class role
type: AnnotationProperty
unique identifier: MO_338
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: DatatypeProperty
type: FunctionalProperty
range: Datatype
  one of: abstract
  one of: concrete
  one of: place_holder

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

deprecation old restriction
type: AnnotationProperty
unique identifier: MO_1015
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

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

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

class source
type: AnnotationProperty
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.
type: DatatypeProperty
type: FunctionalProperty
range: Datatype
  one of: mage
  one of: ontology

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

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

deprecation replacement term
type: AnnotationProperty
unique identifier: MO_1012
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.
type: ObjectProperty

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

synonym
type: AnnotationProperty
unique identifier: MO_333
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.
type: DatatypeProperty
range: string

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Age
type: Class
subclass of: BioMaterialCharacteristics
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
subclass of: Restriction
  on property: has measurement
  some values from: Measurement
unique identifier: MO_178
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
class source: ontology

Allele
type: Class
subclass of: IndividualGeneticCharacteristics
unique identifier: MO_58
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
class source: ontology

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

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

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

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

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

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

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

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

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

BioAssay
type: Class
subclass of: BioAssayPackage
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

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

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

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

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

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

BioMaterialCharacteristicCategory
type: Class
subclass of: BiologicalFactorCategory
comment: General descriptor of a BioMaterialCharacteristic category. Such as strain or line where the name of the strain or line is encoded in the FactorValue.
unique identifier: MO_100

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

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

BioMaterialPurity
type: Class
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.
unique identifier: MO_20
class role: abstract
class source: ontology

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

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

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

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

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

BioSequenceType
type: Class
subclass of: BioSequencePackage
comment: Controlled terms for descriptors indicating the type of biosequence. Types may be physical (e.g. BAC, cDNA clone), or computational (e.g. unigene cluster, consensus).
unique identifier: MO_152
class role: abstract
class source: ontology

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

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

BioSourceType
type: Class
subclass of: BioMaterialCharacteristics
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.
class role: concrete
class source: ontology

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

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

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

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

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

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

CellType
type: Class
subclass of: BioMaterialCharacteristics
subclass of: OntologyEntry
subclass of: Restriction
  on property: has database
  some values from: CellTypeDatabase
comment: CellType, the type of cell used in the experiment if non mixed, if mixed the TargetedCellType should be used, example of instances, epithelial, glial etc.
unique identifier: MO_135
class role: abstract
class source: ontology

CellTypeDatabase
type: Class
subclass of: Database
comment: Database of cell type information.
unique identifier: MO_141
class role: concrete
class source: ontology

CellularComponent
type: Class
subclass of: BioMaterialCharacteristics
subclass of: OntologyEntry
subclass of: Restriction
  on property: has database
  some values from: CellularComponentDatabase
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).
unique identifier: MO_1020
class role: abstract
class source: ontology

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

ChromosomalAberration
type: Class
subclass of: DeprecatedTerms
subclass of: Restriction
  on property: deprecated from version
  has value: version 1.1.7
subclass of: Restriction
  on property: has reason for deprecation
  has value: deleted term
subclass of: Restriction
  on property: has chromosomal aberration classification
  some values from: ChromosomalAberrationClassification
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.
unique identifier: MO_78
class role: abstract
deprecation reason: deleted_term
class source: ontology
deprecation old restriction: some|has_chromosomal_aberration_classification|ChromosomalAberrationClassification
type: NamedIndividual

ChromosomalAberrationClassification
type: Class
subclass of: BioMaterialCharacteristics
comment: An irregularity in the number or structure of chromosomes, usually in the form of a gain (duplication), loss (deletion), exchange (translocation), or alteration in sequence (inversion) of genetic material. Excludes simple changes in sequence such as mutations, and is usually detectable by cytogenetic and microscopic techniques such as FISH.
unique identifier: MO_6
class role: concrete
class source: ontology

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

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

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

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

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

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

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

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

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

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

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

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

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

Database
type: Class
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
comment: Identifiable resource containing data or external ontologies or controlled vocabularies which has uniquely identifiable records.
unique identifier: MO_118
class role: abstract
class source: ontology

DatabaseEntryType
type: Class
subclass of: DescriptionPackage
comment: Controlled set of descriptors for the type of database record such as a protein record (in SWISS-PROT) or a gene object (in SGD).
unique identifier: MO_157
class role: concrete
class source: ontology

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

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

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

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

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

DerivedBioAssayType
type: Class
subclass of: BioAssayPackage
comment: Controlled set of descriptors for the type of derivation of the BioAssay such as averaging features, taking ratios of signal QuantitationTypes, and normalizing BioAssay data.
unique identifier: MO_111
class role: concrete
class source: ontology

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

EnvironmentalStress
type: Class
subclass of: MGEDExtendedOntology
subclass of: Restriction
  on property: has measurement
  some values from: Measurement
comment: Environmental stress is a treatment where some aspect of the environment is perturbed in order to stress the organism or culture, e.g. temperature shock, osmotic shock
unique identifier: MO_227

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

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

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

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

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

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

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

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

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

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

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

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

FamilyHistory
type: Class
subclass of: EnvironmentalHistory
subclass of: Restriction
  on property: has family member
  some values from: FamilyMember
unique identifier: MO_59
comment: Relevant aspects of genetic preconditions or family member's clinical history.
class role: abstract
class source: ontology

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

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

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

FeatureGroup
type: Class
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
unique identifier: MO_54
comment: Technology-based grouping of features representing individual locations on the array.
class role: concrete
class source: mage

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

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

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

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

GeneticMaterial
type: Class
subclass of: MGEDExtendedOntology
comment: Genetic material may be DNA or RNA and identifiable as an entry in a public external database such as EMBL/DDBJ/GenBank or one of the model organism databases.
unique identifier: MO_137

GeneticModification
type: Class
subclass of: BioMaterialCharacteristics
unique identifier: MO_122
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

Genotype
type: Class
subclass of: IndividualGeneticCharacteristics
unique identifier: MO_51
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.
class role: concrete
class source: ontology

GeographicLocation
type: Class
subclass of: EnvironmentalHistory
subclass of: OntologyEntry
subclass of: Restriction
  on property: has database
  some values from: GeographicLocationDatabase
comment: A descriptor of the location from which a BioMaterial was obtained, e.g. country, region, grid reference.
unique identifier: MO_132
class role: abstract
class source: ontology

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

GrowthCondition
type: Class
subclass of: EnvironmentalHistory
subclass of: Restriction
  on property: has maximum measurement
  some values from: Measurement
subclass of: Restriction
  on property: has value
  some values from: string
subclass of: Restriction
  on property: has measurement
  some values from: Measurement
comment: A description of the conditions used to grow organisms or parts of the organism. This includes isolated environments such as cultures and open environments such as field studies.
unique identifier: MO_183
class role: abstract
class source: ontology

Haplotype
type: Class
subclass of: IndividualGeneticCharacteristics
unique identifier: MO_146
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
class role: place_holder

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

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

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

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

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).
unique identifier: MO_47
class role: concrete
class source: ontology

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

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

HistoryFactor
type: Class
subclass of: MGEDExtendedOntology
comment: Factors that are measured or observed parts of the study but not induced or under the control of the experiment. These factors do not have protocols (e.g., epidemiology factors).
unique identifier: MO_82

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

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

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

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

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

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

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

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

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

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

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

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

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

MGEDExtendedOntology
type: Class
subclass of: MGEDOntology
comment: Location for those classes that are not in the Core ontology as they do are not containable in MAGE. It is not yet structured to work with the Core ontology
unique identifier: MO_196

MGEDOntology
type: Class
subclass of: Thing
subclass of: Restriction
  on property: is user defined
  some values from: BibliographicReference
subclass of: Restriction
  on property: is user defined
  some values from: Contact
unique identifier: MO_174
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 role: abstract
class source: ontology

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

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

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

MaterialType
type: Class
subclass of: BioMaterialPackage
comment: Controlled terms for the state of the BioMaterial. Each state (BioSource, different BioSamples, and LabeledExtract) have MaterialTypes. Examples are population of an organism, organism, organism part, cell, etc.
unique identifier: MO_32
class role: concrete
class source: ontology

