An ontology for microarray experiments in support of MAGE v.1. February 9, 2007 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 The MGED Ontology 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 1.3.1.1 ontology MO_26 concrete class to hold instances used as the filler for the property has_cancer_site Description of the source of the nucleic acid used to generate labeled material for the microarray experiment. MO_182 mage abstract ontology abstract 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. Water consumed by or enveloping the organism that the biosource is derived from. ontology abstract MO_153 The MAGE package for defining classes for quantitation. abstract mage MO_130 The developmental stage of the organism's life cycle during which the biomaterial was extracted. abstract MO_120 ontology Refers to the bedding material present in an animals housing. place_holder MO_154 ontology concrete mage A parameter is a variable within a protocol. MO_110 ontology concrete Database for sequence annotation information. MO_83 abstract MAGE package for measurement. MO_89 mage Database of tumor grading information ontology concrete MO_187 Measured values and units. mage concrete MO_144 MO_198 Controlled terms for descriptors for coating of the substrate. ontology concrete ontology class to hold instances used as the filler for the property has_result MO_65 concrete 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. concrete MO_213 ontology The expected shape of the feature on the array. concrete ontology MO_8 abstract ontology The BioMaterial's (i.e., the patient's) medical record as background information relevant to the experiment. MO_189 ontology MO_188 Member of the biosource's family. abstract Controlled terms for how the sequence features were determined (e.g., experimental, computational, etc.) MO_207 ontology concrete MO_40 BioAssayData refers to the data files including images generated from one or more BioAssays. Controlled terms for descriptors of the role of contact, e.g. submitter, biosource_provider. MO_180 concrete ontology MO_113 concrete Controlled terms for descriptors of types of hardware. ontology MO_226 mage Description of the processing state of the biomaterial for use in the microarray hybridization. abstract concrete ontology MO_156 Quantity units not specified in MAGE. 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. abstract MO_101 Organisms or organism parts used as a designed part of the culture (e.g., red blood cells, stromal cells). ontology ontology A descriptor of the location from which a BioMaterial was obtained, e.g. country, region, grid reference. abstract MO_132 MO_165 The process by which derived BioAssays are created from measured BioAssays and/or derived BioAssays. concrete ontology A methodological experiment design type investigates differences caused by application of protocols, hardware, software and bioassay relationships, e.g. quality control, replicates, loop. ontology MO_2 concrete ontology 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). abstract MO_178 place_holder MO_38 ontology The effects of different investigators, laboratories, or organizations on experimental results are studied. ontology abstract MO_162 ReplicateDescription provides details about the type of replication used in the experiment. ontology Physical properties of the BioMaterial e. g. mass or height abstract MO_129 ontology MO_41 Controlled terms for descriptors of the warnings associated with reporters. concrete concrete MO_6 ontology 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. concrete ontology MO_117 Factors that relate to properties of the environmental history of the biomaterial, its treatment, or its growth. MO_64 concrete ontology Database of taxonomic information. 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. ontology MO_174 abstract place_holder MO_169 ontology Identifier or name of the individual organism from which the biomaterial was derived. MO_136 mage A marking on the surface of the array that can be used to identify the origin of the array. concrete The value of an ExperimentFactor. mage concrete MO_203 MO_221 concrete The BioSample after labeling for detection of the nucleic acids. mage MO_109 concrete The software application used. 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. mage concrete concrete MO_30 Database of strain, line, cultivar or ecotype information. ontology MAGE package for BioAssayData. MO_186 An array group is a physical platform that contains one or more arrays that are separately addressable or a virtual grouping of arrays. MO_34 concrete mage MO_5 Properties of the biomaterial before treated in any manner for the purposes of the experiment. abstract ontology 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). abstract MO_152 ontology place_holder 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. ontology MO_43 MO_195 The type of method used to preserve (keep in stasis) the organism or biosource. ontology Microscopic morphology of tissues. abstract MO_194 A descriptor of the strand type the sequence feature belongs to. e.g. forward, reverse MO_7 mage concrete 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. MO_112 abstract MO_15 The MAGE package for describing the elements located on the array. mage Controlled terms for descriptors of the image file format (TIFF, JPEG, GIF, etc.) concrete ontology MO_211 mage A technical manufacturer described defect for features. concrete MO_138 mage MO_191 abstract MAGE package for biological sequences (biosequence). ontology concrete MO_160 Controlled set of terms for describing the type of values (e.g., Euclidean distance). The organism has had non-genetic parts removed, added, or rearranged. MO_44 place_holder The genotype of a single chromosome (i.e., the haploid genotype) that is known and relevant to the experiment being performed. ontology MO_146 Concentration units not specified in MAGE. ontology concrete MO_86 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. Uniform Resource Identifier MO_12 ontology abstract Controlled set of descriptors for the type of database record such as a protein record (in SWISS-PROT) or a gene object (in SGD). concrete ontology MO_157 mage The MAGE package for protocols. MO_63 abstract TestResult is the recorded value of the test outcome. ontology MO_96 abstract MO_31 The descriptions associated with the Experiment package of MAGE abstract mage Units used for volume measurements. concrete ontology MO_179 concrete MO_202 ontology Controlled terms that provide descriptors for the type of software. Controlled terms for descriptors of the type of publication such as those used by Medline (review, book, etc.). concrete MO_208 ontology mage Description of the material placed on a feature (spot). MO_74 concrete concrete MO_201 A bibliographic reference is a published citation in a journal, book, other format e.g. web resource mage Descriptor of the Test performed e.g. Leukocyte count ontology abstract MO_218 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). abstract MO_1020 ontology MO_185 MO_1033 Version of the MGEDOntology. ontology deleted_term The term was deleted from the MGED CoreOntology. MO_1023 1.2.0 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. place_holder mage MO_228 abstract MAGE package for HigherLevelAnalysis The genus and species (and subspecies) of the organism from which the biomaterial is derived from. abstract ontology MO_229 MAGE package that describes the array layout and design. The array may be physical or virtual. abstract MO_33 mage concrete MO_94 ontology class to hold instances used as the filler for the property has_reason_for_deprecation Identifiable resource containing data or external ontologies or controlled vocabularies which has uniquely identifiable records. ontology MO_118 abstract MO_168 ontology concrete 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. concrete 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. ontology abstract ontology MO_184 Tests and results for pathogens infecting organism from which the biosource is derived concrete MO_91 Database of terms for observations such as 'abnormal coat', 'skin pigment abnormality' describing macroscopic examinations. ontology The identifier for the established culture of a metazoan cell if one was used as a biomaterial. ontology abstract MO_49 MO_61 Units used for concentration measurements. concrete ontology MO_90 ontology Complex actions are composed of multiple steps (as opposed to AtomicAction) e.g. mRNA labeling, protein purification. concrete ontology MO_98 concrete Controlled terms for descriptors of failures (as in PCR) associated with reporters. MO_148 Version of the MGEDOntology. MO_1032 deleted_term 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. place_holder ontology 1.1.9 some|has_value|string MO_45 ontology concrete Database of targeted cell type information. Units used for mass measurements. concrete ontology MO_149 MO_55 ontology abstract A description of the conditions the organism has been exposed to that are not one of the variables under study. abstract The resource (e.g. company, hospital, geographical location) used to obtain or purchase the biomaterial. MO_230 ontology concrete MO_52 ontology Controlled descriptors for the type of replication. MAGE package for description of annotations and references to annotations. mage abstract MO_167 abstract MO_126 ontology 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. MO_46 ontology The concentration range of the organism. abstract Units used for time measurements. MO_166 concrete ontology A protocol which yields a dataset(s) from which biological conclusions can be derived. E.g. clustering (not normalization or averaging). concrete ontology MO_47 ontology An assay performed on a biomaterial for the purposes of determining one or more biomaterial characteristics e.g. clinical chemistry. MO_197 abstract MO_181 concrete Database of disease state information. ontology concrete MO_22 mage Controlled terms for descriptors of types of array substrates. MO_79 ontology concrete place_holder MO_155 ontology Volume units not specified in MAGE. A descriptor used in cancer biology to describe abnormalities of tumor cells. E.g. an instance from NCI Thesaurus. MO_28 abstract ontology ontology 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. concrete MO_58 MO_107 mage MAGE package for describing the process by which arrays were manufactured. abstract MO_214 mage concrete Documentation of the set of steps taken in a procedure. 