Chris Stoeckert, Helen Parkinson, Trish Whetzel, Paul Spellman, Catherine A. Ball, Joseph White, John Matese, Liju Fan, Gilberto Fragoso, Mervi Heiskanen, Susanna Sansone, Helen Causton, Laurence Game, Chris Taylor
February 9, 2007
Concepts, definitions, terms, and resources for standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1
An ontology for microarray experiments in support of MAGE v.1.
The MGED Ontology
1.3.1.1
Examples of a Creator include a person, an organization, or a service. Typically, the name of a Creator should be used to indicate the entity.
1999-07-02
An entity primarily responsible for making the resource.
Creator
A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/creator) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.
Date may be used to express temporal information at any level of granularity. Recommended practice is to express the date, date/time, or period of time according to ISO 8601-1 [[ISO 8601-1](https://www.iso.org/iso-8601-date-and-time-format.html)] or a published profile of the ISO standard, such as the W3C Note on Date and Time Formats [[W3CDTF](https://www.w3.org/TR/NOTE-datetime)] or the Extended Date/Time Format Specification [[EDTF](http://www.loc.gov/standards/datetime/)]. If the full date is unknown, month and year (YYYY-MM) or just year (YYYY) may be used. Date ranges may be specified using ISO 8601 period of time specification in which start and end dates are separated by a '/' (slash) character. Either the start or end date may be missing.
1999-07-02
A point or period of time associated with an event in the lifecycle of the resource.
Date
A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/date) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.
Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.
1999-07-02
An account of the resource.
Description
A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/description) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.
Typically, the subject will be represented using keywords, key phrases, or classification codes. Recommended best practice is to use a controlled vocabulary.
1999-07-02
The topic of the resource.
Subject
A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/subject) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.
1999-07-02
A name given to the resource.
Title
A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/title) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.
MO_299
property indicating the version of the MGED Ontology that the term was deprecated from
MO_260
property indicating that the class has an association to a MAGE description
MO_340
property indicating that the class has a URI
MO_312
property indicating that the class has an action
MO_314
property indicating that the class has an additive
MO_309
property indicating that the class has an affiliation to an institution
MO_259
property indicating that the class has an atmospheric component
MO_341
property indicating that the class has been treated
MO_252
property indicating that the class has bioassaydata
MO_238
property indicating that the class has bioassays
MO_272
property indicating that the class has biomaterial characteristics
MO_315
property indicating that the class has a biosource type
MO_248
property indicating that the class has a cancer site
MO_249
property indicating that the class has a category
MO_253
property indicating that the class has a chromosomal aberration classification
MO_274
property indicating that the class has a citation
MO_316
property indicating that the class has a clinical finding
MO_247
property indicating that the class has a clinical record
MO_282
property indicating that the class has a clinical treatment
MO_302
property indicating that the class has a compound
MO_245
property indicating that the class contains a cubic volume measurement
MO_233
property indicating that the class has a database
MO_240
property indicating that the class has a database entry type
MO_301
property indicating that the class has a diameter
MO_290
property indicating the location of the disease.
MO_275
property indicating that the class has disease staging
MO_305
property indicating that the class has a disease state
MO_342
property indicating that the class has a donor
MO_291
property indicating that the class has an experiment design
MO_288
property indicating that the class has an experiment design type
MO_328
property indicating that the class has experiment factors
MO_236
property indicating that the class has a factor value
MO_263
property indicating that the class has an ontology entry
MO_243
property indicating that the class has a family member
MO_250
property indicating that the class has a family relationship
MO_268
property indicating that the class has a feature shape
MO_267
property indicating that the class has fiducials
MO_286
property indicating that the class has hardware
MO_317
property indicating that the class has a height
MO_313
property indicating that the class has a host
MO_283
property indicating that the class has a host part
MO_234
property indicating that the class has an image format
MO_327
property indicating that the class has an individual
MO_254
property indicating that the class has individual genetic characteristics
MO_292
property indicating that the class has an individual time point
MO_281
property indicating that the class has a laboratory test
MO_232
property indicating that the class has a manufacturer
MO_280
property indicating that the class has a mass
MO_297
property indicating that the class has a maximum measurement
MO_325
property indicating that the class has a measurement
MO_242
property indicating that the class has a measurement type
MO_310
property indicating that the class has a node value
MO_264
property indicating that the class has a node value type
MO_307
property indicating that the class has a node
MO_321
property indicating that the class has a nutrient component
MO_285
property indicating that the class has an organism part
MO_278
property indicating that the class has an owner
MO_257
property indicating that the class has a parent organization
MO_241
property indicating that the class has a modified part
MO_273
property indicating that the protocol has a performer or contact person
MO_276
property indicating that the class has a prior disease state
MO_266
property indicating that the class has a property set
MO_300
property indicating that the class has a protocol
MO_303
property indicating that the class has providers
MO_306
property to indicate the reason for deprecating a term
MO_324
property indicating the class has a result
MO_287
property indicating that the class has a scale
MO_284
property indicating that the class has software
MO_320
property indicating that the class has species
MO_244
property indicating that the test has a test protocol
MO_261
property indicating that the test has a test result
MO_311
property indicating that the class has a clinical test
MO_262
property indicating that the class has a treatment
MO_319
property indicating that the class has a type
MO_269
property indicating that the class has units
MO_279
property indicating that the class is user defined
MO_304
instance property to indicate what the term was replaced by
MO_265
property indicating that the class was tested for
abstract
concrete
place_holder
mage
ontology
1.1.7
1.1.8
1.1.9
1.2.0
1.3.0
1.3.1.1
deleted_term
merged_term
replaced_term
split_term
MO_323
property indicating that the class has an identifier
MO_231
property indicating that the class has an accession number
MO_339
property indicating that the class has an accession number version
MO_277
property indicating that the class has an address
MO_318
property indicating that the class has authors
MO_334
property indicating that the class has a description
MO_256
property indicating that the class has an editor
MO_293
property indicating that the class has an email address
MO_289
property indicating that the class has a fax
MO_258
property indicating that the class has a first name
MO_330
property indicating that the contents found at this uri are human readable
MO_294
property indicating that the class has an issue
MO_255
property indicating that the class has a last name
MO_336
property indicating that the contents found at this uri are machine readable (i.e. in a standard format)
MO_271
property indicating that the class has a make
MO_237
property indicating that the class has a middle initials
MO_270
property indicating that the class has a model
MO_296
property indicating that the class has a name
MO_335
property indicating that the class has an order
MO_246
property indicating that the class has pages
MO_235
property indicating that the class has a phone
MO_251
property indicating that the class has a publication
MO_295
property indicating that the class has a publisher
MO_298
property indicating that the class has text
MO_337
property indicating that the class has a title
MO_329
property indicating that the class has a toll free phone
MO_326
property indicating that the class has a value
MO_239
property indicating that the class has a version
MO_308
property indicating that the class has a volume
MO_322
property indicating that the class has a year
MO_332
property indicating that the class is a solvent
Action
abstract
ontology
MO_193
Procedures used during treatment.
Age
abstract
ontology
MO_178
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).
Allele
concrete
ontology
MO_58
One of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on phenotype or sequence. Polymorphisms are included in this definition.
ArrayDesignPackage
abstract
mage
MO_33
MAGE package that describes the array layout and design. The array may be physical or virtual.
ArrayGroup
concrete
mage
MO_34
An array group is a physical platform that contains one or more arrays that are separately addressable or a virtual grouping of arrays.
ArrayPackage
abstract
mage
MO_107
MAGE package for describing the process by which arrays were manufactured.
Atmosphere
abstract
ontology
MO_219
The atmospheric conditions used to culture or grow an organism.
AtomicAction
concrete
ontology
MO_68
An atomic action is a single step process on the biomaterial, e.g. mix by inversion, wait, add
AuditAndSecurityPackage
abstract
mage
MO_172
MAGE package for contacts including organizations and people.
BarrierFacility
abstract
ontology
MO_97
Rating of containment system for the protection of organisms from infectious agents.
Bedding
place_holder
ontology
MO_154
Refers to the bedding material present in an animals housing.
BibliographicReference
concrete
mage
MO_201
A bibliographic reference is a published citation in a journal, book, other format e.g. web resource
BioAssay
abstract
mage
MO_56
A bioassay is an abstract class representing physical and computational groupings of biomaterials and arrays.
BioAssayData
MO_40
BioAssayData refers to the data files including images generated from one or more BioAssays.
BioAssayDataCluster
concrete
mage
MO_116
A grouping of bioassay data that has been organized by one or more mathematical functions into nodes.
BioAssayDataPackage
MO_186
MAGE package for BioAssayData.
BioAssayPackage
abstract
mage
MO_0
MAGE package for bioassay.
BioMaterial
abstract
mage
MO_226
Description of the processing state of the biomaterial for use in the microarray hybridization.
BioMaterialCharacteristics
abstract
ontology
MO_5
Properties of the biomaterial before treated in any manner for the purposes of the experiment.
BioMaterialPackage
abstract
mage
MO_182
Description of the source of the nucleic acid used to generate labeled material for the microarray experiment.
BioMaterialPurity
abstract
ontology
MO_20
A measure of homogeneity of a biomaterial. For example, an expression of the percentage of a tumor biopsy that is tumor cells.
BioMolecularAnnotation
concrete
ontology
MO_213
BioMolecularAnnotation experiment design types are those which are designed to investigate functions, processes, locations and identity at the molecular level e.g. binding site identification, genotyping.
BioSample
concrete
mage
MO_93
The BioSource after any treatment.
BioSampleType
concrete
ontology
MO_161
Used to tell when the BioSample is an extract or not.
BioSequence
concrete
mage
MO_163
A representation of a DNA, RNA, or protein sequence.
BioSequencePackage
abstract
mage
MO_191
MAGE package for biological sequences (biosequence).
BioSequenceType
abstract
ontology
MO_152
Controlled terms for descriptors indicating the type of biosequence. Types may be physical (e.g. BAC, cDNA clone), or computational (e.g. unigene cluster, consensus).
BioSource
concrete
mage
MO_77
The BioSource is the original source material before any treatment events.
BioSourceProvider
abstract
ontology
MO_230
The resource (e.g. company, hospital, geographical location) used to obtain or purchase the biomaterial.