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

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

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

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

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

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

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

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

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

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

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

Nutrients
type: Class
subclass of: GrowthCondition
subclass of: Restriction
  on property: has nutrient component
  some values from: Compound
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

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

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

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

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

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

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

OrganismPart
type: Class
subclass of: BioMaterialCharacteristics
subclass of: OntologyEntry
subclass of: Restriction
  on property: has database
  some values from: OrganismPartDatabase
unique identifier: MO_1
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).
class role: abstract
class source: ontology

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

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

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

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

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

PathogenTest
type: Class
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
class role: abstract
class source: ontology

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

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

Phenotype
type: Class
subclass of: BioMaterialCharacteristics
subclass of: OntologyEntry
subclass of: Restriction
  on property: has database
  some values from: PhenotypeDatabase
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
class source: ontology

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

SamplingTimePoint
type: Class
subclass of: EnvironmentalHistory
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
class role: abstract
class source: ontology

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

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

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

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

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

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

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

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

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

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

StrainOrLine
type: Class
subclass of: BioMaterialCharacteristics
subclass of: OntologyEntry
subclass of: Restriction
  on property: has species
  some values from: Organism
subclass of: Restriction
  on property: has database
  some values from: StrainOrLineDatabase
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.
unique identifier: MO_9
class role: abstract
class source: ontology

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

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

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

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

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

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

TechnologicalDesign
type: Class
subclass of: ExperimentDesignType
unique identifier: MO_21
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
class source: ontology

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

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

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

Test
type: Class
subclass of: BioMaterialCharacteristics
subclass of: Restriction
  on property: has performer
  some values from: Contact
subclass of: Restriction
  on property: has test type
  some values from: TestType
subclass of: Restriction
  on property: has test result
  some values from: TestResult
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
class source: ontology

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

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

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

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

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

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

Transformation
type: Class
subclass of: BioAssayDataPackage
subclass of: Restriction
  on property: has protocol
  some values from: Protocol
unique identifier: MO_216
comment: The process by which BioAssays (data, elements, quantitation types) are averaged normalized, selected, filtered, or otherwise changed into a new set of BioAssay data.

Treatment
type: Class
subclass of: BioMaterialPackage
subclass of: Restriction
  on property: has order
  some values from: int
subclass of: Restriction
  on property: has action
  some values from: Action
subclass of: Restriction
  on property: has protocol
  some values from: Protocol
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
class source: mage

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

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

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

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

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

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

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

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

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

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

http://mged.sourceforge.net/ontologies/MGEDOntology.owl#A
type: NamedIndividual
type: DistanceUnit
comment: Angstrom, unit of distance, 1 angstrom is one tenth of a nanometer
unique identifier: MO_515

ATCC Cultures
type: NamedIndividual
type: CellLineDatabase
type: StrainOrLineDatabase
unique identifier: MO_979
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

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

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

Affymetrix average difference
type: NamedIndividual
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.

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

CABRI Bacteria and Archaea Strains
type: NamedIndividual
type: StrainOrLineDatabase
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.
unique identifier: MO_1008
has human readable URI: http://www.cabri.org/HyperCat/bact/all_A.htm

CABRI Filamentous Fungi Strains
type: NamedIndividual
type: StrainOrLineDatabase
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.
unique identifier: MO_1009
has human readable URI: http://www.cabri.org/HyperCat/fun/all_A.htm

CABRI HLA typed B Cell lines
type: NamedIndividual
type: CellLineDatabase
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.
unique identifier: MO_1005
has human readable URI: http://www.cabri.org/HyperCat/cells/hla.htm

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

CABRI Hybridomas
type: NamedIndividual
type: CellLineDatabase
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.
unique identifier: MO_1006
has human readable URI: http://www.cabri.org/HyperCat/cells/hybrid.htm

CABRI Yeasts Strains
type: NamedIndividual
type: StrainOrLineDatabase
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
has human readable URI: http://www.cabri.org/HyperCat/yeast/all_A.htm

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

CLDB Human and Animal Cell Line
type: NamedIndividual
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

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

ChEBI
type: NamedIndividual
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

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

Ci
type: NamedIndividual
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

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

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

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

DNA sequencer
type: NamedIndividual
type: HardwareType
comment: An instrument that produces DNA sequences.
unique identifier: MO_676

EMAP
type: NamedIndividual
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

EST
type: NamedIndividual
type: DeprecatedTerms
deprecation in version: 1.2.0
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 reason: deleted_term
deprecation old parent: TheoreticalBioSequenceType
deprecation replacement term: TheoreticalBioSequenceType
has reason for deprecation: deleted term
deprecated from version: version 1.2.0

Euclidean distance
type: NamedIndividual
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).

http://mged.sourceforge.net/ontologies/MGEDOntology.owl#F
type: NamedIndividual
type: Sex
unique identifier: MO_717
comment: mating type indicating the presence of F plasmid in a bacterial cell

FMA
type: NamedIndividual
type: OrganismPartDatabase
unique identifier: MO_468
comment: The Foundational Model of Anatomy (FMA) is concerned with the representation of concepts and relationships necessary for the symbolic modeling of the structure of the human body.
has human readable URI: http://sig.biostr.wahington.edu/projects/fm/

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

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

FlyBase organism part database
type: NamedIndividual
type: OrganismPartDatabase
unique identifier: MO_504
comment: curated database containing information on Drosophila genes, alleles etc
has machine readable URI: http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fly/

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

GRAMENE
type: NamedIndividual
type: StrainOrLineDatabase
comment: A Comparative Mapping Resource for Grains.
unique identifier: MO_678
has human readable URI: http://www.gramene.org/

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

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

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

ICD-9-CM
type: NamedIndividual
type: DiseaseStateDatabase
comment: Database entry from ICD 9 2001, international classification of diseases 9, clinical modification 2001.
unique identifier: MO_654
has machine readable URI: ftp://ftp.cdc.gov/pub/Health_Statistics/NCHS/Publications/ICD9-CM/2002

IU
type: NamedIndividual
type: QuantityUnit
synonym: International unit
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.
synonym: UI

IUPAC Clinical Chemistry Guidelines
type: NamedIndividual
type: TestTypeDatabase
comment: A resource of vocabularies for describing clinical tests, e.g. blood chemistry.
unique identifier: MO_593
has human readable URI: http://www.iupac.org/publications/pac/2000/205/205olesen.html

JAX mouse strains
type: NamedIndividual
type: StrainOrLineDatabase
comment: Database entry from the resource at The Jackson Laboratory which has details of approved mouse strain nomenclature.
unique identifier: MO_369
has human readable URI: http://www.informatics.jax.org/external/festing/mouse/STRAINS.shtml

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

http://mged.sourceforge.net/ontologies/MGEDOntology.owl#K
type: NamedIndividual
type: TemperatureUnit
comment: Kelvin, unit of temperature
unique identifier: MO_614

http://mged.sourceforge.net/ontologies/MGEDOntology.owl#L
type: NamedIndividual
type: VolumeUnit
unique identifier: MO_444
comment: liter, unit of volume

LOINC
type: NamedIndividual
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

http://mged.sourceforge.net/ontologies/MGEDOntology.owl#M
type: NamedIndividual
type: ConcentrationUnit
unique identifier: MO_936
comment: Mole per liter or molarity, concentration unit

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

MAS4 average difference
type: NamedIndividual
type: DerivedBioAssayType
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.
unique identifier: MO_782

MAS5 signal
type: NamedIndividual
type: DerivedBioAssayType
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.
unique identifier: MO_653

MAS5 signal log ratio
type: NamedIndividual
type: DerivedBioAssayType
unique identifier: MO_938
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.

MBEI
type: NamedIndividual
type: DerivedBioAssayType
unique identifier: MO_756
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.

