatabase
has human readable URI: http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp
unique identifier: MO_790
comment: a controlled vocabulary for disease states

acclimatization
type: ExperimentalProtocolType
type: ComplexAction
comment: The action of stabilizing an organism prior to treatment
unique identifier: MO_776

nuclear RNA
type: MaterialType
unique identifier: MO_679
comment: RNA obtained from the nucleus.

rectangular feature
type: FeatureShape
unique identifier: MO_897
comment: The shape of the feature on the array is rectangular.

um
type: DistanceUnit
comment: micrometer, unit of distance
unique identifier: MO_421

beginning of stage
type: InitialTimePoint
comment: time point that indicates the start of some developmental stage
unique identifier: MO_608

polyploid
type: Ploidy
unique identifier: MO_394
comment: Describes a cell, nucleus or organism with three or more copies of each chromosome.

mating type h minus
type: Sex
comment: Mating type of S.pombe.
unique identifier: MO_407

log base e
type: Scale
comment: The values presented are logarithm, base e.
unique identifier: MO_554

fM
type: ConcentrationUnit
comment: femtomolar, concentration unit
unique identifier: MO_898

strain or line
type: BioMaterialCharacteristicCategory
unique identifier: MO_859
comment: A descriptor of FactorValue where comparisons of strains or lines are made.

synthetic RNA
type: MaterialType
synonym: complementary RNA
synonym: cRNA
synonym: aRNA
synonym: amplified RNA
comment: RNA which is generated by chemical or enzymatic (non cellular) means. E.g. T7 promotor generated RNA. Non-exact synonym: cRNA, complementary RNA aRNA, amplified RNA
unique identifier: MO_543

centrifuge
type: HardwareType
unique identifier: MO_476
comment: An instrument capable of applying centrifugal force to tubes or microtiter plates.

nucleic acid extraction
type: ExperimentalProtocolType
unique identifier: MO_607
comment: The procedure of extracting nucleic acid from the biomaterial.
type: ComplexAction

NCI strain or line database
type: StrainOrLineDatabase
comment: a controlled vocabulary for strains or lines
unique identifier: MO_397
has human readable URI: http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp

MAS5 signal log ratio
type: DerivedBioAssayType
comment: The difference in expression level for a transcript between data from two arrays, expressed as the log2ratio. A signal log ratio of 1 is the same as a Fold Change of 2.
unique identifier: MO_938

mating type alpha
type: Sex
unique identifier: MO_637
comment: Mating type of S. cerevisiae.

biological resource record
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
unique identifier: MO_989

NCI disease staging database
type: DiseaseStagingDatabase
unique identifier: MO_422
has human readable URI: http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp
comment: a controlled vocabulary for disease stages

whole organism
type: MaterialType
comment: one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria
unique identifier: MO_566

HUMAT
type: DevelopmentalStageDatabase
has machine readable URI: http://obo.sourceforge.net/list.shtml
unique identifier: MO_844
comment: Ontology of human developmental anatomy for Carnegie stages 1-20.

unique identifier
type: AnnotationProperty
type: DatatypeProperty
unique identifier: MO_331
comment: A unique alphanumeric identifier for the term. This will exist in the form of MO_someNumber, e.g. MO_123.

mean and standard deviation
type: DerivedBioAssayType
comment: the mean and standard deviation values resulting from computationally combining 2 or more sets of BioAssayData
unique identifier: MO_445

list of positive integers
type: DataType
unique identifier: MO_873
comment: An ordered, finite set of positive integers.

dye swap quality control
type: QualityControlDescriptionType
unique identifier: MO_524
comment: Indicates that a dye swap was performed for some or all hybridizations within an experiment

merged term
type: DeprecationReason
comment: the term has been subsumed into a more general term
unique identifier: MO_1025

list of nonpositive floats
type: DataType
comment: An ordered, finite set of nonpositive floats.
unique identifier: MO_1000

Affymetrix DAT
type: ImageFormat
comment: A proprietary image data format that is lossless and containing one channel of data.
unique identifier: MO_786

hardware manufacturer
type: Roles
unique identifier: MO_763
comment: Person or organization that manufactured the hardware.

RNA
type: PolymerType
unique identifier: MO_594
comment: Ribonucleic acid.

IU
type: QuantityUnit
synonym: International unit
synonym: UI
unique identifier: MO_1011
comment: The International unit is a unit of measurement for the amount of a substance, based on measured biological activity. It is used for vitamins, hormones, some drugs, vaccines, blood products and similar biologically active substances. The precise definition of one IU differs from substance to substance and is established by international agreement and is based on a reference provided by the Committee on Biological Standardization of the World Health Organization.

mating type h plus
type: Sex
unique identifier: MO_855
comment: Mating type of S.pombe.

quantile normalization protocol type
type: DataTransformationProtocolType
unique identifier: MO_457
comment: Application of a normalization of type quantile_normalization.

version 1.3.1
type: MGEDOntologyVersion
comment: Version of the MGED Ontology.
unique identifier: MO_1034

stimulated design type
type: PerturbationalDesign
comment: A design in which a behavior is invoked by a variable controlled by the experimenter - e.g. administration of a drug that effects aggressivity.
unique identifier: MO_958

genomic region amplification
type: ChromosomalAberrationClassification
unique identifier: MO_609
comment: increment in copy number of a genomic region, includes gene amplification, genomic amplification, and DNA amplification

clinical record
type: DatabaseEntryType
unique identifier: MO_852
comment: record which describes and identifies clinical information about an organism

compound based treatment
type: ComplexAction
type: ExperimentalProtocolType
comment: The treatment is effected by a defined chemical or biological compound. The compound may be a drug, solvent, chemical, etc., with a property that can be measured such as concentration.
unique identifier: MO_798

missing feature or zone
type: DefectType
unique identifier: MO_405
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.

uncentered Pearson correlation
type: NodeValueType
comment: The uncentered Pearson correlation is defined as the Pearson correlation for two data series where the mean of each data series is assumed to be zero.
unique identifier: MO_974

signal
type: DerivedBioAssayType
unique identifier: MO_534
comment: A quantitative measure of the relative abundance of a transcript (MAS 4.0 version of the Affymetrix analysis software).

dpm
type: RadiationUnit
unique identifier: MO_583
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.

list of floats
type: DataType
unique identifier: MO_760
comment: An ordered, finite set of floats.

alexa 546
type: LabelCompound
comment: Absorbs at 556 nm, emission maxima at 573 nm (orange). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble.
unique identifier: MO_493

binding site identification design
type: TechnologicalDesign
type: BioMolecularAnnotation
comment: A binding site identification design type investigates protein binding sites on nucleic acids non-exact synonym: ChIP, chromatin immunoprecipitation, chromatin IP
unique identifier: MO_933
synonym: chromatin immunoprecipitation
synonym: chromatin IP
synonym: chromatin_immunoprecipitation
synonym: ChIP-chip

bedding
type: DeprecatedTerms
deprecated from version: version 1.1.7
unique identifier: MO_615
comment: The material (e.g. straw) that an animal sleeps on
deprecation old parent: BioMaterialCharacteristicCategory
deprecation replacement term: BioMaterialCharacteristicCategory
has reason for deprecation: deleted term
deprecation reason: deleted_term
deprecation in version: 1.1.7

image acquisition software
type: SoftwareType
synonym: scanning software
unique identifier: MO_1003
comment: Software to control a scanner and manipulate and save images. Exact synonym: scanning software

R
type: RadiationUnit
comment: Roentgen. Unit of exposure to gamma or x-rays in the air. 1 R= 2.58E-4 coulombs per kg.
unique identifier: MO_725

Mammalian Phenotype Ontology
type: ObservationDatabase
comment: A community effort to provide standard terms for annotating phenotypic data.
has human readable URI: http://www.informatics.jax.org/searches/Phat.cgi
unique identifier: MO_704

signal log ratio
type: DeprecatedTerms
unique identifier: MO_941
has reason for deprecation: deleted term
deprecation in version: 1.1.7
deprecated from version: version 1.1.7
deprecation old parent: DerivedBioAssayType
deprecation reason: deleted_term
comment: The change in expression level for a transcript between a baseline and an experiment array. This change is expressed as the log2 ratio. A signal log ratio of 1 is the same as a Fold Change of 2.
deprecation replacement term: DerivedBioAssayType

unknown protocol type
type: ExperimentalProtocolType
unique identifier: MO_460
comment: ProtocolType of unknown type.

element design
type: ExperimentalProtocolType
unique identifier: MO_523
comment: protocol that describes how the features, reporters and composites were designed and or selected for inclusion in an array design

33P
type: LabelCompound
unique identifier: MO_427
comment: 33 P, radioactive isotope of phosphorus, used for labeling/detection purposes.

degrees C
type: TemperatureUnit
comment: degrees celsius, unit of temperature
unique identifier: MO_980

ms
type: TimeUnit
unique identifier: MO_920
comment: millisecond, time unit

cytoplasmic RNA
type: MaterialType
comment: RNA obtained from the cytoplasm.
unique identifier: MO_978

replicate analysis
type: DataTransformationProtocolType
unique identifier: MO_433
comment: A transformation method in which replicate intensity or ratio data sets are combined. Analysis of the mean and standard deviation values for replicate data points can be used to identify and potentially exclude low quality data.

control empty
type: ControlType
comment: A Reporter where no material or buffer was deposited on the array
unique identifier: MO_830

NCBI taxonomy
type: OrganismDatabase
has human readable URI: http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/
unique identifier: MO_773
comment: identifier for a taxon provided by the NCBI taxonomy database
type: StrainOrLineDatabase

remove
type: AtomicAction
unique identifier: MO_713
comment: The procedure of extracting/taking out a part of a reaction/contents of a container.

pedigree record
type: DatabaseEntryType
unique identifier: MO_969
comment: A record which describes and identifies a pedigree or lineage for a strain, line, individual or cell whose lineage traceable e.g. a wormbase cell lineage record, or a pedigree record for a mouse

linear regression normalization
type: NormalizationDescriptionType
unique identifier: MO_823
comment: A method to re-scale paired-assay data from one data set relative to the other, based on regression of the values in the one set to those in the other, where the latter utilizes either all values in the data set, or an appropriate subset of these (e.g. special control Features on a microarray, or 2DE spots containing constitutively expressed proteins). The slope of the regression line is used to re-scale all the values in the data set being normalized. This single parameter method assumes that there is a linear relationship between the data sets. A similar approach could be employed to re-scale data from a standalone assay to another standalone (baseline) assay.

gene fragment
type: DeprecatedTerms
unique identifier: MO_853
comment: sequence of part of a gene, which is missing one or both ends
deprecation in version: 1.3.1.1
deprecation replacement term: TheoreticalBioSequenceType
deprecation reason: deleted_term
deprecation old parent: TheoreticalBioSequenceType

wait
type: AtomicAction
comment: Allow time to pass. It's measurement should be a unit of time.
unique identifier: MO_988

FMA
type: OrganismPartDatabase
has human readable URI: http://sig.biostr.wahington.edu/projects/fm/
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.
unique identifier: MO_468

organellar DNA
type: MaterialType
unique identifier: MO_645
comment: DNA from organelles such as the mitochondria or chloroplast.

imprinting design
type: BiologicalProperty
unique identifier: MO_914
comment: An experiment design type where differences in genetic imprinting of maternally- and paternally-inherited chromosomes (e.g., due to in vivo differences in chemical modification and/or chromatin structure) are compared.

concentrate
type: AtomicAction
unique identifier: MO_883
comment: Increasing the concentration of solutes in a solution or suspension.

