November 8, 2006 The MGED Ontology 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 An ontology for microarray experiments in support of MAGE v.1. 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 MO_5 Properties of the biomaterial before treated in any manner for the purposes of the experiment. abstract ontology Database of taxonomic information. MO_64 ontology 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. MO_213 ontology concrete class to hold instances used as the filler for the property has_measurement_type ontology concrete MO_72 MAGE package for description of annotations and references to annotations. mage abstract MO_167 Description of the source of the nucleic acid used to generate labeled material for the microarray experiment. MO_182 mage abstract Units used for quantity measurements. concrete MO_210 ontology Factors that relate to properties of the biomaterial, its treatment, or its growth. ontology abstract MO_190 ontology MO_224 concrete A biological property experiment design type is where an intrinsic characteristic of an organism(s) or biological system is examined. MO_225 Database of disease staging information concrete ontology MO_124 abstract a plant variety obtained in agriculture in horticulture ontology A marking on the surface of the array that can be used to identify the origin of the array. MO_136 concrete mage ontology MO_26 class to hold instances used as the filler for the property has_cancer_site concrete MO_198 concrete Controlled terms for descriptors for coating of the substrate. ontology QualityControlDescription provides details of the quality control aspects of the experiment. abstract ontology MO_88 abstract MO_188 ontology Member of the biosource's family. abstract MO_15 The MAGE package for describing the elements located on the array. mage ontology A theoretical biosequence type is an abstraction used for annotation design of elements, e.g. gene, intron. MO_42 concrete abstract MAGE package for biological sequences (biosequence). mage MO_191 The term was deleted from the MGED CoreOntology. MO_78 deleted_term Version of the MGED Ontology. 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. 1.1.7 abstract some|has_chromosomal_aberration_classification|ChromosomalAberrationClassification ontology place_holder MO_159 ontology An antigenic property of a cell (e.g. bacteria, RBC) or virus identified by serological methods MO_56 mage abstract A bioassay is an abstract class representing physical and computational groupings of biomaterials and arrays. MO_74 mage concrete Description of the material placed on a feature (spot). Concentration units not specified in MAGE. ontology MO_86 concrete The identifier for the established culture of a metazoan cell if one was used as a biomaterial. abstract ontology MO_49 MO_128 A DesignElementGroup holds information on Features, Reporters, or CompositeSequences. mage abstract The technology type or platform of the reporters on the array. ontology MO_18 concrete place_holder Mass units not specified in MAGE. MO_11 ontology ontology MO_16 concrete Defects associated with features or zones such as those that are missing or moved. ontology MO_55 A description of the conditions the organism has been exposed to that are not one of the variables under study. abstract Units of measure. ontology abstract MO_3 The scale (linear, log10, ln, etc) used to represent the value. concrete ontology MO_108 MO_31 The descriptions associated with the Experiment package of MAGE abstract mage MO_13 concrete ontology Compounds that are used for labeling extracts. concrete ontology Controlled terms for descriptors of the warnings associated with reporters. MO_41 MO_222 ontology place_holder The effects of different software, software packages, or software versions on experimental results are studied. The effects of different protocols or changes in protocols on experimental results are studied. MO_140 MO_215 ontology Database of developmental stage information. concrete Controlled terms for descriptors of the role of contact, e.g. submitter, biosource_provider. MO_180 concrete 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. ontology MO_85 ontology concrete Controlled terms for descriptors of the type of polymer (RNA, DNA, protein) of the biosequence. MO_102 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. concrete MO_221 The BioSample after labeling for detection of the nucleic acids. mage 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). concrete MO_165 ontology The process by which derived BioAssays are created from measured BioAssays and/or derived BioAssays. Controlled set of descriptors for indicating the specific type of a Feature, Reporter, or CompositeSequence. ontology concrete MO_14 concrete ontology MO_208 Controlled terms for descriptors of the type of publication such as those used by Medline (review, book, etc.). place_holder some|has_value|string 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_217 ontology deleted_term 1.1.9 Version of the MGEDOntology. concrete ontology MO_166 Units used for time measurements. Controlled terms for how the sequence features were determined (e.g., experimental, computational, etc.) concrete ontology MO_207 ontology MO_152 Controlled terms for descriptors indicating the type of biosequence. Types may be physical (e.g. BAC, cDNA clone), or computational (e.g. unigene cluster, consensus). abstract ontology 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. place_holder MO_43 ontology abstract A descriptor used in cancer biology to describe abnormalities of tumor cells. E.g. an instance from NCI Thesaurus. MO_28 Identifiable resource containing data or external ontologies or controlled vocabularies which has uniquely identifiable records. abstract MO_118 ontology MO_94 ontology class to hold instances used as the filler for the property has_reason_for_deprecation concrete place_holder ontology MO_38 The effects of different investigators, laboratories, or organizations on experimental results are studied. The humidity that the biosource is exposed to. MO_29 abstract ontology A physical bioassay is the combination of arrays and biomaterials as in a hybridization. mage MO_99 concrete MO_194 Microscopic morphology of tissues. abstract ontology concrete ontology MO_156 Quantity units not specified in MAGE. ontology 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. MO_122 concrete ontology concrete Controlled descriptors for the normalization strategy used for the experiment. MO_27 MAGE package for HigherLevelAnalysis abstract MO_228 mage abstract ontology The BioMaterial's (i.e., the patient's) medical record as background information relevant to the experiment. MO_189 The number of single sets of chromosomes in the cell or an organism e.g., haploid, diploid, triploid, etc. concrete MO_220 ontology ontology place_holder MO_143 Distance units not specified in MAGE. MO_169 place_holder Identifier or name of the individual organism from which the biomaterial was derived. ontology MO_19 The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil) . ontology concrete MO_35 concrete Database of geographic locations. ontology concrete Factors that relate to properties of the environmental history of the biomaterial, its treatment, or its growth. ontology MO_117 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. MO_36 ontology A type of relationship applicable to mammals to describe the genetic relatedness of the individual under study. E.g. brother or mother. concrete MO_90 ontology concrete Complex actions are composed of multiple steps (as opposed to AtomicAction) e.g. mRNA labeling, protein purification. MAGE package that describes the array layout and design. The array may be physical or virtual. abstract MO_33 mage The BioSource after any treatment. MO_93 mage concrete The organism has had non-genetic parts removed, added, or rearranged. MO_44 place_holder The effects of different hardware, types of hardware, or models of hardware on experimental results are studied. MO_81 ontology 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 MO_186 MAGE package for BioAssayData. MO_147 abstract Organizations or individuals that may be contacted. mage abstract MO_60 The photoperiod and type (e.g., natural, restricted wavelength) of light exposure. ontology MO_164 Descriptors for protocol parameter types, e.g. compound concentration, media type. 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. abstract MO_123 ontology abstract MO_218 Descriptor of the Test performed e.g. Leukocyte count 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. ontology MO_139 abstract MO_37 ontology Anatomical location(s) of disease. concrete concrete ontology 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. MO_95 ontology An epidemiological experiment design type is where the biosource history is studied e.g. environmental, clinical and family history. concrete MO_142 MO_171 The temperature that a biosource is exposed to. ontology abstract concrete MO_22 mage ontology abstract The resource (e.g. company, hospital, geographical location) used to obtain or purchase the biomaterial. MO_230 concrete ontology MO_119 Units for measuring the intensity of light. ontology concrete The point from which measurements of age were taken. MO_80 abstract An assay performed on a biomaterial for the purposes of determining one or more biomaterial characteristics e.g. clinical chemistry. MO_197 ontology concrete mage A technical manufactured described defect for zones. MO_105 The developmental stage of the organism's life cycle during which the biomaterial was extracted. ontology abstract MO_120 ontology MO_184 abstract Tests and results for pathogens infecting organism from which the biosource is derived ontology abstract 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. MO_174 ontology A protocol which yields a dataset(s) from which biological conclusions can be derived. E.g. clustering (not normalization or averaging). concrete MO_47 MO_201 A bibliographic reference is a published citation in a journal, book, other format e.g. web resource mage concrete Controlled terms for descriptors for the type of control design element. ontology concrete MO_50 place_holder ontology The genotype of a single chromosome (i.e., the haploid genotype) that is known and relevant to the experiment being performed. MO_146 General descriptor of a BioMaterialCharacteristic category. Such as strain or line where the name of the strain or line is encoded in the FactorValue. MO_100 concrete mage A representation of a DNA, RNA, or protein sequence. MO_163 Units for measuring decay of a radioactive isotope over time. concrete MO_204 ontology MO_155 ontology place_holder Volume units not specified in MAGE. abstract MO_0 mage MAGE package for bioassay. mage The machine or instrument used. MO_134 concrete MO_157 Controlled set of descriptors for the type of database record such as a protein record (in SWISS-PROT) or a gene object (in SGD). ontology concrete abstract MO_87 External (to the MGED ontology) controlled vocabulary or ontology that can be referred such as ICD-9 or Gene Ontology. ontology MO_68 An atomic action is a single step process on the biomaterial, e.g. mix by inversion, wait, add ontology concrete ontology Descriptors of biosequence based on the Sequence Ontology (SO) project. MO_25 abstract a biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler abstract MO_71 ontology MO_158 ontology abstract The ExperimentDesignType is the high level description for studies such as "time series", "dose response", etc. mage MO_116 concrete A grouping of bioassay data that has been organized by one or more mathematical functions into nodes. 