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. MO_137 MO_19 The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil) . ontology concrete MO_73 mage concrete A node is an individual component of BioAssayDataCluster that groups design elements, quantitation types, and BioAssays together. A node may contain other nodes. MO_158 ontology abstract The ExperimentDesignType is the high level description for studies such as "time series", "dose response", etc. MO_77 concrete mage The BioSource is the original source material before any treatment events. The point from which measurements of age were taken. ontology MO_80 concrete class to hold instances used as the filler for the property has_measurement_type concrete MO_72 ontology MO_119 ontology Units for measuring the intensity of light. concrete abstract Rating of containment system for the protection of organisms from infectious agents. ontology MO_97 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. abstract External (to the MGED ontology) controlled vocabulary or ontology that can be referred such as ICD-9 or Gene Ontology. MO_87 ontology Units used for distance measurements. concrete MO_4 ontology Distance units not specified in MAGE. MO_143 place_holder ontology ontology The effects of different hardware, types of hardware, or models of hardware on experimental results are studied. MO_81 place_holder mage MO_116 A grouping of bioassay data that has been organized by one or more mathematical functions into nodes. concrete MO_176 Method and type of preserving the organism or biosource (i.e. keeping it in stasis). ontology concrete 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. MO_51 concrete The version of the MGED Ontology. MO_115 ontology 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. concrete ontology Database of developmental stage information. MO_215 abstract Organizations or individuals that may be contacted. MO_147 mage ontology abstract The humidity that the biosource is exposed to. MO_29 MO_163 mage A representation of a DNA, RNA, or protein sequence. concrete MO_205 ontology A factor category describes factors which are examined in the experiment, e.g. disease_state, where the factor values are ALL and AML. abstract MO_48 ontology concrete Units used for temperature measurements. concrete Controlled terms for descriptors for the type of control design element. MO_50 ontology ontology concrete Used to tell when the BioSample is an extract or not. MO_161 ontology concrete MO_121 Controlled descriptors for the quality control strategy for an experiment. ontology MO_224 A biological property experiment design type is where an intrinsic characteristic of an organism(s) or biological system is examined. concrete ontology concrete Database of disease staging information MO_225 A descriptor that indicates the type of the fiducial such as chrome border of an Affymetrix array or a laser ablation mark. ontology MO_17 concrete The number of single sets of chromosomes in the cell or an organism e.g., haploid, diploid, triploid, etc. concrete MO_220 ontology MO_75 All protocols which involve treatment of a biomaterial or an array during the course of a microarray experiment. concrete ontology mage A treatment is the process or action by which a biomaterial is created from an input biomaterial. MO_23 concrete MO_88 abstract QualityControlDescription provides details of the quality control aspects of the experiment. ontology Design elements are reporters, features, and composite elements as defined by MAGE. ontology concrete MO_173 MO_68 ontology An atomic action is a single step process on the biomaterial, e.g. mix by inversion, wait, add concrete A bioassay is an abstract class representing physical and computational groupings of biomaterials and arrays. MO_56 abstract mage concrete ontology MO_142 An epidemiological experiment design type is where the biosource history is studied e.g. environmental, clinical and family history. abstract MO_193 ontology Procedures used during treatment. 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. concrete abstract ontology 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. MO_139 Observation will record the macroscopic examination of the biomaterial. abstract MO_53 ontology concrete 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. ontology MO_32 MO_10 The factors in the study that are experimental parameters or regarded as influencing the experimental results. mage concrete The machine or instrument used. concrete mage MO_134 MO_84 ontology The stage premortem or postmortem at which the sample was processed for extraction of biomaterials. concrete concrete ontology MO_37 Anatomical location(s) of disease. The photoperiod and type (e.g., natural, restricted wavelength) of light exposure. MO_60 abstract ontology ontology MO_69 abstract The current clinical treatment(s) of the patient from which the biosource is derived. concrete Node values allow the organization of the nodes in relation to other nodes produced by mathematical functions such as a clustering algorithm. mage MO_104 concrete MO_175 Database of histology information. ontology ontology abstract MO_71 a biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler abstract ontology 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. MO_123 mage MO_54 Technology-based grouping of features representing individual locations on the array. concrete ontology abstract A drug, solvent, chemical, etc., with a property that can be measured such as concentration. MO_70 Database of compound information. concrete MO_151 ontology 1.1.7 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. deleted_term abstract MO_78 MO_1031 Version of the MGED Ontology. some|has_chromosomal_aberration_classification|ChromosomalAberrationClassification ontology abstract 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. MO_85 ontology MO_99 A physical bioassay is the combination of arrays and biomaterials as in a hybridization. concrete mage Units for measuring decay of a radioactive isotope over time. ontology MO_204 concrete MO_164 Descriptors for protocol parameter types, e.g. compound concentration, media type. Database of organism part information. ontology concrete MO_200 concrete MO_24 mage The individual to contact regarding something provided such as a biomaterial. 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. concrete ontology ontology Primitive data types found in computing languages such as float, boolean, etc. MO_125 concrete A controlled set of terms to provide a descriptor for the type of protocol. ontology abstract MO_150 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 abstract ontology 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_1 MO_159 An antigenic property of a cell (e.g. bacteria, RBC) or virus identified by serological methods place_holder ontology ontology The effects of different software, software packages, or software versions on experimental results are studied. place_holder MO_222 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. concrete MO_21 ontology concrete Time units not specified in MAGE. ontology MO_103 Units of measure. ontology abstract MO_3 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). MO_140 The effects of different protocols or changes in protocols on experimental results are studied. concrete ontology Class to hold deprecated instances and classes. MO_206 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. ontology MO_183 abstract ontology MO_76 concrete Database of codes for clinical findings. Controlled descriptors for the normalization strategy used for the experiment. ontology MO_27 concrete Controlled set of descriptors for indicating the specific type of a Feature, Reporter, or CompositeSequence. ontology concrete MO_14 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. concrete concrete MO_42 ontology A theoretical biosequence type is an abstraction used for annotation design of elements, e.g. gene, intron. mage MO_172 MAGE package for contacts including organizations and people. abstract MO_171 The temperature that a biosource is exposed to. ontology abstract concrete ontology Units used for quantity measurements. MO_210 abstract MO_219 The atmospheric conditions used to culture or grow an organism. ontology abstract MO_0 mage MAGE package for bioassay. A perturbational design type is where the organism(s) are treated or manipulated or modified, for example a genetic modification, somatic modification ontology concrete MO_106 mage MO_128 A DesignElementGroup holds information on Features, Reporters, or CompositeSequences. abstract concrete mage The BioSource after any treatment. MO_93 ontology MO_16 concrete Defects associated with features or zones such as those that are missing or moved. place_holder Mass units not specified in MAGE. MO_11 ontology deleted_term place_holder MO_217 1.1.9 some|has_value|string ontology 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. MO_141 Database of cell type information. concrete ontology ontology MO_133 The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression. abstract ontology Controlled terms for descriptors of the type of polymer (RNA, DNA, protein) of the biosequence. MO_102 concrete User is a way to id a person in a database MO_62 concrete ontology Database of phenotype information MO_39 abstract MO_66 The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. ontology ontology NormalizationDescription provides details of the normalization strategy for the experiment. MO_131 abstract MO_108 ontology The scale (linear, log10, ln, etc) used to represent the value. concrete ontology concrete Database of cell line information. MO_145 MO_223 Method used to deliver a compound for treatment. Factors that relate to properties of the biomaterial, its treatment, or its growth. ontology abstract MO_190 abstract MO_59 Relevant aspects of genetic preconditions or family member's clinical history. ontology ontology Other units are those types not specified in MAGE such as lumens, radioactivity, etc. MO_199 concrete MO_127 The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.). abstract ontology abstract MO_67 mage The QuantitationType provides a method for calculating a single datum of the BioAssayData matrix. MO_212 mage Descriptions pertaining to the array. concrete MO_114 Database of clinical treatment information concrete ontology 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. abstract A technical manufactured described defect for zones. concrete MO_105 mage mage concrete The organization (e.g. company, hospital) to contact to obtain or purchase something. MO_177 ontology concrete The technology type or platform of the reporters on the array. MO_18 a plant variety obtained in agriculture in horticulture abstract ontology MO_124 MO_13 concrete ontology Compounds that are used for labeling extracts. 