NCI cell type database
type: CellTypeDatabase
unique identifier: MO_687
comment: a controlled vocabulary of cell types
has human readable URI: http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp

decontaminate
type: ComplexAction
comment: Treatment to remove organisms present that were not planned as part of the study (e.g., mycoplasma).
type: ExperimentalProtocolType
unique identifier: MO_389

mean log normalization
type: DataTransformationProtocolType
comment: Application of a normalization of type mean_log_centering.
unique identifier: MO_657

heavy background
type: DefectType
unique identifier: MO_571
comment: The Zone is excluded due to smearing, streaking, or dense background in the Zone.

water
type: EnvironmentalFactorCategory
comment: Water consumed by or enveloping the organism that the biosource is derived from.
unique identifier: MO_380

vortexer
type: HardwareType
unique identifier: MO_983
comment: An instrument that mixes by rapid oscillation.

biosequence provider
type: Roles
unique identifier: MO_881
comment: Provider of biosequences (clones, oligos etc) for deposition on the array.

cosmid
type: DeprecatedTerms
unique identifier: MO_888
deprecation in version: 1.2.0
comment: sequence from cosmid, a hybrid cloning vector containing cos sites, usually of ~40kB size
deprecation reason: deleted_term
deprecated from version: version 1.2.0
deprecation old parent: PhysicalBioSequenceType
has reason for deprecation: deleted term
deprecation replacement term: PhysicalBioSequenceType

flag filter
type: DataTransformationProtocolType
comment: transformation method that involves removal of values in a data set based on visual or computed flags (e.g. the GenePix feature_extraction software standard flags). This includes low-intensity filtering methods, where the flag indicates low intensity values in the data set (for microarrays and gels the threshold for exclusion is usually based on some estimation of local or global background intensity; for mass spectrometry and NMR, it is usually based on the signal-to-noise ratio in the spectrum).
unique identifier: MO_1024

blood
type: DeprecatedTerms
comment: A biomaterial obtained as fluid consisting of plasma, blood cells and platelets.
deprecation in version: 1.1.9
deprecation reason: deleted_term
unique identifier: MO_409
deprecated from version: version 1.1.9
deprecation old parent: BioSourceType
has reason for deprecation: deleted term
deprecation replacement term: BioSourceType

control buffer
type: ControlType
comment: A Reporter where only buffer was deposited on the array
unique identifier: MO_505

disease state
type: BioMaterialCharacteristicCategory
comment: A descriptor for FactorValue where DiseaseState is compared.
unique identifier: MO_787

predicted gene
type: DeprecatedTerms
deprecation replacement term: TheoreticalBioSequenceType
deprecation in version: 1.3.1.1
comment: gene sequence which has been computationally predicted
deprecation old parent: TheoreticalBioSequenceType
unique identifier: MO_838
deprecation reason: deleted_term

inconclusive
type: Result
unique identifier: MO_744
comment: a result which can not be interpreted as positive or negative

real time PCR quality control
type: QualityControlDescriptionType
comment: A PCR based quantitative validation of a subset of the array based data used for experimental QC purposes.
unique identifier: MO_434

waterbath
type: HardwareType
comment: A device for controlling temperature by immersion in water.
unique identifier: MO_541

ml
type: VolumeUnit
comment: milliliter, volume unit
unique identifier: MO_488

log base 10
type: Scale
comment: The values presented are logarithm, base 10.
unique identifier: MO_735

years
type: TimeUnit
unique identifier: MO_948
comment: 365 days, time unit

subcutaneous
type: DeliveryMethod
comment: Delivery method whereby a drug or compound is administered under the skin of the organism.
unique identifier: MO_960

acrossBioAssay mean and variance
type: DerivedBioAssayType
comment: The mean and variance values resulting from computationally combining 2 or more sets of bioassay data.
unique identifier: MO_400

ug
type: MassUnit
comment: microgram, unit of mass
unique identifier: MO_438

ontology record
type: DatabaseEntryType
comment: A record which describes and identifies a term, class or instance in an ontology or controlled vocabulary e.g. ICD
unique identifier: MO_529

CABRI Hybridomas
type: CellLineDatabase
unique identifier: MO_1006
has human readable URI: http://www.cabri.org/HyperCat/cells/hybrid.htm
comment: List of CABRI hybridomas sorted by name. It includes 397 resources that are available from European collections participating in the CABRI (Common Access to Biological Resources and Information) initiative (see http://www.cabri.org/ ). Detailed descriptions can be reached from the list and cell lines of interest can be requested.

daughter
type: FamilyRelationship
unique identifier: MO_665
comment: The female offspring of the patient or individual under study.

agar stab
type: BioSourceType
unique identifier: MO_971
comment: agar stab, a cell culture inoculated into agar for long term storage

mix by inversion
type: AtomicAction
unique identifier: MO_700
comment: Mix through the process of inverting.

behavior design
type: DeprecatedTerms
split to term: stimulated design type
deprecation reason: split_term
split to term: innate behavior design
deprecation in version: 1.1.9
deprecation old parent: BiologicalProperty
unique identifier: MO_532
has reason for deprecation: split term
comment: The specific actions or reactions of an organism in response to external or internal stimuli. Patterned activity of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.
deprecated from version: version 1.1.9

innate behavior design
type: BiologicalProperty
comment: A design in which the innate behavior of the organism is examined, e.g. path finding in bees.
unique identifier: MO_355

array manufacturer
type: Roles
comment: Person or organization that manufactured the array.
unique identifier: MO_890

change temperature
type: AtomicAction
unique identifier: MO_677
comment: Change in temperature.

MAD stage
type: OrganismPartDatabase
has human readable URI: http://www.informatics.jax.org/mgihome/GXD/AD/
type: DevelopmentalStageDatabase
type: TargetedCellTypeDatabase
unique identifier: MO_693
comment: database entry from mouse anatomical dictionary for developmental stage term

molecules
type: QuantityUnit
unique identifier: MO_707
comment: number of molecules, quantity unit

pearson correlation coefficient
type: NodeValueType
unique identifier: MO_558
comment: The Pearson's correlation coefficient between two variables. Its values can range between -1.00 to +1.00. The closer the absolute value of the Pearson correlation coefficient is to 0, the smaller the linear relationship between the two variables. A Pearson correlation coefficient with absolute value 1 indicates perfect linear relationship.

Cy3
type: LabelCompound
unique identifier: MO_739
comment: fluorophore used for labeling/detection purposes

feature extraction
type: ExperimentalProtocolType
comment: The process of obtaining quantifiable values from the scanned image of the array. Exact synonyms: image analysis, image quantification
synonym: image analysis
synonym: image quantification
unique identifier: MO_928

operon
type: DeprecatedTerms
deprecation reason: deleted_term
has reason for deprecation: deleted term
deprecation old parent: TheoreticalBioSequenceType
deprecation replacement term: TheoreticalBioSequenceType
comment: sequence which represents an operon, a unit of genetically linked genes displaying coordinated and regulated gene activity, originally described in prokaryotes
deprecated from version: version 1.2.0
unique identifier: MO_759
deprecation in version: 1.2.0

list of nonnegative floats
type: DataType
comment: An ordered, finite set of nonnegative floats.
unique identifier: MO_360

list of nonpositive integers
type: DataType
unique identifier: MO_804
comment: An ordered, finite set of nonpositive integers.

preservation
type: ExperimentalProtocolType
type: ComplexAction
comment: The type of protocol used to preserve (including storage or keep in stasis) the biomaterial.
unique identifier: MO_415

spin
type: AtomicAction
synonym: centrifuge
comment: The procedure of applying a centrifugal force to a physical object. Exact synonym: centrifuge
unique identifier: MO_879

exemplar mRNA
type: DeprecatedTerms
deprecation reason: deleted_term
unique identifier: MO_621
deprecation replacement term: TheoreticalBioSequenceType
comment: An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group.
deprecation old parent: TheoreticalBioSequenceType
deprecation in version: 1.3.1.1

MAS4 average difference
type: DerivedBioAssayType
unique identifier: MO_782
comment: A quantitative measure of the relative abundance of a transcript. Used in the MAS4.0 Affymetrix software to obtain an averaged 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.

class role
type: AnnotationProperty
range: DataRange
  one of: abstract
  one of: place_holder
  one of: concrete
comment: This property is used to identify the type of class of the term. The value "abstract" indicates that the class is used for organizational purposes. The value "instantiated" indicates that the class contains Individuals that can be used as annotation terms. The value "abstract" indicates that the class is used to provide organization within the MGED Ontology. The value "place_holder" indicates that this class represents the location in the ontology where terms of this class would be located.
type: FunctionalProperty
type: DatatypeProperty
unique identifier: MO_338

nonpositive integer
type: DataType
comment: An integer less than or equal to zero.
unique identifier: MO_623

dye swap replicate reduction
type: DerivedBioAssayType
comment: Results of data reduction involving computation of a representative value from identical reporters or features obtained from two, or more, hybridizations in which each LabelExtract is labeled with each of the labels or dyes. Computation of a representative value for reporter X using data from Hybridizations 1 and 2, where LabeledExtract A is labeled with Cy3 (and LabeledExtract B is labeled with Cy5) in Hybridization 1 and LabeledExtract A is labeled with Cy5 (and LabeledExtract B is labeled with Cy3) in Hybridization 2.
unique identifier: MO_750

behavioral design type
type: DeprecatedTerms
deprecation reason: replaced_term
replaced with term: innate behavior design
unique identifier: MO_766
has reason for deprecation: replaced term
deprecated from version: version 1.1.9
deprecation old parent: PerturbationalDesign
was replaced by: innate behavior design
comment: A design type in which some behavior(s) of an organism is studied. The behavior can be innate, such as path finding in bees, or in response to an experimental behavioral stimulus such as sleep deprivation.
deprecation in version: 1.1.9

fl
type: VolumeUnit
comment: femtoliter, unit of volume
unique identifier: MO_721

specified biomaterial action
type: ExperimentalProtocolType
unique identifier: MO_968
type: ComplexAction
type: AtomicAction
comment: Conceptual action for specified protocol applied in treatment.

dl
type: VolumeUnit
comment: deciliter, unit of volume
unique identifier: MO_624

place
type: AtomicAction
comment: The procedure of putting a physical object in a container/physical space.
unique identifier: MO_470

pool
type: ExperimentalProtocolType
unique identifier: MO_779
comment: The process of combining two or more BioMaterials. Exact synonym: combine
synonym: combine
type: ComplexAction

biopsy
type: ComplexAction
unique identifier: MO_711
comment: The process of removing tissue from a living organism.

boolean
type: DataType
unique identifier: MO_826
comment: The values are either TRUE or FALSE, which can be expressed as 1 and 0.

sampling time point
type: BioMaterialCharacteristicCategory
comment: The time point that a sample was taken. Not to be used where the sample is part of a time course. SamplingTimePoint is not related to age. An instance could be summer, a date, a time, or a range value
unique identifier: MO_866

JPEG
type: ImageFormat
unique identifier: MO_746
comment: Joint Photographic Experts Group format, a common image data format containing grayscale or RGB data compressed with little to high data loss.

eclosion
type: InitialTimePoint
comment: Emergence of an adult insect from its pupa or cocoon.
unique identifier: MO_876

PCR
type: DesignElement
comment: Polymerase chain reaction. An element generated using this procedure.
unique identifier: MO_915

array manufacturing
type: ExperimentalProtocolType
comment: The process of physically creating the array.
unique identifier: MO_818

gram percent
type: ConcentrationUnit
unique identifier: MO_582
comment: grams per deciliter, concentration unit

polyA RNA
type: MaterialType
unique identifier: MO_600
synonym: mRNA
synonym: polyA+_RNA
comment: RNA which has been obtained by selection for polyA tracts. Exact synonym: polyA+_RNA Non-exact synonym: mRNA

genetic modification
type: ExperimentalProtocolType
comment: An action whereby an organism(s) has had genetic material removed, added, or rearranged.
unique identifier: MO_927
type: ComplexAction

soil
type: Media
comment: soil, growth media for plants and other soil living organisms
unique identifier: MO_821

biomaterial provider
type: Roles
unique identifier: MO_591
type: BioMaterialCharacteristicCategory
comment: Term used to describe a role or factor value for the person or organization that provides a BioMaterial.

brother
type: FamilyRelationship
comment: A male having the same genetic parents as another, or one genetic parent in common with another.
unique identifier: MO_655