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. Units used for distance measurements. concrete MO_4 ontology MO_70 A drug, solvent, chemical, etc., with a property that can be measured such as concentration. ontology abstract ontology MO_160 concrete Controlled set of terms for describing the type of values (e.g., Euclidean distance). MO_168 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. ontology 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. MO_170 mage concrete mage The BioSource is the original source material before any treatment events. concrete MO_77 MO_178 abstract 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). MO_195 The type of method used to preserve (keep in stasis) the organism or biosource. ontology concrete A descriptor that indicates the type of the fiducial such as chrome border of an Affymetrix array or a laser ablation mark. MO_17 The stage premortem or postmortem at which the sample was processed for extraction of biomaterials. MO_84 concrete ontology MO_223 Method used to deliver a compound for treatment. 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 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 ontology Documentation of the set of steps taken in a procedure. mage concrete MO_214 mage A treatment is the process or action by which a biomaterial is created from an input biomaterial. MO_23 concrete abstract MO_96 ontology TestResult is the recorded value of the test outcome. concrete MO_203 mage The value of an ExperimentFactor. MO_112 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. mage concrete ontology Other units are those types not specified in MAGE such as lumens, radioactivity, etc. MO_199 ontology abstract Observation will record the macroscopic examination of the biomaterial. MO_53 MO_150 ontology abstract A controlled set of terms to provide a descriptor for the type of protocol. concrete MO_209 A BioAssay that is created by the transformation of measured or derived BioAssays. mage 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. ontology abstract MO_145 ontology concrete Database of cell line information. concrete ontology 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. MO_111 ontology Procedures used during treatment. abstract MO_193 abstract MO_126 The name of the pathology diagnosed in the organism from which the biomaterial was derived. The disease state is normal if no disease has been diagnosed. ontology concrete Controlled terms for descriptors of failures (as in PCR) associated with reporters. ontology MO_98 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 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 deleted_term some|has_value|string 1.1.9 ontology MO_148 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. deleted_term ontology place_holder MO_185 Version of the MGEDOntology. concrete MO_54 Technology-based grouping of features representing individual locations on the array. mage MO_176 Method and type of preserving the organism or biosource (i.e. keeping it in stasis). mage abstract MO_172 MAGE package for contacts including organizations and people. The process by which BioAssays (data, elements, quantitation types) are averaged normalized, selected, filtered, or otherwise changed into a new set of BioAssay data. MO_216 mage concrete Measured values and units. MO_144 concrete Database of targeted cell type information. MO_45 ontology ontology Primitive data types found in computing languages such as float, boolean, etc. MO_125 concrete ontology concrete MO_106 A perturbational design type is where the organism(s) are treated or manipulated or modified, for example a genetic modification, somatic modification The genus and species (and subspecies) of the organism from which the biomaterial is derived from. abstract ontology MO_229 abstract Organisms or organism parts used as a designed part of the culture (e.g., red blood cells, stromal cells). ontology MO_101 Database of organism part information. ontology concrete MO_200 concrete Controlled descriptors for the type of replication. MO_52 ontology mage The QuantitationType provides a method for calculating a single datum of the BioAssayData matrix. MO_67 abstract MO_107 mage MAGE package for describing the process by which arrays were manufactured. abstract MO_132 ontology A descriptor of the location from which a BioMaterial was obtained, e.g. country, region, grid reference. abstract Uniform Resource Identifier MO_12 ontology abstract concrete The organization (e.g. company, hospital) to contact to obtain or purchase something. MO_177 mage A factor category describes factors which are examined in the experiment, e.g. disease_state, where the factor values are ALL and AML. abstract ontology MO_205 Controlled terms for descriptors of types of array substrates. MO_79 ontology concrete concrete MO_30 Database of strain, line, cultivar or ecotype information. ontology MO_10 The factors in the study that are experimental parameters or regarded as influencing the experimental results. mage concrete abstract MAGE package for measurement. MO_89 mage ontology MO_57 abstract An ontology developed by the Microarray Gene Expression Data (MGED) Society to provide descriptors required for MAGE v.1 documents. A descriptor of the strand type the sequence feature belongs to. e.g. forward, reverse MO_7 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 Units used for volume measurements. ontology MO_179 concrete MO_69 ontology The current clinical treatment(s) of the patient from which the biosource is derived. abstract The individual to contact regarding something provided such as a biomaterial. MO_24 mage concrete ontology concrete Database of histology information. MO_175 MO_130 mage The MAGE package for defining classes for quantitation. abstract MO_121 ontology Controlled descriptors for the quality control strategy for an experiment. concrete ontology MO_103 Time units not specified in MAGE. concrete ontology MO_127 The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.). abstract Controlled terms that provide descriptors for the type of software. MO_202 concrete ontology concrete MO_113 Controlled terms for descriptors of types of hardware. ontology ontology concrete Database of terms for observations such as 'abnormal coat', 'skin pigment abnormality' describing macroscopic examinations. MO_91 concrete Node values allow the organization of the nodes in relation to other nodes produced by mathematical functions such as a clustering algorithm. MO_104 mage The expected shape of the feature on the array. concrete ontology MO_8 MO_135 abstract 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. ontology MO_133 The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression. ontology abstract MO_58 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 User is a way to id a person in a database MO_62 Database of tumor grading information ontology MO_187 concrete An array group is a physical platform that contains one or more arrays that are separately addressable or a virtual grouping of arrays. mage concrete MO_34 concrete MO_212 Descriptions pertaining to the array. mage class to hold instances used as the filler for the property has_result ontology concrete MO_65 ontology abstract MO_219 The atmospheric conditions used to culture or grow an organism. Units used for mass measurements. concrete ontology MO_149 MO_63 The MAGE package for protocols. abstract mage ontology concrete The version of the MGED Ontology. MO_115 MO_39 ontology Database of phenotype information concrete concrete MO_83 ontology Database for sequence annotation information. mage MO_226 abstract Description of the processing state of the biomaterial for use in the microarray hybridization. MO_129 abstract Physical properties of the BioMaterial e. g. mass or height ontology MO_161 ontology Used to tell when the BioSample is an extract or not. concrete ontology MO_153 Water consumed by or enveloping the organism that the biosource is derived from. abstract ontology MO_173 concrete Design elements are reporters, features, and composite elements as defined by MAGE. The software application used. MO_109 concrete mage 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 abstract MO_97 Rating of containment system for the protection of organisms from infectious agents. 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 ontology The concentration range of the organism. abstract MO_46 ontology A physical biosequence type represents biological sequence that can be physically placed (spotted or synthesized) on an array e.g. BAC, PAC. MO_92 concrete ontology MO_154 Refers to the bedding material present in an animals housing. place_holder ontology abstract MO_59 Relevant aspects of genetic preconditions or family member's clinical history. Class to hold deprecated instances and classes. concrete MO_206 ontology MO_48 ontology Units used for temperature measurements. concrete MO_114 ontology Database of clinical treatment information concrete concrete MO_138 A technical manufacturer described defect for features. mage ontology All protocols which involve treatment of a biomaterial or an array during the course of a microarray experiment. MO_75 concrete concrete A parameter is a variable within a protocol. MO_110 mage ReplicateDescription provides details about the type of replication used in the experiment. abstract ontology MO_162 Database of disease state information. concrete ontology MO_181 Database of codes for clinical findings. ontology concrete MO_76 NormalizationDescription provides details of the normalization strategy for the experiment. MO_131 ontology abstract Database of compound information. ontology MO_151 concrete concrete ontology 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. MO_32 ontology concrete Units used for concentration measurements. MO_61 concrete Database of cell type information. ontology MO_141 ontology abstract The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. MO_66 MO_40 BioAssayData refers to the data files including images generated from one or more BioAssays. concrete MO_73 A node is an individual component of BioAssayDataCluster that groups design elements, quantitation types, and BioAssays together. A node may contain other nodes. mage MO_137 Genetic material may be DNA or RNA and identifiable as an entry in a public external database such as EMBL/DDBJ/GenBank or one of the model organism databases. concrete MO_211 ontology Controlled terms for descriptors of the image file format (TIFF, JPEG, GIF, etc.) MO_254 property indicating that the class has individual genetic characteristics MO_282 property indicating that the class has a clinical treatment MO_280 property indicating that the class has a mass property indicating that the class has an experiment design MO_291 property indicating that the class has a measurement MO_325 property indicating that the class has an ontology entry MO_263 property indicating that the class has hardware MO_286 MO_247 property indicating that the class has a clinical record property indicating that the class has a disease state MO_305 MO_313 property indicating that the class has a host property indicating that the class has a treatment MO_262 property indicating that the class has an experiment design type MO_288 MO_279 