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

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

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

NASC
type: NamedIndividual
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

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

NCI Thesaurus
type: NamedIndividual
type: DeprecatedTerms
deprecation in version: 1.1.7
comment: A description logic namespace that contains controlled terminology used at NCI.
unique identifier: MO_456
has human readable URI: http://nciterms.nci.nih.gov
deprecation reason: split_term
deprecation old parent: CellLineDatabase
deprecation old parent: ClinicalTreatmentDatabase
deprecation old parent: CompoundDatabase
deprecation old parent: DiseaseStateDatabase
deprecation old parent: GeographicLocationDatabase
split to term: NCI cell type database
split to term: NCI compound database
split to term: NCI disease state database
split to term: NCI geographic location database
split to term: NCI organism part database
split to term: NCI strain or line database
split to term: NCI targeted cell type database
split to term: NCI tumor grading database
deprecation old parent: OrganismPartDatabase
deprecation old parent: StrainOrLineDatabase
deprecation old parent: TargetedCellTypeDatabase
deprecation old parent: TumorGradingDatabase
has reason for deprecation: split term
deprecated from version: version 1.1.7

NCI cell type database
type: NamedIndividual
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

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

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

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

NCI geographic location database
type: NamedIndividual
type: GeographicLocationDatabase
unique identifier: MO_630
comment: a controlled vocabulary for geographic locations
has human readable URI: http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp

NCI histology database
type: NamedIndividual
type: HistologyDatabase
unique identifier: MO_537
comment: a controlled vocabulary for histology
has human readable URI: http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp

NCI organism part database
type: NamedIndividual
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

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

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

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

ORF
type: NamedIndividual
type: DeprecatedTerms
deprecation in version: 1.2.0
unique identifier: MO_413
deprecation reason: deleted_term
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 replacement term: TheoreticalBioSequenceType
deprecation old parent: TheoreticalBioSequenceType
has reason for deprecation: deleted term
deprecated from version: version 1.2.0

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

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

PCR amplicon
type: NamedIndividual
type: DeprecatedTerms
deprecation in version: 1.2.0
comment: BioSequence generated by means of polymerase chain reaction
unique identifier: MO_450
deprecation reason: deleted_term
deprecation replacement term: PhysicalBioSequenceType
deprecation old parent: PhysicalBioSequenceType
has reason for deprecation: deleted term
deprecated from version: version 1.2.0

PCR amplification
type: NamedIndividual
type: ComplexAction
type: ExperimentalProtocolType
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

PCR fail
type: NamedIndividual
type: FailType
unique identifier: MO_667
comment: PCR where no products of any kind appear in gel-separated reaction products.

PCR primer
type: NamedIndividual
type: DeprecatedTerms
deprecation in version: 1.2.0
unique identifier: MO_651
deprecation reason: deleted_term
comment: single oligo used for polymerase chain reaction direction unspecified
deprecation old parent: PhysicalBioSequenceType
deprecation replacement term: PhysicalBioSequenceType
has reason for deprecation: deleted term
deprecated from version: version 1.2.0

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

PCR primer reverse
type: NamedIndividual
type: DeprecatedTerms
deprecation in version: 1.2.0
unique identifier: MO_640
deprecation reason: deleted_term
comment: single stranded oligo used for polymerase chain reaction
deprecation old parent: PhysicalBioSequenceType
deprecation replacement term: PhysicalBioSequenceType
has reason for deprecation: deleted term
deprecated from version: version 1.2.0

PCR questionable
type: NamedIndividual
type: FailType
unique identifier: MO_620
comment: PCR with multiple bands, or smear, in gel-separated reaction products

PNG
type: NamedIndividual
type: ImageFormat
unique identifier: MO_1001
comment: Portable Network Graphic, a lossless image data format.

Pathbase
type: NamedIndividual
type: HistologyDatabase
unique identifier: MO_972
comment: database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice
has human readable URI: http://eulep.anat.cam.ac.uk/Search_Pathbase/index.php

Pearson correlation
type: NamedIndividual
type: NodeValueType
unique identifier: MO_632
comment: The Pearson correlation is defined as the covariance of two data series divided by the product of their standard deviations.

http://mged.sourceforge.net/ontologies/MGEDOntology.owl#R
type: NamedIndividual
type: RadiationUnit
unique identifier: MO_725
comment: Roentgen. Unit of exposure to gamma or x-rays in the air. 1 R= 2.58E-4 coulombs per kg.

RMA
type: NamedIndividual
type: DerivedBioAssayType
unique identifier: MO_987
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.

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

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

Rad
type: NamedIndividual
type: RadiationUnit
unique identifier: MO_585
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.

Rem
type: NamedIndividual
type: RadiationUnit
unique identifier: MO_908
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.

SequenceOntology
type: NamedIndividual
type: SequenceOntologyDatabase
unique identifier: MO_724
comment: The Sequence Ontology is a set of terms used to describe features on a nucleotide or protein sequence.
has machine readable URI: http://song.sourceforge.net/

Spearmans rank correlation
type: NamedIndividual
type: NodeValueType
comment: Computed as the ordinary Pearson correlation coefficient between two groups of rankings.
unique identifier: MO_552

TAIR
type: NamedIndividual
type: CellTypeDatabase
type: StrainOrLineDatabase
unique identifier: MO_660
comment: The Arabidopsis Information Resource.
has human readable URI: http://www.arabidopsis.org/servlets/Search

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

TAIR arabidopsis development ontology
type: NamedIndividual
type: DevelopmentalStageDatabase
comment: An ontology of stages of growth and development of the model plant Arabidopsis thaliana.
unique identifier: MO_919
has machine readable URI: http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/developmental/plant_development/Arabidopsis/temporal.tair

TDMS
type: NamedIndividual
type: DiseaseStateDatabase
type: HistologyDatabase
type: OrganismPartDatabase
type: TestTypeDatabase
unique identifier: MO_718
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

TIFF
type: NamedIndividual
type: ImageFormat
unique identifier: MO_638
comment: Tag Image File Format (TIFF) is a common format to describe and store raster image data from scanners and other imaging devices. TIFFs may contain one or more channels and the data may be compressed using a lossless compression algorithm.

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

U per L
type: NamedIndividual
type: ConcentrationUnit
unique identifier: MO_875
comment: units per liter

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

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

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

32P
type: NamedIndividual
type: LabelCompound
comment: 32 P, radioactive isotope of phosphorus used for labeling/detection purposes
unique identifier: MO_839

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

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

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

acrossBioAssay mean and coefficient of variation
type: NamedIndividual
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.

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

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

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

across bioassay data set function
type: NamedIndividual
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

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

ad libitum
type: NamedIndividual
type: DeliveryMethod
comment: A delivery method for compounds/drugs where the compound or drug is freely available.
unique identifier: MO_592

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

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

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

age
type: NamedIndividual
type: BioMaterialCharacteristicCategory
comment: A descriptor for FactorValue where age is compared.
unique identifier: MO_467

alexa 350
type: NamedIndividual
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

alexa 430
type: NamedIndividual
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

alexa 488
type: NamedIndividual
type: LabelCompound
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.
unique identifier: MO_446

alexa 532
type: NamedIndividual
type: LabelCompound
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.
unique identifier: MO_375

alexa 546
type: NamedIndividual
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

alexa 568
type: NamedIndividual
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

alexa 594
type: NamedIndividual
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

alexa 633
type: NamedIndividual
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

alexa 660
type: NamedIndividual
type: LabelCompound
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.
unique identifier: MO_547

alexa 680
type: NamedIndividual
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

all pairs
type: NamedIndividual
type: MethodologicalDesign
comment: An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
unique identifier: MO_565

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

aminosilane
type: NamedIndividual
type: SurfaceType
unique identifier: MO_747
comment: a surface coating type for immobilization with the compound aminosilane

amol
type: NamedIndividual
type: QuantityUnit
unique identifier: MO_977
comment: attomole, quantity unit

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

antibody
type: NamedIndividual
type: PhysicalBioSequenceType
unique identifier: MO_833
comment: glycoprotein of the immunoglobulin family that can combine specifically non-covalently, reversibly with a corresponding antigen

array manufacture software
type: NamedIndividual
type: SoftwareType
unique identifier: MO_502
comment: Software to control an arrayer.