ChEBI
type: CompoundDatabase
comment: A freely available dictionary of small molecular entities. The term molecular entity encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.
unique identifier: MO_857
has human readable URI: http://www.ebi.ac.uk/chebi

feeding
type: DeliveryMethod
comment: Delivery method where a compound/drug is administered in food or water.
unique identifier: MO_993

cell type
type: BioMaterialCharacteristicCategory
unique identifier: MO_548
comment: A descriptor for FactorValue where CellType is compared.

trisomy
type: DeprecatedTerms
deprecation in version: 1.1.9
replaced with term: polysomy
deprecated from version: version 1.1.9
has reason for deprecation: replaced term
deprecation old parent: ChromosomalAberrationClassification
unique identifier: MO_494
deprecation reason: replaced_term
was replaced by: polysomy
comment: The possession of a third chromosome of any one type in an otherwise diploid cell.

polysomy
type: ChromosomalAberrationClassification
comment: A state or condition describing a cell or organism that has more copies of a single chromosome than the usual complement.
unique identifier: MO_1030

single stranded
type: StrandType
unique identifier: MO_576
comment: a nucleic acid consisting of a single polynucleotide chain.

unknown surface type
type: SurfaceType
unique identifier: MO_359
comment: A SurfaceType of unknown type.

synonym
type: AnnotationProperty
unique identifier: MO_333
range: string
type: DatatypeProperty
comment: This property is used to indicate additional terms that have the same meaning as the term that the property is applied to. The terms that have the same meaning as the term that this property is applied to will be the value of the property.

light duration
type: EnvironmentalFactorCategory
unique identifier: MO_604
synonym: photoperiod
comment: The length of the light period that a sample is subjected to. Exact synonym:photoperiod

in vivo design
type: MethodologicalDesign
comment: An experiment design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model.
unique identifier: MO_454

lowess global normalization
type: DataTransformationProtocolType
unique identifier: MO_692
comment: Application of a normalization of type lowess_normalization where the same normalization curve is used for all members of the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample.

mg per ml
type: ConcentrationUnit
comment: milligrams per milliliter, concentration unit
unique identifier: MO_522

alexa 350
type: LabelCompound
comment: Absorbs at 346 nm, emission maxima at 442 nm (blue). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble.
unique identifier: MO_512

WebRENI
type: DiseaseStateDatabase
has human readable URI: http://www.item.fraunhofer.de/reni/index/htm
unique identifier: MO_737
comment: database entry from WebReni A resource for rat and mouse unified nomenclature describing lesions

BAC
type: DeprecatedTerms
synonym: bacterial artificial chromosome
comment: sequence from a bacterial artificial chromosome exact synonym: bacterial artificial chromosome
deprecated from version: version 1.2.0
deprecation replacement term: PhysicalBioSequenceType
deprecation old parent: PhysicalBioSequenceType
unique identifier: MO_985
deprecation in version: 1.2.0
has reason for deprecation: deleted term
deprecation reason: deleted_term

timepoint
type: ComplexAction
comment: Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point.
unique identifier: MO_738

computational feature
type: SeqFeatureBasis
unique identifier: MO_411
comment: Computationally derived sequence feature.

cell line
type: BioMaterialCharacteristicCategory
unique identifier: MO_562
comment: A descriptor for FactorValue where CellLine is compared.

snRNA gene
type: DeprecatedTerms
deprecation in version: 1.2.0
synonym: small nuclear RNA gene
comment: sequence from gene coding for small nuclear RNA exact synonym: small nuclear RNA gene
unique identifier: MO_961
deprecated from version: version 1.2.0
deprecation reason: deleted_term
deprecation old parent: deleted_term
deprecation replacement term: TheoreticalBioSequenceType
has reason for deprecation: deleted term

software variation design
type: MethodologicalDesign
unique identifier: MO_643
comment: A software variation design type compares different types of software for performance, accuracy, precision and reproducibility.

unknown sequence
type: TheoreticalBioSequenceType
unique identifier: MO_535
comment: BioSequence of unknown type
type: PhysicalBioSequenceType

ratio
type: DerivedBioAssayType
unique identifier: MO_597
comment: Result of data reduction involving computation of the quotient of a pair of numerical values, such as signal intensities obtained from the hybridization of two or more labeled extracts to one or more microarrays; volumes of matched spots from comparative 2D gel electrophoresis of two or more labeled extracts; or comparative profiling of a particular metabolite in health and disease by NMR.

fractionate
type: ComplexAction
type: ExperimentalProtocolType
unique identifier: MO_872
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).

A
type: DistanceUnit
unique identifier: MO_515
comment: Angstrom, unit of distance, 1 angstrom is one tenth of a nanometer

promoter
type: DeprecatedTerms
unique identifier: MO_911
deprecation in version: 1.2.0
deprecation replacement term: TheoreticalBioSequenceType
deprecation old parent: TheoreticalBioSequenceType
comment: genomic sequence 5' to a gene where the transcription initiation complex forms.
has reason for deprecation: deleted term
deprecated from version: version 1.2.0
deprecation reason: deleted_term

grandson
type: FamilyRelationship
unique identifier: MO_831
comment: A son of one's son or daughter.

mating type a
type: Sex
unique identifier: MO_659
comment: Mating type of S. cerevisiae.

fresh sample
type: BioSourceType
comment: A sample freshly obtained from the organism(s). E.g. a liver freshly removed from a rat.
unique identifier: MO_730

chromosomal translocation
type: ChromosomalAberrationClassification
unique identifier: MO_368
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.

openGALEN
type: OrganismPartDatabase
comment: OpenGALEN Human Anatomy - open source database of approx. ten thousand human anatomy concepts together with extensive semantic relationships between them including part-of, connects, branch-of, serves, laterality. Also includes some human physiological processes together with functional relationships between these and the anatomy concepts.
unique identifier: MO_613
has human readable URI: http://www.opengalen.org/open/crm/crm-anatomy.html

dissect
type: ComplexAction
type: ExperimentalProtocolType
comment: The action of removing one or more organism parts.
unique identifier: MO_374

m
type: DistanceUnit
unique identifier: MO_367
comment: meter, distance unit

microeinstein per minute and square meter
type: LightUnit
comment: Microeinstein per minute and square meter (µE m-2 min-1 or uEinstein m-2 min-1). One einstein is one mole or 6.02x10e23 (avogadro constant) photons. It is commonly used as a unit for photosynthetically active radiation (PAR), however the einstein is not an SI unit. Therefore, microEinsteins per m2 per second is identical to micromoles per m2 per second (SI unit for light irradiance). i.e. (1000 µE m-2 s-1 = 1000 µmol m-2 s-1).
unique identifier: MO_526

log base 2
type: Scale
comment: The values presented are logarithm, base 2.
unique identifier: MO_647

birth
type: InitialTimePoint
comment: the action of emergence and separation of offspring from the mother.
unique identifier: MO_710

fertilization
type: InitialTimePoint
unique identifier: MO_701
comment: The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. (from the GO)

nutrients
type: EnvironmentalFactorCategory
unique identifier: MO_867
comment: The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.).

YAC
type: DeprecatedTerms
has reason for deprecation: deleted term
deprecation replacement term: PhysicalBioSequenceType
unique identifier: MO_794
deprecated from version: version 1.2.0
deprecation old parent: PhysicalBioSequenceType
deprecation reason: deleted_term
deprecation in version: 1.2.0
comment: sequence from yeast artificial chromosome

double stranded
type: StrandType
comment: a nucleic acid consisting 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.
unique identifier: MO_828

sex
type: BioMaterialCharacteristicCategory
comment: A descriptor for FactorValue where Sex is compared.
unique identifier: MO_680

curated gene record
type: DatabaseEntryType
unique identifier: MO_913
comment: A record which describes and identifies nucleic acid sequence which has been identified as a gene by a curator. e.g. Flybase gene record

EMAP
type: DevelopmentalStageDatabase
unique identifier: MO_357
comment: The Edinburgh Mouse Atlas Project (EMAP) ontology of mouse developmental anatomy covers the 26 developmental stages (Theiler Stages) from fertilization to birth.
has human readable URI: http://genex.hgu.mrc.ac.uk

sacrifice
type: ExperimentalProtocolType
type: ComplexAction
comment: The procedure of euthanizing an organism.
unique identifier: MO_602

frozen sample
type: BioSourceType
comment: A biomaterial obtained frozen
unique identifier: MO_610

short oligo
type: DesignElement
unique identifier: MO_749
comment: An element that is an oligonucleotide of less than 50 nucleotides in length (usually 20 to 25 nt as in Affymetrix probes).

data analyst
type: Roles
comment: A contact who performs data analysis, e.g. statistician.
unique identifier: MO_753

father
type: FamilyRelationship
comment: A male parent.
unique identifier: MO_762

temperature
type: EnvironmentalFactorCategory
comment: Temperature associated with a particular environment.
unique identifier: MO_791

array scanner
type: HardwareType
comment: An instrument capable of acquiring images of arrays.
unique identifier: MO_824

F minus
type: Sex
unique identifier: MO_682
comment: mating type indicating the absence of F plasmid in a bacterial cell

deprecation old parent
type: AnnotationProperty
unique identifier: MO_1016
type: ObjectProperty
comment: The value indicates the parent of the term before the term was deprecated.

heating block
type: HardwareType
unique identifier: MO_663
comment: A device for controlling temperature.

glass
type: SubstrateType
unique identifier: MO_742
comment: The array is made on a glass slide.

mm
type: DistanceUnit
unique identifier: MO_648
comment: millimeter, unit of distance

cm
type: DistanceUnit
comment: centimeter, a unit of distance
unique identifier: MO_837

nonnegative float
type: DataType
unique identifier: MO_386
comment: A float greater than or equal to 0.

cDNA clone
type: DeprecatedTerms
synonym: complementary DNA
synonym: cDNA
deprecation replacement term: PhysicalBioSequenceType
unique identifier: MO_966
deprecation reason: deleted_term
deprecation in version: 1.2.0
has reason for deprecation: deleted term
deprecation old parent: PhysicalBioSequenceType
comment: sequence of complementary cDNA copy of an RNA molecule contained on a plasmid including the plasmid sequence, used when the entire clone is spotted non-exact synonym: cDNA, complementary DNA
deprecated from version: version 1.2.0

primary protein structure record
type: DatabaseEntryType
comment: A record which describes and identifies an experimentally derived protein structure e.g. MSD
unique identifier: MO_785

acrossBioAssay mean and standard deviation
type: DerivedBioAssayType
comment: The mean and standard deviation values resulting from computationally combining 2 or more sets of bioassay data.
unique identifier: MO_946

genotyping design
type: BioMolecularAnnotation
unique identifier: MO_560
comment: A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's.

us
type: TimeUnit
unique identifier: MO_795
comment: microsecond, unit of time

virus
type: MaterialType
comment: one or more DNA or RNA based non cellular infective agent, including bacteriophage
unique identifier: MO_372

computer
type: HardwareType
comment: A device capable of applying software.
unique identifier: MO_510

intravenous
type: DeliveryMethod
unique identifier: MO_432
comment: delivery method whereby a compound or drug is administered via a vein

replicate design
type: MethodologicalDesign
unique identifier: MO_885
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.

alexa 594
type: LabelCompound
comment: Absorbs at 590 nm, emission maxima at 617 nm (red). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble.
unique identifier: MO_461

funder
type: Roles
unique identifier: MO_520
comment: Contact which provides funding for experiments.

ss oligo
type: DeprecatedTerms
deprecation in version: 1.2.0
comment: sequence of a single stranded synthesized oligonucleotide
deprecation reason: deleted_term
deprecation old parent: PhysicalBioSequenceType
has reason for deprecation: deleted term
deprecation replacement term: PhysicalBioSequenceType
unique identifier: MO_570
deprecated from version: version 1.2.0

control hybridization quality
type: ControlType
unique identifier: MO_385
comment: A Reporter that could be used to determine the quality and general performance of the labeled extract. An example is a pool of BioSequences representing widely-expressed genes (i.e., housekeeping genes).

non-targeted transgenic variation design
type: PerturbationalDesign
unique identifier: MO_775
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.

optimization design
type: MethodologicalDesign
comment: An optimization experiment design type is where different protocols or protocol parameters are compared.
unique identifier: MO_934

consensus mRNA
type: DeprecatedTerms
deprecation replacement term: TheoreticalBioSequenceType
unique identifier: MO_423
comment: mRNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple sequences as input.
deprecation reason: deleted_term
deprecation in version: 1.3.1.1
deprecation old parent: TheoreticalBioSequenceType

physiological process design
type: BiologicalProperty
comment: Those processes specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. This includes those processes that exhibit an endogenous periodicity independently of any daily variation in the environment such as circadian rhythm or aging.
unique identifier: MO_1029

feces
type: DeprecatedTerms
comment: A biosource obtained as fecal matter.
deprecated from version: version 1.1.9
has reason for deprecation: deleted term
deprecation reason: deleted_term
deprecation replacement term: BioSourceType
deprecation old parent: BioSourceType
deprecation in version: 1.1.9
unique identifier: MO_636

total intensity normalization paired
type: DataTransformationProtocolType
comment: A method to normalize paired-assay data that uses as a normalization coefficient the sum of intensity values from one assay divided by the sum of intensities from the other, where those sums are taken over all data points, or an appropriate subset of these (e.g. special control Features on a microarray, or 2DE spots containing constitutively expressed proteins). This normalization coefficient is used to rescale the intensity data in one data set relative to the other. Note that a normalization method that employs the average intensity rather than the sum (of all data points, or an appropriate subset) falls into this category as well.
unique identifier: MO_686

aunt
type: FamilyRelationship
unique identifier: MO_354
comment: The sister of one's father or mother.