BiologicalFactorCategory
abstract
ontology
MO_190
Factors that relate to properties of the biomaterial, its treatment, or
its growth.
Biometrics
abstract
ontology
MO_129
Physical properties of the BioMaterial e. g. mass or height
CancerSite
concrete
ontology
MO_26
class to hold instances used as the filler for the property has_cancer_site
CellLine
abstract
ontology
MO_49
The identifier for the established culture of a metazoan cell if one was used as a biomaterial.
CellType
abstract
ontology
MO_135
CellType, the type of cell used in the experiment if non mixed, if mixed the TargetedCellType should be used, example of instances, epithelial, glial etc.
CellTypeDatabase
concrete
ontology
MO_141
Database of cell type information.
CellularComponent
abstract
ontology
MO_1020
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).
CellularComponentDatabase
concrete
ontology
MO_1021
A resource for terms to describe cellular components, e.g. GO Cellular Component ontology.
ClinicalHistory
abstract
ontology
MO_189
The BioMaterial's (i.e., the patient's) medical record as background information relevant to the experiment.
ClinicalTreatment
abstract
ontology
MO_69
The current clinical treatment(s) of the patient from which the biosource is derived.
Compound
abstract
ontology
MO_70
A drug, solvent, chemical, etc., with a property that can be measured such as concentration.
ConcentrationUnit
concrete
ontology
MO_61
Units used for concentration measurements.
ConcentrationUnitOther
concrete
ontology
MO_86
Concentration units not specified in MAGE.
Contact
abstract
mage
MO_147
Organizations or individuals that may be contacted.
ControlType
concrete
ontology
MO_50
Controlled terms for descriptors for the type of control design element.
Cultivar
abstract
ontology
MO_124
a plant variety obtained in agriculture in horticulture
DataType
concrete
ontology
MO_125
Primitive data types found in computing languages such as float, boolean, etc.
Database
abstract
ontology
MO_118
Identifiable resource containing data or external ontologies or controlled vocabularies which has uniquely identifiable records.
DatabaseEntryType
concrete
ontology
MO_157
Controlled set of descriptors for the type of database record such as a protein record (in SWISS-PROT) or a gene object (in SGD).
DefectType
concrete
ontology
MO_16
Defects associated with features or zones such as those that are missing or moved.
DeliveryMethod
MO_223
Method used to deliver a compound for treatment.
DeprecatedTerms
concrete
ontology
MO_206
Class to hold deprecated instances and classes.
DeprecationReason
concrete
ontology
MO_94
class to hold instances used as the filler for the property has_reason_for_deprecation
DerivedBioAssay
concrete
mage
MO_209
A BioAssay that is created by the transformation of measured or derived BioAssays.
DescriptionPackage
abstract
mage
MO_167
MAGE package for description of annotations and references to annotations.
DesignElement
concrete
ontology
MO_173
Design elements are reporters, features, and composite elements as defined by MAGE.
DesignElementGroup
abstract
mage
MO_128
A DesignElementGroup holds information on Features, Reporters, or CompositeSequences.
DesignElementGroupType
concrete
ontology
MO_14
Controlled set of descriptors for indicating the specific type of a Feature, Reporter, or CompositeSequence.
DesignElementPackage
abstract
mage
MO_15
The MAGE package for describing the elements located on the array.
DevelopmentalStage
abstract
ontology
MO_120
The developmental stage of the organism's life cycle during which the biomaterial was extracted.
DevelopmentalStageDatabase
concrete
ontology
MO_215
Database of developmental stage information.
DiseaseLocation
concrete
ontology
MO_37
Anatomical location(s) of disease.
DiseaseStaging
abstract
ontology
MO_133
The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression.
DiseaseStagingDatabase
concrete
ontology
MO_225
Database of disease staging information
DiseaseState
abstract
ontology
MO_126
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.
DistanceUnit
concrete
ontology
MO_4
Units used for distance measurements.
DistanceUnitOther
place_holder
ontology
MO_143
Distance units not specified in MAGE.
Ecotype
abstract
ontology
MO_71
a biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler
EnvironmentalFactorCategory
concrete
ontology
MO_117
Factors that relate to properties of the environmental history of the biomaterial, its treatment, or its growth.
EnvironmentalHistory
abstract
ontology
MO_55
A description of the conditions the organism has been exposed to that are not one of the variables under study.
EnvironmentalStress
MO_227
Environmental stress is a treatment where some aspect of the environment is perturbed in order to stress the organism or culture, e.g. temperature shock, osmotic shock
EpidemiologicalDesign
concrete
ontology
MO_142
An epidemiological experiment design type is where the biosource history is studied e.g. environmental, clinical and family history.
Experiment
concrete
mage
MO_112
The complete set of bioassays (hybridizations) and their descriptions performed as an experiment for a common purpose. Here we take experiment to mean an observational or perturbing study. An experiment will be often equivalent to a publication.
ExperimentDesign
concrete
mage
MO_170
ExperimentDesign refers to both observational and experimental (perturbational) studies. The organizing principles of the study including the relationships between assays and the steps taken to interpret the data.
ExperimentDesignType
abstract
ontology
MO_158
The ExperimentDesignType is the high level description for studies such as "time series", "dose response", etc.
ExperimentalFactor
concrete
mage
MO_10
The factors in the study that are experimental parameters or regarded as influencing the experimental results.
ExperimentalFactorCategory
abstract
ontology
MO_205
A factor category describes factors which are examined in the experiment, e.g. disease_state, where the factor values are ALL and AML.
FactorValue
concrete
mage
MO_203
The value of an ExperimentFactor.
FailType
concrete
ontology
MO_98
Controlled terms for descriptors of failures (as in PCR) associated with reporters.
FamilyHistory
abstract
ontology
MO_59
Relevant aspects of genetic preconditions or family member's clinical history.
FamilyMember
abstract
ontology
MO_188
Member of the biosource's family.
FamilyRelationship
concrete
ontology
MO_36
A type of relationship applicable to mammals to describe the genetic relatedness of the individual under study. E.g. brother or mother.
FeatureDefect
concrete
mage
MO_138
A technical manufacturer described defect for features.
FeatureGroup
concrete
mage
MO_54
Technology-based grouping of features representing individual locations on the array.
FeatureShape
concrete
ontology
MO_8
The expected shape of the feature on the array.
Fiducial
concrete
mage
MO_136
A marking on the surface of the array that can be used to identify the origin of the array.
FiducialType
concrete
ontology
MO_17
A descriptor that indicates the type of the fiducial such as chrome border of an Affymetrix array or a laser ablation mark.
Generation
place_holder
ontology
MO_43
The number of cell passages if the organism or organism part that is cultured is unicellular or a cell culture otherwise the number of generations.
GeneticMaterial
MO_137
Genetic material may be DNA or RNA and identifiable as an entry in a public external database such as EMBL/DDBJ/GenBank or one of the model organism databases.
GeneticModification
concrete
ontology
MO_122
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.
Genotype
concrete
ontology
MO_51
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.
GeographicLocation
abstract
ontology
MO_132
A descriptor of the location from which a BioMaterial was obtained, e.g. country, region, grid reference.
GrowthCondition
abstract
ontology
MO_183
A description of the conditions used to grow organisms or parts of the organism. This includes isolated environments such as cultures and open environments such as field studies.
Haplotype
place_holder
ontology
MO_146
The genotype of a single chromosome (i.e., the haploid genotype) that is known and relevant to the experiment being performed.
Hardware
concrete
mage
MO_134
The machine or instrument used.
HardwareType
concrete
ontology
MO_113
Controlled terms for descriptors of types of hardware.
HardwareVariation
place_holder
ontology
MO_81
The effects of different hardware, types of hardware, or models of hardware on experimental results are studied.
HigherLevelAnalysisPackage
abstract
mage
MO_228
MAGE package for HigherLevelAnalysis
HigherLevelAnalysisProtocolType
concrete
ontology
MO_47
A protocol which yields a dataset(s) from which biological conclusions can be derived. E.g. clustering (not normalization or averaging).
Histology
abstract
ontology
MO_194
Microscopic morphology of tissues.
HistologyDatabase
concrete
ontology
MO_175
Database of histology information.
HistoryFactor
MO_82
Factors that are measured or observed parts of the study but not induced or under the control of the experiment. These factors do not have protocols (e.g., epidemiology factors).
Host
abstract
ontology
MO_101
Organisms or organism parts used as a designed part of the culture (e.g., red blood cells, stromal cells).
Humidity
abstract
ontology
MO_29
The humidity that the biosource is exposed to.
Image
concrete
mage
MO_22
ImageFormat
concrete
ontology
MO_211
Controlled terms for descriptors of the image file format (TIFF, JPEG, GIF, etc.)
Individual
place_holder
ontology
MO_169
Identifier or name of the individual organism from which the biomaterial was derived.
InitialTimePoint
concrete
ontology
MO_80
The point from which measurements of age were taken.
LabelCompound
concrete
ontology
MO_13
Compounds that are used for labeling extracts.
LabeledExtract
concrete
mage
MO_221
The BioSample after labeling for detection of the nucleic acids.
Light
abstract
ontology
MO_60
The photoperiod and type (e.g., natural, restricted wavelength) of light exposure.
LightUnit
concrete
ontology
MO_119
Units for measuring the intensity of light.
MGEDCoreOntology
abstract
ontology
MO_57
An ontology developed by the Microarray Gene Expression Data (MGED) Society to provide descriptors required for MAGE v.1 documents.
MGEDExtendedOntology
MO_196
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
MGEDOntology
abstract
ontology
MO_174
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.
MGEDOntologyVersion
concrete
ontology
MO_115
The version of the MGED Ontology.
MassUnit
concrete
ontology
MO_149
Units used for mass measurements.
MassUnitOther
place_holder
ontology
MO_11
Mass units not specified in MAGE.
MaterialType
concrete
ontology
MO_32
Controlled terms for the state of the BioMaterial. Each state (BioSource, different BioSamples, and LabeledExtract) have MaterialTypes. Examples are population of an organism, organism, organism part, cell, etc.
Measurement
concrete
mage
MO_144
Measured values and units.