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

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

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

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

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

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

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

averaged intensity
type: NamedIndividual
type: DerivedBioAssayType
unique identifier: MO_362
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.

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

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

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

behavior design
type: NamedIndividual
type: DeprecatedTerms
deprecation in version: 1.1.9
unique identifier: MO_532
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.
deprecation reason: split_term
deprecation old parent: BiologicalProperty
split to term: innate behavior design
has reason for deprecation: split term
split to term: stimulated design type
deprecated from version: version 1.1.9

behavioral design type
type: NamedIndividual
type: DeprecatedTerms
deprecation in version: 1.1.9
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.
unique identifier: MO_766
deprecation reason: replaced_term
deprecation old parent: PerturbationalDesign
was replaced by: innate behavior design
replaced with term: innate behavior design
has reason for deprecation: replaced term
deprecated from version: version 1.1.9

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

bibliographic record
type: NamedIndividual
type: DatabaseEntryType
comment: A record which describes and identifies a paper publication e.g. a medline record
unique identifier: MO_923

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

bioassay data transformation software
type: NamedIndividual
type: SoftwareType
unique identifier: MO_672
comment: Software used to transform the Measured or DerivedBioAssay data e.g. normalization. Non-exact synonym: normalization software
synonym: normalization software

bioassay replicate reduction
type: NamedIndividual
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.

biological fluid collection
type: NamedIndividual
type: ComplexAction
type: ExperimentalProtocolType
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.

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

biological resource record
type: NamedIndividual
type: DatabaseEntryType
comment: A record which describes and identifies a biological resource such as a cone or strain e.g. an ATCC record Jax strain list
unique identifier: MO_989

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

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

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

biotin
type: NamedIndividual
type: LabelCompound
unique identifier: MO_793
comment: a compound used for labeling/detection purposes

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

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

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

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

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

cDNA clone
type: NamedIndividual
type: DeprecatedTerms
deprecation in version: 1.2.0
unique identifier: MO_966
synonym: cDNA
synonym: complementary DNA
deprecation reason: deleted_term
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
deprecation replacement term: PhysicalBioSequenceType
deprecation old parent: PhysicalBioSequenceType
has reason for deprecation: deleted term
deprecated from version: version 1.2.0

candela
type: NamedIndividual
type: LightUnit
unique identifier: MO_572
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
synonym: candle power

candelas per square meter
type: NamedIndividual
type: LightUnit
unique identifier: MO_813
comment: Unit of brightness or luminance.

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

cell
type: NamedIndividual
type: MaterialType
unique identifier: MO_612
comment: One or more dissociated cell(s) possibly heterogeneous, excluding single cell organisms.

cell component comparison design
type: NamedIndividual
type: BiologicalProperty
comment: A design in which RNA from different cell components is examined.
unique identifier: MO_1019

cell cycle design
type: NamedIndividual
type: BiologicalProperty
comment: A cell cycle design experiment design type is one that assays events that occurs in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells.
unique identifier: MO_822

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

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

cell ontology
type: NamedIndividual
type: CellTypeDatabase
type: TargetedCellTypeDatabase
unique identifier: MO_404
comment: database of cell ontology terms
has machine readable URI: http://cvs.sourceforge.net/views.py/obo/obo/ontology/anatomy/cell_type/cell.ontology

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

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

cells per ml
type: NamedIndividual
type: ConcentrationUnitOther
unique identifier: MO_727
comment: the number of cells per ml

cellular modification design
type: NamedIndividual
type: PerturbationalDesign
type: TechnologicalDesign
comment: A cellular modification design type is where a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.
unique identifier: MO_392
synonym: RNAi

cellular process design
type: NamedIndividual
type: BiologicalProperty
unique identifier: MO_810
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.

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

cfu per ml
type: NamedIndividual
type: ConcentrationUnitOther
unique identifier: MO_788
comment: the number of colony forming units per ml

change biomaterial characteristics
type: NamedIndividual
type: ComplexAction
type: ExperimentalProtocolType
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
synonym: change environment
synonym: change growth condition

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

change light
type: NamedIndividual
type: AtomicAction
comment: Change in light intensity or wavelength.
unique identifier: MO_549

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

chrome border
type: NamedIndividual
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)

chromosomal deletion
type: NamedIndividual
type: ChromosomalAberrationClassification
unique identifier: MO_922
comment: The loss of a segment of the genetic material from a chromosome.

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

chromosomal insertion
type: NamedIndividual
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.

chromosomal inversion
type: NamedIndividual
type: ChromosomalAberrationClassification
comment: Chromosome segments that have been turned through 180 degrees with the result that the gene sequence for the segment is reversed with respect to the rest of the chromosome.
unique identifier: MO_622

chromosomal substitution
type: NamedIndividual
type: GeneticModification
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.
unique identifier: MO_995

chromosomal translocation
type: NamedIndividual
type: ChromosomalAberrationClassification
comment: A type of aberration characterized by fragmentation of a chromosome and transfer of the broken-off portion to another chromosome, often of a different pair.
unique identifier: MO_368

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

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

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

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

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

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

clone of unknown source
type: NamedIndividual
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.

clustered data
type: NamedIndividual
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.

clustering software
type: NamedIndividual
type: SoftwareType
unique identifier: MO_464
comment: Software used to cluster the data.

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

co-expression design
type: NamedIndividual
type: BioMolecularAnnotation
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
unique identifier: MO_904
synonym: guilt by association

coitus
type: NamedIndividual
type: InitialTimePoint
unique identifier: MO_783
synonym: copulation
synonym: insemination
comment: the physical act of copulation that occurs during the process of sexual reproduction synonyms: copulation, insemination

collapsed spot replicate
type: NamedIndividual
type: DerivedBioAssayType
unique identifier: MO_789
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.

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

compound based treatment
type: NamedIndividual
type: ComplexAction
type: ExperimentalProtocolType
unique identifier: MO_798
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.

compound record
type: NamedIndividual
type: DatabaseEntryType
unique identifier: MO_546
comment: a record which describes and identifies a compound e.g. drug record part of NCI thesaurus

compound treatment design
type: NamedIndividual
type: PerturbationalDesign
comment: A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.
unique identifier: MO_555

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

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

computed nucleic acid sequence feature record
type: NamedIndividual
type: DatabaseEntryType
comment: A record which identifies and describes a nucleic sequence feature which has been computationally determined or predicted E.g. and Ensembl record
unique identifier: MO_774

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

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

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

condition specificity
type: NamedIndividual
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

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

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

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

consultant
type: NamedIndividual
type: Roles
comment: A contact who provides some service related to some aspect of the experiment which is not data coding or analysis. E.g. help with an experimental design.
unique identifier: MO_984

control biosequence
type: NamedIndividual
type: ControlType
comment: A Reporter associated with a BioSequence that has a context dependent predicted signal. e.g. a yeast reporter on a human array is a control_biosequence expected to be of low signal if no spikes are used. If spikes are used, the signal is expected to be high.
unique identifier: MO_940

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

control design element group type
type: NamedIndividual
type: DesignElementGroupType
comment: A grouping of DesignElements features/Reporters/Composites which are not designed to detect a signal in the biomaterial and which are on the array for control purposes e.g. a grouping of controls used for spiking.
unique identifier: MO_414

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

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

control hybridization quality
type: NamedIndividual
type: ControlType
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).
unique identifier: MO_385

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

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

control spike calibration
type: NamedIndividual
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

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

cosine distance
type: NamedIndividual
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.