Adult Mouse Anatomy
type: OrganismPartDatabase
unique identifier: MO_992
has machine readable URI: http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/MA.ontology
comment: This ontology describes the anatomy of the adult mouse. It contains anatomical structures for the postnatal mouse (Theiler stage 28).

circadian rhythm design
type: DeprecatedTerms
deprecation reason: replaced_term
replaced with term: physiological process design
deprecation in version: 1.1.7
was replaced by: physiological process design
deprecation old parent: 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.
has reason for deprecation: replaced term
deprecated from version: version 1.1.7
unique identifier: MO_539

degrees F
type: TemperatureUnit
unique identifier: MO_812
comment: degrees Fahrenheit, unit of temperature

median log normalization
type: DataTransformationProtocolType
unique identifier: MO_931
comment: Application of a normalization of type median_log_centering.

class source
type: AnnotationProperty
range: DataRange
  one of: mage
  one of: ontology
type: FunctionalProperty
type: DatatypeProperty
unique identifier: MO_343
comment: The property indicates the derivation of the class. A value of "mage" means that the class is derived from the MAGE-OM and the value "ontology" indicates that the class is derived from the ontology. This property is being added since the MGED Ontology was developed in such a way to include classes that exist in the MAGE-OM as well as classes that exist only in the MGED Ontology.

nm
type: DistanceUnit
unique identifier: MO_862
comment: nanometer distance unit

loop design
type: MethodologicalDesign
comment: A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design
synonym: circular design
unique identifier: MO_912

operator variation design
type: MethodologicalDesign
comment: An operator variation experiment design type assesses the operator performance and relation to data consistency and quality.
unique identifier: MO_519

genomic DNA
type: MaterialType
unique identifier: MO_599
comment: high molecular weight DNA

cell lysate
type: MaterialType
unique identifier: MO_903
comment: cell lysate, a collection of cells whose membranes have been disrupted

time series design
type: MethodologicalDesign
unique identifier: MO_887
comment: Groups of assays that are related as part of a time series.

flip-dye consistency
type: NormalizationDescriptionType
has reason for deprecation: replaced term
deprecated from version: version 1.2.0
was replaced by: dye swap merge
unique identifier: MO_907
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.

dye swap merge
type: DataTransformationProtocolType
unique identifier: MO_448
comment: A method of merging expression results from 2 dye-swap hybridizations on a Feature by Feature basis, with possible flagging if the results do not pass consistency checking criteria.

percent weight per weight
type: ConcentrationUnit
unique identifier: MO_474
comment: percent weight per weight, concentration unit

granddaughter
type: FamilyRelationship
comment: A daughter of one's son or daughter.
unique identifier: MO_703

cell type comparison design
type: BiologicalProperty
unique identifier: MO_764
comment: A cell type comparison design experiment design type compares cells of different type for example different cell lines.

arrayer
type: HardwareType
comment: An instrument capable of manufacturing arrays by spotting material.
unique identifier: MO_697

deprecation reason
type: AnnotationProperty
range: DataRange
  one of: deleted_term
  one of: split_term
  one of: merged_term
  one of: replaced_term
type: DatatypeProperty
unique identifier: MO_1013
comment: Indicates the why the term was deprecated. The possible values are: deleted_term, split_term, merged_term, replaced_term.

MESH
type: DiseaseStateDatabase
unique identifier: MO_580
has human readable URI: http://www.nlm.nih.gov/mesh/filelist.html
comment: database entry from MESH, medical subject headings vocabulary resource

TIFF
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.
unique identifier: MO_638

not sequence verified
type: WarningType
comment: The sequence of the BioSequence that relates to this reporter has not been sequence verified by the experimenter.
unique identifier: MO_970

lowess normalization
type: NormalizationDescriptionType
unique identifier: MO_720
comment: A method of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria.

ex vivo design
type: MethodologicalDesign
unique identifier: MO_808
comment: An experiment design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment.

mean and confidence indicators
type: DeprecatedTerms
deprecation old parent: DerivedBioAssayType
deprecation replacement term: DerivedBioAssayType
unique identifier: MO_702
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.
deprecation in version: 1.2.0
has reason for deprecation: deleted term
deprecation reason: deleted_term
deprecated from version: version 1.2.0

polypeptide
type: DeprecatedTerms
deprecated from version: version 1.2.0
has reason for deprecation: deleted term
deprecation in version: 1.2.0
deprecation reason: deleted_term
deprecation replacement term: TheoreticalBioSequenceType
comment: sequence of a protein, a linear amino acid polymer
deprecation replacement term: PhysicalBioSequenceType
deprecation old parent: TheoreticalBioSequenceType
unique identifier: MO_530
deprecation old parent: PhysicalBioSequenceType

chromosome
type: DeprecatedTerms
deprecation replacement term: TheoreticalBioSequenceType
deprecated from version: version 1.2.0
has reason for deprecation: deleted term
deprecation reason: deleted_term
deprecation old parent: TheoreticalBioSequenceType
deprecation replacement term: PhysicalBioSequenceType
comment: Physical or theoretical sequence of, or representing a chromosome, one of the DNA molecules that comprises the genome.
deprecation old parent: PhysicalBioSequenceType
deprecation in version: 1.2.0
unique identifier: MO_578

light intensity
type: EnvironmentalFactorCategory
comment: The amount of light actually striking the surface of samples which are being assayed. It has a unit association as well, usually uEinstein /m2 /min or uEinstein /m2/s.
unique identifier: MO_517

amino acid primary sequence record
type: DatabaseEntryType
unique identifier: MO_829
comment: A record which describes and identifies an amino acid sequence which is encoded by a CDS from a primary_nucleic_acid_sequence_record

kg
type: MassUnit
comment: kilogram, 1000 grams, unit of mass
unique identifier: MO_846

dye swap replicate
type: ReplicateDescriptionType
comment: One of a pair of replicate assays in which LabeledExtracts derived from the same BioMaterial used for both assays (e.g., a hybridization or a 2-D gel run) differ only in that the dyes used for labeling have been reversed, e.g., assay 1: A-Cy3 vs. B-Cy5, and assay 2: A-Cy5 vs. B-Cy3. The purpose of using dye-swap replicate pairs is to assess or remove dye-specific biases from the combined experimental results.
unique identifier: MO_901

seed dormancy
type: PreservationType
comment: preservation type whereby the seed is maintained in a dormant state
unique identifier: MO_666

mixed design element group type
type: DesignElementGroupType
comment: a design element group consisting of multiple types
unique identifier: MO_528

no
type: DeprecatedTerms
has reason for deprecation: deleted term
deprecation reason: deleted_term
comment: false
deprecation in version: 1.1.7
unique identifier: MO_556
deprecated from version: version 1.1.7

diploid
type: Ploidy
unique identifier: MO_836
comment: Describes a cell, nucleus or an organism with two copies of each chromosome.

PCR primer forward
type: DeprecatedTerms
deprecation reason: deleted_term
deprecated from version: version 1.2.0
unique identifier: MO_381
deprecation replacement term: PhysicalBioSequenceType
deprecation in version: 1.2.0
has reason for deprecation: deleted term
deprecation old parent: PhysicalBioSequenceType
comment: single stranded oligo used for polymerase chain reaction

agar
type: Media
comment: A type of solid media commonly used for growing organisms
unique identifier: MO_935

Rem
type: RadiationUnit
comment: Roentgen Equivalent Man. Unit of dose equivalent, i.e., the measure of potential biological damage caused by exposure and absorption of radiation. Rem = absorbed dose (rad) x quality factor (Q). Q is unique to the type of incident radiation.
unique identifier: MO_908

log ratio
type: DerivedBioAssayType
comment: Logarithmic transformation of ratio data.
unique identifier: MO_896

germination
type: InitialTimePoint
comment: The physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth (from the GO).
unique identifier: MO_590

add
type: AtomicAction
comment: The procedure of placing one physical object in the same container/physical space as another.
unique identifier: MO_815

RMA
type: DerivedBioAssayType
comment: Robust Multiarray Average. A quantitative measure of the relative abundance of a transcript. RMA is a summary measure of related perfect match Features on an Affymetrix array. The values are background-adjusted, normalized and log-transformed values.
unique identifier: MO_987

environmental history design
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.
unique identifier: MO_698

paraffin sample
type: BioSourceType
comment: A biomaterial obtained embedded in paraffin (wax).
unique identifier: MO_990

computed protein structure record
type: DatabaseEntryType
unique identifier: MO_765
comment: a record which describes and identifies a protein structure e.g. PDB

gene knock in
type: GeneticModification
comment: A modification whereby a functional gene, or a functional part of a gene, is inserted into an organism', e.g. by recombination, P-element insertion.
unique identifier: MO_437

set temperature
type: AtomicAction
unique identifier: MO_393
comment: An action where the temperature is specified.

growth condition design
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.
unique identifier: MO_588

institution
type: Roles
unique identifier: MO_601
comment: A contact's affiliation, e.g. university, research institute or business.

loess group normalization
type: DataTransformationProtocolType
comment: Application of a normalization of type loess_normalization where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed.
unique identifier: MO_377

clinical information
type: BioMaterialCharacteristicCategory
unique identifier: MO_816
comment: A descriptor for FactorValue where ClinicalInformation is compared.

sowing
type: InitialTimePoint
unique identifier: MO_748
comment: the process of placing a seed or spore in some media with the intention to invoke germination.

relative humidity
type: EnvironmentalFactorCategory
comment: The amount of moisture in the air expressed as a percentage of the maximum amount the air is capable of holding.
unique identifier: MO_453

MAS5 signal
type: DerivedBioAssayType
unique identifier: MO_653
comment: A quantitative measure of the relative abundance of a transcript. Used in the MAS5.0 Affymetrix software to obtain a smoothed signal intensity from a group of related Features.

normalized ratios
type: DerivedBioAssayType
comment: Results obtained by either taking the pair wise ratios of two bioassay data sets and then normalizing, or normalizing each bioassay data set and then taking ratios.
unique identifier: MO_664

tRNA gene
type: DeprecatedTerms
comment: sequence from a gene coding for transfer RNA exact synonym: transfer RNA gene
deprecation in version: 1.2.0
unique identifier: MO_850
deprecation replacement term: TheoreticalBioSequenceType
deprecation reason: deleted_term
has reason for deprecation: deleted term
deprecation old parent: TheoreticalBioSequenceType
synonym: transfer RNA gene
deprecated from version: version 1.2.0

x times
type: ConcentrationUnitOther
unique identifier: MO_496
comment: multiple of stock solution concentration, concentration unit

differential expression software
type: SoftwareType
comment: A software implementing a Higher Level Analysis protocol of type differential_expresssion.
unique identifier: MO_350

loess normalization
type: NormalizationDescriptionType
unique identifier: MO_428
comment: A method of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria.