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 ontology MO_57 abstract An ontology developed by the Microarray Gene Expression Data (MGED) Society to provide descriptors required for MAGE v.1 documents. MO_25 ontology abstract Descriptors of biosequence based on the Sequence Ontology (SO) project. ontology A resource for terms to describe cellular components, e.g. GO Cellular Component ontology. MO_1021 concrete 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. ontology concrete MO_111 ontology Database of geographic locations. MO_35 concrete A BioAssay that is created by the transformation of measured or derived BioAssays. MO_209 mage concrete MO_319 property indicating that the class has a type property indicating that the class has a factor value MO_236 property indicating that the class has an association to a MAGE description MO_260 property indicating that the class has a clinical finding MO_316 property indicating that the class has a nutrient component MO_321 property indicating that the class has a node value type MO_264 property to indicate the reason for deprecating a term MO_306 property indicating that the class has a measurement type MO_242 property indicating that the class has an ontology entry MO_263 MO_328 property indicating that the class has experiment factors property indicating that the class has a host MO_313 property indicating that the class has a height MO_317 MO_320 property indicating that the class has species MO_248 property indicating that the class has a cancer site MO_249 property indicating that the class has a category property indicating that the class has a chromosomal aberration classification MO_253 property indicating that the class has a mass MO_280 property indicating that the class has a clinical test MO_311 MO_252 property indicating that the class has bioassaydata MO_324 property indicating the class has a result property indicating that the class has a citation MO_274 MO_290 property indicating the location of the disease. MO_259 property indicating that the class has an atmospheric component property indicating that the class has an action MO_312 property indicating that the class has a family member MO_243 property indicating the version of the MGED Ontology that the term was deprecated from MO_299 MO_303 property indicating that the class has providers property indicating that the class has a compound MO_302 MO_257 property indicating that the class has a parent organization MO_314 property indicating that the class has an additive MO_269 property indicating that the class has units property indicating that the class has a modified part MO_241 property indicating that the class has a family relationship MO_250 MO_307 property indicating that the class has a node MO_291 property indicating that the class has an experiment design MO_232 property indicating that the class has a manufacturer property indicating that the class has a node value MO_310 MO_262 property indicating that the class has a treatment MO_265 property indicating that the class was tested for MO_304 instance property to indicate what the term was replaced by property indicating that the class has a database MO_233 property indicating that the class has disease staging MO_275 property indicating that the class has an experiment design type MO_288 MO_279 property indicating that the class is user defined MO_301 property indicating that the class has a diameter property indicating that the test has a test result MO_261 property indicating that the class has a feature shape MO_268 MO_267 property indicating that the class has fiducials property indicating that the class has individual genetic characteristics MO_254 property indicating that the class has a prior disease state MO_276 property indicating that the class has an individual MO_327 MO_240 property indicating that the class has a database entry type MO_244 property indicating that the test has a test protocol MO_273 property indicating that the protocol has a performer or contact person property indicating that the class has software MO_284 MO_285 property indicating that the class has an organism part property indicating that the class has a protocol MO_300 MO_286 property indicating that the class has hardware MO_297 property indicating that the class has a maximum measurement property indicating that the class has a disease state MO_305 MO_247 property indicating that the class has a clinical record property indicating that the class has an affiliation to an institution MO_309 property indicating that the class has a scale MO_287 property indicating that the class has an image format MO_234 MO_283 property indicating that the class has a host part property indicating that the class has a laboratory test MO_281 property indicating that the class has a property set MO_266 MO_238 property indicating that the class has bioassays MO_272 property indicating that the class has biomaterial characteristics MO_325 property indicating that the class has a measurement property indicating that the class has a clinical treatment MO_282 property indicating that the class contains a cubic volume measurement MO_245 property indicating that the class has an editor MO_256 MO_251 property indicating that the class has a publication MO_335 property indicating that the class has an order MO_296 property indicating that the class has a name property indicating that the class has an issue MO_294 property indicating that the class has a first name MO_258 property indicating that the class has an accession number version MO_339 MO_289 property indicating that the class has a fax property indicating that the class has an email address MO_293 MO_295 property indicating that the class has a publisher MO_323 property indicating that the class has an identifier MO_246 property indicating that the class has pages MO_271 property indicating that the class has a make property indicating that the class has a model MO_270 MO_330 property indicating that the contents found at this uri are human readable property indicating that the class has a phone MO_235 property indicating that the class has a version MO_239 property indicating that the class has a year MO_322 property indicating that the class has a value MO_326 property indicating that the class has a toll free phone MO_329 MO_334 property indicating that the class has a description property indicating that the class has an address MO_277 property indicating that the class has an accession number MO_231 MO_308 property indicating that the class has a volume property indicating that the class has a last name MO_255 property indicating that the class has text MO_298 property indicating that the contents found at this uri are machine readable (i.e. in a standard format) MO_336 property indicating that the class has a middle initials MO_237 property indicating that the class has a title MO_337 MO_318 property indicating that the class has authors property indicating that the class is a solvent MO_332 property indicating that the class has an owner MO_278 MO_342 property indicating that the class has a donor MO_341 property indicating that the class has been treated property indicating that the class has a URI MO_340 property indicating that the class has a biosource type MO_315 property indicating that the class has an individual time point MO_292 Graphics Interchange Format , a common image data format containing RGB data compressed with fairly high data loss. MO_963 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_1012 MO_767 The point at which the egg(s) is laid by an organism. A chamber in which the hybridization is performed which maintains constant conditions. MO_563 nanoliter unit of volume MO_754 MO_650 The concentration range of the organism. MO_905 picoliter, volume unit MO_696 An instrument designed to remove excess liquid by vacuum and heating. 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. MO_756 MO_527 An experiment design type where genotype, haplotype, or other individual genetic characteristics are compared. 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_902 MO_469 Version of the MGED Ontology. MO_581 deleted_term 1.3.1.1 sequence from the mitochondrial genome a measurement where the value is independent of other measurements MO_741 d 24 hours, time unit MO_513 MO_614 Kelvin, unit of temperature MO_825 gram, unit of mass deleted_term MO_463 sequence from the region between genes 1.2.0 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_1028 A state or condition describing a cell or organism that has fewer copies of a single chromosome than the usual complement. MO_674 The organism is forced to respond to a stimulus with some behavior (e.g., avoidance, obtaining a reward, etc.) 