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

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

cpm
type: NamedIndividual
type: RadiationUnit
unique identifier: MO_348
comment: counts per minute, unit of light emissions produced by ionizing radiation.

ctDNA
type: NamedIndividual
type: DeprecatedTerms
deprecation in version: 1.3.1.1
unique identifier: MO_586
synonym: chloroplast DNA
comment: ctDNA: sequence from the chloroplast synonym: chloroplast DNA
deprecation reason: deleted_term
deprecation old parent: PhysicalBioSequenceType
deprecation replacement term: PhysicalBioSequenceType

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

curated gene record
type: NamedIndividual
type: DatabaseEntryType
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
unique identifier: MO_913

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

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

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

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

data coder
type: NamedIndividual
type: Roles
unique identifier: MO_695
comment: person who prepares the MAGE-ML file

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

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

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

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

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

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

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

development or differentiation design
type: NamedIndividual
type: BiologicalProperty
comment: A development or differentiation experiment design type assays events associated with development or differentiation or moving through a life cycle. Development applies to organism(s) acquiring a mature state, and differentiation applies to cells acquiring specialized functions.
unique identifier: MO_892

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

diameter aberration
type: NamedIndividual
type: DefectType
unique identifier: MO_781
comment: The diameter of the Feature is much smaller or much larger than expected based on the spotting pin diameter.

differential expression
type: NamedIndividual
type: HigherLevelAnalysisProtocolType
comment: An analysis aimed at identifying differentially expressed genes in two or more conditions.
unique identifier: MO_874

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

dilute
type: NamedIndividual
type: AtomicAction
comment: Decreasing the concentration of solutes in a solution or suspension.
unique identifier: MO_962

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

disease staging
type: NamedIndividual
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.

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

disease state design
type: NamedIndividual
type: EpidemiologicalDesign
type: PerturbationalDesign
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

displaced feature or zone
type: NamedIndividual
type: DefectType
comment: The Feature or Zone is displaced from its expected position, due to e.g. a bent spotting pin(s).
unique identifier: MO_959

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

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

dose response design
type: NamedIndividual
type: PerturbationalDesign
comment: A dose response design type examines the relationship between the size of the administered dose and the extent of the response of the organism(s).
unique identifier: MO_485

double stranded
type: NamedIndividual
type: StrandType
unique identifier: MO_828
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.

dpm
type: NamedIndividual
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.

ds oligo
type: NamedIndividual
type: DeprecatedTerms
comment: a double stranded oligonucleotide
deprecation in version: 1.2.0
unique identifier: MO_344
deprecation reason: deleted_term
deprecation old parent: PhysicalBioSequenceType
deprecation replacement term: PhysicalBioSequenceType
has reason for deprecation: deleted term
deprecated from version: version 1.2.0

dye swap design
type: NamedIndividual
type: MethodologicalDesign
comment: An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip
unique identifier: MO_858
synonym: dye flip
synonym: flip dye

dye swap merge
type: NamedIndividual
type: DataTransformationProtocolType
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.
unique identifier: MO_448

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

dye swap replicate
type: NamedIndividual
type: ReplicateDescriptionType
unique identifier: MO_901
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.

dye swap replicate reduction
type: NamedIndividual
type: DerivedBioAssayType
unique identifier: MO_750
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.

eVOC
type: NamedIndividual
type: CellTypeDatabase
type: DevelopmentalStageDatabase
type: DiseaseStateDatabase
type: OrganismPartDatabase
unique identifier: MO_684
comment: Ontology of human terms that describe the sample source of human cDNA and SAGE libraries.
has human readable URI: http://www.sanbi.ac.za/evoc/ontologies.html

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

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

element design
type: NamedIndividual
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

ellipsoid feature
type: NamedIndividual
type: FeatureShape
unique identifier: MO_459
comment: The shape of the feature on the array is circular or oval.

environmental history design
type: NamedIndividual
type: EnvironmentalHistory
comment: An environmental history design type is where some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc.
unique identifier: MO_698

ex vivo design
type: NamedIndividual
type: MethodologicalDesign
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.
unique identifier: MO_808

exemplar mRNA
type: NamedIndividual
type: DeprecatedTerms
deprecation in version: 1.3.1.1
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.
unique identifier: MO_621
deprecation reason: deleted_term
deprecation old parent: TheoreticalBioSequenceType
deprecation replacement term: TheoreticalBioSequenceType

exon
type: NamedIndividual
type: DeprecatedTerms
deprecation in version: 1.2.0
unique identifier: MO_619
deprecation reason: deleted_term
comment: sequence which represents regions of a transcript that are joined to another exon during splicing
deprecation old parent: TheoreticalBioSequenceType
deprecation replacement term: TheoreticalBioSequenceType
has reason for deprecation: deleted term
deprecated from version: version 1.2.0

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

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

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

extract
type: NamedIndividual
type: BioSampleType
unique identifier: MO_895
comment: The BioSample immediately before labeling.

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

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

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

feature extraction
type: NamedIndividual
type: ExperimentalProtocolType
unique identifier: MO_928
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

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

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

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

female
type: NamedIndividual
type: Sex
unique identifier: MO_506
comment: of, pertaining to, or designating the sex that only produces gametes that can be fertilized by male gametes.

fertilization
type: NamedIndividual
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)

fg
type: NamedIndividual
type: MassUnit
unique identifier: MO_732
comment: femtogram, unit of mass

filtered data
type: NamedIndividual
type: DerivedBioAssayType
comment: Data from which a subset has been removed based on some criteria, e.g. data below an intensity threshhold.
unique identifier: MO_625

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

flag filter
type: NamedIndividual
type: DataTransformationProtocolType
unique identifier: MO_1024
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).

flip-dye consistency
type: NamedIndividual
type: NormalizationDescriptionType
comment: A method of checking the consistency of expression levels between a pair of features from flip-dye hybridizations by studying the distribution of the logarithm of ratios of intensity ratios from the two spots.
unique identifier: MO_907
was replaced by: dye swap merge
has reason for deprecation: replaced term
deprecated from version: version 1.2.0

float
type: NamedIndividual
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

fmol
type: NamedIndividual
type: QuantityUnit
unique identifier: MO_689
comment: femtomole, unit of quantity

forward
type: NamedIndividual
type: StrandType
synonym: +
unique identifier: MO_820
comment: the forward strand exact synonym: +

fractionate
type: NamedIndividual
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).

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

french railway distance
type: NamedIndividual
type: NodeValueType
unique identifier: MO_964
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.

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

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

frozen storage
type: NamedIndividual
type: PreservationType
unique identifier: MO_481
comment: Storage where the thing stored is stored below 0 degrees celsius.

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

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

http://mged.sourceforge.net/ontologies/MGEDOntology.owl#g
type: NamedIndividual
type: MassUnit
unique identifier: MO_825
comment: gram, unit of mass

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

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

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

gene knock in
type: NamedIndividual
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

gene knock out
type: NamedIndividual
type: GeneticModification
unique identifier: MO_771
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.

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

genetic modification design
type: NamedIndividual
type: PerturbationalDesign
comment: A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out
unique identifier: MO_447

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

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

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

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

germination
type: NamedIndividual
type: InitialTimePoint
unique identifier: MO_590
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).

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

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

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

grandfather
type: NamedIndividual
type: FamilyRelationship
unique identifier: MO_478
comment: The father of one's father or mother.

grandmother
type: NamedIndividual
type: FamilyRelationship
unique identifier: MO_924
comment: The mother of one's father or mother.

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

grow
type: NamedIndividual
type: ComplexAction
type: ExperimentalProtocolType
comment: A ComplexAction or ProtocolType describing growth of an organism or cell culture.
unique identifier: MO_758

growth condition design
type: NamedIndividual
type: PerturbationalDesign
comment: A growth condition experiment design type is where some part of the growth condition is changed for the purposes of the experiment, examples of growth conditions changed are media, temperature, humidity, light, nutrients.
unique identifier: MO_588

half-life
type: NamedIndividual
type: TimeUnitOther
unique identifier: MO_595
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.

haploid
type: NamedIndividual
type: Ploidy
comment: Describes a cell, nucleus or an organism with one copy of each chromosome.
unique identifier: MO_719

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

hardware variation design
type: NamedIndividual
type: MethodologicalDesign
comment: A hardware variation experiment design type compares different types of hardware for performance, reproducibility, accuracy and precision.
unique identifier: MO_734

harvest
type: NamedIndividual
type: ComplexAction
type: ExperimentalProtocolType
unique identifier: MO_982
comment: The process of harvesting cells from culture.

hatching
type: NamedIndividual
type: InitialTimePoint
unique identifier: MO_745
comment: The point at which an organism emerges from an egg.

