An ontology for microarray experiments in support of MAGE v.1. February 9, 2007 Chris Stoeckert, Helen Parkinson, Trish Whetzel, Paul Spellman, Catherine A. Ball, Joseph White, John Matese, Liju Fan, Gilberto Fragoso, Mervi Heiskanen, Susanna Sansone, Helen Causton, Laurence Game, Chris Taylor The MGED Ontology Concepts, definitions, terms, and resources for standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1 1.3.1.1 ontology MO_26 concrete class to hold instances used as the filler for the property has_cancer_site Description of the source of the nucleic acid used to generate labeled material for the microarray experiment. MO_182 mage abstract ontology abstract MO_9 A strain or line is an animal or plant offspring that has a single ancestral breeding pair or parent as a result of brother x sister or parent x offspring matings. This class is extended to include F1 offspring and established breeding lines. For microbes, these are isolates derived from nature or in the laboratory. Water consumed by or enveloping the organism that the biosource is derived from. ontology abstract MO_153 The MAGE package for defining classes for quantitation. abstract mage MO_130 The developmental stage of the organism's life cycle during which the biomaterial was extracted. abstract MO_120 ontology Refers to the bedding material present in an animals housing. place_holder MO_154 ontology concrete mage A parameter is a variable within a protocol. MO_110 ontology concrete Database for sequence annotation information. MO_83 abstract MAGE package for measurement. MO_89 mage Database of tumor grading information ontology concrete MO_187 Measured values and units. mage concrete MO_144 MO_198 Controlled terms for descriptors for coating of the substrate. ontology concrete ontology class to hold instances used as the filler for the property has_result MO_65 concrete BioMolecularAnnotation experiment design types are those which are designed to investigate functions, processes, locations and identity at the molecular level e.g. binding site identification, genotyping. concrete MO_213 ontology The expected shape of the feature on the array. concrete ontology MO_8 abstract ontology The BioMaterial's (i.e., the patient's) medical record as background information relevant to the experiment. MO_189 ontology MO_188 Member of the biosource's family. abstract Controlled terms for how the sequence features were determined (e.g., experimental, computational, etc.) MO_207 ontology concrete MO_40 BioAssayData refers to the data files including images generated from one or more BioAssays. Controlled terms for descriptors of the role of contact, e.g. submitter, biosource_provider. MO_180 concrete ontology MO_113 concrete Controlled terms for descriptors of types of hardware. ontology MO_226 mage Description of the processing state of the biomaterial for use in the microarray hybridization. abstract concrete ontology MO_156 Quantity units not specified in MAGE. MO_216 The process by which BioAssays (data, elements, quantitation types) are averaged normalized, selected, filtered, or otherwise changed into a new set of BioAssay data. abstract MO_101 Organisms or organism parts used as a designed part of the culture (e.g., red blood cells, stromal cells). ontology ontology A descriptor of the location from which a BioMaterial was obtained, e.g. country, region, grid reference. abstract MO_132 MO_165 The process by which derived BioAssays are created from measured BioAssays and/or derived BioAssays. concrete ontology A methodological experiment design type investigates differences caused by application of protocols, hardware, software and bioassay relationships, e.g. quality control, replicates, loop. ontology MO_2 concrete ontology The time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise the identifiable point must be specified such as planting (e.g. 3 days post planting). abstract MO_178 place_holder MO_38 ontology The effects of different investigators, laboratories, or organizations on experimental results are studied. ontology abstract MO_162 ReplicateDescription provides details about the type of replication used in the experiment. ontology Physical properties of the BioMaterial e. g. mass or height abstract MO_129 ontology MO_41 Controlled terms for descriptors of the warnings associated with reporters. concrete concrete MO_6 ontology An irregularity in the number or structure of chromosomes, usually in the form of a gain (duplication), loss (deletion), exchange (translocation), or alteration in sequence (inversion) of genetic material. Excludes simple changes in sequence such as mutations, and is usually detectable by cytogenetic and microscopic techniques such as FISH. concrete ontology MO_117 Factors that relate to properties of the environmental history of the biomaterial, its treatment, or its growth. MO_64 concrete ontology Database of taxonomic information. The MGED Ontology is a top level container for the MGEDCoreOntology and the MGEDExtendedOntology. The MGED ontology describes microarray experiments and is split into the MGEDCoreOntology, which supports MAGE-OM v1.0 and is organized consistently with MAGE, and the MGEDExtendedOntology, which expands MAGE v1.0 and contains concepts and relationships which are not included in MAGE. ontology MO_174 abstract place_holder MO_169 ontology Identifier or name of the