property indicating that the class is user defined property indicating that the class has a measurement type MO_242 property indicating that the class has an atmospheric component MO_259 property indicating that the class has a factor value MO_236 property indicating that the class has a compound MO_302 MO_241 property indicating that the class has a modified part MO_324 property indicating the class has a result property indicating that the class has software MO_284 property indicating that the class has an action MO_312 property indicating that the class has fiducials MO_267 MO_297 property indicating that the class has a maximum measurement MO_281 property indicating that the class has a laboratory test MO_311 property indicating that the class has a clinical test MO_269 property indicating that the class has units property indicating that the class has a category MO_249 MO_268 property indicating that the class has a feature shape MO_287 property indicating that the class has a scale property indicating that the class has a family relationship MO_250 property indicating that the class has a diameter MO_301 property indicating that the class has a nutrient component MO_321 MO_299 property indicating the version of the MGED Ontology that the term was deprecated from property indicating that the class has disease staging MO_275 property indicating that the class has experiment factors MO_328 property indicating that the class has a parent organization MO_257 MO_319 property indicating that the class has a type property indicating that the class has bioassaydata MO_252 MO_248 property indicating that the class has a cancer site MO_306 property to indicate the reason for deprecating a term MO_244 property indicating that the test has a test protocol MO_320 property indicating that the class has species MO_232 property indicating that the class has a manufacturer MO_240 property indicating that the class has a database entry type MO_307 property indicating that the class has a node property indicating that the class has an image format MO_234 MO_303 property indicating that the class has providers property indicating that the class has biomaterial characteristics MO_272 MO_310 property indicating that the class has a node value property indicating that the class has an individual MO_327 property indicating that the class has a citation MO_274 property indicating the location of the disease. MO_290 MO_304 instance property to indicate what the term was replaced by property indicating that the test has a test result MO_261 MO_273 property indicating that the protocol has a performer or contact person property indicating that the class has a clinical finding MO_316 MO_266 property indicating that the class has a property set property indicating that the class has an organism part MO_285 MO_253 property indicating that the class has a chromosomal aberration classification MO_260 property indicating that the class has an association to a MAGE description MO_317 property indicating that the class has a height property indicating that the class has a host part MO_283 MO_245 property indicating that the class contains a cubic volume measurement MO_276 property indicating that the class has a prior disease state MO_238 property indicating that the class has bioassays property indicating that the class was tested for MO_265 MO_314 property indicating that the class has an additive MO_300 property indicating that the class has a protocol property indicating that the class has an affiliation to an institution MO_309 property indicating that the class has a node value type MO_264 property indicating that the class has a database MO_233 property indicating that the class has a family member MO_243 property indicating that the class has a title MO_337 MO_329 property indicating that the class has a toll free phone property indicating that the class has an email address MO_293 MO_239 property indicating that the class has a version MO_318 property indicating that the class has authors property indicating that the class has a last name MO_255 MO_294 property indicating that the class has an issue MO_336 property indicating that the contents found at this uri are machine readable (i.e. in a standard format) MO_231 property indicating that the class has an accession number property indicating that the class has a name MO_296 property indicating that the class has an editor MO_256 property indicating that the class has an identifier MO_323 property indicating that the class has a publication MO_251 MO_332 property indicating that the class is a solvent property indicating that the class has an accession number version MO_339 property indicating that the class has a first name MO_258 MO_334 property indicating that the class has a description property indicating that the class has a volume MO_308 MO_246 property indicating that the class has pages property indicating that the class has a middle initials MO_237 MO_295 property indicating that the class has a publisher property indicating that the class has text MO_298 property indicating that the class has a year MO_322 MO_277 property indicating that the class has an address MO_335 property indicating that the class has an order property indicating that the class has a phone MO_235 MO_326 property indicating that the class has a value MO_270 property indicating that the class has a model property indicating that the class has a make MO_271 property indicating that the class has a fax MO_289 property indicating that the contents found at this uri are human readable MO_330 property indicating that the class has a URI MO_340 MO_278 property indicating that the class has an owner MO_292 property indicating that the class has an individual time point property indicating that the class has a donor MO_342 property indicating that the class has a biosource type MO_315 property indicating that the class has been treated MO_341 The source DNA for a Feature was not uniformly deposited. MO_906 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. deleted_term sequence of a protein, a linear amino acid polymer MO_530 1.2.0 MO_482 A relative measurement of homogeneity of a biomaterial e.g. tumor biopsy. MO_989 A record which describes and identifies a biological resource such as a cone or strain e.g. an ATCC record Jax strain list MO_891 An ordered, finite set of integers. MO_985 bacterial artificial chromosome sequence from a bacterial artificial chromosome exact synonym: bacterial artificial chromosome 1.2.0 deleted_term TechnologyType of FeatureGroup where bacterial or other colonies are spotted directly. MO_618 MO_389 Treatment to remove organisms present that were not planned as part of the study (e.g., mycoplasma). MO_487 A design aimed at identifying genes expressed in biomaterials of interest. 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. a controlled vocabulary of organism parts MO_690 http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C13007 MO_669 The perimeter of the spotted DNA on the slide is irregular. The mean and standard deviation values resulting from computationally combining 2 or more sets of bioassay data. MO_946 The unit of total light output from a light source. MO_603 Results of an analysis method that groups data based on a measure of similarity, e.g. Pearson correlation coefficient, Euclidean distance. MO_418 Mating type of S. cerevisiae. MO_659 A Reporter of whose BioSequence is of known length used as a methodological control for hybridization efficiency. MO_431 MO_610 A biomaterial obtained frozen 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. A grouping of DesignElements, Features, Reporters, Composite Sequences on the basis of a common species. MO_395 A state or condition describing a cell or organism that has more copies of a single chromosome than the usual complement. MO_596 The process of applying a solvent (e.g. water) or a solution (e.g. SSC/SDS) to a BioMaterial or an array to remove impurities or unwanted compounds. MO_740 Micromole per liter or micromolar, concentration unit MO_796 nanogram, a mass unit sequence from yeast artificial chromosome deleted_term 1.2.0 MO_794 Database entry from CABRI, a database listing sources such as cell lines, bacteria, plasmids etc. MO_536 http://www.cabri.org/HyperCat/cells/all.htm MO_526 Microeinstein per minute and square meter (µE m-2 min-1 or uEinstein m-2 min-1). One einstein is one mole or 6.02x10e23 (avogadro constant) photons. It is commonly used as a unit for photosynthetically active radiation (PAR), however the einstein is not an SI unit. Therefore, microEinsteins per m2 per second is identical to micromoles per m2 per second (SI unit for light irradiance). i.e. (1000 µE m-2 s-1 = 1000 µmol m-2 s-1). MO_499 A descriptor for the TechnologyType for a group of features where double stranded DNA is spotted on the array e.g. a PCR of a cDNA clone. MO_763 Person or organization that manufactured the hardware. MO_884 The process of incubating one or more labeled extracts with an array. 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_349 MO_445 the mean and standard deviation values resulting from computationally combining 2 or more sets of BioAssayData MO_425 the mean and coefficient of variation values resulting from computationally combining 2 or more sets of BioAssayData MO_978 RNA obtained from the cytoplasm. MO_465 The male offspring of the patient or individual under study. MO_670 number of items or events per day MO_746 Joint Photographic Experts Group format, a common image data format containing grayscale or RGB data compressed with little to high data loss. A dose response design type examines the relationship between the size of the administered dose and the extent of the response of the organism(s). MO_485 MO_898 femtomolar, concentration unit micrometer, unit of distance MO_421 MO_723 A female having the same genetic parents as another, or one genetic parent in common with another. MO_964 The "French railway distance" is based on the fact that (at least in the past) most of the railways in France headed straight to Paris. Thus, the French railway distance between two points is the usual distance if the straight line through them passes to a designated ÒParisÓ point, or is the sum of their distances to the ÒParisÓ point otherwise. MO_947 http://www.nlm.nih.gov/research/umls/ Database resource, unified medical language system, an ontology constructed by merging several disparate ontologies, available from NIH. MO_811 A method of normalizing log ratio data by subtraction of the median log ratios computed across all data points, or an appropriate subset of these (e.g. special control Features on a microarray, or 2DE spots containing constitutively expressed proteins). MO_635 semisolid media type 1.2.0 sequence which represents an operon, a unit of genetically linked genes displaying coordinated and regulated gene activity, originally described in prokaryotes MO_759 deleted_term A quantitative measure of the relative abundance of a transcript. Used in the MAS5.0 Affymetrix software to obtain a smoothed signal intensity from a group of related Features. MO_653 MO_912 A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design circular design - the reverse strand exact synonym: - MO_402 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 MO_348 counts per minute, unit of light emissions produced by ionizing radiation. MO_647 The values presented are logarithm, base 2. A descriptor for FactorValue where ClinicalInformation is compared. MO_816 MO_999 organism(s) whose sex is unknown MO_749 An element that is an oligonucleotide of less than 50 nucleotides in length (usually 20 to 25 nt as in Affymetrix probes). 