MeasurementPackage
abstract
mage
MO_89
MAGE package for measurement.
MeasurementType
concrete
ontology
MO_72
class to hold instances used as the filler for the property has_measurement_type
Media
concrete
ontology
MO_19
The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil) .
MethodologicalDesign
concrete
ontology
MO_2
A methodological experiment design type investigates differences caused by application of protocols, hardware, software and bioassay relationships, e.g. quality control, replicates, loop.
MethodologicalFactorCategory
abstract
ontology
MO_85
The effects on results of changing protocols, hardware, software, or people performing the experiments are studied Examples are comparison of data across different labeling protocols, scanners, image quantification software, or laboratories.
Node
concrete
mage
MO_73
A node is an individual component of BioAssayDataCluster that groups design elements, quantitation types, and BioAssays together. A node may contain other nodes.
NodeValue
concrete
mage
MO_104
Node values allow the organization of the nodes in relation to other nodes produced by mathematical functions such as a clustering algorithm.
NormalizationDescription
abstract
ontology
MO_131
NormalizationDescription provides details of the normalization strategy for the experiment.
Nutrients
abstract
ontology
MO_127
The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.).
Observation
abstract
ontology
MO_53
Observation will record the macroscopic examination of the biomaterial.
ObservationDatabase
concrete
ontology
MO_91
Database of terms for observations such as 'abnormal coat', 'skin pigment abnormality' describing macroscopic examinations.
OntologyEntry
abstract
ontology
MO_87
External (to the MGED ontology) controlled vocabulary or ontology that can be referred such as ICD-9 or Gene Ontology.
OperatorVariation
place_holder
ontology
MO_38
The effects of different investigators, laboratories, or organizations on experimental results are studied.
Organism
abstract
ontology
MO_229
The genus and species (and subspecies) of the organism from which the biomaterial is derived from.
OrganismDatabase
concrete
ontology
MO_64
Database of taxonomic information.
OrganismPart
abstract
ontology
MO_1
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).
OrganismStatus
concrete
ontology
MO_84
The stage premortem or postmortem at which the sample was processed for extraction of biomaterials.
Organization
concrete
mage
MO_177
The organization (e.g. company, hospital) to contact to obtain or purchase something.
OtherUnit
concrete
ontology
MO_199
Other units are those types not specified in MAGE such as lumens, radioactivity, etc.
Parameter
concrete
mage
MO_110
A parameter is a variable within a protocol.
PathogenTest
abstract
ontology
MO_184
Tests and results for pathogens infecting organism from which the biosource is derived
Person
concrete
mage
MO_24
The individual to contact regarding something provided such as a biomaterial.
Phenotype
abstract
ontology
MO_192
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.
PhenotypeDatabase
concrete
ontology
MO_39
Database of phenotype information
PhysicalArrayDesign
concrete
mage
MO_212
Descriptions pertaining to the array.
PhysicalBioAssay
concrete
mage
MO_99
A physical bioassay is the combination of arrays and biomaterials as in a hybridization.
Ploidy
concrete
ontology
MO_220
The number of single sets of chromosomes in the cell or an organism e.g., haploid, diploid, triploid, etc.
PolymerType
concrete
ontology
MO_102
Controlled terms for descriptors of the type of polymer (RNA, DNA, protein) of the biosequence.
PopulationDensity
abstract
ontology
MO_46
The concentration range of the organism.
Preservation
MO_176
Method and type of preserving the organism or biosource (i.e. keeping it in stasis).
PreservationType
MO_195
The type of method used to preserve (keep in stasis) the organism or biosource.
Protocol
concrete
mage
MO_214
Documentation of the set of steps taken in a procedure.
ProtocolPackage
abstract
mage
MO_63
The MAGE package for protocols.
ProtocolParameterType
MO_164
Descriptors for protocol parameter types, e.g. compound concentration, media type.
ProtocolType
abstract
ontology
MO_150
A controlled set of terms to provide a descriptor for the type of protocol.
ProtocolVariation
MO_140
The effects of different protocols or changes in protocols on experimental results are studied.
PublicationType
concrete
ontology
MO_208
Controlled terms for descriptors of the type of publication such as those used by Medline (review, book, etc.).
QualityControlDescription
abstract
ontology
MO_88
QualityControlDescription provides details of the quality control aspects of the experiment.
QualityControlDescriptionType
concrete
ontology
MO_121
Controlled descriptors for the quality control strategy for an experiment.
QuantitationType
abstract
mage
MO_67
The QuantitationType provides a method for calculating a single datum of the BioAssayData matrix.
QuantitationTypePackage
abstract
mage
MO_130
The MAGE package for defining classes for quantitation.
QuantityUnit
concrete
ontology
MO_210
Units used for quantity measurements.
QuantityUnitOther
concrete
ontology
MO_156
Quantity units not specified in MAGE.
RadiationUnit
concrete
ontology
MO_204
Units for measuring decay of a radioactive isotope over time.
ReplicateDescription
abstract
ontology
MO_162
ReplicateDescription provides details about the type of replication used in the experiment.
ReplicateDescriptionType
concrete
ontology
MO_52
Controlled descriptors for the type of replication.
Reporter
concrete
mage
MO_74
Description of the material placed on a feature (spot).
Result
concrete
ontology
MO_65
class to hold instances used as the filler for the property has_result
Roles
concrete
ontology
MO_180
Controlled terms for descriptors of the role of contact, e.g. submitter, biosource_provider.
SamplingTimePoint
abstract
ontology
MO_139
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.
Scale
concrete
ontology
MO_108
The scale (linear, log10, ln, etc) used to represent the value.
SeqFeatureBasis
concrete
ontology
MO_207
Controlled terms for how the sequence features were determined (e.g., experimental, computational, etc.)
SequenceOntologyBioSequenceType
abstract
ontology
MO_25
Descriptors of biosequence based on the Sequence Ontology (SO) project.
SequenceOntologyDatabase
concrete
ontology
MO_83
Database for sequence annotation information.
Serotype
place_holder
ontology
MO_159
An antigenic property of a cell (e.g. bacteria, RBC) or virus identified by serological methods
Software
concrete
mage
MO_109
The software application used.
SoftwareType
concrete
ontology
MO_202
Controlled terms that provide descriptors for the type of software.
SoftwareVariation
place_holder
ontology
MO_222
The effects of different software, software packages, or software versions on experimental results are studied.
SomaticModification
MO_44
The organism has had non-genetic parts removed, added, or rearranged.
StrainOrLine
abstract
ontology
MO_9
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.
StrandType
MO_7
A descriptor of the strand type the sequence feature belongs to. e.g. forward, reverse
SubstrateType
concrete
ontology
MO_79
Controlled terms for descriptors of types of array substrates.
SurfaceType
concrete
ontology
MO_198
Controlled terms for descriptors for coating of the substrate.
TargetedCellType
abstract
ontology
MO_123
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.
TechnologicalDesign
concrete
ontology
MO_21
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.
TechnologyType
concrete
ontology
MO_18
The technology type or platform of the reporters on the array.
Temperature
abstract
ontology
MO_171
The temperature that a biosource is exposed to.
TemperatureUnit
concrete
ontology
MO_48
Units used for temperature measurements.
Test
abstract
ontology
MO_197
An assay performed on a biomaterial for the purposes of determining one or more biomaterial characteristics e.g. clinical chemistry.
TestResult
abstract
ontology
MO_96
TestResult is the recorded value of the test outcome.
TestType
abstract
ontology
MO_218
Descriptor of the Test performed e.g. Leukocyte count
TestTypeDatabase
concrete
ontology
MO_76
Database of codes for clinical findings.
TimeUnit
concrete
ontology
MO_166
Units used for time measurements.
TimeUnitOther
concrete
ontology
MO_103
Time units not specified in MAGE.
Transformation
MO_216
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
concrete
mage
MO_23
A treatment is the process or action by which a biomaterial is created from an input biomaterial.
TumorGrading
abstract
ontology
MO_28
A descriptor used in cancer biology to describe abnormalities of tumor cells. E.g. an instance from NCI Thesaurus.
URI
abstract
ontology
MO_12
Uniform Resource Identifier
Unit
abstract
ontology
MO_3
Units of measure.
User
MO_62
User is a way to id a person in a database
VolumeUnit
concrete
ontology
MO_179
Units used for volume measurements.
VolumeUnitOther
place_holder
ontology
MO_155
Volume units not specified in MAGE.
WarningType
concrete
ontology
MO_41
Controlled terms for descriptors of the warnings associated with reporters.
Water
abstract
ontology
MO_153
Water consumed by or enveloping the organism that the biosource is derived from.
ZoneDefect
concrete
mage
MO_105
A technical manufactured described defect for zones.
DIRECTED-BINARY-RELATION
PAL-CONSTRAINT
owl:Thing
MO_515
Angstrom, unit of distance, 1 angstrom is one tenth of a nanometer
http://www.atcc.org/Cultures/Products.cfm
MO_979
database resource for bacteria, bacteriophages, cell lines, fungi and yeast, plant tissue cultures, plant seeds, protozoa and algae and plant and animal viruses
http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/MA.ontology?rev=1.1&view=markup
MO_992
This ontology describes the anatomy of the adult mouse. It contains anatomical structures for the postnatal mouse (Theiler stage 28).
MO_786
A proprietary image data format that is lossless and containing one channel of data.
MO_649
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.
1.2.0
deleted_term
bacterial artificial chromosome
MO_985
sequence from a bacterial artificial chromosome
exact synonym: bacterial artificial chromosome
http://www.cabri.org/HyperCat/bact/all_A.htm
MO_1008
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.
http://www.cabri.org/HyperCat/fun/all_A.htm
MO_1009
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.
http://www.cabri.org/HyperCat/cells/hla.htm
MO_1005
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.
http://www.cabri.org/HyperCat/cells/all.htm
MO_536
Database entry from CABRI, a database listing sources such as cell lines, bacteria, plasmids etc.
http://www.cabri.org/HyperCat/cells/hybrid.htm
MO_1006
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.
http://www.cabri.org/HyperCat/yeast/all_A.htm
MO_1010
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.
http://www.cbil.upenn.edu/anatomy.php3
MO_886
a controlled vocabulary provided by CBIL
MO_1007
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.
http://portal.bioengineering.elyt.ods.org/ontology/
MO_967
Ontology describing anatomical and physiological relationships.
http://www.ebi.ac.uk/chebi
MO_857
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.
http://chem.sis.nlm.nih.gov/chemidplus
MO_426
Database entry from the ChemIDplus database which stores information on the structure, identifiers etc for compounds.