experimental design element group type
type: DesignElementGroupType
unique identifier: MO_755
comment: A grouping of DesignElements, Features/Reporters/Composite Sequences which are expected to detect a signal in the biomaterial.

histological slide preparation
type: ExperimentalProtocolType
comment: The action of preparing a slide for the microscopical examination of organism parts or cell types.
type: ComplexAction
unique identifier: MO_611

intron
type: DeprecatedTerms
has reason for deprecation: deleted term
deprecation replacement term: TheoreticalBioSequenceType
deprecation in version: 1.2.0
unique identifier: MO_709
comment: sequence spliced out from a transcript
deprecation old parent: TheoreticalBioSequenceType
deprecation reason: deleted_term
deprecated from version: version 1.2.0

U per week
type: OtherUnit
comment: units per week, e.g. the number of units of alcohol consumed over a period of 7 days
unique identifier: MO_388

activity units per ml
type: OtherUnit
unique identifier: MO_870
has reason for deprecation: deleted term
deprecated from version: version 1.3.1
comment: Units of defined biological activity, e.g. cytokine stimulation, per ml.

reference design
type: MethodologicalDesign
comment: A reference experiment design type is where all samples are compared to a common reference.
unique identifier: MO_699

Hfr
type: DeprecatedTerms
unique identifier: MO_419
deprecated from version: version 1.1.7
deprecation reason: deleted_term
deprecation replacement term: Sex
has reason for deprecation: deleted term
deprecation in version: 1.1.7
deprecation old parent: Sex
comment: High frequency recombinant, mating type that indicates that the F plasmid has integrated into the chromosome

transcript
type: DeprecatedTerms
deprecation replacement term: TheoreticalBioSequenceType
comment: sequence that represents the product of an RNA polymerase engaged in transcription
unique identifier: MO_827
deprecation old parent: TheoreticalBioSequenceType
deprecation in version: 1.3.1.1
deprecation reason: deleted_term

hours
type: TimeUnit
synonym: h
unique identifier: MO_486
comment: 60 minutes, time unit

kat per L
type: ConcentrationUnitOther
unique identifier: MO_869
comment: katal per liter, catalytic-activity concentration unit

rRNA gene
type: DeprecatedTerms
deprecation reason: deleted_term
deprecation old parent: TheoreticalBioSequenceType
synonym: ribosomal RNA gene
deprecated from version: version 1.2.0
deprecation in version: 1.2.0
comment: sequence from gene coding for ribosomal RNA exact synonym: ribosomal RNA gene
unique identifier: MO_955
has reason for deprecation: deleted term
deprecation replacement term: TheoreticalBioSequenceType

quality control testing design
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
unique identifier: MO_981

manhattan distance
type: NodeValueType
comment: The "Manhattan distance" is the shortest path between two points in a block format, e.g. the length of the path along Manthattan city streets.
unique identifier: MO_567

alexa 568
type: LabelCompound
comment: Absorbs at 556 nm, emission maxima at 573 nm (orange). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble.
unique identifier: MO_736

organellar RNA
type: MaterialType
comment: RNA obtained from an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus.
unique identifier: MO_574

negative float
type: DataType
comment: A float that is < 0.
unique identifier: MO_728

homogenizer
type: HardwareType
comment: An instrument which fragments tissues or other biomaterials.
unique identifier: MO_714

Cy5
type: LabelCompound
comment: fluorophore used for labeling/detection purposes
unique identifier: MO_646

plasmid
type: DeprecatedTerms
deprecation in version: 1.2.0
deprecation old parent: PhysicalBioSequenceType
unique identifier: MO_439
has reason for deprecation: deleted term
comment: sequence from a plasmid, an extrachromosomal autonomously replicating piece of DNA excluding mitochondria and chloroplasts
deprecation replacement term: PhysicalBioSequenceType
deprecated from version: version 1.2.0
deprecation reason: deleted_term

integer
type: DataType
unique identifier: MO_435
comment: A value which is a whole number (e.g. 10).

son
type: FamilyRelationship
unique identifier: MO_465
comment: The male offspring of the patient or individual under study.

developmental stage
type: BioMaterialCharacteristicCategory
unique identifier: MO_878
comment: A descriptor for FactorValue where DevelopmentalStage is compared.

feature extraction software
type: SoftwareType
synonym: image quantification software
synonym: image analysis software
unique identifier: MO_633
comment: Software to create MeasuredBioAssayData from images. Exact Synonym: image analysis software, image quantification software.

oral gavage
type: DeliveryMethod
unique identifier: MO_975
comment: delivery method for drug or compound whereby the drug is administered via the mouth

CABRI HLA typed B Cell lines
type: CellLineDatabase
unique identifier: MO_1005
comment: List of CABRI HLA typed B cell lines sorted by name. It includes 238 resources that are available from a European collection participating in the CABRI (Common Access to Biological Resources and Information) initiative (see http://www.cabri.org/ ). Detailed descriptions can be reached from the list and cell lines of interest can be requested.
has human readable URI: http://www.cabri.org/HyperCat/cells/hla.htm

linlog normalization
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.
has reason for deprecation: replaced term
deprecated from version: version 1.2.0
unique identifier: MO_956

candela
type: LightUnit
comment: One lumen per steradian. A steradian is a fraction of the surface area of a sphere that is equal to the square of the radius divided by the total surface area. This is approximately 8% of the total surface area. Exact synonym: candle power
unique identifier: MO_572
synonym: candle power

nitrocellulose
type: SubstrateType
comment: The array is made on a nitrocellulose filter.
unique identifier: MO_455

cc
type: VolumeUnit
unique identifier: MO_834
comment: a cubic centimeter, volume unit

protein
type: PolymerType
unique identifier: MO_683
comment: Polymer of amino acids.
type: MaterialType

nmol
type: QuantityUnit
comment: nanomoles, quantity unit
unique identifier: MO_743

DNA
type: MaterialType
unique identifier: MO_945
comment: Deoxyribonucleic acid.
type: PolymerType

pM
type: ConcentrationUnit
unique identifier: MO_628
comment: picomolar, concentration unit

g per L
type: ConcentrationUnit
comment: grams per liter, concentration unit
unique identifier: MO_805

monosomy
type: DeprecatedTerms
deprecation in version: 1.1.9
deprecation old parent: ChromosomalAberrationClassification
comment: Absence of one chromosome of a pair of homologous chromosomes. In a normally diploid cell it is represented symbolically as 2N-1.
deprecation reason: replaced_term
deprecated from version: version 1.1.9
was replaced by: oligosomy
has reason for deprecation: replaced term
replaced with term: oligosomy
unique identifier: MO_424

chromosomal substitution
type: GeneticModification
unique identifier: MO_995
comment: A state/condition describing a cell, or organism, in which all, or part, of a chromosome from a donor replaces that of the recipient. Examples include strains created by repeated backcrossing as well as those created by recombinant methods. For single gene insertion, use the term gene_knock_in.

tau rank correlation
type: DeprecatedTerms
deprecation in version: 1.1.7
deprecated from version: version 1.1.7
deprecation reason: deleted_term
unique identifier: MO_673
has reason for deprecation: deleted term
deprecation replacement term: NodeValueType
comment: a nonparametric measure of the agreement between two rankings
deprecation old parent: NodeValueType

tiling path design
type: BioMolecularAnnotation
unique identifier: MO_507
comment: An experiment in which gene expression on a genome-wide basis is evaluated, without bias toward coding or noncoding regions, using arrays containing oligonucleotides that are either overlapping or spaced at regular intervals.

french railway distance
type: NodeValueType
comment: The "French railway distance" is based on the fact that (at least in the past) most of the railways in France headed straight to Paris. Thus, the French railway distance between two points is the usual distance if the straight line through them passes to a designated Paris point, or is the sum of their distances to the Paris point otherwise.
unique identifier: MO_964

TDMS
type: HistologyDatabase
comment: Toxicology Data Management System, a database resource for systems, organs, pathology, etc.
has human readable URI: http://hazel.niehs.nih.gov/user_spt/pct_terms.htm
unique identifier: MO_718
type: TestTypeDatabase
type: OrganismPartDatabase
type: DiseaseStateDatabase

PAC
type: DeprecatedTerms
has reason for deprecation: deleted term
deprecation in version: 1.2.0
unique identifier: MO_909
deprecation replacement term: PhysicalBioSequenceType
deprecation reason: deleted_term
comment: sequence from a P1 artificial chromosome
deprecation old parent: PhysicalBioSequenceType
deprecated from version: version 1.2.0

minutes
type: TimeUnit
synonym: m
unique identifier: MO_877
comment: 60 seconds, unit of time

gene
type: DeprecatedTerms
deprecation reason: deleted_term
deprecation replacement term: TheoreticalBioSequenceType
deprecated from version: version 1.2.0
unique identifier: MO_503
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
deprecation old parent: TheoreticalBioSequenceType
has reason for deprecation: deleted term
deprecation in version: 1.2.0

number per day
type: OtherUnit
comment: number of items or events per day
unique identifier: MO_670

sonicator
type: HardwareType
unique identifier: MO_477
comment: An instrument for sonicating biomaterials.

acrossBioAssay mean and p values
type: DerivedBioAssayType
comment: The mean and associated p-values resulting from computationally combining 2 or more sets of bioassay data.
unique identifier: MO_671

mol
type: QuantityUnit
unique identifier: MO_998
comment: mole, unit of quantity

ATCC Cultures
type: StrainOrLineDatabase
type: CellLineDatabase
comment: database resource for bacteria, bacteriophages, cell lines, fungi and yeast, plant tissue cultures, plant seeds, protozoa and algae and plant and animal viruses
has human readable URI: http://www.atcc.org/Cultures/Products.cfm
unique identifier: MO_979

micromole per second and square meter
type: OtherUnit
comment: Number of photons in a certain waveband incident per unit time (s) on a unit area (m2) divided by the Avogadro constant (6.022 x 10e23 mol-1). It is used commonly to describe photosynthetically active radiation (PAR) in the 400-700 nm waveband.
unique identifier: MO_848

freeze dried sample
type: BioSourceType
unique identifier: MO_589
comment: A biomaterial that has been lyophilized or dried by freezing under a vacuum.

consortium member
type: Roles
comment: A member of a consortium of institutions.
unique identifier: MO_778

spotted ss PCR amplicon features
type: TechnologyType
comment: A descriptor for the TechnologyType for a group of features where single stranded DNA PCR product is spotted on the array.
unique identifier: MO_921

seconds
type: TimeUnit
comment: time unit
unique identifier: MO_391

control unknown type
type: ControlType
unique identifier: MO_925
comment: A Reporter indicated as being a control of unknown type.

unknown sex
type: Sex
unique identifier: MO_999
comment: organism(s) whose sex is unknown

frozen storage
type: PreservationType
comment: Storage where the thing stored is stored below 0 degrees celsius.
unique identifier: MO_481

spotted antibody features
type: TechnologyType
comment: TechnologyType of FeatureGroup where antibodies are spotted directly.
unique identifier: MO_483

loess global normalization
type: DataTransformationProtocolType
comment: Application of a normalization of type loess_normalization where the same normalization curve is used for all points in the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample.
unique identifier: MO_443

thermal cycler
type: HardwareType
unique identifier: MO_854
comment: An instrument designed to automatically raise and lower the temperature of wells or tubes. Usually used to perform PCR. Exact Synonym: thermocycler

long oligo
type: DesignElement
comment: An element that is an oligonucleotide of at least 50 nucleotides in length.
unique identifier: MO_598

hatching
type: InitialTimePoint
unique identifier: MO_745
comment: The point at which an organism emerges from an egg.