1.2.0 Physical or theoretical sequence of, or representing a chromosome, one of the DNA molecules that comprises the genome. MO_578 deleted_term MO_979 http://www.atcc.org/Cultures/Products.cfm database resource for bacteria, bacteriophages, cell lines, fungi and yeast, plant tissue cultures, plant seeds, protozoa and algae and plant and animal viruses MO_773 http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ identifier for a taxon provided by the NCBI taxonomy database 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 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_784 A Reporter where only buffer was deposited on the array MO_505 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_620 PCR with multiple bands, or smear, in gel-separated reaction products 33 P, radioactive isotope of phosphorus, used for labeling/detection purposes. MO_427 MO_390 An integer >= 0. The diameter of the Feature is much smaller or much larger than expected based on the spotting pin diameter. MO_781 Hardware for automated liquid transfer and handling. MO_868 A descriptor for FactorValue where CellLine is compared. MO_562 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_430 A article published in a print or online journal having an ISSN. 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 sequence from a P1 artificial chromosome MO_909 deleted_term 1.2.0 Roentgen. Unit of exposure to gamma or x-rays in the air. 1 R= 2.58E-4 coulombs per kg. MO_725 MO_403 milliliter per kilogram MO_397 a controlled vocabulary for strains or lines http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C16403 deleted_term false MO_556 1.1.7 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 MO_867 The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.). MO_614 Kelvin, unit of temperature The array is made on a glass slide. MO_742 A cellular modification design type is where a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. MO_392 RNAi The process of introducing a foreign agent such as serum, vaccine, antigenic substance or organism. MO_559 infect 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_573 MO_870 Units of defined biological activity, e.g. cytokine stimulation, per ml. MO_579 The TechnologyType of the FeatureGroup is spotted single stranded oligonucleotides (of any length) on the substrate. MO_874 An analysis aimed at identifying differentially expressed genes in two or more conditions. deleted_term 1.2.0 sequence spliced out from a transcript MO_709 MO_491 the chrome border on an Affymetrix type array which is used as a point of reference for orientation (fiducial) A delivery method for compounds/drugs where the compound or drug is freely available. MO_592 MO_481 Storage where the thing stored is stored below 0 degrees celsius. MO_689 femtomole, unit of quantity The values are a sequence of one or more characters. MO_352 MO_758 A ComplexAction or ProtocolType describing growth of an organism or cell culture. MO_444 liter, unit of volume Logarithmic transformation of ratio data. MO_896 deciliter, unit of volume MO_624 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_448 Sequence feature whose derivation is unknown. MO_525 MO_521 Application of a scale adjustment following loess_group_normalization, to render the group variances similar. MO_435 A value which is a whole number (e.g. 10). MO_331 A unique alphanumeric identifier for the term. This will exist in the form of MO_someNumber, e.g. MO_123. MO_478 The father of one's father or mother. MO_959 The Feature or Zone is displaced from its expected position, due to e.g. a bent spotting pin(s). 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. The action of stabilizing an organism prior to treatment MO_776 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. 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_333 a surface coating for immobilization with the polypeptide, polylysine MO_569 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 femtogram, unit of mass MO_732 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 MO_411 Computationally derived sequence feature. the process of placing a seed or spore in some media with the intention to invoke germination. MO_748 The sister of one's father or mother. MO_354 MO_417 An analysis aimed at ranking genes or transcripts according to the uniformity of expression across a set of conditions. For example, the analysis can be used to rank genes according to the degree of tissue or developmental stage specificity. MO_1008 List of CABRI bacteria and archaea strains sorted by genus and species. It includes more than 40,000 resources that are available from seven European collections participating in the CABRI (Common Access to Biological Resources and Information) initiative (see http://www.cabri.org/ ). Detailed descriptions can be reached from the list and strains of interest can be requested. http://www.cabri.org/HyperCat/bact/all_A.htm MO_853 sequence of part of a gene, which is missing one or both ends An ordered, finite set of nonpositive floats. MO_1000 A replicate that consists of independent biological replicates made from different individual BioSources. MO_952 MO_825 gram, unit of mass MO_943 the mean and associated p-values resulting from computationally combining 2 or more sets of BioAssayData units per week, e.g. the number of units of alcohol consumed over a period of 7 days MO_388 An instrument which fragments tissues or other biomaterials. MO_714 An action where the temperature is specified. MO_393 MO_661 osmolality per kilogram of water, concentration of the solute per unit of solvent MO_815 The procedure of placing one physical object in the same container/physical space as another. MO_878 A descriptor for FactorValue where DevelopmentalStage is compared. MO_656 A float less than or equal to zero. MO_587 Time stated in terms of the day, month, and year. MO_416 biomaterial removed after the death of the organism MO_814 potential of hydrogen MO_503 deleted_term 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 MO_471 The procedure of labeling a biosample. MO_353 milligram per kilogram per day MO_846 kilogram, 1000 grams, unit of mass The mother of one's father or mother. MO_924 The mean and associated p-values resulting from computationally combining 2 or more sets of bioassay data. MO_671 MO_900 An ordered, finite set of negative integers. 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_708 Reporter used as a control where some label has been deposited. This includes fluor and radioactively labeled oligos and fluors alone. MO_675 A species experiment design type assays differences between distinct species. Indicates the why the term was deprecated. The possible values are: deleted_term, split_term, merged_term, replaced_term. merged_term replaced_term split_term deleted_term MO_1013 mating type indicating the presence of F plasmid in a bacterial cell MO_717 insemination copulation the physical act of copulation that occurs during the process of sexual reproduction synonyms: copulation, insemination MO_783 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 Software to control an arrayer. MO_502 http://nciterm.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C1908 a controlled vocabulary for compounds MO_376 MO_535 BioSequence of unknown type MO_962 Decreasing the concentration of solutes in a solution or suspension. http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C4741 a controlled vocabulary for histology MO_537 a design element group consisting of multiple types MO_528 MO_707 number of molecules, quantity unit 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_558 An ordered, finite set of positive floats. MO_777 The values are either TRUE or FALSE, which can be expressed as 1 and 0. MO_826 Describes a cell, nucleus or an organism with two copies of each chromosome. MO_836 Deoxyribonucleic acid. MO_945 A descriptor for FactorValue where DiseaseState is compared. MO_787 MO_931 Application of a normalization of type median_log_centering. The material (e.g. straw) that an animal sleeps on deleted_term MO_615 1.1.7 MO_665 The female offspring of the patient or individual under study. The process of generating an image from the array. MO_929 MO_817 The shape of the feature on the array is square. MO_362 Results of data reduction involving computation of the average of multiple intensities of identical type. These could include identical Features, Reporters or CompositeSequences in different microarray hybridizations, matched replicate spots on 2D gels run from the same sample, or repeat measurements of the same metabolite in replicate cell cultures. 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. MO_654 MO_747 a surface coating type for immobilization with the compound aminosilane MO_666 preservation type whereby the seed is maintained in a dormant state MO_462 A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. MO_779 combine The process of combining two or more BioMaterials. Exact synonym: combine MO_948 365 days, time unit MO_555 A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed. MO_802 false or no MO_454 An experiment design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model. MO_916 percentage volume per volume, concentration unit a nucleic acid consisting of a single polynucleotide chain. MO_576 MO_888 sequence from cosmid, a hybrid cloning vector containing cos sites, usually of ~40kB size 1.2.0 deleted_term The Pearson correlation is defined as the covariance of two data series divided by the product of their standard deviations. MO_632 MO_930 Hardware for synthesizing oligos. microsecond, unit of time MO_795 MO_727 the number of cells per ml Software used to transform the Measured or DerivedBioAssay data e.g. normalization. Non-exact synonym: normalization software MO_672 normalization software 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 photoperiod The length of the light period that a sample is subjected to. Exact synonym:photoperiod MO_604 MO_1017 The value of the property indicates a replacement term since the term was split. A female parent. MO_387 Conceptual action for specified protocol applied in treatment. MO_968 media type, usually some sort of broth MO_715 MO_488 milliliter, volume unit MO_533 transcription profiling gene expression A transcript identification design type characterizes the length and position of transcripts and allows identification of all forms of transcripts in the genome. transcription_profiling gene_expression expression_profiling expression profiling percent weight per volume, concentration unit MO_420 MO_699 A reference experiment design type is where all samples are compared to a common reference. The procedure of putting a physical object in a container/physical space. MO_470 MO_437 A modification whereby a functional gene, or a functional part of a gene, is inserted into an organism', e.g. by recombination, P-element insertion. MO_766 MO_355 A design in which the innate behavior of the organism is examined, e.g. path finding in bees. 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. replaced_term 1.1.9 The term name was changed to one more appropriate to the intent of the definition. MO_554 The values presented are logarithm, base e. 