MO_642
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).
MO_739
fluorophore used for labeling/detection purposes
MO_646
fluorophore used for labeling/detection purposes
MO_945
Deoxyribonucleic acid.
MO_676
An instrument that produces DNA sequences.
http://genex.hgu.mrc.ac.uk
MO_357
The Edinburgh Mouse Atlas Project (EMAP) ontology of mouse developmental anatomy covers the 26 developmental stages (Theiler Stages) from fertilization to birth.
1.2.0
deleted_term
MO_412
Sequence derived from expressed sequence tag. EST's are likely to be partial, single read and low quality sequences.
MO_932
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).
MO_717
mating type indicating the presence of F plasmid in a bacterial cell
http://sig.biostr.wahington.edu/projects/fm/
MO_468
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.
MO_682
mating type indicating the absence of F plasmid in a bacterial cell
http://cvs.sourceforge.net/viewcvs.py/*checkout*/obo/obo/ontology/developmental/animal_development/fly/fly_development.ontology?content-type=text/plain&rev=1.1
MO_865
uri for FlyBase developmental stage terms
http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fly/
MO_504
curated database containing information on Drosophila genes, alleles etc
MO_963
Graphics Interchange Format , a common image data format containing RGB data compressed with fairly high data loss.
http://www.gramene.org/
MO_678
A Comparative Mapping Resource for Grains.
http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo
MO_1022
The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.
http://obo.sourceforge.net/list.shtml
MO_844
Ontology of human developmental anatomy for Carnegie stages 1-20.
1.1.7
deleted_term
MO_419
High frequency recombinant, mating type that indicates that the F plasmid has integrated into the chromosome
ftp://ftp.cdc.gov/pub/Health_Statistics/NCHS/Publications/ICD9-CM/2002
MO_654
Database entry from ICD 9 2001, international classification of diseases 9, clinical modification 2001.
International unit
UI
MO_1011
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.
http://www.iupac.org/publications/pac/2000/205/205olesen.html
MO_593
A resource of vocabularies for describing clinical tests, e.g. blood chemistry.
http://www.informatics.jax.org/external/festing/mouse/STRAINS.shtml
MO_369
Database entry from the resource at The Jackson Laboratory which has details of approved mouse strain nomenclature.
MO_746
Joint Photographic Experts Group format, a common image data format containing grayscale or RGB data compressed with little to high data loss.
MO_614
Kelvin, unit of temperature
MO_444
liter, unit of volume
http://www.loinc.org/download
MO_731
Database resource for universal identifiers for laboratory and other clinical observations
MO_936
Mole per liter or molarity, concentration unit
http://www.informatics.jax.org/mgihome/GXD/AD/
MO_693
database entry from mouse anatomical dictionary for developmental stage term
MO_782
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.
MO_653
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.
MO_938
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.
MO_756
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.
http://www.nlm.nih.gov/mesh/filelist.html
MO_580
database entry from MESH, medical subject headings vocabulary resource
http://tumor.informatics.jax.org
MO_942
Database entry from the mouse tumor biology database, a resource for nomenclature of mouse tumors.
http://www.informatics.jax.org/searches/Phat.cgi?id=MP:0000001
MO_704
A community effort to provide standard terms for annotating phenotypic data.
http://arabidopsis.info/catalogue.html
MO_379
The Nottingham Arabidopsis Stock Centre (NASC). Provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.
http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/
MO_773
identifier for a taxon provided by the NCBI taxonomy database
http://nciterms.nci.nih.gov
1.1.7
split_term
MO_456
A description logic namespace that contains controlled terminology used at NCI.
http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=12596
MO_687
a controlled vocabulary of cell types
http://nciterm.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C1908
MO_376
a controlled vocabulary for compounds
http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C28108
MO_422
a controlled vocabulary for disease stages
http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C7057
MO_790
a controlled vocabulary for disease states
http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C16632
MO_630
a controlled vocabulary for geographic locations
http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C4741
MO_537
a controlled vocabulary for histology
http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C13007
MO_690
a controlled vocabulary of organism parts
http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C16403
MO_397
a controlled vocabulary for strains or lines
http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12596
MO_351
a controlled vocabulary of targeted cell types
http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C28076
MO_819
a controlled vocabulary of tumor grading terms
1.2.0
deleted_term
MO_413
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.
1.2.0
deleted_term
MO_909
sequence from a P1 artificial chromosome
MO_915
Polymerase chain reaction. An element generated using this procedure.
1.2.0
deleted_term
MO_450
BioSequence generated by means of polymerase chain reaction
MO_358
Amplification of nucleic acid sequence by use of the polymerase chain reaction whereby the number of templates grows geometrically with each cycle.
MO_667
PCR where no products of any kind appear in gel-separated reaction products.
1.2.0
deleted_term
MO_651
single oligo used for polymerase chain reaction direction unspecified
1.2.0
deleted_term
MO_381
single stranded oligo used for polymerase chain reaction
1.2.0
deleted_term
MO_640
single stranded oligo used for polymerase chain reaction
MO_620
PCR with multiple bands, or smear, in gel-separated reaction products
MO_1001
Portable Network Graphic, a lossless image data format.
http://eulep.anat.cam.ac.uk/Search_Pathbase/index.php
MO_972
database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice
MO_632
The Pearson correlation is defined as the covariance of two data series divided by the product of their standard deviations.
MO_725
Roentgen. Unit of exposure to gamma or x-rays in the air. 1 R= 2.58E-4 coulombs per kg.
MO_987
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.
MO_594
Ribonucleic acid.
MO_553
A RNA stability experiment design type examines the stability and/or decay of RNA transcripts.
MO_585
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.
MO_908
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.
http://song.sourceforge.net/
MO_724
The Sequence Ontology is a set of terms used to describe features on a nucleotide or protein sequence.
MO_552
Computed as the ordinary Pearson correlation coefficient between two groups of rankings.
http://www.arabidopsis.org/servlets/Search?action=new_search&type=ecotype
MO_660
The Arabidopsis Information Resource.
http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/anatomy/gross_anatomy/plant_gross_anatomy/Arabidopsis/Attic/arabidopsis_anatomy.ontology
MO_809
A structured controlled vocabulary for the anatomy of Arabidopsis.
http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/developmental/plant_development/Arabidopsis/temporal.tair?rev=1.21&view=markup
MO_919
An ontology of stages of growth and development of the model plant Arabidopsis thaliana.
http://hazel.niehs.nih.gov/user_spt/pct_terms.htm
MO_718
Toxicology Data Management System, a database resource for systems, organs, pathology, etc.
MO_638
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.
http://www.nlm.nih.gov/research/umls/
MO_947
Database resource, unified medical language system, an ontology constructed by merging several disparate ontologies, available from NIH.
MO_875
units per liter
MO_388
units per week, e.g. the number of units of alcohol consumed over a period of 7 days
http://www.item.fraunhofer.de/reni/index/htm
MO_737
database entry from WebReni A resource for rat and mouse unified nomenclature describing lesions
1.2.0
deleted_term
MO_794
sequence from yeast artificial chromosome
MO_839
32 P, radioactive isotope of phosphorus used for labeling/detection purposes
MO_427
33 P, radioactive isotope of phosphorus, used for labeling/detection purposes.
MO_741
a measurement where the value is independent of other measurements
MO_776
The action of stabilizing an organism prior to treatment
MO_840
The mean and coefficient of variation values resulting from computationally combining 2 or more sets of bioassay data.
MO_671
The mean and associated p-values resulting from computationally combining 2 or more sets of bioassay data.
MO_946
The mean and standard deviation values resulting from computationally combining 2 or more sets of bioassay data.
MO_400
The mean and variance values resulting from computationally combining 2 or more sets of bioassay data.
MO_606
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.
MO_870
Units of defined biological activity, e.g. cytokine stimulation, per ml.
MO_592
A delivery method for compounds/drugs where the compound or drug is freely available.
MO_815
The procedure of placing one physical object in the same container/physical space as another.
MO_935
A type of solid media commonly used for growing organisms
MO_971
agar stab, a cell culture inoculated into agar for long term storage
MO_467
A descriptor for FactorValue where age is compared.
MO_512
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.
MO_401
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.
MO_446
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.
MO_375
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.
MO_493
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.
MO_736
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.
MO_461
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.
MO_345
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.
MO_547
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.
MO_799
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.
MO_565
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
MO_829
A record which describes and identifies an amino acid sequence which is encoded by a CDS from a primary_nucleic_acid_sequence_record
MO_747
a surface coating type for immobilization with the compound aminosilane
MO_977
attomole, quantity unit
MO_918
Describes a cell, nucleus or an organism whose chromosome number is not an exact multiple of the haploid number (n).
MO_833
glycoprotein of the immunoglobulin family that can combine specifically non-covalently, reversibly with a corresponding antigen
MO_502
Software to control an arrayer.
MO_890
Person or organization that manufactured the array.
MO_818
The process of physically creating the array.
MO_899
An experiment in which the array platform is compared, e.g. Agilent versus
Affy.
MO_824
An instrument capable of acquiring images of arrays.
MO_697
An instrument capable of manufacturing arrays by spotting material.
MO_498
The atmospheric conditions used to culture or grow an organism.
MO_354
The sister of one's father or mother.
MO_362
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.
MO_511
The rating of containment system used to protect organisms from infectious agents.
1.1.7
deleted_term
MO_615
The material (e.g. straw) that an animal sleeps on
MO_608
time point that indicates the start of some developmental stage
1.1.9
split_term
MO_532
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.
1.1.9
replaced_term
MO_766
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.
MO_674
The organism is forced to respond to a stimulus with some behavior (e.g., avoidance, obtaining a reward, etc.)