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_627 A publication type which has an ISBN. MO_498 The atmospheric conditions used to culture or grow an organism. An operon identification experiment type is designed to identify locations and members of operons in a genome. MO_772 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_669 The perimeter of the spotted DNA on the slide is irregular. An experiment in which the array platform is compared, e.g. Agilent versus Affy. MO_899 A delivery method for compound or drug whereby the substance is administered via the peritoneum. MO_473 Amplification of nucleic acid sequence by use of the polymerase chain reaction whereby the number of templates grows geometrically with each cycle. MO_358 The value of the property indicates a replacement term since the term was split. MO_1017 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. MO_417 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. Time stated in terms of the day, month, and year. MO_587 MO_865 uri for FlyBase developmental stage terms 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_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. Depriving an organism of food or nutrients MO_370 sample which has been removed prior to the death of an organism MO_705 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_1015 MO_629 An integer > 0. MO_952 A replicate that consists of independent biological replicates made from different individual BioSources. MO_740 Micromole per liter or micromolar, concentration unit MO_516 Sequence features derived by both computational and experimental methods. 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. Database resource for universal identifiers for laboratory and other clinical observations MO_731 http://www.loinc.org/download MO_797 a record which describes and identifies an amino acid feature which is computationally derived e.g. PFAM 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_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. The process of incubating one or more labeled extracts with an array. MO_884 MO_542 The values are unordered and have no scale. MO_430 A article published in a print or online journal having an ISSN. Reporter used as a control where some label has been deposited. This includes fluor and radioactively labeled oligos and fluors alone. MO_708 Database entry from the ChemIDplus database which stores information on the structure, identifiers etc for compounds. http://chem.sis.nlm.nih.gov/chemidplus MO_426 MO_847 Software upon which other software runs. A translational bias is an experiment design which characterizes the association of transcripts and translation machinery. MO_939 MO_918 Describes a cell, nucleus or an organism whose chromosome number is not an exact multiple of the haploid number (n). 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. A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. MO_462 MO_544 A family history design type is where the family history such as traits, characteristics, susceptibility to disease is studied A RNA stability experiment design type examines the stability and/or decay of RNA transcripts. MO_553 MO_926 microliter, unit of volume The value of the property indicates what version of the ontology the term was deprecated from. 1.1.7 1.1.9 1.3.1.1 1.3.0 1.1.8 1.2.0 MO_1014 MO_500 Unit for a simple count of things Person who contributed to the study. MO_769 MO_991 A publication type which is available online and which is not an online journal article, e.g. a web site or service. deleted_term 1.2.0 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. MO_531 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_499 MO_451 A record which describes and identifies an amino acid sequence which has been curated MO_726 An injury experiment design type is where the response of an organism(s) to injury or damage is studied. The values are a sequence of one or more characters. MO_352 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_489 MO_929 The process of generating an image from the array. A population of multiple sexes, e.g. a mixture of females and males, or males and hermaphrodites. MO_436 liter, unit of volume MO_444 MO_796 nanogram, a mass unit MO_631 Unit of time corresponding to approx. one cycle of the moon's phases. 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_401 MO_365 An experiment which has a peer reviewed publication attached. 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://arabidopsis.info/catalogue.html MO_819 http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C28076 a controlled vocabulary of tumor grading terms MO_856 Experiment design type in which genomic content is studied using an array based assay. array_CGH array CGH CGH A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied. MO_832 thermocycler MO_716 Hardware for measuring light at different wavelengths. a controlled vocabulary for compounds MO_376 http://nciterm.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C1908 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_345 MO_949 milligram, mass unit 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_994 A descriptor for FactorValue where GeneticVariation is compared. 1.1.8 deleted_term MO_557 A record which identifies a nucleic acid sequence feature(s) and which has been curated. MO_644 MO_757 A record which describes and identifies a primary sequence record e.g. DDBJ/EMBL/Genbank Database entry from CABRI, a database listing sources such as cell lines, bacteria, plasmids etc. http://www.cabri.org/HyperCat/cells/all.htm MO_536 MO_626 An instrument designed to mechanically wash or stain arrays. http://tumor.informatics.jax.org MO_942 Database entry from the mouse tumor biology database, a resource for nomenclature of mouse tumors. An instrument which controls hybridization conditions, into which a hybridization chamber may fit. MO_497 the mean and variance values resulting from computationally combining 2 or more sets of BioAssayData MO_458 An experiment in which spikes were introduced into some or all of the hybridizations for quality control or data transformation purposes. MO_937 http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12596 a controlled vocabulary of targeted cell types MO_351 MO_564 The modification of the genetic material (either coding or non-coding) of an organism by mutagenic compounds or irradiation. MO_484 SubstrateType of unknown type. MO_403 milliliter per kilogram MO_384 A descriptor for a clinical treatment for a patient. http://www.cabri.org/HyperCat/yeast/all_A.htm 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. MO_1010 MO_967 http://portal.bioengineering.elyt.ods.org/ontology/ Ontology describing anatomical and physiological relationships. 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_861 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_642 micromoles, quantity unit MO_752 the term has been decomposed into more specific terms MO_1027 MO_809 A structured controlled vocabulary for the anatomy of Arabidopsis. http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/anatomy/gross_anatomy/plant_gross_anatomy/Arabidopsis/Attic/arabidopsis_anatomy.ontology Database resource, unified medical language system, an ontology constructed by merging several disparate ontologies, available from NIH. http://www.nlm.nih.gov/research/umls/ MO_947 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. Delivery method for a compound or drug where the substance is administered via an injection into the muscle. MO_617 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_364 Sequence feature whose derivation is unknown. MO_525 intersex MO_356 an organism with both male and female sexual organs in one individual synonym: intersex http://www.cbil.upenn.edu/anatomy.php3 a controlled vocabulary provided by CBIL MO_886 deleted_term 1.3.1.1 MO_361 DNA sequence produced from some base calling or alignment algorithm which uses multiple sequence as input A grouping of DesignElements, Features, Reporters, Composite Sequences on the basis of a common species. MO_395 MO_658 kg/m2 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 potential of hydrogen MO_814 The rating of containment system used to protect organisms from infectious agents. MO_511 MO_575 A sex experiment design type assays differences associated with an organism's sex, gender or mating type. The action of changing the relative humidity, e.g. from 1% to 10%. MO_917 an unspecified collection of heterogeneous molecules, e.g. lipids, carbohydrate , nucleic acids and proteins MO_889 MO_449 A Reporter where genomic DNA has been deposited, the genomic DNA may be fragmented, e.g. salmon sperm DNA, Cot1DNA. MO_950 The brother of one's father or mother. MO_482 A relative measurement of homogeneity of a biomaterial e.g. tumor biopsy. MO_691 A record which describes and identifies an image, e.g. an image from the mouse atlas MO_538 a record which identifies and describes the function of a gene product, e.g. E.C. record The value of the property indicates the replacement term. MO_1018 1.2.0 deleted_term 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_551 MO_717 mating type indicating the presence of F plasmid in a bacterial cell 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. 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. 