chrome border
type: FiducialType
unique identifier: MO_491
comment: the chrome border on an Affymetrix type array which is used as a point of reference for orientation (fiducial)

filtered data
type: DerivedBioAssayType
unique identifier: MO_625
comment: Data from which a subset has been removed based on some criteria, e.g. data below an intensity threshhold.

coitus
type: InitialTimePoint
unique identifier: MO_783
comment: the physical act of copulation that occurs during the process of sexual reproduction synonyms: copulation, insemination
synonym: insemination
synonym: copulation

loess scaled group normalization
type: DataTransformationProtocolType
comment: Application of a scale adjustment following loess_group_normalization, to render the group variances similar.
unique identifier: MO_521

PCR questionable
type: FailType
comment: PCR with multiple bands, or smear, in gel-separated reaction products
unique identifier: MO_620

DNA sequencer
type: HardwareType
comment: An instrument that produces DNA sequences.
unique identifier: MO_676

computed nucleic acid sequence feature record
type: DatabaseEntryType
unique identifier: MO_774
comment: A record which identifies and describes a nucleic sequence feature which has been computationally determined or predicted E.g. and Ensembl record

purify
type: ComplexAction
unique identifier: MO_406
type: ExperimentalProtocolType
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).

cell component comparison design
type: BiologicalProperty
unique identifier: MO_1019
comment: A design in which RNA from different cell components is examined.

bioassay data transformation software
type: SoftwareType
unique identifier: MO_672
synonym: normalization software
comment: Software used to transform the Measured or DerivedBioAssay data e.g. normalization. Non-exact synonym: normalization software

clustering software
type: SoftwareType
comment: Software used to cluster the data.
unique identifier: MO_464

jackknife Pearson correlation
type: NodeValueType
unique identifier: MO_784
comment: The jackknife Pearson correlation is the lowest Pearson correlation between two data series where one pair of values in the data series are omitted.

age
type: BioMaterialCharacteristicCategory
unique identifier: MO_467
comment: A descriptor for FactorValue where age is compared.

ad libitum
type: DeliveryMethod
comment: A delivery method for compounds/drugs where the compound or drug is freely available.
unique identifier: MO_592

across bioassay data set function
type: DataTransformationProtocolType
comment: A function applied to corresponding values coming from a set of compatible Measured/Derived bioassay data sets. Two Measured/Derived bioassay data sets are compatible if there is a natural one-to-one correspondence between them.
unique identifier: MO_606

lowess scaled group normalization
type: DataTransformationProtocolType
comment: Application of a scale adjustment following lowess_group_normalization, to render the group variances similar.
unique identifier: MO_410

array manufacture software
type: SoftwareType
unique identifier: MO_502
comment: Software to control an arrayer.

GRAMENE
type: StrainOrLineDatabase
unique identifier: MO_678
comment: A Comparative Mapping Resource for Grains.
has human readable URI: http://www.gramene.org/

list of negative integers
type: DataType
unique identifier: MO_900
comment: An ordered, finite set of negative integers.

dye swap design
type: MethodologicalDesign
unique identifier: MO_858
synonym: dye flip
synonym: flip dye
comment: An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip

irradiate
type: ExperimentalProtocolType
comment: treatment of a biomaterial with radiation e.g. electromagnetic radiation
unique identifier: MO_770
type: ComplexAction

CLDB Human and Animal Cell Line
type: CellLineDatabase
comment: List of cell lines available in the Cell Line Database (CLDB), that includes more than 4,000 resources from many European collections and Italian laboratories. Indexes are given by species/strain, pathology, tumor, tissue/organ, and transforming agent.
unique identifier: MO_1007

TAIR arabidopsis development ontology
type: DevelopmentalStageDatabase
unique identifier: MO_919
has machine readable URI: http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/developmental/plant_development/Arabidopsis/temporal.tair
comment: An ontology of stages of growth and development of the model plant Arabidopsis thaliana.

cell cycle design
type: BiologicalProperty
unique identifier: MO_822
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.

32P
type: LabelCompound
comment: 32 P, radioactive isotope of phosphorus used for labeling/detection purposes
unique identifier: MO_839

cpm
type: RadiationUnit
unique identifier: MO_348
comment: counts per minute, unit of light emissions produced by ionizing radiation.

list of positive floats
type: DataType
comment: An ordered, finite set of positive floats.
unique identifier: MO_777

collapsed spot replicate
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.
unique identifier: MO_789

IUPAC Clinical Chemistry Guidelines
type: TestTypeDatabase
has human readable URI: http://www.iupac.org/publications/pac/2000/205/205olesen.html
unique identifier: MO_593
comment: A resource of vocabularies for describing clinical tests, e.g. blood chemistry.

compound record
type: DatabaseEntryType
comment: a record which describes and identifies a compound e.g. drug record part of NCI thesaurus
unique identifier: MO_546

list of nonnegative integers
type: DataType
unique identifier: MO_973
comment: An ordered, finite set of nonnegative integers.

mL per L
type: ConcentrationUnit
comment: milliliters per liter, concentration unit
unique identifier: MO_801

transcript identification design
type: TechnologicalDesign
unique identifier: MO_533
synonym: transcription_profiling
synonym: gene expression
synonym: expression_profiling
type: BioMolecularAnnotation
synonym: gene_expression
synonym: transcription profiling
comment: A transcript identification design type characterizes the length and position of transcripts and allows identification of all forms of transcripts in the genome.
synonym: expression profiling

percent vol per vol
type: ConcentrationUnit
unique identifier: MO_916
comment: percentage volume per volume, concentration unit

stimulus or stress design
type: PerturbationalDesign
unique identifier: MO_568
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.

mean log centering
type: NormalizationDescriptionType
unique identifier: MO_398
comment: A method of normalizing log ratio data by subtraction of the mean log ratios computed across all data points, or an appropriate subset of these (e.g. special control Features on a microarray, or 2DE spots containing constitutively expressed proteins).

transfection
type: GeneticModification
comment: Introduction of genetic material into an organism often in the form of a plasmid.
unique identifier: MO_366

software manufacturer
type: Roles
unique identifier: MO_475
comment: Person or organization that manufactured the software.

SequenceOntology
type: SequenceOntologyDatabase
has machine readable URI: http://song.sourceforge.net/
comment: The Sequence Ontology is a set of terms used to describe features on a nucleotide or protein sequence.
unique identifier: MO_724

total intensity normalization
type: DeprecatedTerms
deprecated from version: version 1.2.0
has reason for deprecation: deleted term
deprecation in version: 1.2.0
deprecation reason: deleted_term
deprecation replacement term: NormalizationDescriptionType
comment: A method of re-scaling intensity data from one channel relative to another based on the ratio of the sums of the fluorescent intensities from each channel for all Features: N = sum(Ri) / sum(Gi) . The ratio is used to re-scale the intensities in one channel for each Feature. This is a single parameter linear normalization method.
unique identifier: MO_441
deprecation old parent: NormalizationDescriptionType

Euclidean distance
type: NodeValueType
unique identifier: MO_932
comment: The straight line distance between two points. In n dimensions, the Euclidean distance between two points p and q is square root of (sum (pi-qi)2) where pi (or qi) is the i-th coordinate of p (or q).

species design
type: BiologicalProperty
unique identifier: MO_675
comment: A species experiment design type assays differences between distinct species.

control biosequence
type: ControlType
unique identifier: MO_940
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.

mix general
type: AtomicAction
unique identifier: MO_944
comment: The procedure of agitating 2 or more materials in order to combine them. The materials may be of any state solid/liquid/gas.

pathogenicity design
type: PerturbationalDesign
unique identifier: MO_807
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.

urine
type: BioSourceType
unique identifier: MO_399
comment: The fluid and dissolved substances excreted by the kidney.

all pairs
type: MethodologicalDesign
unique identifier: MO_565
comment: An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.

ctDNA
type: DeprecatedTerms
synonym: chloroplast DNA
deprecation replacement term: PhysicalBioSequenceType
unique identifier: MO_586
comment: ctDNA: sequence from the chloroplast synonym: chloroplast DNA
deprecation old parent: PhysicalBioSequenceType
deprecation reason: deleted_term
deprecation in version: 1.3.1.1

linear scale
type: Scale
unique identifier: MO_751
comment: The scale is a standard base 10, non logarithmic scale.

list of integers
type: DataType
unique identifier: MO_891
comment: An ordered, finite set of integers.

moving average
type: DataTransformationProtocolType
unique identifier: MO_681
comment: A type of data transformation in which an average, usually the mean, is calculated across values within a sliding window. e.g. The moving average of signal intensity, or array CGH, data may be used in normalization.

reverse
type: StrandType
synonym: -
unique identifier: MO_402
comment: the reverse strand exact synonym: -

individual
type: BioMaterialCharacteristicCategory
unique identifier: MO_639
comment: A descriptor for FactorValue where BioSources are compared.

CABRI Bacteria and Archaea Strains
type: StrainOrLineDatabase
unique identifier: MO_1008
has human readable URI: http://www.cabri.org/HyperCat/bact/all_A.htm
comment: List of CABRI bacteria and archaea strains sorted by genus and species. It includes more than 40,000 resources that are available from seven European collections participating in the CABRI (Common Access to Biological Resources and Information) initiative (see http://www.cabri.org/ ). Detailed descriptions can be reached from the list and strains of interest can be requested.

percent confluence
type: ConcentrationUnitOther
unique identifier: MO_378
comment: A measure of the density of an attached or monolayer culture (e.g., cell culture), e.g., 80 percent_confluence.

lumen
type: LightUnit
unique identifier: MO_603
comment: The unit of total light output from a light source.

change light
type: AtomicAction
comment: Change in light intensity or wavelength.
unique identifier: MO_549

cells per ml
type: ConcentrationUnitOther
comment: the number of cells per ml
unique identifier: MO_727

organism status
type: BioMaterialCharacteristicCategory
comment: The stage premortem or postmortem at which the sample was processed for extraction of biomaterials.
unique identifier: MO_871

M
type: ConcentrationUnit
unique identifier: MO_936
comment: Mole per liter or molarity, concentration unit

float
type: DataType
comment: A value which is a floating point number (i.e. real number) with arbitrary precision (e.g. 2.34).
unique identifier: MO_860

bibliographic record
type: DatabaseEntryType
comment: A record which describes and identifies a paper publication e.g. a medline record
unique identifier: MO_923

ellipsoid feature
type: FeatureShape
comment: The shape of the feature on the array is circular or oval.
unique identifier: MO_459

in medium
type: DeliveryMethod
unique identifier: MO_733
comment: Delivery method where a compound/drug is administered in the culture medium (e.g., for in vitro treatment).

pmol
type: QuantityUnit
comment: picomoles, quantity unit
unique identifier: MO_688

ratio statistics normalization
type: NormalizationDescriptionType
unique identifier: MO_349
comment: A method to re-scale paired-assay data from one data set relative to the other, based on an iterative regression method of calculating single parameter linear normalization factors. This method allows calculation of the mean, standard deviation and confidence interval limits for the distribution of measured ratio values.

mOsm per kg H2O
type: ConcentrationUnitOther
unique identifier: MO_661
comment: osmolality per kilogram of water, concentration of the solute per unit of solvent

data coder
type: Roles
comment: person who prepares the MAGE-ML file
unique identifier: MO_695

media
type: EnvironmentalFactorCategory
comment: The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil)
unique identifier: MO_545

self vs self design
type: MethodologicalDesign
unique identifier: MO_490
comment: A self vs. self experiment design investigates variance and error estimates in the experimental system, and is where the same extract is compared.