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_917 The action of changing the relative humidity, e.g. from 1% to 10%. An ordered, finite set of booleans. MO_712 MO_861 Application of a normalization of type lowess_normalization where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed. Absence of one chromosome of a pair of homologous chromosomes. In a normally diploid cell it is represented symbolically as 2N-1. 1.1.9 replaced_term A state or condition describing a cell or organism that has fewer copies of a single chromosome than the usual complement. MO_424 A community effort to provide standard terms for annotating phenotypic data. MO_704 http://www.informatics.jax.org/searches/Phat.cgi?id=MP:0000001 The Edinburgh Mouse Atlas Project (EMAP) ontology of mouse developmental anatomy covers the 26 developmental stages (Theiler Stages) from fertilization to birth. MO_357 http://genex.hgu.mrc.ac.uk deleted_term 1.2.0 sequence from the region between genes MO_463 ribosomal RNA gene sequence from gene coding for ribosomal RNA exact synonym: ribosomal RNA gene MO_955 deleted_term 1.2.0 MO_515 Angstrom, unit of distance, 1 angstrom is one tenth of a nanometer MO_575 A sex experiment design type assays differences associated with an organism's sex, gender or mating type. array_CGH array CGH CGH Experiment design type in which genomic content is studied using an array based assay. MO_856 The shape of the feature on the array is circular or oval. MO_459 MO_655 A male having the same genetic parents as another, or one genetic parent in common with another. The mean and variance values resulting from computationally combining 2 or more sets of bioassay data. MO_400 A cell cycle design experiment design type is one that assays events that occurs in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells. MO_822 MO_494 1.1.9 The possession of a third chromosome of any one type in an otherwise diploid cell. replaced_term MO_780 a record which identifies and describes biological pathways, e.g. a KEGG record Change in temperature. MO_677 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_907 MO_566 one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria MO_377 Application of a normalization of type loess_normalization where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed. cell lysate, a collection of cells whose membranes have been disrupted MO_903 MO_862 nanometer distance unit MO_974 The uncentered Pearson correlation is defined as the Pearson correlation for two data series where the mean of each data series is assumed to be zero. MO_937 An experiment in which spikes were introduced into some or all of the hybridizations for quality control or data transformation purposes. http://www.iupac.org/publications/pac/2000/205/205olesen.html MO_593 A resource of vocabularies for describing clinical tests, e.g. blood chemistry. MO_685 The action of collecting biological fluids including bodily secretions, exudates, transudates etc. and sampling of cytoplasm. The purpose of sampling may range from collecting other organisms (i.e. pathogens) to studying fluid composition. MO_791 Temperature associated with a particular environment. MO_824 An instrument capable of acquiring images of arrays. <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_660 The Arabidopsis Information Resource. http://www.arabidopsis.org/servlets/Search?action=new_search&type=ecotype DNA from organelles such as the mitochondria or chloroplast. MO_645 The procedure of placing a physical object under specified conditions e.g. time, temperature, humidity for the purposes of obtaining a different product. MO_965 http://arabidopsis.info/catalogue.html The Nottingham Arabidopsis Stock Centre (NASC). Provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. MO_379 Sequence from some nucleic acid copy and the associated vector for which the source clone supplier is unknown. MO_371 the action of emergence and separation of offspring from the mother. MO_710 A float that is < 0. MO_728 a cubic centimeter, volume unit MO_834 MO_920 millisecond, time unit MO_638 Tag Image File Format (TIFF) is a common format to describe and store raster image data from scanners and other imaging devices. TIFFs may contain one or more channels and the data may be compressed using a lossless compression algorithm. 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 The procedure of placing a physical object under specified conditions e.g. time, temperature, humidity, for the purposes of keeping it in the same state. MO_442 MO_644 A record which identifies a nucleic acid sequence feature(s) and which has been curated. a record which describes and identifies a compound e.g. drug record part of NCI thesaurus MO_546 An instrument that mixes by rapid oscillation. MO_983 MO_582 grams per deciliter, concentration unit 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_961 1.2.0 small nuclear RNA gene deleted_term sequence from gene coding for small nuclear RNA exact synonym: small nuclear RNA gene deleted_term MO_384 A descriptor for a clinical treatment for a patient. MO_522 milligrams per milliliter, concentration unit MO_359 A SurfaceType of unknown type. MO_648 millimeter, unit of distance MO_628 picomolar, concentration unit MO_529 A record which describes and identifies a term, class or instance in an ontology or controlled vocabulary e.g. ICD MO_981 A quality control testing experiment design type is where some aspect of the experiment is quality controlled for the purposes of quality assurance MO_736 Absorbs at 556 nm, emission maxima at 573 nm (orange). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble. MO_360 An ordered, finite set of nonnegative floats. MO_753 A contact who performs data analysis, e.g. statistician. MO_564 The modification of the genetic material (either coding or non-coding) of an organism by mutagenic compounds or irradiation. A descriptor for FactorValue where BioSources are compared. MO_639 MO_608 time point that indicates the start of some developmental stage MO_828 a nucleic acid consisting of two polynucleotide chains having antiparallel orientation and being bound together by hydrogen bonding between the chains. This would apply to DNA and some RNA genomes, but not to rRNA or tRNA, etc. An instrument capable of applying centrifugal force to tubes or microtiter plates. MO_476 MO_871 The stage premortem or postmortem at which the sample was processed for extraction of biomaterials. MO_990 A biomaterial obtained embedded in paraffin (wax). An ontology of stages of growth and development of the model plant Arabidopsis thaliana. http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/developmental/plant_development/Arabidopsis/temporal.tair?rev=1.21&view=markup MO_919 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_428 Unit of time corresponding to approx. one cycle of the moon's phases. MO_631 A quantitative measure of the relative abundance of a transcript (MAS 4.0 version of the Affymetrix analysis software). MO_534 image analysis image quantification MO_928 The process of obtaining quantifiable values from the scanned image of the array. Exact synonyms: image analysis, image quantification MO_786 A proprietary image data format that is lossless and containing one channel of data. MO_863 A descriptor for FactorValue where PhysicalCharacteristics are compared. High frequency recombinant, mating type that indicates that the F plasmid has integrated into the chromosome MO_419 1.1.7 deleted_term Absorbs at 532 nm, emission maxima at 554 nm (yellow). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble. MO_375 The organism is forced to respond to a stimulus with some behavior (e.g., avoidance, obtaining a reward, etc.) MO_674 An operator variation experiment design type assesses the operator performance and relation to data consistency and quality. MO_519 Ontology of human developmental anatomy for Carnegie stages 1-20. MO_844 http://obo.sourceforge.net/list.shtml MO_754 nanoliter unit of volume A member of a consortium of institutions. MO_778 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 Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point. MO_738 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_649 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. An ordered, finite set of floats. MO_760 The process of harvesting cells from culture. MO_982 protocol that describes how the features, reporters and composites were designed and or selected for inclusion in an array design MO_523 MO_745 The point at which an organism emerges from an egg. person who prepares the MAGE-ML file MO_695 The action of removing one or more organism parts. MO_374 MO_819 http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C28076 a controlled vocabulary of tumor grading terms the term has been decomposed into more specific terms http://nciterms.nci.nih.gov MO_630 a controlled vocabulary for geographic locations http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C16632 MO_456 a controlled vocabulary for disease states MO_790 http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C7057 a controlled vocabulary of cell types MO_687 http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=12596 http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12596 MO_351 a controlled vocabulary of targeted cell types 1.1.7 A description logic namespace that contains controlled terminology used at NCI. split_term MO_668 A function applied to subsets of values from the same Measured/Derived bioassay data set. a measurement where the value is dependent on another measurement MO_396 MO_646 fluorophore used for labeling/detection purposes MO_590 The physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth (from the GO). MO_755 A grouping of DesignElements, Features/Reporters/Composite Sequences which are expected to detect a signal in the biomaterial. MO_453 The amount of moisture in the air expressed as a percentage of the maximum amount the air is capable of holding. The process of removing tissue from a living organism. MO_711 A chamber in which the hybridization is performed which maintains constant conditions. MO_563 MO_440 Version of the MGEDOntology. An element that is an oligonucleotide of at least 50 nucleotides in length. MO_598 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 Portable Network Graphic, a lossless image data format. MO_1001 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. Describes a cell, nucleus or organism with three or more copies of each chromosome. MO_394 MO_434 A PCR based quantitative validation of a subset of the array based data used for experimental QC purposes. MO_407 Mating type of S.pombe. MO_545 The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil) high molecular weight DNA MO_599 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. The procedure of agitating 2 or more materials in order to combine them. The materials may be of any state solid/liquid/gas. MO_944 MO_495 The act of placing a plant in media (e.g. soil) to allow it to grow. This excludes sowing. ontology mage 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. a record which identifies and describes the function of a gene product, e.g. E.C. record MO_538 MO_347 An experiment done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture. the number of colony forming units per ml MO_788 http://cvs.sourceforge.net/viewcvs.py/*checkout*/obo/obo/ontology/developmental/animal_development/fly/fly_development.ontology?content-type=text/plain&rev=1.1 MO_865 uri for FlyBase developmental stage terms MO_391 time unit MO_774 A record which identifies and describes a nucleic sequence feature which has been computationally determined or predicted E.g. and Ensembl record fluorophore used for labeling/detection purposes MO_739 MO_634 ExperimentDesignType of unknown type. TechnologyType of FeatureGroup where protein (other than antibody) is spotted directly. MO_996 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. sequence from the mitochondrial genome MO_581 MO_835 sample The procedure of separating a BioMaterial into two or more BioMaterials of similar composition e.g. aliquoting a sample. The BioMaterial may be a BioSource (e.g., a tissue) or a BioSample (e.g. RNA extracted from a BioSource). Non exact Synonym: sample MO_544 A family history design type is where the family history such as traits, characteristics, susceptibility to disease is studied nanomoles, quantity unit MO_743 Polymer of amino acids. MO_683 MO_551 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. 