1.3.0 The organism (or organism part) has been exposed to a virus or pathogen. MO_559 The process of introducing a foreign agent such as serum, vaccine, antigenic substance or organism. infect MO_440 Version of the MGEDOntology. replaced_term The term name was changed to one more appropriate to the intent of the definition. MO_1026 MO_616 MO_803 sequence of a processed transcript capable of directing protein synthesis deleted_term 1.2.0 MO_492 The array is made on a nylon membrane. An irregularity in the number of chromosomes, usually in the form of a gain of genetic material. MO_1002 MO_723 A female having the same genetic parents as another, or one genetic parent in common with another. An experiment done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture. MO_347 percent weight per volume, concentration unit MO_420 MO_893 person who checks the consistency of the data and MAGE-ML file TechnologyType of FeatureGroup where protein (other than antibody) is spotted directly. MO_996 An experimentally defined sequence feature. MO_452 A Reporter of whose BioSequence is of known length used as a methodological control for hybridization efficiency. MO_431 MO_894 The BioSample at any stage other than immediately before labeling. MO_864 An integer < 0. http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C7057 MO_790 a controlled vocabulary for disease states The action of stabilizing an organism prior to treatment MO_776 MO_679 RNA obtained from the nucleus. MO_897 The shape of the feature on the array is rectangular. micrometer, unit of distance MO_421 time point that indicates the start of some developmental stage MO_608 MO_394 Describes a cell, nucleus or organism with three or more copies of each chromosome. Mating type of S.pombe. MO_407 The values presented are logarithm, base e. MO_554 femtomolar, concentration unit MO_898 MO_859 A descriptor of FactorValue where comparisons of strains or lines are made. complementary RNA cRNA aRNA amplified RNA 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 MO_543 MO_476 An instrument capable of applying centrifugal force to tubes or microtiter plates. MO_607 The procedure of extracting nucleic acid from the biomaterial. a controlled vocabulary for strains or lines MO_397 http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C16403 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_938 MO_637 Mating type of S. cerevisiae. A record which describes and identifies a biological resource such as a cone or strain e.g. an ATCC record Jax strain list MO_989 MO_422 http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C28108 a controlled vocabulary for disease stages one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria MO_566 http://obo.sourceforge.net/list.shtml MO_844 Ontology of human developmental anatomy for Carnegie stages 1-20. MO_331 A unique alphanumeric identifier for the term. This will exist in the form of MO_someNumber, e.g. MO_123. the mean and standard deviation values resulting from computationally combining 2 or more sets of BioAssayData MO_445 MO_873 An ordered, finite set of positive integers. MO_524 Indicates that a dye swap was performed for some or all hybridizations within an experiment the term has been subsumed into a more general term MO_1025 An ordered, finite set of nonpositive floats. MO_1000 A proprietary image data format that is lossless and containing one channel of data. MO_786 MO_763 Person or organization that manufactured the hardware. MO_594 Ribonucleic acid. 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. MO_855 Mating type of S.pombe. MO_457 Application of a normalization of type quantile_normalization. Version of the MGED Ontology. MO_1034 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_958 MO_609 increment in copy number of a genomic region, includes gene amplification, genomic amplification, and DNA amplification MO_852 record which describes and identifies clinical information about an organism 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_798 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. 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_974 MO_534 A quantitative measure of the relative abundance of a transcript (MAS 4.0 version of the Affymetrix analysis software). 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. MO_760 An ordered, finite set of floats. 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_493 A binding site identification design type investigates protein binding sites on nucleic acids non-exact synonym: ChIP, chromatin immunoprecipitation, chromatin IP MO_933 chromatin immunoprecipitation chromatin IP chromatin_immunoprecipitation ChIP-chip MO_615 The material (e.g. straw) that an animal sleeps on deleted_term 1.1.7 scanning software MO_1003 Software to control a scanner and manipulate and save images. Exact synonym: scanning software Roentgen. Unit of exposure to gamma or x-rays in the air. 1 R= 2.58E-4 coulombs per kg. MO_725 A community effort to provide standard terms for annotating phenotypic data. http://www.informatics.jax.org/searches/Phat.cgi?id=MP:0000001 MO_704 MO_941 1.1.7 deleted_term 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_460 ProtocolType of unknown type. MO_523 protocol that describes how the features, reporters and composites were designed and or selected for inclusion in an array design MO_427 33 P, radioactive isotope of phosphorus, used for labeling/detection purposes. degrees celsius, unit of temperature MO_980 MO_920 millisecond, time unit RNA obtained from the cytoplasm. MO_978 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. A Reporter where no material or buffer was deposited on the array MO_830 http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ MO_773 identifier for a taxon provided by the NCBI taxonomy database MO_713 The procedure of extracting/taking out a part of a reaction/contents of a container. 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_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_853 sequence of part of a gene, which is missing one or both ends 1.3.1.1 deleted_term Allow time to pass. It's measurement should be a unit of time. MO_988 http://sig.biostr.wahington.edu/projects/fm/ 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_468 MO_645 DNA from organelles such as the mitochondria or chloroplast. 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_883 Increasing the concentration of solutes in a solution or suspension. MO_687 a controlled vocabulary of cell types http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=12596 Treatment to remove organisms present that were not planned as part of the study (e.g., mycoplasma). MO_389 Application of a normalization of type mean_log_centering. MO_657 MO_571 The Zone is excluded due to smearing, streaking, or dense background in the Zone. Water consumed by or enveloping the organism that the biosource is derived from. MO_380 MO_983 An instrument that mixes by rapid oscillation. MO_881 Provider of biosequences (clones, oligos etc) for deposition on the array. MO_888 1.2.0 sequence from cosmid, a hybrid cloning vector containing cos sites, usually of ~40kB size deleted_term 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_1024 A biomaterial obtained as fluid consisting of plasma, blood cells and platelets. 1.1.9 deleted_term MO_409 A Reporter where only buffer was deposited on the array MO_505 A descriptor for FactorValue where DiseaseState is compared. MO_787 1.3.1.1 gene sequence which has been computationally predicted MO_838 deleted_term MO_744 a result which can not be interpreted as positive or negative A PCR based quantitative validation of a subset of the array based data used for experimental QC purposes. MO_434 A device for controlling temperature by immersion in water. MO_541 milliliter, volume unit MO_488 The values presented are logarithm, base 10. MO_735 MO_948 365 days, time unit Delivery method whereby a drug or compound is administered under the skin of the organism. MO_960 The mean and variance values resulting from computationally combining 2 or more sets of bioassay data. MO_400 microgram, unit of mass MO_438 A record which describes and identifies a term, class or instance in an ontology or controlled vocabulary e.g. ICD MO_529 MO_1006 http://www.cabri.org/HyperCat/cells/hybrid.htm 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. MO_665 The female offspring of the patient or individual under study. MO_971 agar stab, a cell culture inoculated into agar for long term storage MO_700 Mix through the process of inverting. split_term A design in which the innate behavior of the organism is examined, e.g. path finding in bees. MO_355 1.1.9 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. Person or organization that manufactured the array. MO_890 MO_677 Change in temperature. http://www.informatics.jax.org/mgihome/GXD/AD/ MO_693 database entry from mouse anatomical dictionary for developmental stage term MO_707 number of molecules, quantity unit 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_739 fluorophore used for labeling/detection purposes The process of obtaining quantifiable values from the scanned image of the array. Exact synonyms: image analysis, image quantification image analysis image quantification MO_928 deleted_term sequence which represents an operon, a unit of genetically linked genes displaying coordinated and regulated gene activity, originally described in prokaryotes MO_759 1.2.0 An ordered, finite set of nonnegative floats. MO_360 MO_804 An ordered, finite set of nonpositive integers. The type of protocol used to preserve (including storage or keep in stasis) the biomaterial. MO_415 centrifuge The procedure of applying a centrifugal force to a physical object. Exact synonym: centrifuge MO_879 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. 1.3.1.1 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. place_holder concrete abstract 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_338 An integer less than or equal to zero. MO_623 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. MO_750 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. 1.1.9 femtoliter, unit of volume MO_721 MO_968 Conceptual action for specified protocol applied in treatment. deciliter, unit of volume MO_624 The procedure of putting a physical object in a container/physical space. MO_470 MO_779 The process of combining two or more BioMaterials. Exact synonym: combine combine MO_711 The process of removing tissue from a living organism. MO_826 The values are either TRUE or FALSE, which can be expressed as 1 and 0. <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_866 MO_746 Joint Photographic Experts Group format, a common image data format containing grayscale or RGB data compressed with little to high data loss. Emergence of an adult insect from its pupa or cocoon. MO_876 Polymerase chain reaction. An element generated using this procedure. MO_915 The process of physically creating the array. MO_818 MO_582 grams per deciliter, concentration unit MO_600 mRNA polyA+_RNA RNA which has been obtained by selection for polyA tracts. Exact synonym: polyA+_RNA Non-exact synonym: mRNA An action whereby an organism(s) has had genetic material removed, added, or rearranged. MO_927 soil, growth media for plants and other soil living organisms MO_821 MO_591 Term used to describe a role or factor value for the person or organization that provides a BioMaterial. A male having the same genetic parents as another, or one genetic parent in common with another. MO_655 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. MO_857 http://www.ebi.ac.uk/chebi Delivery method where a compound/drug is administered in food or water. MO_993 MO_548 A descriptor for FactorValue where CellType is compared. 