MO_923
A record which describes and identifies a paper publication e.g. a medline record
ChIP-chip
chromatin IP
chromatin immunoprecipitation
chromatin_immunoprecipitation
MO_933
A binding site identification design type investigates protein binding sites on nucleic acids
non-exact synonym: ChIP, chromatin immunoprecipitation, chromatin IP
normalization software
MO_672
Software used to transform the Measured or DerivedBioAssay data e.g. normalization.
Non-exact synonym: normalization software
MO_976
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.
MO_685
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.
MO_952
A replicate that consists of independent biological replicates made from different individual BioSources.
MO_989
A record which describes and identifies a biological resource such as a cone or strain e.g. an ATCC record Jax strain list
MO_591
Term used to describe a role or factor value for the person or organization that provides a BioMaterial.
MO_711
The process of removing tissue from a living organism.
MO_881
Provider of biosequences (clones, oligos etc) for deposition on the array.
MO_793
a compound used for labeling/detection purposes
MO_710
the action of emergence and separation of offspring from the mother.
1.1.9
deleted_term
MO_409
A biomaterial obtained as fluid consisting of plasma, blood cells and platelets.
MO_627
A publication type which has an ISBN.
MO_826
The values are either TRUE or FALSE, which can be expressed as 1 and 0.
MO_655
A male having the same genetic parents as another, or one genetic parent in common with another.
1.2.0
deleted_term
cDNA
complementary DNA
MO_966
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
candle power
MO_572
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
MO_813
Unit of brightness or luminance.
MO_834
a cubic centimeter, volume unit
MO_612
One or more dissociated cell(s) possibly heterogeneous, excluding single cell organisms.
MO_1019
A design in which RNA from different cell components is examined.
MO_822
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.
MO_562
A descriptor for FactorValue where CellLine is compared.
MO_903
cell lysate, a collection of cells whose membranes have been disrupted
http://cvs.sourceforge.net/views.py/obo/obo/ontology/anatomy/cell_type/cell.ontology?rev=HEAD&content-type=text/vnd.viewcvs-markup
MO_404
database of cell ontology terms
MO_548
A descriptor for FactorValue where CellType is compared.
MO_764
A cell type comparison design experiment design type compares cells of different type for example different cell lines.
MO_727
the number of cells per ml
RNAi
MO_392
A cellular modification design type is where a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.
MO_810
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.
MO_476
An instrument capable of applying centrifugal force to tubes or microtiter plates.
MO_788
the number of colony forming units per ml
change environment
change growth condition
MO_383
Indicates that one or more BioMaterialCharacteristics have changed during the treatment of a BioMaterial.
Non exact synonym: change growth condition, change environment
MO_917
The action of changing the relative humidity, e.g. from 1% to 10%.
MO_549
Change in light intensity or wavelength.
MO_677
Change in temperature.
MO_491
the chrome border on an Affymetrix type array which is used as a point of
reference for orientation (fiducial)
MO_922
The loss of a segment of the genetic material from a chromosome.
MO_1002
An irregularity in the number of chromosomes, usually in the form of a gain of genetic material.
MO_518
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.
MO_622
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.
MO_995
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.
MO_368
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.
1.2.0
deleted_term
MO_578
Physical or theoretical sequence of, or representing a chromosome, one of the DNA molecules that comprises the genome.
1.1.7
replaced_term
MO_539
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.
MO_832
A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied.
MO_816
A descriptor for FactorValue where ClinicalInformation is compared.
MO_852
record which describes and identifies clinical information about an organism
MO_384
A descriptor for a clinical treatment for a patient.
MO_371
Sequence from some nucleic acid copy and the associated vector for which the source clone supplier is unknown.
MO_418
Results of an analysis method that groups data based on a measure of similarity, e.g. Pearson correlation coefficient, Euclidean distance.
MO_464
Software used to cluster the data.
MO_837
centimeter, a unit of distance
guilt by association
MO_904
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
copulation
insemination
MO_783
the physical act of copulation that occurs during the process of sexual reproduction
synonyms: copulation, insemination
MO_789
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.
CGH
array CGH
array_CGH
MO_856
Experiment design type in which genomic content is studied using an array based assay.
MO_798
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.
MO_546
a record which describes and identifies a compound e.g. drug record part of NCI thesaurus
MO_555
A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.
MO_411
Computationally derived sequence feature.
MO_797
a record which describes and identifies an amino acid feature which is computationally derived e.g. PFAM
MO_774
A record which identifies and describes a nucleic sequence feature which has been computationally determined or predicted E.g. and Ensembl record
MO_765
a record which describes and identifies a protein structure e.g. PDB
MO_510
A device capable of applying software.
MO_883
Increasing the concentration of solutes in a solution or suspension.
MO_417
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.
1.3.1.1
deleted_term
MO_361
DNA sequence produced from some base calling or alignment algorithm which uses multiple sequence as input
1.3.1.1
deleted_term
MO_423
mRNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple sequences as input.
MO_778
A member of a consortium of institutions.
MO_984
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.
MO_940
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.
MO_505
A Reporter where only buffer was deposited on the array
MO_414
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.
MO_830
A Reporter where no material or buffer was deposited on the array
MO_449
A Reporter where genomic DNA has been deposited, the genomic DNA may be fragmented, e.g. salmon sperm DNA, Cot1DNA.
MO_385
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).
MO_708
Reporter used as a control where some label has been deposited. This includes fluor and radioactively labeled oligos and fluors alone.
MO_431
A Reporter of whose BioSequence is of known length used as a methodological control for hybridization efficiency.
MO_364
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.
MO_925
A Reporter indicated as being a control of unknown type.
MO_550
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.
1.2.0
deleted_term
MO_888
sequence from cosmid, a hybrid cloning vector containing cos sites, usually of ~40kB size
MO_500
Unit for a simple count of things
MO_348
counts per minute, unit of light emissions produced by ionizing radiation.
1.3.1.1
deleted_term
chloroplast DNA
MO_586
ctDNA: sequence from the chloroplast
synonym: chloroplast DNA
MO_451
A record which describes and identifies an amino acid sequence which has been curated
MO_913
A record which describes and identifies nucleic acid sequence which has been identified as a gene by a curator. e.g. Flybase gene record
MO_644
A record which identifies a nucleic acid sequence feature(s) and which has been curated.
MO_893
person who checks the consistency of the data and MAGE-ML file
MO_978
RNA obtained from the cytoplasm.
MO_753
A contact who performs data analysis, e.g. statistician.
MO_695
person who prepares the MAGE-ML file
MO_587
Time stated in terms of the day, month, and year.
MO_665
The female offspring of the patient or individual under study.
d
MO_513
24 hours, time unit
MO_389
Treatment to remove organisms present that were not planned as part of the study (e.g., mycoplasma).
MO_980
degrees celsius, unit of temperature
MO_812
degrees Fahrenheit, unit of temperature
MO_1023
The term was deleted from the MGED CoreOntology.
MO_892
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.
MO_878
A descriptor for FactorValue where DevelopmentalStage is compared.
MO_781
The diameter of the Feature is much smaller or much larger than expected based on the spotting pin diameter.
MO_874
An analysis aimed at identifying differentially expressed genes in two or more conditions.
MO_350
A software implementing a Higher Level Analysis protocol of type differential_expresssion.
MO_962
Decreasing the concentration of solutes in a solution or suspension.
MO_836
Describes a cell, nucleus or an organism with two copies of each chromosome.
MO_792
The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression.
MO_787
A descriptor for FactorValue where DiseaseState is compared.
MO_902
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.
MO_959
The Feature or Zone is displaced from its expected position, due to e.g. a bent spotting pin(s).
MO_374
The action of removing one or more organism parts.
MO_624
deciliter, unit of volume
MO_485
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).
MO_828
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.
MO_583
disintegrations per minute, unit of atom disintegrations per minute. dpm = (cpm - measured background)/efficiency. Efficiency is dependent on the radioisotope used and the instrument.
1.2.0
deleted_term
MO_344
a double stranded oligonucleotide
dye flip
flip dye
MO_858
An experiment design type where the label orientations are reversed.
exact synonym: flip dye, dye flip
MO_448
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.
MO_524
Indicates that a dye swap was performed for some or all hybridizations within an experiment
MO_901
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.
MO_750
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.
http://www.sanbi.ac.za/evoc/ontologies.html
MO_684
Ontology of human terms that describe the sample source of human cDNA and SAGE libraries.
MO_876
Emergence of an adult insect from its pupa or cocoon.
MO_767
The point at which the egg(s) is laid by an organism.
MO_523
protocol that describes how the features, reporters and composites were designed and or selected for inclusion in an array design
MO_459
The shape of the feature on the array is circular or oval.
MO_698
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.
MO_808
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.
1.3.1.1
deleted_term
MO_621
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.
1.2.0
deleted_term
MO_619
sequence which represents regions of a transcript that are joined to another exon during splicing
MO_516
Sequence features derived by both computational and experimental methods.
MO_755
A grouping of DesignElements, Features/Reporters/Composite Sequences which are expected to detect a signal in the biomaterial.
MO_452
An experimentally defined sequence feature.
MO_895
The BioSample immediately before labeling.
MO_898
femtomolar, concentration unit
MO_544
A family history design type is where the family history such as traits, characteristics, susceptibility to disease is studied
MO_762
A male parent.
image analysis
image quantification
MO_928
The process of obtaining quantifiable values from the scanned image of the
array. Exact synonyms: image analysis, image quantification
image analysis software
image quantification software
MO_633
Software to create MeasuredBioAssayData from images.
Exact Synonym: image analysis software, image quantification software.
1.1.9
deleted_term
MO_636
A biosource obtained as fecal matter.
MO_993
Delivery method where a compound/drug is administered in food or water.
MO_506
of, pertaining to, or designating the sex that only produces gametes that can be fertilized by male gametes.
MO_701
The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. (from the GO)
MO_732
femtogram, unit of mass
MO_625
Data from which a subset has been removed based on some criteria, e.g. data below an intensity threshhold.
MO_721
femtoliter, unit of volume
MO_1024
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).
MO_907
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.
MO_860
A value which is a floating point number (i.e. real number) with arbitrary precision (e.g. 2.34).
MO_689
femtomole, unit of quantity
+
MO_820
the forward strand
exact synonym: +
MO_872
The action of separating a BioMaterial into one or more fractions e.g. differential centrifugation or FACS when used for cell sorting (see purify).