1.2.0 MO_700 Mix through the process of inverting. Ribonucleic acid. MO_594 MO_818 The process of physically creating the array. 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 A PCR based semi quantitative validation of a subset of the array based data used for experimental QC purposes. MO_986 deleted_term MO_911 1.2.0 genomic sequence 5' to a gene where the transcription initiation complex forms. Database resource for universal identifiers for laboratory and other clinical observations MO_731 http://www.loinc.org/download 1.2.0 MO_531 A method of analyzing the significant expression level of a Feature by calculating the intensity-dependent Z distribution value for the logarithm of the intensity ratios from the two channels. deleted_term MO_370 Depriving an organism of food or nutrients An ordered, finite set of nonpositive integers. MO_804 MO_586 ctDNA: sequence from the chloroplast synonym: chloroplast DNA chloroplast DNA MO_447 A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out MO_479 Mix by drawing up and down with a pipette. 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 MO_877 m 60 seconds, unit of time 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_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). An ordered, finite set of positive integers. MO_873 Unit for a simple count of things MO_500 An experiment in which the array platform is compared, e.g. Agilent versus Affy. MO_899 MO_622 Chromosome segments that have been turned through 180 degrees with the result that the gene sequence for the segment is reversed with respect to the rest of the chromosome. MO_423 mRNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple sequences as input. Delivery method for a compound or drug where the substance is administered via an injection into the muscle. MO_617 MO_921 A descriptor for the TechnologyType for a group of features where single stranded DNA PCR product is spotted on the array. The procedure of applying a centrifugal force to a physical object. Exact synonym: centrifuge centrifuge MO_879 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. d MO_513 24 hours, time unit An integer less than or equal to zero. MO_623 MO_571 The Zone is excluded due to smearing, streaking, or dense background in the Zone. multiple of stock solution concentration, concentration unit MO_496 MO_885 A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. MO_607 The procedure of extracting nucleic acid from the biomaterial. 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_358 Amplification of nucleic acid sequence by use of the polymerase chain reaction whereby the number of templates grows geometrically with each cycle. MO_373 Total cellular and nuclear RNA. MO_733 Delivery method where a compound/drug is administered in the culture medium (e.g., for in vitro treatment). the array is made on silicon MO_382 DNA sequence produced from some base calling or alignment algorithm which uses multiple sequence as input MO_361 MO_567 The "Manhattan distance" is the shortest path between two points in a block format, e.g. the length of the path along Manthattan city streets. MO_508 one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria MO_386 A float greater than or equal to 0. Sequence derived from expressed sequence tag. EST's are likely to be partial, single read and low quality sequences. 1.2.0 MO_412 deleted_term The procedure of euthanizing an organism. MO_602 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 MO_923 A record which describes and identifies a paper publication e.g. a medline record MO_851 An ordered, finite set of negative floats. http://www.informatics.jax.org/external/festing/mouse/STRAINS.shtml Database entry from the resource at The Jackson Laboratory which has details of approved mouse strain nomenclature. MO_369 MO_957 A method of re-scaling ratio data by iteratively subtracting the mean log base 2 ratio from each log2(ratio). This adjusts the mean log2(ratio) to zero. In each subsequent iteration, outliers are removed based on user-specified criteria, the mean log(2) ratio is recalculated based on the remaining data, and the entire data set is rescaled again. This continues until the mean log(2) ratio converges. MO_724 The Sequence Ontology is a set of terms used to describe features on a nucleotide or protein sequence. http://song.sourceforge.net/ A software implementing a Higher Level Analysis protocol of type differential_expresssion. MO_350 MO_629 An integer > 0. 1.2.0 deleted_term MO_850 transfer RNA gene sequence from a gene coding for transfer RNA exact synonym: transfer RNA gene MO_832 A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied. MO_938 The difference in expression level for a transcript between data from two arrays, expressed as the log2ratio. A signal log ratio of 1 is the same as a Fold Change of 2. MO_372 one or more DNA or RNA based non cellular infective agent, including bacteriophage MO_1002 An irregularity in the number of chromosomes, usually in the form of a gain of genetic material. MO_881 Provider of biosequences (clones, oligos etc) for deposition on the array. http://www.gramene.org/ A Comparative Mapping Resource for Grains. MO_678 MO_512 Absorbs at 346 nm, emission maxima at 442 nm (blue). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble. MO_890 Person or organization that manufactured the array. A population of multiple sexes, e.g. a mixture of females and males, or males and hermaphrodites. MO_436 MO_901 One of a pair of replicate assays in which LabeledExtracts derived from the same BioMaterial used for both assays (e.g., a hybridization or a 2-D gel run) differ only in that the dyes used for labeling have been reversed, e.g., assay 1: A-Cy3 vs. B-Cy5, and assay 2: A-Cy5 vs. B-Cy3. The purpose of using dye-swap replicate pairs is to assess or remove dye-specific biases from the combined experimental results. 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_694 1.2.0 MO_344 deleted_term a double stranded oligonucleotide The value of the property indicates the replacement term. MO_1018 MO_612 One or more dissociated cell(s) possibly heterogeneous, excluding single cell organisms. MO_860 A value which is a floating point number (i.e. real number) with arbitrary precision (e.g. 2.34). MO_833 glycoprotein of the immunoglobulin family that can combine specifically non-covalently, reversibly with a corresponding antigen The atmospheric conditions used to culture or grow an organism. MO_498 MO_771 The modification of an organism that renders a gene non-functional e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods. agar stab, a cell culture inoculated into agar for long term storage MO_971 MO_813 Unit of brightness or luminance. MO_975 delivery method for drug or compound whereby the drug is administered via the mouth MO_682 mating type indicating the absence of F plasmid in a bacterial cell MO_680 A descriptor for FactorValue where Sex is compared. 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 sequence that represents the product of an RNA polymerase engaged in transcription MO_827 The procedure in which solid material is dispensed or dissolved in a liquid. MO_466 MO_843 A descriptor used in cancer biology to describe abnormalities of tumor cells. Polymerase chain reaction. An element generated using this procedure. MO_915 guilt by association MO_904 A co-expression experiment design type identifies genes which are coordinately expressed and are potentially used to infer a role in a biological process(es) non-exact synonym: guilt by association An optimization experiment design type is where different protocols or protocol parameters are compared. MO_934 A type of solid media commonly used for growing organisms MO_935 attomole, quantity unit MO_977 MO_993 Delivery method where a compound/drug is administered in food or water. SubstrateType of unknown type. MO_484 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. MO_368 MO_633 Software to create MeasuredBioAssayData from images. Exact Synonym: image analysis software, image quantification software. image quantification software image analysis software A software variation design type compares different types of software for performance, accuracy, precision and reproducibility. MO_643 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. MO_565 An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. MO_857 http://www.ebi.ac.uk/chebi 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. A descriptor for FactorValue where age is compared. MO_467 MO_657 Application of a normalization of type mean_log_centering. http://www.cabri.org/HyperCat/yeast/all_A.htm MO_1010 List of CABRI yeasts strains sorted by genus and species. It includes more than 30,000 resources that are available from four European collections participating in the CABRI (Common Access to Biological Resources and Information) initiative (see http://www.cabri.org/ ). Detailed descriptions can be reached from the list and strains of interest can be requested. the term has been subsumed into a more general term A RNA stability experiment design type examines the stability and/or decay of RNA transcripts. MO_553 The value indicates the parent of the term before the term was deprecated. MO_1016 MO_480 Generation of a DNA strand from an RNA strand using reverse transcriptase. MO_767 The point at which the egg(s) is laid by an organism. 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_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). The gain of a segment of the genetic material in a chromosome by fragmentation of a chromosome and transfer of the broken-off portion of another chromosome or other sources. MO_518 TechnologyType of FeatureGroup where antibodies are spotted directly. MO_483 A Reporter where genomic DNA has been deposited, the genomic DNA may be fragmented, e.g. salmon sperm DNA, Cot1DNA. MO_449 MO_852 record which describes and identifies clinical information about an organism Absorbs at 495 nm, emission maxima at 519 nm (green). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble. MO_446 MO_991 A publication type which is available online and which is not an online journal article, e.g. a web site or service. concrete place_holder 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 http://www.cbil.upenn.edu/anatomy.php3 a controlled vocabulary provided by CBIL MO_886 Software used to control automated liquid handler. MO_761 MO_658 The mass of an object in kilograms divided by the surface area in meters squared. Also known as the Body Mass Index (when applied to a person) which is a measure of leaness/obesity. Exact synonym:kg/m2 kg/m2 MO_876 Emergence of an adult insect from its pupa or cocoon. MO_601 A contact's affiliation, e.g. university, research institute or business. 