1.1.9 A state or condition describing a cell or organism that has more copies of a single chromosome than the usual complement. MO_1030 MO_494 replaced_term The possession of a third chromosome of any one type in an otherwise diploid cell. MO_576 a nucleic acid consisting of a single polynucleotide chain. MO_359 A SurfaceType of unknown type. 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_604 photoperiod The length of the light period that a sample is subjected to. Exact synonym:photoperiod An experiment design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model. MO_454 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. milligrams per milliliter, concentration unit MO_522 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_512 http://www.item.fraunhofer.de/reni/index/htm MO_737 database entry from WebReni A resource for rat and mouse unified nomenclature describing lesions bacterial artificial chromosome sequence from a bacterial artificial chromosome exact synonym: bacterial artificial chromosome MO_985 1.2.0 deleted_term Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point. MO_738 MO_411 Computationally derived sequence feature. MO_562 A descriptor for FactorValue where CellLine is compared. 1.2.0 small nuclear RNA gene sequence from gene coding for small nuclear RNA exact synonym: small nuclear RNA gene MO_961 deleted_term deleted_term MO_643 A software variation design type compares different types of software for performance, accuracy, precision and reproducibility. MO_535 BioSequence of unknown type 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_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_515 Angstrom, unit of distance, 1 angstrom is one tenth of a nanometer MO_911 1.2.0 genomic sequence 5' to a gene where the transcription initiation complex forms. deleted_term MO_831 A son of one's son or daughter. MO_659 Mating type of S. cerevisiae. A sample freshly obtained from the organism(s). E.g. a liver freshly removed from a rat. MO_730 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. 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_613 http://www.opengalen.org/open/crm/crm-anatomy.html The action of removing one or more organism parts. MO_374 MO_367 meter, distance unit 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_526 The values presented are logarithm, base 2. MO_647 the action of emergence and separation of offspring from the mother. MO_710 MO_701 The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. (from the GO) MO_867 The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.). MO_794 deleted_term 1.2.0 sequence from yeast artificial chromosome 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_828 A descriptor for FactorValue where Sex is compared. MO_680 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_357 The Edinburgh Mouse Atlas Project (EMAP) ontology of mouse developmental anatomy covers the 26 developmental stages (Theiler Stages) from fertilization to birth. http://genex.hgu.mrc.ac.uk The procedure of euthanizing an organism. MO_602 A biomaterial obtained frozen MO_610 MO_749 An element that is an oligonucleotide of less than 50 nucleotides in length (usually 20 to 25 nt as in Affymetrix probes). A contact who performs data analysis, e.g. statistician. MO_753 A male parent. MO_762 Temperature associated with a particular environment. MO_791 An instrument capable of acquiring images of arrays. MO_824 MO_682 mating type indicating the absence of F plasmid in a bacterial cell MO_1016 The value indicates the parent of the term before the term was deprecated. MO_663 A device for controlling temperature. MO_742 The array is made on a glass slide. MO_648 millimeter, unit of distance centimeter, a unit of distance MO_837 MO_386 A float greater than or equal to 0. complementary DNA cDNA MO_966 deleted_term 1.2.0 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 A record which describes and identifies an experimentally derived protein structure e.g. MSD MO_785 The mean and standard deviation values resulting from computationally combining 2 or more sets of bioassay data. MO_946 MO_560 A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. MO_795 microsecond, unit of time one or more DNA or RNA based non cellular infective agent, including bacteriophage MO_372 A device capable of applying software. MO_510 MO_432 delivery method whereby a compound or drug is administered via a vein 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. 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_461 MO_520 Contact which provides funding for experiments. 1.2.0 sequence of a single stranded synthesized oligonucleotide deleted_term MO_570 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_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. An optimization experiment design type is where different protocols or protocol parameters are compared. MO_934 MO_423 mRNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple sequences as input. deleted_term 1.3.1.1 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_1029 A biosource obtained as fecal matter. deleted_term 1.1.9 MO_636 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_686 MO_354 The sister of one's father or mother. MO_992 http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/MA.ontology?rev=1.1&view=markup This ontology describes the anatomy of the adult mouse. It contains anatomical structures for the postnatal mouse (Theiler stage 28). replaced_term 1.1.7 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_539 MO_812 degrees Fahrenheit, unit of temperature MO_931 Application of a normalization of type median_log_centering. mage ontology 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_862 nanometer distance unit A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design circular design MO_912 An operator variation experiment design type assesses the operator performance and relation to data consistency and quality. MO_519 MO_599 high molecular weight DNA MO_903 cell lysate, a collection of cells whose membranes have been disrupted MO_887 Groups of assays that are related as part of a time series. 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_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_474 percent weight per weight, concentration unit A daughter of one's son or daughter. MO_703 MO_764 A cell type comparison design experiment design type compares cells of different type for example different cell lines. An instrument capable of manufacturing arrays by spotting material. MO_697 split_term replaced_term merged_term deleted_term MO_1013 Indicates the why the term was deprecated. The possible values are: deleted_term, split_term, merged_term, replaced_term. MO_580 http://www.nlm.nih.gov/mesh/filelist.html database entry from MESH, medical subject headings vocabulary resource 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. MO_638 The sequence of the BioSequence that relates to this reporter has not been sequence verified by the experimenter. MO_970 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_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. 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. 1.2.0 deleted_term 1.2.0 deleted_term sequence of a protein, a linear amino acid polymer MO_530 deleted_term Physical or theoretical sequence of, or representing a chromosome, one of the DNA molecules that comprises the genome. 1.2.0 MO_578 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. MO_517 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 kilogram, 1000 grams, unit of mass MO_846 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_901 preservation type whereby the seed is maintained in a dormant state MO_666 a design element group consisting of multiple types MO_528 deleted_term false 1.1.7 MO_556 MO_836 Describes a cell, nucleus or an organism with two copies of each chromosome. deleted_term MO_381 1.2.0 single stranded oligo used for polymerase chain reaction A type of solid media commonly used for growing organisms MO_935 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. MO_908 Logarithmic transformation of ratio data. MO_896 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_590 The procedure of placing one physical object in the same container/physical space as another. MO_815 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_987 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_698 A biomaterial obtained embedded in paraffin (wax). MO_990 MO_765 a record which describes and identifies a protein structure e.g. PDB 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_437 MO_393 An action where the temperature is specified. 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_588 MO_601 A contact's affiliation, e.g. university, research institute or business. 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_377 MO_816 A descriptor for FactorValue where ClinicalInformation is compared. MO_748 the process of placing a seed or spore in some media with the intention to invoke germination. The amount of moisture in the air expressed as a percentage of the maximum amount the air is capable of holding. MO_453 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. 