MO_589
A biomaterial that has been lyophilized or dried by freezing under a vacuum.
MO_964
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.
MO_730
A sample freshly obtained from the organism(s). E.g. a liver freshly removed from a rat.
MO_610
A biomaterial obtained frozen
MO_481
Storage where the thing stored is stored below 0 degrees celsius.
MO_538
a record which identifies and describes the function of a gene product, e.g. E.C. record
MO_520
Contact which provides funding for experiments.
MO_825
gram, unit of mass
MO_805
grams per liter, concentration unit
1.2.0
deleted_term
MO_503
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
1.3.1.1
deleted_term
MO_853
sequence of part of a gene, which is missing one or both ends
MO_437
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.
MO_771
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.
MO_927
An action whereby an organism(s) has had genetic material removed, added, or rearranged.
MO_447
A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out
1.1.8
deleted_term
MO_557
A descriptor for FactorValue where GeneticVariation is compared.
MO_599
high molecular weight DNA
MO_609
increment in copy number of a genomic region, includes gene amplification, genomic amplification, and DNA amplification
MO_560
A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's.
MO_590
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).
MO_742
The array is made on a glass slide.
MO_582
grams per deciliter, concentration unit
MO_703
A daughter of one's son or daughter.
MO_478
The father of one's father or mother.
MO_924
The mother of one's father or mother.
MO_831
A son of one's son or daughter.
MO_758
A ComplexAction or ProtocolType describing growth of an organism or cell culture.
MO_588
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.
MO_595
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.
MO_719
Describes a cell, nucleus or an organism with one copy of each chromosome.
MO_763
Person or organization that manufactured the hardware.
MO_734
A hardware variation experiment design type compares different types of hardware for performance, reproducibility, accuracy and precision.
MO_982
The process of harvesting cells from culture.
MO_745
The point at which an organism emerges from an egg.
MO_663
A device for controlling temperature.
MO_571
The Zone is excluded due to smearing, streaking, or dense background in the Zone.
intersex
MO_356
an organism with both male and female sexual organs in one individual
synonym: intersex
MO_611
The action of preparing a slide for the microscopical examination of organism parts or cell types.
MO_714
An instrument which fragments tissues or other biomaterials.
h
MO_486
60 minutes, time unit
MO_884
The process of incubating one or more labeled extracts with an array.
MO_563
A chamber in which the hybridization is performed which maintains constant conditions.
MO_497
An instrument which controls hybridization conditions, into which a hybridization chamber may fit.
MO_929
The process of generating an image from the array.
scanning software
MO_1003
Software to control a scanner and manipulate and save images.
Exact synonym: scanning software
MO_691
A record which describes and identifies an image, e.g. an image from the mouse atlas
MO_914
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.
MO_733
Delivery method where a compound/drug is administered in the culture medium (e.g., for in vitro treatment).
MO_514
The TechnologyType of the FeatureGroup is manufactured using in situ methods such as photolithography (e.g. Affymetrix) or chemical synthesis (e.g. Agilent)
MO_347
An experiment done in a test tube or a culture dish, e.g.
A bacterial invasion assay in an established cell culture.
MO_454
An experiment design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model.
MO_744
a result which can not be interpreted as positive or negative
MO_965
The procedure of placing a physical object under specified conditions e.g. time, temperature, humidity for the purposes of obtaining a different product.
MO_639
A descriptor for FactorValue where BioSources are compared.
MO_722
A descriptor for FactorValue where IndividualGeneticCharacteristic is compared.
MO_527
An experiment design type where genotype, haplotype, or other individual genetic characteristics are compared.
MO_564
The modification of the genetic material (either coding or non-coding) of an organism by mutagenic compounds or irradiation.
1.3.0
replaced_term
MO_616
The organism (or organism part) has been exposed to a virus or pathogen.
MO_726
An injury experiment design type is where the response of an organism(s) to injury or damage is studied.
MO_355
A design in which the innate behavior of the organism is examined, e.g.
path finding in bees.
infect
MO_559
The process of introducing a foreign agent such as serum, vaccine, antigenic substance or organism.
MO_601
A contact's affiliation, e.g. university, research institute or business.
MO_435
A value which is a whole number (e.g. 10).
1.2.0
deleted_term
MO_463
sequence from the region between genes
MO_617
Delivery method for a compound or drug where the substance is administered via an injection into the muscle.
MO_473
A delivery method for compound or drug whereby the substance is administered via the peritoneum.
MO_432
delivery method whereby a compound or drug is administered via a vein
1.2.0
deleted_term
MO_709
sequence spliced out from a transcript
MO_769
Person who contributed to the study.
MO_770
treatment of a biomaterial with radiation e.g. electromagnetic radiation
MO_669
The perimeter of the spotted DNA on the slide is irregular.
MO_489
The clone used to originate the BioSequence which corresponds to the reporter was found to be contaminated (e.g. well-well contamination) on examination.
MO_487
A design aimed at identifying genes expressed in biomaterials of interest.
MO_957
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.
MO_784
The jackknife Pearson correlation is the lowest Pearson correlation between two data series where one pair of values in the data series are omitted.
MO_430
A article published in a print or online journal having an ISSN.
MO_869
katal per liter, catalytic-activity concentration unit
MO_846
kilogram, 1000 grams, unit of mass
kg/m2
MO_658
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
MO_471
The procedure of labeling a biosample.
MO_910
mark made on slide using a laser which is used as a point of reference for orientation (fiducial)
photoperiod
MO_604
The length of the light period that a sample is subjected to.
Exact synonym:photoperiod
MO_517
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.
Eberwine procedure
MO_997
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
MO_823
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.
MO_751
The scale is a standard base 10, non logarithmic scale.
MO_956
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.
MO_845
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.
MO_715
media type, usually some sort of broth
MO_868
Hardware for automated liquid transfer and handling.
MO_761
Software used to control automated liquid handler.
MO_712
An ordered, finite set of booleans.
MO_760
An ordered, finite set of floats.
MO_891
An ordered, finite set of integers.
MO_851
An ordered, finite set of negative floats.
MO_900
An ordered, finite set of negative integers.
MO_360
An ordered, finite set of nonnegative floats.
MO_973
An ordered, finite set of nonnegative integers.
MO_1000
An ordered, finite set of nonpositive floats.
MO_804
An ordered, finite set of nonpositive integers.
MO_777
An ordered, finite set of positive floats.
MO_873
An ordered, finite set of positive integers.
MO_800
An ordered, finite set of strings.
MO_443
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.
MO_377
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.
MO_428
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.
MO_521
Application of a scale adjustment following loess_group_normalization, to render the group variances similar.
MO_735
The values presented are logarithm, base 10.
MO_647
The values presented are logarithm, base 2.
MO_554
The values presented are logarithm, base e.
MO_896
Logarithmic transformation of ratio data.
MO_598
An element that is an oligonucleotide of at least 50 nucleotides in length.
circular design
MO_912
A loop experiment design is where labeled extracts are compared in consecutive pairs.
synonym: circular design
1.3.0
replaced_term
MO_706
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.
MO_692
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.
MO_861
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.
MO_720
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.
MO_410
Application of a scale adjustment following lowess_group_normalization, to render the group variances similar.
MO_603
The unit of total light output from a light source.
MO_573
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.
MO_367
meter, distance unit
MO_801
milliliters per liter, concentration unit
MO_509
milimolar, concentration unit
MO_661
osmolality per kilogram of water, concentration of the solute per unit of solvent
1.2.0
deleted_term
MO_803
sequence of a processed transcript capable of directing protein synthesis
MO_652
individual whose sex organs contain only male gametes
MO_567
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.
MO_659
Mating type of S. cerevisiae.
MO_637
Mating type of S. cerevisiae.
MO_407
Mating type of S.pombe.
MO_855
Mating type of S.pombe.
MO_425
the mean and coefficient of variation values resulting from computationally combining 2 or more sets of BioAssayData
1.2.0
deleted_term
MO_702
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.
MO_943
the mean and associated p-values resulting from computationally combining 2 or more sets of BioAssayData
MO_445
the mean and standard deviation values resulting from computationally combining 2 or more sets of BioAssayData
MO_458
the mean and variance values resulting from computationally combining 2 or more sets of BioAssayData
MO_398
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).
MO_657
Application of a normalization of type mean_log_centering.
MO_545
The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil)
MO_811
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).
MO_931
Application of a normalization of type median_log_centering.
MO_1025
the term has been subsumed into a more general term
MO_806
the organism part in which additional tumors are identified remote from the primary site
MO_949
milligram, mass unit
MO_353
milligram per kilogram per day
MO_522
milligrams per milliliter, concentration unit
MO_346
A record which describes and identifies a microarray experiment e.g. GEO
MO_526
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).
MO_584
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).
MO_848
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.
m
MO_877
60 seconds, unit of time
MO_405
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.
MO_700
Mix through the process of inverting.
MO_479
Mix by drawing up and down with a pipette.
MO_880
Mix through the use of a vortexer.
MO_944
The procedure of agitating 2 or more materials in order to combine them. The materials may be of any state solid/liquid/gas.
MO_528
a design element group consisting of multiple types
MO_436
A population of multiple sexes, e.g. a mixture of females and males, or males and hermaphrodites.
MO_488
milliliter, volume unit
MO_403
milliliter per kilogram
MO_648
millimeter, unit of distance
MO_998
mole, unit of quantity
MO_889
an unspecified collection of heterogeneous molecules, e.g. lipids, carbohydrate , nucleic acids and proteins
MO_707
number of molecules, quantity unit
1.1.9
replaced_term
MO_424
Absence of one chromosome of a pair of homologous chromosomes. In a normally diploid cell it is represented symbolically as 2N-1.
MO_631
Unit of time corresponding to approx. one cycle of the moon's phases.
MO_387
A female parent.
MO_681
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.
MO_920
millisecond, time unit
1.3.1.1
deleted_term
MO_581
sequence from the mitochondrial genome
MO_561
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.
MO_802
false or no
MO_728
A float that is < 0.
MO_864
An integer < 0.
MO_796
nanogram, a mass unit
MO_455
The array is made on a nitrocellulose filter.