individual organism from which the biomaterial was derived. MO_136 mage A marking on the surface of the array that can be used to identify the origin of the array. concrete The value of an ExperimentFactor. mage concrete MO_203 MO_221 concrete The BioSample after labeling for detection of the nucleic acids. mage MO_109 concrete The software application used. mage MO_170 ExperimentDesign refers to both observational and experimental (perturbational) studies. The organizing principles of the study including the relationships between assays and the steps taken to interpret the data. mage concrete concrete MO_30 Database of strain, line, cultivar or ecotype information. ontology MAGE package for BioAssayData. MO_186 An array group is a physical platform that contains one or more arrays that are separately addressable or a virtual grouping of arrays. MO_34 concrete mage MO_5 Properties of the biomaterial before treated in any manner for the purposes of the experiment. abstract ontology Controlled terms for descriptors indicating the type of biosequence. Types may be physical (e.g. BAC, cDNA clone), or computational (e.g. unigene cluster, consensus). abstract MO_152 ontology place_holder The number of cell passages if the organism or organism part that is cultured is unicellular or a cell culture otherwise the number of generations. ontology MO_43 MO_195 The type of method used to preserve (keep in stasis) the organism or biosource. ontology Microscopic morphology of tissues. abstract MO_194 A descriptor of the strand type the sequence feature belongs to. e.g. forward, reverse MO_7 mage concrete The complete set of bioassays (hybridizations) and their descriptions performed as an experiment for a common purpose. Here we take experiment to mean an observational or perturbing study. An experiment will be often equivalent to a publication. MO_112 abstract MO_15 The MAGE package for describing the elements located on the array. mage Controlled terms for descriptors of the image file format (TIFF, JPEG, GIF, etc.) concrete ontology MO_211 mage A technical manufacturer described defect for features. concrete MO_138 mage MO_191 abstract MAGE package for biological sequences (biosequence). ontology concrete MO_160 Controlled set of terms for describing the type of values (e.g., Euclidean distance). The organism has had non-genetic parts removed, added, or rearranged. MO_44 place_holder The genotype of a single chromosome (i.e., the haploid genotype) that is known and relevant to the experiment being performed. ontology MO_146 Concentration units not specified in MAGE. ontology concrete MO_86 abstract ontology MO_135 CellType, the type of cell used in the experiment if non mixed, if mixed the TargetedCellType should be used, example of instances, epithelial, glial etc. Uniform Resource Identifier MO_12 ontology abstract Controlled set of descriptors for the type of database record such as a protein record (in SWISS-PROT) or a gene object (in SGD). concrete ontology MO_157 mage The MAGE package for protocols. MO_63 abstract TestResult is the recorded value of the test outcome. ontology MO_96 abstract MO_31 The descriptions associated with the Experiment package of MAGE abstract mage Units used for volume measurements. concrete ontology MO_179 concrete MO_202 ontology Controlled terms that provide descriptors for the type of software. Controlled terms for descriptors of the type of publication such as those used by Medline (review, book, etc.). concrete MO_208 ontology mage Description of the material placed on a feature (spot). MO_74 concrete concrete MO_201 A bibliographic reference is a published citation in a journal, book, other format e.g. web resource mage Descriptor of the Test performed e.g. Leukocyte count ontology abstract MO_218 A structure within a cell, such as an anatomical structure (e.g. rough endoplasmic reticulum or nucleus) or a gene product group (e.g. ribosome, proteasome or a protein dimer). abstract MO_1020 ontology MO_185 MO_1033 Version of the MGEDOntology. ontology deleted_term The term was deleted from the MGED CoreOntology. MO_1023 1.2.0 An abnormality in the number or structure of chromosomes in the biomaterial from an individual organism, detected by karyotyping or other methods. E.g., a B-cell lymphoma from a patient has an abnormal karyotype 48,XY,t(1;2)(p22;p11),+3,+12. place_holder mage MO_228 abstract MAGE package for HigherLevelAnalysis The genus and species (and subspecies) of the organism from which the biomaterial is derived from. abstract ontology MO_229 MAGE package that describes the array layout and design. The array may be physical or virtual. abstract MO_33 mage concrete MO_94 ontology class to hold instances used as the filler for the property has_reason_for_deprecation Identifiable resource containing data or external ontologies or controlled vocabularies which has uniquely identifiable records. ontology MO_118 abstract MO_168 ontology concrete Term applied to any organism able to undergo sexual reproduction in order to differentiate the individuals or types involved. Sexual reproduction is defined as the ability to exchange genetic material with the potential of recombinant progeny. concrete MO_95 The form in which the BioMaterial was obtained/maintained e.g. frozen, fresh etc. Note can be used to describe BioSamples as well as BioSources. ontology abstract ontology