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 A record which describes and identifies a primary sequence record e.g. DDBJ/EMBL/Genbank MO_757 MO_611 The action of preparing a slide for the microscopical examination of organism parts or cell types. percent weight per weight, concentration unit MO_474 sequence which represents regions of a transcript that are joined to another exon during splicing 1.2.0 MO_619 deleted_term 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_698 An environmental history design type is where some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc. Allow time to pass. It's measurement should be a unit of time. MO_988 Data from which a subset has been removed based on some criteria, e.g. data below an intensity threshhold. MO_625 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_973 An ordered, finite set of nonnegative integers. person who checks the consistency of the data and MAGE-ML file MO_893 32 P, radioactive isotope of phosphorus used for labeling/detection purposes MO_839 MO_468 The Foundational Model of Anatomy (FMA) is concerned with the representation of concepts and relationships necessary for the symbolic modeling of the structure of the human body. http://sig.biostr.wahington.edu/projects/fm/ A descriptor for FactorValue where CellType is compared. MO_548 MO_580 http://www.nlm.nih.gov/mesh/filelist.html database entry from MESH, medical subject headings vocabulary resource http://www.informatics.jax.org/mgihome/GXD/AD/ MO_693 database entry from mouse anatomical dictionary for developmental stage term Graphics Interchange Format , a common image data format containing RGB data compressed with fairly high data loss. MO_963 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. MO_550 MO_895 The BioSample immediately before labeling. database entry from WebReni A resource for rat and mouse unified nomenclature describing lesions MO_737 http://www.item.fraunhofer.de/reni/index/htm MO_953 An organism part comparison experiment design type compares tissues, regions, organs within or between organisms MO_399 The fluid and dissolved substances excreted by the kidney. 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_842 7 days, unit of time 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_807 MO_859 A descriptor of FactorValue where comparisons of strains or lines are made. sample which has been removed prior to the death of an organism MO_705 MO_458 the mean and variance values resulting from computationally combining 2 or more sets of BioAssayData increment in copy number of a genomic region, includes gene amplification, genomic amplification, and DNA amplification MO_609 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 An instrument designed to automatically raise and lower the temperature of wells or tubes. Usually used to perform PCR. Exact Synonym: thermocycler MO_854 Person who contributed to the study. MO_769 A record which describes and identifies the relationship between species and is computationally determined and based on sequences e.g. Treebase record MO_662 Ontology describing anatomical and physiological relationships. MO_967 http://portal.bioengineering.elyt.ods.org/ontology/ MO_380 Water consumed by or enveloping the organism that the biosource is derived from. Increasing the concentration of solutes in a solution or suspension. MO_883 MO_492 The array is made on a nylon membrane. MO_506 of, pertaining to, or designating the sex that only produces gametes that can be fertilized by male gametes. 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. DNA which is generated by chemical or enzymatic (non cellular) means. non-exact synonym: cDNA cDNA MO_577 MO_918 Describes a cell, nucleus or an organism whose chromosome number is not an exact multiple of the haploid number (n). MO_713 The procedure of extracting/taking out a part of a reaction/contents of a container. MO_547 Absorbs at 663 nm, emission maxima at 690 nm (far-red). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble. MO_792 The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression. A float > 0. MO_501 A state/condition describing a cell, or organism, in which all, or part, of a chromosome from a donor replaces that of the recipient. Examples include strains created by repeated backcrossing as well as those created by recombinant methods. For single gene insertion, use the term gene_knock_in. MO_995 Robust Multiarray Average. A quantitative measure of the relative abundance of a transcript. RMA is a summary measure of related Ôperfect matchÕ Features on an Affymetrix array. The values are background-adjusted, normalized and log-transformed values. MO_987 An operon identification experiment type is designed to identify locations and members of operons in a genome. MO_772 MO_650 The concentration range of the organism. MO_805 grams per liter, concentration unit MO_998 mole, unit of quantity MO_589 A biomaterial that has been lyophilized or dried by freezing under a vacuum. 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). 1.2.0 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 deleted_term MO_880 Mix through the use of a vortexer. MO_926 microliter, unit of volume BioSequence generated by means of polymerase chain reaction MO_450 MO_606 A function applied to corresponding values coming from a set of compatible Measured/Derived bioassay data sets. Two Measured/Derived bioassay data sets are compatible if there is a natural one-to-one correspondence between them. MO_882 Person who is the primary contact for data submitted to a database. MO_686 A method to normalize paired-assay data that uses as a normalization coefficient the sum of intensity values from one assay divided by the sum of intensities from the other, where those sums are taken over all data points, or an appropriate subset of these (e.g. special control Features on a microarray, or 2DE spots containing constitutively expressed proteins). This normalization coefficient is used to rescale the intensity data in one data set relative to the other. Note that a normalization method that employs the average intensity rather than the sum (of all data points, or an appropriate subset) falls into this category as well. MO_457 Application of a normalization of type quantile_normalization. MO_673 deleted_term a nonparametric measure of the agreement between two rankings 1.1.7 MO_730 A sample freshly obtained from the organism(s). E.g. a liver freshly removed from a rat. MO_799 Absorbs at 679 nm, emission maxima at 702 nm (far-red). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble. A transformation method in which low intensities are linearly scaled while high intensities are logarithmically scaled. The transition point is determined by minimizing the absolute deviation of the variance of log ratios. MO_845 MO_789 Results of data reduction involving computation of a representative value, e.g. by averaging, for a group of replicated Features, Reporters or CompositeSequences from a single hybridization. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. MO_560 1.2.0 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. deleted_term MO_894 The BioSample at any stage other than immediately before labeling. MO_637 Mating type of S. cerevisiae. The array is made on a nitrocellulose filter. MO_455 a record which describes and identifies an amino acid feature which is computationally derived e.g. PFAM MO_797 Software upon which other software runs. MO_847 MO_570 1.2.0 deleted_term sequence of a single stranded synthesized oligonucleotide The mean and coefficient of variation values resulting from computationally combining 2 or more sets of bioassay data. MO_840 A device capable of applying software. MO_510 MO_451 A record which describes and identifies an amino acid sequence which has been curated MO_838 gene sequence which has been computationally predicted MO_821 soil, growth media for plants and other soil living organisms Contact which provides funding for experiments. MO_520 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 picogram, mass unit MO_363 1.1.9 1.1.8 1.3.0 1.2.0 1.1.7 The value of the property indicates what version of the ontology the term was deprecated from. MO_1014 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_808 MO_398 A method of normalizing log ratio data by subtraction of the mean log ratios computed across all data points, or an appropriate subset of these (e.g. special control Features on a microarray, or 2DE spots containing constitutively expressed proteins). MO_509 milimolar, concentration unit An experiment design type where genotype, haplotype, or other individual genetic characteristics are compared. MO_527 MO_936 Mole per liter or molarity, concentration unit UI International unit 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_408 the organism part in which the tumor originated 1.1.7 deleted_term MO_540 true MO_768 the number of plaque forming units per ml List of CABRI hybridomas sorted by name. It includes 397 resources that are available from European collections participating in the CABRI (Common Access to Biological Resources and Information) initiative (see http://www.cabri.org/ ). Detailed descriptions can be reached from the list and cell lines of interest can be requested. http://www.cabri.org/HyperCat/cells/hybrid.htm MO_1006 the organism part in which additional tumors are identified remote from the primary site MO_806 http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C28108 a controlled vocabulary for disease stages MO_422 deleted_term A biomaterial obtained as fluid consisting of plasma, blood cells and platelets. MO_409 1.1.9 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_378 A measure of the density of an attached or monolayer culture (e.g., cell culture), e.g., 80 percent_confluence. MO_992 This ontology describes the anatomy of the adult mouse. It contains anatomical structures for the postnatal mouse (Theiler stage 28). http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/MA.ontology?rev=1.1&view=markup picomoles, quantity unit MO_688 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_940 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_385 deleted_term 1.2.0 single oligo used for polymerase chain reaction direction unspecified MO_651 MO_950 The brother of one's father or mother. MO_752 micromoles, quantity unit 1.1.9 split_term MO_532 The specific actions or reactions of an organism in response to external or internal stimuli. Patterned activity of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions. MO_426 Database entry from the ChemIDplus database which stores information on the structure, identifiers etc for compounds. http://chem.sis.nlm.nih.gov/chemidplus MO_762 A male parent. MO_810 Processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. The sequence of the BioSequence that relates to this reporter has not been sequence verified by the experimenter. MO_970 MO_439 deleted_term sequence from a plasmid, an extrachromosomal autonomously replicating piece of DNA excluding mitochondria and chloroplasts 1.2.0 degrees celsius, unit of temperature MO_980 MO_676 An instrument that produces DNA sequences. MO_933 A binding site