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.