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

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

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

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

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

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

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

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

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

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

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

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

imprinting design
type: NamedIndividual
type: BiologicalProperty
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.
unique identifier: MO_914

in medium
type: NamedIndividual
type: DeliveryMethod
comment: Delivery method where a compound/drug is administered in the culture medium (e.g., for in vitro treatment).
unique identifier: MO_733

in situ oligo features
type: NamedIndividual
type: TechnologyType
unique identifier: MO_514
comment: The TechnologyType of the FeatureGroup is manufactured using in situ methods such as photolithography (e.g. Affymetrix) or chemical synthesis (e.g. Agilent)

in vitro design
type: NamedIndividual
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

in vivo design
type: NamedIndividual
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

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

incubate
type: NamedIndividual
type: ComplexAction
type: ExperimentalProtocolType
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.

individual
type: NamedIndividual
type: BioMaterialCharacteristicCategory
comment: A descriptor for FactorValue where BioSources are compared.
unique identifier: MO_639

individual genetic characteristic
type: NamedIndividual
type: BioMaterialCharacteristicCategory
comment: A descriptor for FactorValue where IndividualGeneticCharacteristic is compared.
unique identifier: MO_722

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

induced mutation
type: NamedIndividual
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.

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

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

innate behavior design
type: NamedIndividual
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

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

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

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

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

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

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

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

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

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

irradiate
type: NamedIndividual
type: ComplexAction
type: ExperimentalProtocolType
unique identifier: MO_770
comment: treatment of a biomaterial with radiation e.g. electromagnetic radiation

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

is contaminated
type: NamedIndividual
type: WarningType
unique identifier: MO_489
comment: The clone used to originate the BioSequence which corresponds to the reporter was found to be contaminated (e.g. well-well contamination) on examination.

is expressed design
type: NamedIndividual
type: BiologicalProperty
comment: A design aimed at identifying genes expressed in biomaterials of interest.
unique identifier: MO_487

iterative mean log centering
type: NamedIndividual
type: NormalizationDescriptionType
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.
unique identifier: MO_957

jackknife Pearson correlation
type: NamedIndividual
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.

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

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

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

kg per m2
type: NamedIndividual
type: OtherUnit
unique identifier: MO_658
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
synonym: kg/m2

labeling
type: NamedIndividual
type: ComplexAction
type: ExperimentalProtocolType
unique identifier: MO_471
comment: The procedure of labeling a biosample.

laser ablation mark
type: NamedIndividual
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)

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

light intensity
type: NamedIndividual
type: EnvironmentalFactorCategory
unique identifier: MO_517
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.

linear amplification
type: NamedIndividual
type: ComplexAction
type: ExperimentalProtocolType
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
synonym: Eberwine procedure
unique identifier: MO_997

linear regression normalization
type: NamedIndividual
type: NormalizationDescriptionType
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.
unique identifier: MO_823

linear scale
type: NamedIndividual
type: Scale
unique identifier: MO_751
comment: The scale is a standard base 10, non logarithmic scale.

linlog normalization
type: NamedIndividual
type: NormalizationDescriptionType
comment: A transformation method in which low intensities are linearly scaled while high intensities are logarithmically scaled. The transition point is determined by minimizing the absolute deviation of the variance of log ratios.
unique identifier: MO_956
has reason for deprecation: replaced term
deprecated from version: version 1.2.0

linlog transformation
type: NamedIndividual
type: DataTransformationProtocolType
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.
unique identifier: MO_845

liquid
type: NamedIndividual
type: Media
unique identifier: MO_715
comment: media type, usually some sort of broth

liquid handler
type: NamedIndividual
type: HardwareType
comment: Hardware for automated liquid transfer and handling.
unique identifier: MO_868

liquid handler software
type: NamedIndividual
type: SoftwareType
unique identifier: MO_761
comment: Software used to control automated liquid handler.

list of booleans
type: NamedIndividual
type: DataType
comment: An ordered, finite set of booleans.
unique identifier: MO_712

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

list of integers
type: NamedIndividual
type: DataType
comment: An ordered, finite set of integers.
unique identifier: MO_891

list of negative floats
type: NamedIndividual
type: DataType
comment: An ordered, finite set of negative floats.
unique identifier: MO_851

list of negative integers
type: NamedIndividual
type: DataType
comment: An ordered, finite set of negative integers.
unique identifier: MO_900

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

list of nonnegative integers
type: NamedIndividual
type: DataType
comment: An ordered, finite set of nonnegative integers.
unique identifier: MO_973

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

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

list of positive floats
type: NamedIndividual
type: DataType
comment: An ordered, finite set of positive floats.
unique identifier: MO_777

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

list of strings
type: NamedIndividual
type: DataType
comment: An ordered, finite set of strings.
unique identifier: MO_800

loess global normalization
type: NamedIndividual
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

loess group normalization
type: NamedIndividual
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

loess normalization
type: NamedIndividual
type: NormalizationDescriptionType
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.
unique identifier: MO_428

loess scaled group normalization
type: NamedIndividual
type: DataTransformationProtocolType
comment: Application of a scale adjustment following loess_group_normalization, to render the group variances similar.
unique identifier: MO_521

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

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

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

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

long oligo
type: NamedIndividual
type: DesignElement
comment: An element that is an oligonucleotide of at least 50 nucleotides in length.
unique identifier: MO_598

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

low intensity filter
type: NamedIndividual
type: DeprecatedTerms
deprecation in version: 1.3.0
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
deprecation reason: replaced_term
deprecation old parent: DataTransformationProtocolType
replaced with term: flag filter
was replaced by: flag filter
has reason for deprecation: replaced term
deprecated from version: version 1.3.0

lowess global normalization
type: NamedIndividual
type: DataTransformationProtocolType
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.
unique identifier: MO_692

lowess group normalization
type: NamedIndividual
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

lowess normalization
type: NamedIndividual
type: NormalizationDescriptionType
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.
unique identifier: MO_720

lowess scaled group normalization
type: NamedIndividual
type: DataTransformationProtocolType
comment: Application of a scale adjustment following lowess_group_normalization, to render the group variances similar.
unique identifier: MO_410

lumen
type: NamedIndividual
type: LightUnit
unique identifier: MO_603
comment: The unit of total light output from a light source.

lux
type: NamedIndividual
type: LightUnit
comment: A metric unit equal to one lumen per square meter. This unit is the modern equivalent of foot-candles where one footcandle is 10.76 lux.
unique identifier: MO_573

http://mged.sourceforge.net/ontologies/MGEDOntology.owl#m
type: NamedIndividual
type: DistanceUnit
unique identifier: MO_367
comment: meter, distance unit

mL per L
type: NamedIndividual
type: ConcentrationUnit
unique identifier: MO_801
comment: milliliters per liter, concentration unit

mM
type: NamedIndividual
type: ConcentrationUnit
unique identifier: MO_509
comment: milimolar, concentration unit

mOsm per kg H2O
type: NamedIndividual
type: ConcentrationUnitOther
unique identifier: MO_661
comment: osmolality per kilogram of water, concentration of the solute per unit of solvent

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

male
type: NamedIndividual
type: Sex
unique identifier: MO_652
comment: individual whose sex organs contain only male gametes

manhattan distance
type: NamedIndividual
type: NodeValueType
unique identifier: MO_567
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.