MO_184 Tests and results for pathogens infecting organism from which the biosource is derived concrete MO_91 Database of terms for observations such as 'abnormal coat', 'skin pigment abnormality' describing macroscopic examinations. ontology The identifier for the established culture of a metazoan cell if one was used as a biomaterial. ontology abstract MO_49 MO_61 Units used for concentration measurements. concrete ontology MO_90 ontology Complex actions are composed of multiple steps (as opposed to AtomicAction) e.g. mRNA labeling, protein purification. concrete ontology MO_98 concrete Controlled terms for descriptors of failures (as in PCR) associated with reporters. MO_148 Version of the MGEDOntology. MO_1032 deleted_term A group of FactorValues which refer to the same condition used to treat or describe a BioMaterial, e.g. 10% glucose, 1 hour OR larval stage, age 24 hours. place_holder ontology 1.1.9 some|has_value|string MO_45 ontology concrete Database of targeted cell type information. Units used for mass measurements. concrete ontology MO_149 MO_55 ontology abstract A description of the conditions the organism has been exposed to that are not one of the variables under study. abstract The resource (e.g. company, hospital, geographical location) used to obtain or purchase the biomaterial. MO_230 ontology concrete MO_52 ontology Controlled descriptors for the type of replication. MAGE package for description of annotations and references to annotations. mage abstract MO_167 abstract MO_126 ontology The name of the pathology diagnosed in the organism from which the biomaterial was derived. The disease state is normal if no disease has been diagnosed. MO_46 ontology The concentration range of the organism. abstract Units used for time measurements. MO_166 concrete ontology A protocol which yields a dataset(s) from which biological conclusions can be derived. E.g. clustering (not normalization or averaging). concrete ontology MO_47 ontology An assay performed on a biomaterial for the purposes of determining one or more biomaterial characteristics e.g. clinical chemistry. MO_197 abstract MO_181 concrete Database of disease state information. ontology concrete MO_22 mage Controlled terms for descriptors of types of array substrates. MO_79 ontology concrete place_holder MO_155 ontology Volume units not specified in MAGE. A descriptor used in cancer biology to describe abnormalities of tumor cells. E.g. an instance from NCI Thesaurus. MO_28 abstract ontology ontology One of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on phenotype or sequence. Polymorphisms are included in this definition. concrete MO_58 MO_107 mage MAGE package for describing the process by which arrays were manufactured. abstract MO_214 mage concrete Documentation of the set of steps taken in a procedure. Genetic material may be DNA or RNA and identifiable as an entry in a public external database such as EMBL/DDBJ/GenBank or one of the model organism databases. MO_137 MO_19 The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil) . ontology concrete MO_73 mage concrete A node is an individual component of BioAssayDataCluster that groups design elements, quantitation types, and BioAssays together. A node may contain other nodes. MO_158 ontology abstract The ExperimentDesignType is the high level description for studies such as "time series", "dose response", etc. MO_77 concrete mage The BioSource is the original source material before any treatment events. The point from which measurements of age were taken. ontology MO_80 concrete class to hold instances used as the filler for the property has_measurement_type concrete MO_72 ontology MO_119 ontology Units for measuring the intensity of light. concrete abstract Rating of containment system for the protection of organisms from infectious agents. ontology MO_97 abstract ontology MO_20 A measure of homogeneity of a biomaterial. For example, an expression of the percentage of a tumor biopsy that is tumor cells. abstract External (to the MGED ontology) controlled vocabulary or ontology that can be referred such as ICD-9 or Gene Ontology. MO_87 ontology Units used for distance measurements. concrete MO_4 ontology Distance units not specified in MAGE. MO_143 place_holder ontology ontology The effects of different hardware, types of hardware, or models of hardware on experimental results are studied. MO_81 place_holder mage MO_116 A grouping of bioassay data that has been organized by one or more mathematical functions into nodes. concrete MO_176 Method and type of preserving the organism or biosource (i.e. keeping it in stasis). ontology concrete The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment. MO_51 concrete The version of the MGED Ontology. MO_115 ontology MO_100 General descriptor of a BioMaterialCharacteristic category. Such as strain or line where the name of the strain or line is encoded in the FactorValue. concrete ontology Database of developmental stage information. MO_215 abstract Organizations or individuals that may be contacted. MO_147 mage ontology abstract The humidity that the biosource is exposed to. MO_29 MO_163 mage A representation of a DNA, RNA, or protein sequence. concrete MO_205 ontology A factor category describes factors which are examined in the experiment, e.g. disease_state, where the factor values are ALL and AML. abstract MO_48