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_664 sequence from a gene coding for transfer RNA exact synonym: transfer RNA gene 1.2.0 MO_850 deleted_term transfer RNA gene MO_496 multiple of stock solution concentration, concentration unit A software implementing a Higher Level Analysis protocol of type differential_expresssion. MO_350 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_755 A grouping of DesignElements, Features/Reporters/Composite Sequences which are expected to detect a signal in the biomaterial. The action of preparing a slide for the microscopical examination of organism parts or cell types. MO_611 1.2.0 MO_709 sequence spliced out from a transcript deleted_term units per week, e.g. the number of units of alcohol consumed over a period of 7 days MO_388 MO_870 Units of defined biological activity, e.g. cytokine stimulation, per ml. A reference experiment design type is where all samples are compared to a common reference. MO_699 MO_419 deleted_term 1.1.7 High frequency recombinant, mating type that indicates that the F plasmid has integrated into the chromosome sequence that represents the product of an RNA polymerase engaged in transcription MO_827 1.3.1.1 deleted_term h MO_486 60 minutes, time unit MO_869 katal per liter, catalytic-activity concentration unit deleted_term ribosomal RNA gene 1.2.0 sequence from gene coding for ribosomal RNA exact synonym: ribosomal RNA gene MO_955 A quality control testing experiment design type is where some aspect of the experiment is quality controlled for the purposes of quality assurance MO_981 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_567 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 RNA obtained from an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus. MO_574 A float that is < 0. MO_728 An instrument which fragments tissues or other biomaterials. MO_714 fluorophore used for labeling/detection purposes MO_646 1.2.0 MO_439 sequence from a plasmid, an extrachromosomal autonomously replicating piece of DNA excluding mitochondria and chloroplasts deleted_term MO_435 A value which is a whole number (e.g. 10). MO_465 The male offspring of the patient or individual under study. MO_878 A descriptor for FactorValue where DevelopmentalStage is compared. image quantification software image analysis software MO_633 Software to create MeasuredBioAssayData from images. Exact Synonym: image analysis software, image quantification software. MO_975 delivery method for drug or compound whereby the drug is administered via the mouth 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/hla.htm 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_956 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_572 candle power The array is made on a nitrocellulose filter. MO_455 MO_834 a cubic centimeter, volume unit MO_683 Polymer of amino acids. nanomoles, quantity unit MO_743 MO_945 Deoxyribonucleic acid. MO_628 picomolar, concentration unit grams per liter, concentration unit MO_805 1.1.9 Absence of one chromosome of a pair of homologous chromosomes. In a normally diploid cell it is represented symbolically as 2N-1. replaced_term MO_424 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. 1.1.7 deleted_term MO_673 a nonparametric measure of the agreement between two rankings 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. 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_964 Toxicology Data Management System, a database resource for systems, organs, pathology, etc. http://hazel.niehs.nih.gov/user_spt/pct_terms.htm MO_718 1.2.0 MO_909 deleted_term sequence from a P1 artificial chromosome m MO_877 60 seconds, unit of time 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 1.2.0 number of items or events per day MO_670 MO_477 An instrument for sonicating biomaterials. The mean and associated p-values resulting from computationally combining 2 or more sets of bioassay data. MO_671 MO_998 mole, unit of quantity database resource for bacteria, bacteriophages, cell lines, fungi and yeast, plant tissue cultures, plant seeds, protozoa and algae and plant and animal viruses http://www.atcc.org/Cultures/Products.cfm MO_979 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. MO_848 MO_589 A biomaterial that has been lyophilized or dried by freezing under a vacuum. A member of a consortium of institutions. MO_778 A descriptor for the TechnologyType for a group of features where single stranded DNA PCR product is spotted on the array. MO_921 time unit MO_391 MO_925 A Reporter indicated as being a control of unknown type. MO_999 organism(s) whose sex is unknown Storage where the thing stored is stored below 0 degrees celsius. MO_481 TechnologyType of FeatureGroup where antibodies are spotted directly. MO_483 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_443 MO_854 An instrument designed to automatically raise and lower the temperature of wells or tubes. Usually used to perform PCR. Exact Synonym: thermocycler An element that is an oligonucleotide of at least 50 nucleotides in length. MO_598 MO_745 The point at which an organism emerges from an egg. MO_491 the chrome border on an Affymetrix type array which is used as a point of reference for orientation (fiducial) MO_625 Data from which a subset has been removed based on some criteria, e.g. data below an intensity threshhold. MO_783 the physical act of copulation that occurs during the process of sexual reproduction synonyms: copulation, insemination insemination copulation Application of a scale adjustment following loess_group_normalization, to render the group variances similar. MO_521 PCR with multiple bands, or smear, in gel-separated reaction products MO_620 An instrument that produces DNA sequences. MO_676 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_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_1019 A design in which RNA from different cell components is examined. MO_672 normalization software Software used to transform the Measured or DerivedBioAssay data e.g. normalization. Non-exact synonym: normalization software Software used to cluster the data. MO_464 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_467 A descriptor for FactorValue where age is compared. A delivery method for compounds/drugs where the compound or drug is freely available. MO_592 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_606 Application of a scale adjustment following lowess_group_normalization, to render the group variances similar. MO_410 MO_502 Software to control an arrayer. MO_678 A Comparative Mapping Resource for Grains. http://www.gramene.org/ MO_900 An ordered, finite set of negative integers. MO_858 dye flip flip dye An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip treatment of a biomaterial with radiation e.g. electromagnetic radiation MO_770 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. MO_1007 MO_919 http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/developmental/plant_development/Arabidopsis/temporal.tair?rev=1.21&view=markup An ontology of stages of growth and development of the model plant Arabidopsis thaliana. 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. 32 P, radioactive isotope of phosphorus used for labeling/detection purposes MO_839 MO_348 counts per minute, unit of light emissions produced by ionizing radiation. An ordered, finite set of positive floats. MO_777 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. MO_789 http://www.iupac.org/publications/pac/2000/205/205olesen.html MO_593 A resource of vocabularies for describing clinical tests, e.g. blood chemistry. a record which describes and identifies a compound e.g. drug record part of NCI thesaurus MO_546 MO_973 An ordered, finite set of nonnegative integers. milliliters per liter, concentration unit MO_801 MO_533 transcription_profiling gene expression expression_profiling gene_expression transcription profiling A transcript identification design type characterizes the length and position of transcripts and allows identification of all forms of transcripts in the genome. expression profiling MO_916 percentage volume per volume, concentration unit 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_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). Introduction of genetic material into an organism often in the form of a plasmid. MO_366 MO_475 Person or organization that manufactured the software. http://song.sourceforge.net/ The Sequence Ontology is a set of terms used to describe features on a nucleotide or protein sequence. MO_724 1.2.0 deleted_term 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_441 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_675 A species experiment design type assays differences between distinct species. 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_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_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_399 The fluid and dissolved substances excreted by the kidney. MO_565 An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. chloroplast DNA MO_586 ctDNA: sequence from the chloroplast synonym: chloroplast DNA deleted_term 1.3.1.1 MO_751 The scale is a standard base 10, non logarithmic scale. MO_891 An ordered, finite set of integers. 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_402 the reverse strand exact synonym: - MO_639 A descriptor for FactorValue where BioSources are compared. MO_1008 http://www.cabri.org/HyperCat/bact/all_A.htm 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. MO_378 A measure of the density of an attached or monolayer culture (e.g., cell culture), e.g., 80 percent_confluence. MO_603 The unit of total light output from a light source. Change in light intensity or wavelength. MO_549 the number of cells per ml MO_727 The stage premortem or postmortem at which the sample was processed for extraction of biomaterials. MO_871 MO_936 Mole per liter or molarity, concentration unit A value which is a floating point number (i.e. real number) with arbitrary precision (e.g. 2.34). MO_860 A record which describes and identifies a paper publication e.g. a medline record MO_923 The shape of the feature on the array is circular or oval. MO_459 MO_733 Delivery method where a compound/drug is administered in the culture medium (e.g., for in vitro treatment). picomoles, quantity unit MO_688 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_661 osmolality per kilogram of water, concentration of the solute per unit of solvent person who prepares the MAGE-ML file MO_695 The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil) MO_545 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_1001 Portable Network Graphic, a lossless image data format. 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_906 The source DNA for a Feature was not uniformly deposited. Eberwine procedure 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_997 one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria MO_508 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_734 A hardware variation experiment design type compares different types of hardware for performance, reproducibility, accuracy and precision. MO_418 Results of an analysis method that groups data based on a measure of similarity, e.g. Pearson correlation coefficient, Euclidean distance. MO_977 attomole, quantity unit 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_584 http://www.arabidopsis.org/servlets/Search?action=new_search&type=ecotype MO_660 The Arabidopsis Information Resource. 