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

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

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

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

mean and coefficient of variation
type: NamedIndividual
type: DerivedBioAssayType
unique identifier: MO_425
comment: the mean and coefficient of variation values resulting from computationally combining 2 or more sets of BioAssayData

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

mean and p values
type: NamedIndividual
type: DerivedBioAssayType
unique identifier: MO_943
comment: the mean and associated p-values resulting from computationally combining 2 or more sets of BioAssayData

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

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

mean log centering
type: NamedIndividual
type: NormalizationDescriptionType
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).
unique identifier: MO_398

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

media
type: NamedIndividual
type: EnvironmentalFactorCategory
unique identifier: MO_545
comment: The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil)

median log centering
type: NamedIndividual
type: NormalizationDescriptionType
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).
unique identifier: MO_811

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

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

metastatic site
type: NamedIndividual
type: CancerSite
unique identifier: MO_806
comment: the organism part in which additional tumors are identified remote from the primary site

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

mg per kg per day
type: NamedIndividual
type: ConcentrationUnitOther
unique identifier: MO_353
comment: milligram per kilogram per day

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

microarray experiment record
type: NamedIndividual
type: DatabaseEntryType
comment: A record which describes and identifies a microarray experiment e.g. GEO
unique identifier: MO_346

microeinstein per minute and square meter
type: NamedIndividual
type: LightUnit
unique identifier: MO_526
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).

microeinstein per second and square meter
type: NamedIndividual
type: LightUnit
unique identifier: MO_584
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).

micromole per second and square meter
type: NamedIndividual
type: OtherUnit
unique identifier: MO_848
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.

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

missing feature or zone
type: NamedIndividual
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.

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

mix by pipette
type: NamedIndividual
type: AtomicAction
unique identifier: MO_479
comment: Mix by drawing up and down with a pipette.

mix by vortex
type: NamedIndividual
type: AtomicAction
unique identifier: MO_880
comment: Mix through the use of a vortexer.

mix general
type: NamedIndividual
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.

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

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

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

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

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

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

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

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

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

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

mother
type: NamedIndividual
type: FamilyRelationship
comment: A female parent.
unique identifier: MO_387

moving average
type: NamedIndividual
type: DataTransformationProtocolType
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.
unique identifier: MO_681

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

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

multiple testing correction
type: NamedIndividual
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.

negative
type: NamedIndividual
type: Result
unique identifier: MO_802
comment: false or no

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

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

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

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

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

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

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

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

non-targeted transgenic variation design
type: NamedIndividual
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.

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

nonnegative integer
type: NamedIndividual
type: DataType
comment: An integer >= 0.
unique identifier: MO_390

nonpositive float
type: NamedIndividual
type: DataType
comment: A float less than or equal to zero.
unique identifier: MO_656

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

normalization testing design
type: NamedIndividual
type: MethodologicalDesign
comment: A normalization testing experiment design tests different normalization procedures.
unique identifier: MO_729

normalized intensities
type: NamedIndividual
type: DerivedBioAssayType
unique identifier: MO_994
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.

normalized ratios
type: NamedIndividual
type: DerivedBioAssayType
unique identifier: MO_664
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.

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

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

not uniform
type: NamedIndividual
type: DefectType
unique identifier: MO_906
comment: The source DNA for a Feature was not uniformly deposited.

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

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

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

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

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

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

oligo synthesizer
type: NamedIndividual
type: HardwareType
comment: Hardware for synthesizing oligos.
unique identifier: MO_930

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

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

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

openGALEN
type: NamedIndividual
type: OrganismPartDatabase
unique identifier: MO_613
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.
has human readable URI: http://www.opengalen.org/open/crm/crm-anatomy.html

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

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

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

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

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

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

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

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

organism
type: NamedIndividual
type: BioMaterialCharacteristicCategory
unique identifier: MO_508
comment: one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria

organism part
type: NamedIndividual
type: BioMaterialCharacteristicCategory
type: MaterialType
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).

organism part comparison design
type: NamedIndividual
type: BiologicalProperty
comment: An organism part comparison experiment design type compares tissues, regions, organs within or between organisms
unique identifier: MO_953

organism status
type: NamedIndividual
type: BioMaterialCharacteristicCategory
unique identifier: MO_871
comment: The stage premortem or postmortem at which the sample was processed for extraction of biomaterials.

organism status design
type: NamedIndividual
type: BiologicalProperty
comment: A design that compares samples from live and dead organisms.
unique identifier: MO_841

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

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

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

pathogenicity design
type: NamedIndividual
type: PerturbationalDesign
comment: A pathogenicity experiment design type is where an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed.
unique identifier: MO_807

pathway record
type: NamedIndividual
type: DatabaseEntryType
unique identifier: MO_780
comment: a record which identifies and describes biological pathways, e.g. a KEGG record

pearson correlation coefficient
type: NamedIndividual
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.

pedigree record
type: NamedIndividual
type: DatabaseEntryType
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
unique identifier: MO_969

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

percent confluence
type: NamedIndividual
type: ConcentrationUnitOther
comment: A measure of the density of an attached or monolayer culture (e.g., cell culture), e.g., 80 percent_confluence.
unique identifier: MO_378

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

percent vol per vol
type: NamedIndividual
type: ConcentrationUnit
unique identifier: MO_916
comment: percentage volume per volume, concentration unit

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

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

pfu per ml
type: NamedIndividual
type: ConcentrationUnitOther
unique identifier: MO_768
comment: the number of plaque forming units per ml

pg
type: NamedIndividual
type: MassUnit
unique identifier: MO_363
comment: picogram, mass unit

phylogeny record
type: NamedIndividual
type: DatabaseEntryType
comment: A record which describes and identifies the relationship between species and is computationally determined and based on sequences e.g. Treebase record
unique identifier: MO_662

physical characteristics
type: NamedIndividual
type: BioMaterialCharacteristicCategory
comment: A descriptor for FactorValue where PhysicalCharacteristics are compared.
unique identifier: MO_863

physiological process design
type: NamedIndividual
type: BiologicalProperty
unique identifier: MO_1029
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.

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

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

planting
type: NamedIndividual
type: InitialTimePoint
unique identifier: MO_495
comment: The act of placing a plant in media (e.g. soil) to allow it to grow. This excludes sowing.

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

pmol
type: NamedIndividual
type: QuantityUnit
unique identifier: MO_688
comment: picomoles, quantity unit

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

polylysine
type: NamedIndividual
type: SurfaceType
unique identifier: MO_569
comment: a surface coating for immobilization with the polypeptide, polylysine

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

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

polysomy
type: NamedIndividual
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

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

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

positive
type: NamedIndividual
type: Result
unique identifier: MO_429
comment: true or yes

positive float
type: NamedIndividual
type: DataType
comment: A float > 0.
unique identifier: MO_501

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

postmortem
type: NamedIndividual
type: OrganismStatus
unique identifier: MO_416
comment: biomaterial removed after the death of the organism

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

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

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

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

primary site
type: NamedIndividual
type: CancerSite
unique identifier: MO_408
comment: the organism part in which the tumor originated

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

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

purify
type: NamedIndividual
type: ComplexAction
type: ExperimentalProtocolType
unique identifier: MO_406
comment: The action of enriching a BioMaterial (organism, cell, nucleic acid etc) or Compound e.g. for FACS for positive selection or RNA cleanup the Action or ProtocolType is purify (see fractionate).

quality control testing design
type: NamedIndividual
type: MethodologicalDesign
comment: A quality control testing experiment design type is where some aspect of the experiment is quality controlled for the purposes of quality assurance
unique identifier: MO_981

quantile normalization
type: NamedIndividual
type: NormalizationDescriptionType
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.
unique identifier: MO_951

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

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

ratio
type: NamedIndividual
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.

ratio statistics normalization
type: NamedIndividual
type: NormalizationDescriptionType
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.
unique identifier: MO_349

real time PCR quality control
type: NamedIndividual
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

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

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

relative
type: NamedIndividual
type: MeasurementType
unique identifier: MO_396
comment: a measurement where the value is dependent on another measurement

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

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

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

replicate analysis
type: NamedIndividual
type: DataTransformationProtocolType
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.
unique identifier: MO_433

replicate design
type: NamedIndividual
type: MethodologicalDesign
comment: A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
unique identifier: MO_885

resuspend
type: NamedIndividual
type: AtomicAction
unique identifier: MO_466
comment: The procedure in which solid material is dispensed or dissolved in a liquid.