MO_754
nanoliter unit of volume
MO_862
nanometer distance unit
MO_743
nanomoles, quantity unit
1.1.7
deleted_term
MO_556
false
MO_775
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.
MO_386
A float greater than or equal to 0.
MO_390
An integer >= 0.
MO_656
A float less than or equal to zero.
MO_623
An integer less than or equal to zero.
MO_729
A normalization testing experiment design tests different normalization procedures.
MO_994
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.
MO_664
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.
MO_894
The BioSample at any stage other than immediately before labeling.
MO_970
The sequence of the BioSequence that relates to this reporter has not been sequence verified by the experimenter.
MO_906
The source DNA for a Feature was not uniformly deposited.
MO_679
RNA obtained from the nucleus.
MO_607
The procedure of extracting nucleic acid from the biomaterial.
MO_757
A record which describes and identifies a primary sequence record e.g. DDBJ/EMBL/Genbank
MO_670
number of items or events per day
MO_867
The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.).
MO_492
The array is made on a nylon membrane.
MO_930
Hardware for synthesizing oligos.
MO_1028
A state or condition describing a cell or organism that has fewer copies of a single chromosome than the usual complement.
MO_991
A publication type which is available online and which is not an online journal article, e.g. a web site or service.
MO_529
A record which describes and identifies a term, class or instance in an ontology or controlled vocabulary e.g. ICD
http://www.opengalen.org/open/crm/crm-anatomy.html
MO_613
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.
MO_847
Software upon which other software runs.
MO_519
An operator variation experiment design type assesses the operator performance and relation to data consistency and quality.
1.2.0
deleted_term
MO_759
sequence which represents an operon, a unit of genetically linked genes displaying coordinated and regulated gene activity, originally described in prokaryotes
MO_772
An operon identification experiment type is designed to identify locations and members of operons in a genome.
MO_934
An optimization experiment design type is where different protocols or protocol parameters are compared.
MO_975
delivery method for drug or compound whereby the drug is administered via the mouth
MO_645
DNA from organelles such as the mitochondria or chloroplast.
MO_574
RNA obtained from an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus.
MO_508
one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria
MO_954
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).
MO_953
An organism part comparison experiment design type compares tissues, regions, organs within or between organisms
MO_871
The stage premortem or postmortem at which the sample was processed for extraction of biomaterials.
MO_841
A design that compares samples from live and dead organisms.
MO_814
potential of hydrogen
MO_628
picomolar, concentration unit
MO_990
A biomaterial obtained embedded in paraffin (wax).
MO_807
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.
MO_780
a record which identifies and describes biological pathways, e.g. a KEGG record
MO_558
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.
MO_969
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
MO_365
An experiment which has a peer reviewed publication attached.
MO_378
A measure of the density of an attached or monolayer culture (e.g., cell culture), e.g., 80 percent_confluence.
MO_482
A relative measurement of homogeneity of a biomaterial e.g. tumor biopsy.
MO_916
percentage volume per volume, concentration unit
MO_420
percent weight per volume, concentration unit
MO_474
percent weight per weight, concentration unit
MO_768
the number of plaque forming units per ml
MO_363
picogram, mass unit
MO_662
A record which describes and identifies the relationship between species and is
computationally determined and based on sequences e.g. Treebase record
MO_863
A descriptor for FactorValue where PhysicalCharacteristics are compared.
MO_1029
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.
MO_905
picoliter, volume unit
MO_470
The procedure of putting a physical object in a container/physical space.
MO_495
The act of placing a plant in media (e.g. soil) to allow it to grow. This excludes sowing.
1.2.0
deleted_term
MO_439
sequence from a plasmid, an extrachromosomal autonomously replicating piece of DNA excluding mitochondria and chloroplasts
MO_688
picomoles, quantity unit
mRNA
polyA+_RNA
MO_600
RNA which has been obtained by selection for polyA tracts.
Exact synonym: polyA+_RNA
Non-exact synonym: mRNA
MO_569
a surface coating for immobilization with the polypeptide, polylysine
1.2.0
deleted_term
MO_530
sequence of a protein, a linear amino acid polymer
MO_394
Describes a cell, nucleus or organism with three or more copies of each chromosome.
MO_1030
A state or condition describing a cell or organism that has more copies of a single chromosome than the usual complement.
combine
MO_779
The process of combining two or more BioMaterials.
Exact synonym: combine
MO_650
The concentration range of the organism.
MO_429
true or yes
MO_501
A float > 0.
MO_629
An integer > 0.
MO_416
biomaterial removed after the death of the organism
1.3.1.1
deleted_term
MO_838
gene sequence which has been computationally predicted
MO_705
sample which has been removed prior to the death of an organism
MO_415
The type of protocol used to preserve (including storage or keep in stasis) the biomaterial.
MO_785
A record which describes and identifies an experimentally derived protein structure e.g. MSD
MO_408
the organism part in which the tumor originated
1.2.0
deleted_term
MO_911
genomic sequence 5' to a gene where the transcription initiation complex forms.
MO_683
Polymer of amino acids.
MO_406
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).
MO_981
A quality control testing experiment design type is where some aspect of the experiment is quality controlled for the purposes of quality assurance
MO_951
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.
MO_457
Application of a normalization of type quantile_normalization.
1.2.0
deleted_term
ribosomal RNA gene
MO_955
sequence from gene coding for ribosomal RNA
exact synonym: ribosomal RNA gene
MO_597
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.
MO_349
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.
MO_434
A PCR based quantitative validation of a subset of the array based data used for experimental QC purposes.
MO_897
The shape of the feature on the array is rectangular.
MO_699
A reference experiment design type is where all samples are compared to a common reference.
MO_396
a measurement where the value is dependent on another measurement
MO_453
The amount of moisture in the air expressed as a percentage of the maximum amount the air is capable of holding.
MO_713
The procedure of extracting/taking out a part of a reaction/contents of a container.
MO_1026
The term name was changed to one more appropriate to the intent of the definition.
MO_433
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.
MO_885
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.
MO_466
The procedure in which solid material is dispensed or dissolved in a liquid.
-
MO_402
the reverse strand
exact synonym: -
MO_480
Generation of a DNA strand from an RNA strand using reverse transcriptase.
MO_986
A PCR based semi quantitative validation of a subset of the array based data used for experimental QC purposes.
MO_602
The procedure of euthanizing an organism.
MO_866
<pre>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</pre>
MO_391
time unit
MO_694
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.
MO_666
preservation type whereby the seed is maintained in a dormant state
MO_490
A self vs. self experiment design investigates variance and error estimates in the experimental system, and is where the same extract is compared.
MO_635
semisolid media type
MO_393
An action where the temperature is specified.
MO_680
A descriptor for FactorValue where Sex is compared.
MO_575
A sex experiment design type assays differences associated with an organism's sex, gender or mating type.
MO_749
An element that is an oligonucleotide of less than 50 nucleotides in length (usually 20 to 25 nt as in Affymetrix probes).
MO_534
A quantitative measure of the relative abundance of a transcript (MAS 4.0 version of the Affymetrix analysis software).
1.1.7
deleted_term
MO_941
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.
MO_382
the array is made on silicon
MO_576
a nucleic acid consisting of a single polynucleotide chain.
MO_723
A female having the same genetic parents as another, or one genetic parent in common with another.
1.2.0
deleted_term
MO_531
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.
1.2.0
deleted_term
deleted_term
small nuclear RNA gene
MO_961
sequence from gene coding for small nuclear RNA
exact synonym: small nuclear RNA gene
MO_475
Person or organization that manufactured the software.
MO_643
A software variation design type compares different types of software for performance, accuracy, precision and reproducibility.
MO_821
soil, growth media for plants and other soil living organisms
MO_465
The male offspring of the patient or individual under study.
MO_477
An instrument for sonicating biomaterials.
MO_748
the process of placing a seed or spore in some media with the intention to invoke germination.
MO_675
A species experiment design type assays differences between distinct species.
MO_395
A grouping of DesignElements, Features, Reporters, Composite Sequences on the basis of a common species.
MO_968
Conceptual action for specified protocol applied in treatment.
thermocycler
MO_716
Hardware for measuring light at different wavelengths.
MO_937
An experiment in which spikes were introduced into some or all of the hybridizations for quality control or data transformation purposes.
centrifuge
MO_879
The procedure of applying a centrifugal force to a physical object.
Exact synonym: centrifuge
sample
MO_835
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
MO_1027
the term has been decomposed into more specific terms
MO_483
TechnologyType of FeatureGroup where antibodies are spotted directly.
MO_618
TechnologyType of FeatureGroup where bacterial or other colonies are spotted directly.
MO_499
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.
MO_996
TechnologyType of FeatureGroup where protein (other than antibody) is spotted directly.
MO_921
A descriptor for the TechnologyType for a group of features where single stranded DNA PCR product is spotted on the array.
MO_579
The TechnologyType of the FeatureGroup is spotted single stranded oligonucleotides (of any length) on the substrate.
MO_817
The shape of the feature on the array is square.
1.2.0
deleted_term
MO_570
sequence of a single stranded synthesized oligonucleotide
MO_370
Depriving an organism of food or nutrients
MO_958
A design in which a behavior is invoked by a variable controlled by the experimenter - e.g. administration of a drug that effects aggressivity.
MO_568
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.
MO_442
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.
MO_859
A descriptor of FactorValue where comparisons of strains or lines are made.
MO_462
A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
MO_352
The values are a sequence of one or more characters.
MO_960
Delivery method whereby a drug or compound is administered under the skin of the organism.
MO_882
Person who is the primary contact for data submitted to a database.
cDNA
MO_577
DNA which is generated by chemical or enzymatic (non cellular) means.
non-exact synonym: cDNA
aRNA
amplified RNA
cRNA
complementary RNA
MO_543
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
1.2.0
deleted_term
transfer RNA gene
MO_850
sequence from a gene coding for transfer RNA
exact synonym: transfer RNA gene
1.1.7
deleted_term
MO_673
a nonparametric measure of the agreement between two rankings
MO_641
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.
MO_791
Temperature associated with a particular environment.
MO_854
An instrument designed to automatically raise and lower the temperature of wells or tubes. Usually used to perform PCR.
Exact Synonym: thermocycler
MO_507
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.