identification design type investigates protein binding sites on nucleic acids non-exact synonym: ChIP, chromatin immunoprecipitation, chromatin IP chromatin immunoprecipitation chromatin IP chromatin_immunoprecipitation ChIP-chip MO_721 femtoliter, unit of volume MO_691 A record which describes and identifies an image, e.g. an image from the mouse atlas MO_549 Change in light intensity or wavelength. An integer < 0. MO_864 MO_640 1.2.0 single stranded oligo used for polymerase chain reaction deleted_term complementary RNA aRNA cRNA amplified RNA MO_543 RNA which is generated by chemical or enzymatic (non cellular) means. E.g. T7 promotor generated RNA. Non-exact synonym: cRNA, complementary RNA aRNA, amplified RNA MO_472 A normalization method that uses as a coefficient the sum of all intensities in the data set, or an appropriate subset of these (e.g. special control Features on a microarray, or 2DE spots containing constitutively expressed proteins). The intensities are normalized through division by such a coefficient (and possible subsequent multiplication by a target constant). Note that a normalization method that employs the average intensity rather than the sum (of all data points, or an appropriate subset) falls into this category as well. MO_875 units per liter degrees Fahrenheit, unit of temperature MO_812 MO_756 Multiarray-Based Expression Index (MBEI). A quantitative measure of the relative abundance of a transcript. MBEI is used in the dChip software to obtain a signal intensity from a group of related Features on an Affymetrix array. MO_966 cDNA complementary DNA 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 MO_557 A descriptor for FactorValue where GeneticVariation is compared. MO_469 Version of the MGED Ontology. deleted_term 1.1.8 MO_703 A daughter of one's son or daughter. Term used to describe a role or factor value for the person or organization that provides a BioMaterial. MO_591 MO_663 A device for controlling temperature. An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip MO_858 dye flip flip dye MO_800 An ordered, finite set of strings. MO_410 Application of a scale adjustment following lowess_group_normalization, to render the group variances similar. MO_585 Radiation absorbed dose. Unit of energy absorbed per unit mass as a result of exposure to radiation. 1 rad = Absorption of 100 ergs per gram of material = 0.01Gy. MO_684 Ontology of human terms that describe the sample source of human cDNA and SAGE libraries. http://www.sanbi.ac.za/evoc/ontologies.html MO_572 candle power 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 A publication type which has an ISBN. MO_627 a compound used for labeling/detection purposes MO_793 the forward strand exact synonym: + + MO_820 MO_910 mark made on slide using a laser which is used as a point of reference for orientation (fiducial) An instrument designed to remove excess liquid by vacuum and heating. MO_696 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, tumour, tissue/organ, and transforming agent. MO_1007 A hardware variation experiment design type compares different types of hardware for performance, reproducibility, accuracy and precision. MO_734 MO_741 a measurement where the value is independent of other measurements microgram, unit of mass MO_438 MO_461 Absorbs at 590 nm, emission maxima at 617 nm (red). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble. MO_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_956 A transformation method in which low intensities are linearly scaled while high intensities are logarithmically scaled. The transition point is determined by minimizing the absolute deviation of the variance of log ratios. a result which can not be interpreted as positive or negative MO_744 MO_905 picoliter, volume unit 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. 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 loss of a segment of the genetic material from a chromosome. MO_922 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. 1.1.7 MO_941 MO_887 Groups of assays that are related as part of a time series. MO_541 A device for controlling temperature by immersion in water. centimeter, a unit of distance MO_837 An instrument designed to mechanically wash or stain arrays. MO_626 An experimentally defined sequence feature. MO_452 http://hazel.niehs.nih.gov/user_spt/pct_terms.htm Toxicology Data Management System, a database resource for systems, organs, pathology, etc. MO_718 scanning software Software to control a scanner and manipulate and save images. Exact synonym: scanning software MO_1003 MO_667 PCR where no products of any kind appear in gel-separated reaction products. MO_751 The scale is a standard base 10, non logarithmic scale. MO_636 1.1.9 A biosource obtained as fecal matter. deleted_term MO_588 A growth condition experiment design type is where some part of the growth condition is changed for the purposes of the experiment, examples of growth conditions changed are media, temperature, humidity, light, nutrients. A descriptor for FactorValue where IndividualGeneticCharacteristic is compared. MO_722 Computed as the ordinary Pearson correlation coefficient between two groups of rankings. MO_552 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 The values are unordered and have no scale. MO_542 An experiment which has a peer reviewed publication attached. MO_365 MO_869 katal per liter, catalytic-activity concentration unit The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. (from the GO) MO_701 Database entry from the mouse tumor biology database, a resource for nomenclature of mouse tumors. MO_942 http://tumor.informatics.jax.org MO_939 A translational bias is an experiment design which characterizes the association of transcripts and translation machinery. MO_652 individual whose sex organs contain only male gametes MO_364 A Reporter that could be hybridized to an exogenously added nucleic acid or protein (spike) before or during hybridization and is used as a control for data processing. It may be deposited at one or more known concentrations (calibration). A reporter may be a spike, a calibration control or both. MO_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_524 Indicates that a dye swap was performed for some or all hybridizations within an experiment An instrument for sonicating biomaterials. MO_477 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_801 milliliters per liter, concentration unit MO_949 milligram, mass unit The type of protocol used to preserve (including storage or keep in stasis) the biomaterial. MO_415 MO_486 h 60 minutes, time unit replaced_term MO_706 1.3.0 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. Describes a cell, nucleus or an organism with one copy of each chromosome. MO_719 MO_616 replaced_term The organism (or organism part) has been exposed to a virus or pathogen. 1.3.0 an organism with both male and female sexual organs in one individual synonym: intersex intersex MO_356 A son of one's son or daughter. MO_831 A normalization testing experiment design tests different normalization procedures. MO_729 Delivery method whereby a drug or compound is administered under the skin of the organism. MO_960 an unspecified collection of heterogeneous molecules, e.g. lipids, carbohydrate , nucleic acids and proteins MO_889 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 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 MO_366 Introduction of genetic material into an organism often in the form of a plasmid. Sequence features derived by both computational and experimental methods. MO_516 MO_460 ProtocolType of unknown type. A cell type comparison design experiment design type compares cells of different type for example different cell lines. MO_764 MO_803 sequence of a processed transcript capable of directing protein synthesis 1.2.0 deleted_term MO_429 true or yes MO_432 delivery method whereby a compound or drug is administered via a vein deleted_term 1.2.0 single stranded oligo used for polymerase chain reaction MO_381 meter, distance unit MO_367 MO_925 A Reporter indicated as being a control of unknown type. The rating of containment system used to protect organisms from infectious agents. MO_511 A record which describes and identifies an experimentally derived protein structure e.g. MSD MO_785 Person or organization that manufactured the software. MO_475 The source DNA was not printed for a Feature or Zone on the slide, possibly due to lack of sample, broken or clogged spotting pin. MO_405 MO_841 A design that compares samples from live and dead organisms. Multiple testing correction uses individual p-values derived from multiple statistical tests to control either the family-wise error rate or the false discovery rate. MO_561 a record which describes and identifies a protein structure e.g. PDB MO_765 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 MO_497 An instrument which controls hybridization conditions, into which a hybridization chamber may fit. thermocycler MO_716 Hardware for measuring light at different wavelengths. A delivery method for compound or drug whereby the substance is administered via the peritoneum. MO_473 MO_830 A Reporter where no material or buffer was deposited on the array Mating type of S.pombe. MO_855 replaced_term MO_539 A circadian rhythm experiment design type assays the events associated with the circadian rhythm which is a biological activity that exhibits an endogenous periodicity independently of any daily variation in the environment. 1.1.7 The values presented are logarithm, base 10. MO_735 An action whereby an organism(s) has had genetic material removed, added, or rearranged. MO_927 MO_584 Microeinstein per second and square meter (µE m-2 s-1 or uEinstein m-2 s-1). One einstein is one mole or 6.02x10e23 (Avogadro constant) photons. It is commonly used as a unit for photosynthetically active radiation (PAR), however the einstein is not an SI unit. Therefore, microEinsteins per m2 per second is identical to micromoles per m2 per second (SI unit for light irradiance). i.e. (1000 µE m-2 s-1 = 1000 µmol m-2 s-1). MO_383 Indicates that one or more BioMaterialCharacteristics have changed during the treatment of a BioMaterial. Non exact synonym: change growth condition, change environment change environment change growth condition MO_346 A record which describes and identifies a microarray experiment e.g. GEO 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_969 MO_972 http://eulep.anat.cam.ac.uk/Search_Pathbase/index.php database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice MO_600 mRNA polyA+_RNA RNA which has been obtained by selection for polyA tracts. Exact synonym: polyA+_RNA Non-exact synonym: mRNA MO_679 RNA obtained from the nucleus. sequence which represents an open reading frame, a series of codon triplets deduced from a DNA sequence, that contain a start and a stop codon. 1.2.0 MO_413 deleted_term 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_823 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 MO_1009 MO_770 treatment of a biomaterial with radiation e.g. electromagnetic radiation RNA obtained from an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus. MO_574 An injury experiment design type is where the response of an organism(s) to injury or damage is studied. MO_726 The shape of the feature on the array is rectangular. MO_897 An instrument capable of manufacturing arrays by spotting material. MO_697 Software used to cluster the data. MO_464