reverse
type: NamedIndividual
type: StrandType
synonym: -
unique identifier: MO_402
comment: the reverse strand exact synonym: -

reverse transcription
type: NamedIndividual
type: ComplexAction
type: ExperimentalProtocolType
comment: Generation of a DNA strand from an RNA strand using reverse transcriptase.
unique identifier: MO_480

reverse transcription PCR quality control
type: NamedIndividual
type: QualityControlDescriptionType
comment: A PCR based semi quantitative validation of a subset of the array based data used for experimental QC purposes.
unique identifier: MO_986

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

sampling time point
type: NamedIndividual
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

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

secreted protein identification design
type: NamedIndividual
type: BioMolecularAnnotation
comment: A secreted protein identification design type identifies transcripts associated with a secretory pathway during translation and is used to infer which proteins are secreted or membrane bound.
unique identifier: MO_694

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

self vs self design
type: NamedIndividual
type: MethodologicalDesign
comment: A self vs. self experiment design investigates variance and error estimates in the experimental system, and is where the same extract is compared.
unique identifier: MO_490

semisolid
type: NamedIndividual
type: Media
unique identifier: MO_635
comment: semisolid media type

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

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

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

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

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

signal log ratio
type: NamedIndividual
type: DeprecatedTerms
deprecation in version: 1.1.7
unique identifier: MO_941
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 reason: deleted_term
deprecation old parent: DerivedBioAssayType
deprecation replacement term: DerivedBioAssayType
has reason for deprecation: deleted term
deprecated from version: version 1.1.7

silicon
type: NamedIndividual
type: SubstrateType
unique identifier: MO_382
comment: the array is made on silicon

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

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

slice analysis
type: NamedIndividual
type: DeprecatedTerms
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
deprecation reason: deleted_term
deprecation old parent: NormalizationDescriptionType
deprecation replacement term: NormalizationDescriptionType
has reason for deprecation: deleted term
deprecated from version: version 1.2.0

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

software manufacturer
type: NamedIndividual
type: Roles
unique identifier: MO_475
comment: Person or organization that manufactured the software.

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

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

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

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

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

species design
type: NamedIndividual
type: BiologicalProperty
comment: A species experiment design type assays differences between distinct species.
unique identifier: MO_675

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

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

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

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

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

split
type: NamedIndividual
type: ComplexAction
type: ExperimentalProtocolType
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

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

spotted antibody features
type: NamedIndividual
type: TechnologyType
unique identifier: MO_483
comment: TechnologyType of FeatureGroup where antibodies are spotted directly.

spotted colony features
type: NamedIndividual
type: TechnologyType
unique identifier: MO_618
comment: TechnologyType of FeatureGroup where bacterial or other colonies are spotted directly.

spotted ds DNA features
type: NamedIndividual
type: TechnologyType
comment: A descriptor for the TechnologyType for a group of features where double stranded DNA is spotted on the array e.g. a PCR of a cDNA clone.
unique identifier: MO_499

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

spotted ss PCR amplicon features
type: NamedIndividual
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

spotted ss oligo features
type: NamedIndividual
type: TechnologyType
unique identifier: MO_579
comment: The TechnologyType of the FeatureGroup is spotted single stranded oligonucleotides (of any length) on the substrate.

square feature
type: NamedIndividual
type: FeatureShape
unique identifier: MO_817
comment: The shape of the feature on the array is square.

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

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

stimulated design type
type: NamedIndividual
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

stimulus or stress design
type: NamedIndividual
type: PerturbationalDesign
comment: A stimulus or stress experiment design type is where the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc.
unique identifier: MO_568

store
type: NamedIndividual
type: ComplexAction
type: ExperimentalProtocolType
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.

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

strain or line design
type: NamedIndividual
type: BiologicalProperty
comment: A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
unique identifier: MO_462

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

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

submitter
type: NamedIndividual
type: Roles
unique identifier: MO_882
comment: Person who is the primary contact for data submitted to a database.

synthetic DNA
type: NamedIndividual
type: MaterialType
comment: DNA which is generated by chemical or enzymatic (non cellular) means. non-exact synonym: cDNA
unique identifier: MO_577
synonym: cDNA

synthetic RNA
type: NamedIndividual
type: MaterialType
unique identifier: MO_543
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
synonym: aRNA
synonym: amplified RNA
synonym: cRNA
synonym: complementary RNA

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

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

technical replicate
type: NamedIndividual
type: QualityControlDescriptionType
type: ReplicateDescriptionType
comment: A replicate where the same BioSample is use e.g. the same pool of RNA used to assess technical (as opposed to biological) variation within an experiment.
unique identifier: MO_641

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

thermal cycler
type: NamedIndividual
type: HardwareType
comment: An instrument designed to automatically raise and lower the temperature of wells or tubes. Usually used to perform PCR. Exact Synonym: thermocycler
unique identifier: MO_854

tiling path design
type: NamedIndividual
type: BioMolecularAnnotation
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.
unique identifier: MO_507

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

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

total RNA
type: NamedIndividual
type: MaterialType
unique identifier: MO_373
comment: Total cellular and nuclear RNA.

total intensity normalization
type: NamedIndividual
type: DeprecatedTerms
deprecation in version: 1.2.0
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 reason: deleted_term
deprecation old parent: NormalizationDescriptionType
deprecation replacement term: NormalizationDescriptionType
has reason for deprecation: deleted term
deprecated from version: version 1.2.0

total intensity normalization paired
type: NamedIndividual
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

total intensity normalization single
type: NamedIndividual
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

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

transcript identification design
type: NamedIndividual
type: BioMolecularAnnotation
type: TechnologicalDesign
comment: A transcript identification design type characterizes the length and position of transcripts and allows identification of all forms of transcripts in the genome.
unique identifier: MO_533
synonym: expression profiling
synonym: expression_profiling
synonym: gene expression
synonym: gene_expression
synonym: transcription profiling
synonym: transcription_profiling

transfect
type: NamedIndividual
type: ComplexAction
type: ExperimentalProtocolType
unique identifier: MO_849
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.

transfection
type: NamedIndividual
type: GeneticModification
comment: Introduction of genetic material into an organism often in the form of a plasmid.
unique identifier: MO_366

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

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

tumor grading
type: NamedIndividual
type: BioMaterialCharacteristicCategory
comment: A descriptor used in cancer biology to describe abnormalities of tumor cells.
unique identifier: MO_843

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

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

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

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

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

uncentered Pearson correlation
type: NamedIndividual
type: NodeValueType
unique identifier: MO_974
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.

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

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

unknown experiment design type
type: NamedIndividual
type: BioMolecularAnnotation
type: BiologicalProperty
type: EpidemiologicalDesign
type: MethodologicalDesign
type: PerturbationalDesign
comment: ExperimentDesignType of unknown type.
unique identifier: MO_634

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

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

unknown sex
type: NamedIndividual
type: Sex
unique identifier: MO_999
comment: organism(s) whose sex is unknown

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

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

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

urine
type: NamedIndividual
type: BioSourceType
unique identifier: MO_399
comment: The fluid and dissolved substances excreted by the kidney.

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

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

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

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

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

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

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

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

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

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

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

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

wash
type: NamedIndividual
type: ComplexAction
type: ExperimentalProtocolType
unique identifier: MO_596
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.

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

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

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

weeks
type: NamedIndividual
type: TimeUnit
comment: 7 days, unit of time
unique identifier: MO_842

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

wild type
type: NamedIndividual
type: Allele
type: Genotype
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.

within bioassay data set function
type: NamedIndividual
type: DataTransformationProtocolType
comment: A function applied to subsets of values from the same Measured/Derived bioassay data set.
unique identifier: MO_668

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

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

yes
type: NamedIndividual
type: DeprecatedTerms
deprecation in version: 1.1.7
unique identifier: MO_540
deprecation reason: deleted_term
comment: true
has reason for deprecation: deleted term
deprecated from version: version 1.1.7