MO_887
Groups of assays that are related as part of a time series.
MO_738
Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point.
MO_373
Total cellular and nuclear RNA.
1.2.0
deleted_term
MO_441
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.
MO_686
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.
MO_472
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.
1.3.1.1
deleted_term
MO_827
sequence that represents the product of an RNA polymerase engaged in transcription
expression profiling
expression_profiling
gene expression
gene_expression
transcription profiling
transcription_profiling
MO_533
A transcript identification design type characterizes the length and
position of transcripts and allows identification of all forms of
transcripts in the genome.
MO_849
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.
MO_366
Introduction of genetic material into an organism often in the form of a plasmid.
MO_939
A translational bias is an experiment design which characterizes the association of transcripts and translation machinery.
1.1.9
replaced_term
MO_494
The possession of a third chromosome of any one type in an otherwise diploid cell.
MO_843
A descriptor used in cancer biology to describe abnormalities of tumor cells.
MO_740
Micromole per liter or micromolar, concentration unit
MO_438
microgram, unit of mass
MO_926
microliter, unit of volume
MO_421
micrometer, unit of distance
MO_752
micromoles, quantity unit
MO_974
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.
MO_950
The brother of one's father or mother.
MO_525
Sequence feature whose derivation is unknown.
MO_634
ExperimentDesignType of unknown type.
MO_460
ProtocolType of unknown type.
MO_535
BioSequence of unknown type
MO_999
organism(s) whose sex is unknown
MO_484
SubstrateType of unknown type.
MO_359
A SurfaceType of unknown type.
MO_542
The values are unordered and have no scale.
MO_399
The fluid and dissolved substances excreted by the kidney.
MO_795
microsecond, unit of time
MO_696
An instrument designed to remove excess liquid by vacuum and heating.
1.2.0
deleted_term
MO_551
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.
MO_1031
Version of the MGED Ontology.
MO_469
Version of the MGED Ontology.
MO_1032
Version of the MGEDOntology.
MO_1033
Version of the MGEDOntology.
MO_440
Version of the MGEDOntology.
MO_1034
Version of the MGED Ontology.
MO_372
one or more DNA or RNA based non cellular infective agent, including bacteriophage
MO_983
An instrument that mixes by rapid oscillation.
MO_988
Allow time to pass. It's measurement should be a unit of time.
MO_596
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.
MO_626
An instrument designed to mechanically wash or stain arrays.
MO_380
Water consumed by or enveloping the organism that the biosource is derived from.
MO_541
A device for controlling temperature by immersion in water.
MO_842
7 days, unit of time
MO_566
one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria
MO_605
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.
MO_668
A function applied to subsets of values from the same Measured/Derived bioassay data set.
MO_496
multiple of stock solution concentration, concentration unit
MO_948
365 days, time unit
1.1.7
deleted_term
MO_540
true
1.3.1.1
Chris Stoeckert, Helen Parkinson, Trish Whetzel, Paul Spellman, Catherine A. Ball, Joseph White, John Matese, Liju Fan, Gilberto Fragoso, Mervi Heiskanen, Susanna Sansone, Helen Causton, Laurence Game, Chris Taylor
February 9, 2007
Concepts, definitions, terms, and resources for standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1
An ontology for microarray experiments in support of MAGE v.1.
The MGED Ontology
1.3.1.1
BioMaterialCharacteristicCategory
MO_100
General descriptor of a BioMaterialCharacteristic category. Such as strain or line where the name of the strain or line is encoded in the FactorValue.
BioSourceType
concrete
ontology
MO_95
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.
BiologicalProperty
concrete
ontology
MO_224
A biological property experiment design type is where an intrinsic characteristic of an organism(s) or biological system is examined.
CellLineDatabase
concrete
ontology
MO_145
Database of cell line information.
ChromosomalAberration
abstract
ontology
1.1.7
some|has_chromosomal_aberration_classification|ChromosomalAberrationClassification
deleted_term
MO_78
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.
ChromosomalAberrationClassification
concrete
ontology
MO_6
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.
ClinicalTreatmentDatabase
concrete
ontology
MO_114
Database of clinical treatment information
ComplexAction
concrete
ontology
MO_90
Complex actions are composed of multiple steps (as opposed to AtomicAction) e.g. mRNA labeling, protein purification.
CompoundDatabase
concrete
ontology
MO_151
Database of compound information.
DataTransformationProtocolType
concrete
ontology
MO_165
The process by which derived BioAssays are created from measured BioAssays and/or derived BioAssays.
DerivedBioAssayType
concrete
ontology
MO_111
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.
DiseaseStateDatabase
concrete
ontology
MO_181
Database of disease state information.
ExperimentPackage
abstract
mage
MO_31
The descriptions associated with the Experiment package of MAGE
ExperimentalProtocolType
concrete
ontology
MO_75
All protocols which involve treatment of a biomaterial or an array during the course of a microarray experiment.
FactorValueDependency
place_holder
ontology
1.1.9
some|has_value|string
deleted_term
MO_148
A group of FactorValues which refer to the same condition used to treat or describe a BioMaterial, e.g. 10% glucose, 1 hour OR larval stage, age 24 hours.
FactorValueSet
place_holder
ontology
1.1.9
some|has_value|string
deleted_term
MO_217
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.
GeographicLocationDatabase
concrete
ontology
MO_35
Database of geographic locations.
IndividualChromosomalAbnormality
place_holder
ontology
1.2.0
deleted_term
MO_185
An abnormality in the number or structure of chromosomes in the biomaterial from an individual organism, detected by karyotyping or other methods. E.g., a B-cell lymphoma from a patient has an abnormal karyotype 48,XY,t(1;2)(p22;p11),+3,+12.
IndividualGeneticCharacteristics
abstract
ontology
MO_66
The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes.
NodeValueType
concrete
ontology
MO_160
Controlled set of terms for describing the type of values (e.g., Euclidean distance).
NormalizationDescriptionType
concrete
ontology
MO_27
Controlled descriptors for the normalization strategy used for the experiment.
OrganismPartDatabase
concrete
ontology
MO_200
Database of organism part information.
PerturbationalDesign
concrete
ontology
MO_106
A perturbational design type is where the organism(s) are treated or manipulated or modified, for example a genetic modification, somatic modification
PhysicalBioSequenceType
concrete
ontology
MO_92
A physical biosequence type represents biological sequence that can be physically placed (spotted or synthesized) on an array e.g. BAC, PAC.
Sex
concrete
ontology
MO_168
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.
StrainOrLineDatabase
concrete
ontology
MO_30
Database of strain, line, cultivar or ecotype information.
TargetedCellTypeDatabase
concrete
ontology
MO_45
Database of targeted cell type information.
TheoreticalBioSequenceType
concrete
ontology
MO_42
A theoretical biosequence type is an abstraction used for annotation design of elements, e.g. gene, intron.
TumorGradingDatabase
concrete
ontology
MO_187
Database of tumor grading information
MO_338
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.
MO_343
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.
MO_1014
The value of the property indicates what version of the ontology the term was deprecated from.
MO_1016
The value indicates the parent of the term before the term was deprecated.
MO_1015
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.
MO_1013
Indicates the why the term was deprecated. The possible values are: deleted_term, split_term, merged_term, replaced_term.
MO_1012
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.
MO_1018
The value of the property indicates the replacement term.
MO_1017
The value of the property indicates a replacement term since the term was split.
MO_333
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.
MO_331
A unique alphanumeric identifier for the term. This will exist in the form of MO_someNumber, e.g. MO_123.
2012-06-14
Dublin Core Metadata Element Set, Version 1.1
The guidelines for using names of persons or organizations as creators also apply to contributors. Typically, the name of a Contributor should be used to indicate the entity.
1999-07-02
An entity responsible for making contributions to the resource.
Contributor
A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/contributor) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.
Spatial topic and spatial applicability may be a named place or a location specified by its geographic coordinates. Temporal topic may be a named period, date, or date range. A jurisdiction may be a named administrative entity or a geographic place to which the resource applies. Recommended practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names [[TGN](https://www.getty.edu/research/tools/vocabulary/tgn/index.html)]. Where appropriate, named places or time periods may be used in preference to numeric identifiers such as sets of coordinates or date ranges.
1999-07-02
The spatial or temporal topic of the resource, spatial applicability of the resource, or jurisdiction under which the resource is relevant.
Coverage
A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/coverage) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.
Recommended practice is to use a controlled vocabulary where available. For example, for file formats one could use the list of Internet Media Types [[MIME](https://www.iana.org/assignments/media-types/media-types.xhtml)].
1999-07-02
The file format, physical medium, or dimensions of the resource.
Format
A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/format) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.
Recommended practice is to identify the resource by means of a string conforming to an identification system.
1999-07-02
An unambiguous reference to the resource within a given context.
Identifier
A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/identifier) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.
Recommended practice is to use either a non-literal value representing a language from a controlled vocabulary such as ISO 639-2 or ISO 639-3, or a literal value consisting of an IETF Best Current Practice 47 [[IETF-BCP47](https://tools.ietf.org/html/bcp47)] language tag.
1999-07-02
A language of the resource.
Language
A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/language) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.
Examples of a Publisher include a person, an organization, or a service. Typically, the name of a Publisher should be used to indicate the entity.
1999-07-02
An entity responsible for making the resource available.
Publisher
A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/publisher) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.
Recommended practice is to identify the related resource by means of a URI. If this is not possible or feasible, a string conforming to a formal identification system may be provided.
1999-07-02
A related resource.
Relation
A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/relation) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.
Typically, rights information includes a statement about various property rights associated with the resource, including intellectual property rights.
1999-07-02
Information about rights held in and over the resource.
Rights
A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/rights) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.
The described resource may be derived from the related resource in whole or in part. Recommended best practice is to identify the related resource by means of a string conforming to a formal identification system.
1999-07-02
A related resource from which the described resource is derived.
Source
A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/source) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.
Recommended practice is to use a controlled vocabulary such as the DCMI Type Vocabulary [[DCMI-TYPE](http://dublincore.org/documents/dcmi-type-vocabulary/)]. To describe the file format, physical medium, or dimensions of the resource, use the Format element.
1999-07-02
The nature or genre of the resource.
Type
A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/type) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.