PNG
type: ImageFormat
unique identifier: MO_1001
comment: Portable Network Graphic, a lossless image data format.

wild type
type: Genotype
type: Allele
unique identifier: MO_605
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.

not uniform
type: DefectType
unique identifier: MO_906
comment: The source DNA for a Feature was not uniformly deposited.

linear amplification
type: ComplexAction
type: ExperimentalProtocolType
synonym: Eberwine procedure
comment: Amplification of nucleic acid sequence by making many copies off the same template. An example is the use of the T7 promoter for amplification by transcribing many RNA copies. non exact synonym: Eberwine procedure
unique identifier: MO_997

organism
type: BioMaterialCharacteristicCategory
comment: one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria
unique identifier: MO_508

FlyBase organism part database
type: OrganismPartDatabase
has machine readable URI: http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fly/
unique identifier: MO_504
comment: curated database containing information on Drosophila genes, alleles etc

hardware variation design
type: MethodologicalDesign
unique identifier: MO_734
comment: A hardware variation experiment design type compares different types of hardware for performance, reproducibility, accuracy and precision.

clustered data
type: DerivedBioAssayType
unique identifier: MO_418
comment: Results of an analysis method that groups data based on a measure of similarity, e.g. Pearson correlation coefficient, Euclidean distance.

amol
type: QuantityUnit
unique identifier: MO_977
comment: attomole, quantity unit

microeinstein per second and square meter
type: LightUnit
comment: Microeinstein per second and square meter (µE m-2 s-1 or uEinstein m-2 s-1). One einstein is one mole or 6.02x10e23 (Avogadro constant) photons. It is commonly used as a unit for photosynthetically active radiation (PAR), however the einstein is not an SI unit. Therefore, microEinsteins per m2 per second is identical to micromoles per m2 per second (SI unit for light irradiance). i.e. (1000 µE m-2 s-1 = 1000 µmol m-2 s-1).
unique identifier: MO_584

TAIR
type: CellTypeDatabase
type: StrainOrLineDatabase
has human readable URI: http://www.arabidopsis.org/servlets/Search
unique identifier: MO_660
comment: The Arabidopsis Information Resource.

wash
type: ExperimentalProtocolType
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.
type: ComplexAction
unique identifier: MO_596

differential expression
type: HigherLevelAnalysisProtocolType
unique identifier: MO_874
comment: An analysis aimed at identifying differentially expressed genes in two or more conditions.

fmol
type: QuantityUnit
comment: femtomole, unit of quantity
unique identifier: MO_689

displaced feature or zone
type: DefectType
unique identifier: MO_959
comment: The Feature or Zone is displaced from its expected position, due to e.g. a bent spotting pin(s).

list of booleans
type: DataType
comment: An ordered, finite set of booleans.
unique identifier: MO_712

primary site
type: CancerSite
comment: the organism part in which the tumor originated
unique identifier: MO_408

candelas per square meter
type: LightUnit
comment: Unit of brightness or luminance.
unique identifier: MO_813

grandmother
type: FamilyRelationship
unique identifier: MO_924
comment: The mother of one's father or mother.

chromosomal deletion
type: ChromosomalAberrationClassification
unique identifier: MO_922
comment: The loss of a segment of the genetic material from a chromosome.

grandfather
type: FamilyRelationship
comment: The father of one's father or mother.
unique identifier: MO_478

resuspend
type: AtomicAction
unique identifier: MO_466
comment: The procedure in which solid material is dispensed or dissolved in a liquid.

postmortem
type: OrganismStatus
comment: biomaterial removed after the death of the organism
unique identifier: MO_416

total intensity normalization single
type: DataTransformationProtocolType
comment: A normalization method that uses as a coefficient the sum of all intensities in the data set, or an appropriate subset of these (e.g. special control Features on a microarray, or 2DE spots containing constitutively expressed proteins). The intensities are normalized through division by such a coefficient (and possible subsequent multiplication by a target constant). Note that a normalization method that employs the average intensity rather than the sum (of all data points, or an appropriate subset) falls into this category as well.
unique identifier: MO_472

gene knock out
type: GeneticModification
comment: The modification of an organism that renders a gene non-functional e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods.
unique identifier: MO_771

yes
type: DeprecatedTerms
unique identifier: MO_540
deprecation reason: deleted_term
deprecated from version: version 1.1.7
deprecation in version: 1.1.7
comment: true
has reason for deprecation: deleted term

EST
type: DeprecatedTerms
has reason for deprecation: deleted term
deprecation reason: deleted_term
unique identifier: MO_412
comment: Sequence derived from expressed sequence tag. EST's are likely to be partial, single read and low quality sequences.
deprecation in version: 1.2.0
deprecation replacement term: TheoreticalBioSequenceType
deprecation old parent: TheoreticalBioSequenceType
deprecated from version: version 1.2.0

mix by vortex
type: AtomicAction
unique identifier: MO_880
comment: Mix through the use of a vortexer.

liquid handler
type: HardwareType
unique identifier: MO_868
comment: Hardware for automated liquid transfer and handling.

change biomaterial characteristics
type: ComplexAction
synonym: change environment
synonym: change growth condition
comment: Indicates that one or more BioMaterialCharacteristics have changed during the treatment of a BioMaterial. Non exact synonym: change growth condition, change environment
unique identifier: MO_383
type: ExperimentalProtocolType

phylogeny record
type: DatabaseEntryType
unique identifier: MO_662
comment: A record which describes and identifies the relationship between species and is computationally determined and based on sequences e.g. Treebase record

extract
type: BioSampleType
comment: The BioSample immediately before labeling.
unique identifier: MO_895

eVOC
type: DevelopmentalStageDatabase
comment: Ontology of human terms that describe the sample source of human cDNA and SAGE libraries.
unique identifier: MO_684
type: DiseaseStateDatabase
type: CellTypeDatabase
type: OrganismPartDatabase
has human readable URI: http://www.sanbi.ac.za/evoc/ontologies.html

aminosilane
type: SurfaceType
unique identifier: MO_747
comment: a surface coating type for immobilization with the compound aminosilane

tumor grading
type: BioMaterialCharacteristicCategory
comment: A descriptor used in cancer biology to describe abnormalities of tumor cells.
unique identifier: MO_843

weeks
type: TimeUnit
unique identifier: MO_842
comment: 7 days, unit of time

mM
type: ConcentrationUnit
unique identifier: MO_509
comment: milimolar, concentration unit

mean and p values
type: DerivedBioAssayType
unique identifier: MO_943
comment: the mean and associated p-values resulting from computationally combining 2 or more sets of BioAssayData

cellular process design
type: BiologicalProperty
comment: Processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
unique identifier: MO_810

antibody
type: PhysicalBioSequenceType
comment: glycoprotein of the immunoglobulin family that can combine specifically non-covalently, reversibly with a corresponding antigen
unique identifier: MO_833

liquid handler software
type: SoftwareType
unique identifier: MO_761
comment: Software used to control automated liquid handler.

Spearmans rank correlation
type: NodeValueType
comment: Computed as the ordinary Pearson correlation coefficient between two groups of rankings.
unique identifier: MO_552

total RNA
type: MaterialType
unique identifier: MO_373
comment: Total cellular and nuclear RNA.

ORF
type: DeprecatedTerms
deprecation replacement term: 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.
deprecation reason: deleted_term
deprecation in version: 1.2.0
unique identifier: MO_413
deprecated from version: version 1.2.0
deprecation old parent: TheoreticalBioSequenceType
has reason for deprecation: deleted term

positive float
type: DataType
comment: A float > 0.
unique identifier: MO_501

genetic modification design
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
unique identifier: MO_447

mean and coefficient of variation
type: DerivedBioAssayType
unique identifier: MO_425
comment: the mean and coefficient of variation values resulting from computationally combining 2 or more sets of BioAssayData

ICD-9-CM
type: DiseaseStateDatabase
unique identifier: MO_654
has machine readable URI: ftp://ftp.cdc.gov/pub/Health_Statistics/NCHS/Publications/ICD9-CM/2002
comment: Database entry from ICD 9 2001, international classification of diseases 9, clinical modification 2001.

submitter
type: Roles
comment: Person who is the primary contact for data submitted to a database.
unique identifier: MO_882

reverse transcription PCR quality control
type: QualityControlDescriptionType
unique identifier: MO_986
comment: A PCR based semi quantitative validation of a subset of the array based data used for experimental QC purposes.

cell
type: MaterialType
unique identifier: MO_612
comment: One or more dissociated cell(s) possibly heterogeneous, excluding single cell organisms.

NCI organism part database
type: OrganismPartDatabase
unique identifier: MO_690
comment: a controlled vocabulary of organism parts
has human readable URI: http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp

cell ontology
type: CellTypeDatabase
unique identifier: MO_404
type: TargetedCellTypeDatabase
has machine readable URI: http://cvs.sourceforge.net/views.py/obo/obo/ontology/anatomy/cell_type/cell.ontology
comment: database of cell ontology terms

biotin
type: LabelCompound
unique identifier: MO_793
comment: a compound used for labeling/detection purposes

NCI Thesaurus
type: DeprecatedTerms
deprecation old parent: StrainOrLineDatabase
deprecation in version: 1.1.7
deprecation old parent: ClinicalTreatmentDatabase
split to term: NCI cell type database
split to term: NCI disease state database
split to term: NCI strain or line database
deprecation old parent: GeographicLocationDatabase
deprecation old parent: TumorGradingDatabase
deprecation old parent: CellLineDatabase
deprecated from version: version 1.1.7
deprecation old parent: TargetedCellTypeDatabase
comment: A description logic namespace that contains controlled terminology used at NCI.
deprecation reason: split_term
split to term: NCI geographic location database
split to term: NCI compound database
deprecation old parent: DiseaseStateDatabase
deprecation old parent: CompoundDatabase
has human readable URI: http://nciterms.nci.nih.gov
split to term: NCI organism part database
split to term: NCI targeted cell type database
deprecation old parent: OrganismPartDatabase
has reason for deprecation: split term
unique identifier: MO_456
split to term: NCI tumor grading database

NCI geographic location database
type: GeographicLocationDatabase
unique identifier: MO_630
has human readable URI: http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp
comment: a controlled vocabulary for geographic locations

median log centering
type: NormalizationDescriptionType
unique identifier: MO_811
comment: A method of normalizing log ratio data by subtraction of the median log ratios computed across all data points, or an appropriate subset of these (e.g. special control Features on a microarray, or 2DE spots containing constitutively expressed proteins).

semisolid
type: Media
comment: semisolid media type
unique identifier: MO_635

list of strings
type: DataType
comment: An ordered, finite set of strings.
unique identifier: MO_800

iterative mean log centering
type: NormalizationDescriptionType
unique identifier: MO_957
comment: A method of re-scaling ratio data by iteratively subtracting the mean log base 2 ratio from each log2(ratio). This adjusts the mean log2(ratio) to zero. In each subsequent iteration, outliers are removed based on user-specified criteria, the mean log(2) ratio is recalculated based on the remaining data, and the entire data set is rescaled again. This continues until the mean log(2) ratio converges.