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_596 MO_874 An analysis aimed at identifying differentially expressed genes in two or more conditions. femtomole, unit of quantity MO_689 MO_959 The Feature or Zone is displaced from its expected position, due to e.g. a bent spotting pin(s). An ordered, finite set of booleans. MO_712 the organism part in which the tumor originated MO_408 Unit of brightness or luminance. MO_813 MO_924 The mother of one's father or mother. MO_922 The loss of a segment of the genetic material from a chromosome. The father of one's father or mother. MO_478 MO_466 The procedure in which solid material is dispensed or dissolved in a liquid. biomaterial removed after the death of the organism MO_416 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. MO_472 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_771 MO_540 deleted_term 1.1.7 true deleted_term MO_412 Sequence derived from expressed sequence tag. EST's are likely to be partial, single read and low quality sequences. 1.2.0 MO_880 Mix through the use of a vortexer. MO_868 Hardware for automated liquid transfer and handling. change environment change growth condition Indicates that one or more BioMaterialCharacteristics have changed during the treatment of a BioMaterial. Non exact synonym: change growth condition, change environment MO_383 MO_662 A record which describes and identifies the relationship between species and is computationally determined and based on sequences e.g. Treebase record The BioSample immediately before labeling. MO_895 Ontology of human terms that describe the sample source of human cDNA and SAGE libraries. MO_684 http://www.sanbi.ac.za/evoc/ontologies.html MO_747 a surface coating type for immobilization with the compound aminosilane A descriptor used in cancer biology to describe abnormalities of tumor cells. MO_843 MO_842 7 days, unit of time MO_509 milimolar, concentration unit MO_943 the mean and associated p-values resulting from computationally combining 2 or more sets of BioAssayData 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_810 glycoprotein of the immunoglobulin family that can combine specifically non-covalently, reversibly with a corresponding antigen MO_833 MO_761 Software used to control automated liquid handler. Computed as the ordinary Pearson correlation coefficient between two groups of rankings. MO_552 MO_373 Total cellular and nuclear RNA. 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. deleted_term 1.2.0 MO_413 A float > 0. MO_501 A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out MO_447 MO_425 the mean and coefficient of variation values resulting from computationally combining 2 or more sets of BioAssayData MO_654 ftp://ftp.cdc.gov/pub/Health_Statistics/NCHS/Publications/ICD9-CM/2002 Database entry from ICD 9 2001, international classification of diseases 9, clinical modification 2001. Person who is the primary contact for data submitted to a database. MO_882 MO_986 A PCR based semi quantitative validation of a subset of the array based data used for experimental QC purposes. MO_612 One or more dissociated cell(s) possibly heterogeneous, excluding single cell organisms. MO_690 a controlled vocabulary of organism parts http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C13007 MO_404 http://cvs.sourceforge.net/views.py/obo/obo/ontology/anatomy/cell_type/cell.ontology?rev=HEAD&content-type=text/vnd.viewcvs-markup database of cell ontology terms MO_793 a compound used for labeling/detection purposes 1.1.7 A description logic namespace that contains controlled terminology used at NCI. split_term MO_630 http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C16632 a controlled vocabulary for geographic locations http://nciterms.nci.nih.gov MO_456 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). semisolid media type MO_635 An ordered, finite set of strings. MO_800 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. deleted_term BioSequence generated by means of polymerase chain reaction MO_450 1.2.0 MO_346 A record which describes and identifies a microarray experiment e.g. GEO sequence which represents regions of a transcript that are joined to another exon during splicing deleted_term MO_619 1.2.0 MO_640 single stranded oligo used for polymerase chain reaction 1.2.0 deleted_term MO_656 A float less than or equal to zero. The procedure of labeling a biosample. MO_471 + MO_820 the forward strand exact synonym: + The Pearson correlation is defined as the covariance of two data series divided by the product of their standard deviations. MO_632 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_799 MO_863 A descriptor for FactorValue where PhysicalCharacteristics are compared. MO_634 ExperimentDesignType of unknown type. MO_982 The process of harvesting cells from culture. A design that compares samples from live and dead organisms. MO_841 MO_537 a controlled vocabulary for histology http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C4741 TechnologyType of FeatureGroup where bacterial or other colonies are spotted directly. MO_618 Describes a cell, nucleus or an organism with one copy of each chromosome. MO_719 MO_577 cDNA DNA which is generated by chemical or enzymatic (non cellular) means. non-exact synonym: cDNA 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_892 An organism part comparison experiment design type compares tissues, regions, organs within or between organisms MO_953 database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice MO_972 http://eulep.anat.cam.ac.uk/Search_Pathbase/index.php 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 guilt by association 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_362 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. 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_585 of, pertaining to, or designating the sex that only produces gametes that can be fertilized by male gametes. MO_506 a record which identifies and describes biological pathways, e.g. a KEGG record MO_780 MO_930 Hardware for synthesizing oligos. 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 sample An integer >= 0. MO_390 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. MO_729 A normalization testing experiment design tests different normalization procedures. A ComplexAction or ProtocolType describing growth of an organism or cell culture. MO_758 A descriptor for FactorValue where IndividualGeneticCharacteristic is compared. MO_722 MO_806 the organism part in which additional tumors are identified remote from the primary site media type, usually some sort of broth MO_715 MO_392 A cellular modification design type is where a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. RNAi MO_768 the number of plaque forming units per ml The TechnologyType of the FeatureGroup is manufactured using in situ methods such as photolithography (e.g. Affymetrix) or chemical synthesis (e.g. Agilent) MO_514 MO_371 Sequence from some nucleic acid copy and the associated vector for which the source clone supplier is unknown. 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. deleted_term MO_651 single oligo used for polymerase chain reaction direction unspecified 1.2.0 MO_792 The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression. 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_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/fun/all_A.htm a measurement where the value is dependent on another measurement MO_396 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_555 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_817 The shape of the feature on the array is square. 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. a surface coating for immobilization with the polypeptide, polylysine MO_569 The diameter of the Feature is much smaller or much larger than expected based on the spotting pin diameter. MO_781 Database entry from the resource at The Jackson Laboratory which has details of approved mouse strain nomenclature. http://www.informatics.jax.org/external/festing/mouse/STRAINS.shtml MO_369 MO_353 milligram per kilogram per day The act of placing a plant in media (e.g. soil) to allow it to grow. This excludes sowing. MO_495 MO_429 true or yes MO_487 A design aimed at identifying genes expressed in biomaterials of interest. MO_788 the number of colony forming units per ml 1.3.0 replaced_term 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_706 An ordered, finite set of negative floats. MO_851 femtogram, unit of mass MO_732 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). A female parent. MO_387 MO_910 mark made on slide using a laser which is used as a point of reference for orientation (fiducial) MO_802 false or no a double stranded oligonucleotide deleted_term 1.2.0 MO_344 Decreasing the concentration of solutes in a solution or suspension. MO_962 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. picogram, mass unit MO_363 MO_875 units per liter individual whose sex organs contain only male gametes MO_652 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. 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_595 MO_667 PCR where no products of any kind appear in gel-separated reaction products. A function applied to subsets of values from the same Measured/Derived bioassay data set. MO_668 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_414 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). Mix by drawing up and down with a pipette. MO_479 MO_480 Generation of a DNA strand from an RNA strand using reverse transcriptase. MO_579 The TechnologyType of the FeatureGroup is spotted single stranded oligonucleotides (of any length) on the substrate. the array is made on silicon MO_382 MO_840 The mean and coefficient of variation values resulting from computationally combining 2 or more sets of bioassay data.