PCR amplicon
type: DeprecatedTerms
has reason for deprecation: deleted term
deprecation reason: deleted_term
deprecation replacement term: PhysicalBioSequenceType
comment: BioSequence generated by means of polymerase chain reaction
deprecated from version: version 1.2.0
unique identifier: MO_450
deprecation old parent: PhysicalBioSequenceType
deprecation in version: 1.2.0

microarray experiment record
type: DatabaseEntryType
unique identifier: MO_346
comment: A record which describes and identifies a microarray experiment e.g. GEO

exon
type: DeprecatedTerms
comment: sequence which represents regions of a transcript that are joined to another exon during splicing
deprecation reason: deleted_term
deprecated from version: version 1.2.0
unique identifier: MO_619
deprecation in version: 1.2.0
has reason for deprecation: deleted term
deprecation replacement term: TheoreticalBioSequenceType
deprecation old parent: TheoreticalBioSequenceType

PCR primer reverse
type: DeprecatedTerms
unique identifier: MO_640
deprecated from version: version 1.2.0
comment: single stranded oligo used for polymerase chain reaction
deprecation in version: 1.2.0
deprecation old parent: PhysicalBioSequenceType
has reason for deprecation: deleted term
deprecation replacement term: PhysicalBioSequenceType
deprecation reason: deleted_term

nonpositive float
type: DataType
unique identifier: MO_656
comment: A float less than or equal to zero.

labeling
type: ComplexAction
comment: The procedure of labeling a biosample.
unique identifier: MO_471
type: ExperimentalProtocolType

forward
type: StrandType
synonym: +
unique identifier: MO_820
comment: the forward strand exact synonym: +

Pearson correlation
type: NodeValueType
comment: The Pearson correlation is defined as the covariance of two data series divided by the product of their standard deviations.
unique identifier: MO_632

alexa 680
type: LabelCompound
comment: Absorbs at 679 nm, emission maxima at 702 nm (far-red). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble.
unique identifier: MO_799

physical characteristics
type: BioMaterialCharacteristicCategory
unique identifier: MO_863
comment: A descriptor for FactorValue where PhysicalCharacteristics are compared.

unknown experiment design type
type: PerturbationalDesign
type: EpidemiologicalDesign
type: BioMolecularAnnotation
type: MethodologicalDesign
type: BiologicalProperty
unique identifier: MO_634
comment: ExperimentDesignType of unknown type.

harvest
type: ExperimentalProtocolType
type: ComplexAction
unique identifier: MO_982
comment: The process of harvesting cells from culture.

organism status design
type: BiologicalProperty
comment: A design that compares samples from live and dead organisms.
unique identifier: MO_841

NCI histology database
type: HistologyDatabase
unique identifier: MO_537
comment: a controlled vocabulary for histology
has human readable URI: http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp

spotted colony features
type: TechnologyType
comment: TechnologyType of FeatureGroup where bacterial or other colonies are spotted directly.
unique identifier: MO_618

haploid
type: Ploidy
comment: Describes a cell, nucleus or an organism with one copy of each chromosome.
unique identifier: MO_719

synthetic DNA
type: MaterialType
unique identifier: MO_577
synonym: cDNA
comment: DNA which is generated by chemical or enzymatic (non cellular) means. non-exact synonym: cDNA

development or differentiation design
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.
unique identifier: MO_892

organism part comparison design
type: BiologicalProperty
comment: An organism part comparison experiment design type compares tissues, regions, organs within or between organisms
unique identifier: MO_953

Pathbase
type: HistologyDatabase
comment: database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice
unique identifier: MO_972
has human readable URI: http://eulep.anat.cam.ac.uk/Search_Pathbase/index.php

co-expression design
type: BioMolecularAnnotation
unique identifier: MO_904
comment: A co-expression experiment design type identifies genes which are coordinately expressed and are potentially used to infer a role in a biological process(es) non-exact synonym: guilt by association
synonym: guilt by association

averaged intensity
type: DerivedBioAssayType
comment: Results of data reduction involving computation of the average of multiple intensities of identical type. These could include identical Features, Reporters or CompositeSequences in different microarray hybridizations, matched replicate spots on 2D gels run from the same sample, or repeat measurements of the same metabolite in replicate cell cultures.
unique identifier: MO_362

alexa 488
type: LabelCompound
unique identifier: MO_446
comment: Absorbs at 495 nm, emission maxima at 519 nm (green). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble.

Rad
type: RadiationUnit
comment: Radiation absorbed dose. Unit of energy absorbed per unit mass as a result of exposure to radiation. 1 rad = Absorption of 100 ergs per gram of material = 0.01Gy.
unique identifier: MO_585

female
type: Sex
comment: of, pertaining to, or designating the sex that only produces gametes that can be fertilized by male gametes.
unique identifier: MO_506

pathway record
type: DatabaseEntryType
comment: a record which identifies and describes biological pathways, e.g. a KEGG record
unique identifier: MO_780

oligo synthesizer
type: HardwareType
unique identifier: MO_930
comment: Hardware for synthesizing oligos.

split
type: ExperimentalProtocolType
type: ComplexAction
unique identifier: MO_835
comment: The procedure of separating a BioMaterial into two or more BioMaterials of similar composition e.g. aliquoting a sample. The BioMaterial may be a BioSource (e.g., a tissue) or a BioSample (e.g. RNA extracted from a BioSource). Non exact Synonym: sample
synonym: sample

nonnegative integer
type: DataType
comment: An integer >= 0.
unique identifier: MO_390

Affymetrix average difference
type: DerivedBioAssayType
unique identifier: MO_649
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.

normalization testing design
type: MethodologicalDesign
unique identifier: MO_729
comment: A normalization testing experiment design tests different normalization procedures.

grow
type: ComplexAction
type: ExperimentalProtocolType
comment: A ComplexAction or ProtocolType describing growth of an organism or cell culture.
unique identifier: MO_758

individual genetic characteristic
type: BioMaterialCharacteristicCategory
comment: A descriptor for FactorValue where IndividualGeneticCharacteristic is compared.
unique identifier: MO_722

metastatic site
type: CancerSite
unique identifier: MO_806
comment: the organism part in which additional tumors are identified remote from the primary site

liquid
type: Media
comment: media type, usually some sort of broth
unique identifier: MO_715

cellular modification design
type: TechnologicalDesign
unique identifier: MO_392
comment: A cellular modification design type is where a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.
synonym: RNAi
type: PerturbationalDesign

pfu per ml
type: ConcentrationUnitOther
unique identifier: MO_768
comment: the number of plaque forming units per ml

in situ oligo features
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)
unique identifier: MO_514

clone of unknown source
type: PhysicalBioSequenceType
unique identifier: MO_371
comment: Sequence from some nucleic acid copy and the associated vector for which the source clone supplier is unknown.

store
type: ComplexAction
unique identifier: MO_442
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.
type: ExperimentalProtocolType

PCR primer
type: DeprecatedTerms
deprecation reason: deleted_term
unique identifier: MO_651
has reason for deprecation: deleted term
deprecation old parent: PhysicalBioSequenceType
deprecation replacement term: PhysicalBioSequenceType
comment: single oligo used for polymerase chain reaction direction unspecified
deprecated from version: version 1.2.0
deprecation in version: 1.2.0

disease staging
type: BioMaterialCharacteristicCategory
unique identifier: MO_792
comment: The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression.

transfect
type: ComplexAction
unique identifier: MO_849
type: ExperimentalProtocolType
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.

CABRI Filamentous Fungi Strains
type: StrainOrLineDatabase
unique identifier: MO_1009
comment: List of CABRI filamentous fungi strains sorted by genus and species. It includes more than 30,000 resources that are available from five European collections participating in the CABRI (Common Access to Biological Resources and Information) initiative (see http://www.cabri.org/ ). Detailed descriptions can be reached from the list and strains of interest can be requested.
has human readable URI: http://www.cabri.org/HyperCat/fun/all_A.htm

relative
type: MeasurementType
comment: a measurement where the value is dependent on another measurement
unique identifier: MO_396

compound treatment design
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.
unique identifier: MO_555

linlog transformation
type: DataTransformationProtocolType
unique identifier: MO_845
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.

square feature
type: FeatureShape
unique identifier: MO_817
comment: The shape of the feature on the array is square.

biological fluid collection
type: ExperimentalProtocolType
type: ComplexAction
unique identifier: MO_685
comment: The action of collecting biological fluids including bodily secretions, exudates, transudates etc. and sampling of cytoplasm. The purpose of sampling may range from collecting other organisms (i.e. pathogens) to studying fluid composition.

polylysine
type: SurfaceType
comment: a surface coating for immobilization with the polypeptide, polylysine
unique identifier: MO_569

diameter aberration
type: DefectType
comment: The diameter of the Feature is much smaller or much larger than expected based on the spotting pin diameter.
unique identifier: MO_781

JAX mouse strains
type: StrainOrLineDatabase
comment: Database entry from the resource at The Jackson Laboratory which has details of approved mouse strain nomenclature.
has human readable URI: http://www.informatics.jax.org/external/festing/mouse/STRAINS.shtml
unique identifier: MO_369

mg per kg per day
type: ConcentrationUnitOther
unique identifier: MO_353
comment: milligram per kilogram per day

planting
type: InitialTimePoint
comment: The act of placing a plant in media (e.g. soil) to allow it to grow. This excludes sowing.
unique identifier: MO_495

positive
type: Result
unique identifier: MO_429
comment: true or yes

is expressed design
type: BiologicalProperty
unique identifier: MO_487
comment: A design aimed at identifying genes expressed in biomaterials of interest.

cfu per ml
type: ConcentrationUnitOther
unique identifier: MO_788
comment: the number of colony forming units per ml

low intensity filter
type: DeprecatedTerms
deprecation in version: 1.3.0
deprecation old parent: DataTransformationProtocolType
deprecation reason: replaced_term
comment: A transformation method that involves removal of low intensity values in a data set. For microarrays and gels the threshold for exclusion is usually based on some estimation of local or global background intensity; for mass spectrometry and NMR, it is usually based on the signal-to-noise ratio in the spectrum.
unique identifier: MO_706
deprecated from version: version 1.3.0
was replaced by: flag filter
replaced with term: flag filter
has reason for deprecation: replaced term

list of negative floats
type: DataType
comment: An ordered, finite set of negative floats.
unique identifier: MO_851

fg
type: MassUnit
comment: femtogram, unit of mass
unique identifier: MO_732

dose response design
type: PerturbationalDesign
unique identifier: MO_485
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).

mother
type: FamilyRelationship
comment: A female parent.
unique identifier: MO_387

laser ablation mark
type: FiducialType
unique identifier: MO_910
comment: mark made on slide using a laser which is used as a point of reference for orientation (fiducial)

negative
type: Result
unique identifier: MO_802
comment: false or no

ds oligo
type: DeprecatedTerms
comment: a double stranded oligonucleotide
deprecation reason: deleted_term
deprecated from version: version 1.2.0
deprecation in version: 1.2.0
deprecation replacement term: PhysicalBioSequenceType
has reason for deprecation: deleted term
unique identifier: MO_344
deprecation old parent: PhysicalBioSequenceType

dilute
type: AtomicAction
comment: Decreasing the concentration of solutes in a solution or suspension.
unique identifier: MO_962

cosine distance
type: NodeValueType
unique identifier: MO_550
comment: The cosine distance of two vectors is the cosine of the angle between them. This measures the difference in direction between two vectors, irrespective of their lengths.

pg
type: MassUnit
comment: picogram, mass unit
unique identifier: MO_363

U per L
type: ConcentrationUnit
unique identifier: MO_875
comment: units per liter

male
type: Sex
comment: individual whose sex organs contain only male gametes
unique identifier: MO_652

quantile normalization
type: NormalizationDescriptionType
unique identifier: MO_951
comment: A method of normalizing a set of MeasuredBioAssayData aimed at rendering the distribution of intensities for each assay in the set the same, by forcing the values of quantiles to be equal across assays.

half-life
type: TimeUnitOther
comment: t1/2. The period over which the activity or concentration of a specified chemical or element falls to half its original activity or concentration. Typically applied to the half-life of radioactive atoms but also applicable to any other situation where the population is of molecules of diminishing concentration or activity.
unique identifier: MO_595

PCR fail
type: FailType
unique identifier: MO_667
comment: PCR where no products of any kind appear in gel-separated reaction products.

within bioassay data set function
type: DataTransformationProtocolType
comment: A function applied to subsets of values from the same Measured/Derived bioassay data set.
unique identifier: MO_668

control design element group type
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.
unique identifier: MO_414

organism part
type: MaterialType
type: BioMaterialCharacteristicCategory
unique identifier: MO_954
comment: The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm).

mix by pipette
type: AtomicAction
comment: Mix by drawing up and down with a pipette.
unique identifier: MO_479

reverse transcription
type: ExperimentalProtocolType
unique identifier: MO_480
comment: Generation of a DNA strand from an RNA strand using reverse transcriptase.
type: ComplexAction

spotted ss oligo features
type: TechnologyType
unique identifier: MO_579
comment: The TechnologyType of the FeatureGroup is spotted single stranded oligonucleotides (of any length) on the substrate.

silicon
type: SubstrateType
comment: the array is made on silicon
unique identifier: MO_382

acrossBioAssay mean and coefficient of variation
type: DerivedBioAssayType
unique identifier: MO_840
comment: The mean and coefficient of variation values resulting from computationally combining 2 or more sets of bioassay data.