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 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 1.3.0.1 May 17, 2006 An ontology for microarray experiments in support of MAGE v.1. mage MAGE package for bioassay. 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). abstract abstract Units of measure. ontology ontology concrete A methodological experiment design type investigates differences caused by application of protocols, hardware, software and bioassay relationships, e.g. quality control, replicates, loop. concrete ontology Units used for distance measurements. ontology abstract Properties of the biomaterial before treated in any manner for the purposes of the experiment. concrete 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. A descriptor of the strand type the sequence feature belongs to. e.g. forward, reverse The expected shape of the feature on the array. concrete ontology 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. abstract ontology mage concrete The factors in the study that are experimental parameters or regarded as influencing the experimental results. Mass units not specified in MAGE. place_holder ontology abstract ontology Uniform Resource Identifier Compounds that are used for labeling extracts. ontology concrete Controlled set of descriptors for indicating the specific type of a Feature, Reporter, or CompositeSequence. ontology concrete The MAGE package for describing the elements located on the array. abstract mage Defects associated with features or zones such as those that are missing or moved. ontology concrete concrete The technology type or platform of the reporters on the array. ontology A descriptor that indicates the type of the fiducial such as chrome border of an Affymetrix array or a laser ablation mark. ontology concrete ontology concrete The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil) . A measure of homogeneity of a biomaterial. For example, an expression of the percentage of a tumor biopsy that is tumor cells. ontology abstract concrete ontology 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 mage concrete A treatment is the process or action by which a biomaterial is created from an input biomaterial. mage The individual to contact regarding something provided such as a biomaterial. concrete mage Descriptors of biosequence based on the Sequence Ontology (SO) project. abstract ontology class to hold instances used as the filler for the property has_cancer_site ontology concrete concrete ontology Controlled descriptors for the normalization strategy used for the experiment. abstract A descriptor used in cancer biology to describe abnormalities of tumor cells. E.g. an instance from NCI Thesaurus. ontology ontology abstract The humidity that the biosource is exposed to. concrete ontology Database of strain, line, cultivar or ecotype information. abstract mage The descriptions associated with the Experiment package of MAGE ontology concrete Controlled terms for the state of the BioMaterial. Each state (BioSource, different BioSamples, and LabeledExtract) have MaterialTypes. Examples are population of an organism, organism, organism part, cell, etc. MAGE package that describes the array layout and design. The array may be physical or virtual. abstract mage An array group is a physical platform that contains one or more arrays that are separately addressable or a virtual grouping of arrays. concrete mage ontology concrete Database of geographic locations. concrete A type of relationship applicable to mammals to describe the genetic relatedness of the individual under study. E.g. brother or mother. ontology the organism part in which additional tumors are identified remote from the primary site the organism part in which the tumor originated ontology Anatomical location(s) of disease. concrete place_holder The effects of different investigators, laboratories, or organizations on experimental results are studied. ontology concrete Database of phenotype information ontology BioAssayData refers to the data files including images generated from one or more BioAssays. ontology concrete Controlled terms for descriptors of the warnings associated with reporters. concrete ontology A theoretical biosequence type is an abstraction used for annotation design of elements, e.g. gene, intron. place_holder 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. The organism has had non-genetic parts removed, added, or rearranged. concrete Database of targeted cell type information. ontology The concentration range of the organism. ontology abstract ontology A protocol which yields a dataset(s) from which biological conclusions can be derived. E.g. clustering (not normalization or averaging). concrete ontology Units used for temperature measurements. concrete The identifier for the established culture of a metazoan cell if one was used as a biomaterial. ontology abstract Controlled terms for descriptors for the type of control design element. concrete ontology 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. Controlled descriptors for the type of replication. ontology concrete abstract ontology Observation will record the macroscopic examination of the biomaterial. Technology-based grouping of features representing individual locations on the array. mage concrete ontology A description of the conditions the organism has been exposed to that are not one of the variables under study. abstract A bioassay is an abstract class representing physical and computational groupings of biomaterials and arrays. mage abstract ontology An ontology developed by the Microarray Gene Expression Data (MGED) Society to provide descriptors required for MAGE v.1 documents. abstract 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. ontology concrete Relevant aspects of genetic preconditions or family member's clinical history. abstract ontology ontology The photoperiod and type (e.g., natural, restricted wavelength) of light exposure. abstract ontology Units used for concentration measurements. concrete mage abstract The MAGE package for protocols. User is a way to id a person in a database concrete Database of taxonomic information. ontology class to hold instances used as the filler for the property has_result ontology concrete ontology abstract The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. The QuantitationType provides a method for calculating a single datum of the BioAssayData matrix. mage abstract An atomic action is a single step process on the biomaterial, e.g. mix by inversion, wait, add concrete ontology The current clinical treatment(s) of the patient from which the biosource is derived. abstract ontology ontology A drug, solvent, chemical, etc., with a property that can be measured such as concentration. abstract a biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler abstract ontology ontology class to hold instances used as the filler for the property has_measurement_type concrete concrete A node is an individual component of BioAssayDataCluster that groups design elements, quantitation types, and BioAssays together. A node may contain other nodes. mage concrete mage Description of the material placed on a feature (spot). ontology concrete All protocols which involve treatment of a biomaterial or an array during the course of a microarray experiment. ontology Database of codes for clinical findings. concrete The BioSource is the original source material before any treatment events. concrete mage Version of the MGED Ontology. abstract 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. The term was deleted from the MGED CoreOntology. Controlled terms for descriptors of types of array substrates. ontology concrete ontology concrete The point from which measurements of age were taken. ontology The effects of different hardware, types of hardware, or models of hardware on experimental results are studied. place_holder 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 ontology The stage premortem or postmortem at which the sample was processed for extraction of biomaterials. ontology concrete Database for sequence annotation information. 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 ontology Concentration units not specified in MAGE. concrete ontology abstract External (to the MGED ontology) controlled vocabulary or ontology that can be referred such as ICD-9 or Gene Ontology. ontology abstract QualityControlDescription provides details of the quality control aspects of the experiment. MAGE package for measurement. abstract mage Complex actions are composed of multiple steps (as opposed to AtomicAction) e.g. mRNA labeling, protein purification. ontology concrete ontology Database of terms for observations such as 'abnormal coat', 'skin pigment abnormality' describing macroscopic examinations. concrete concrete ontology A physical biosequence type represents biological sequence that can be physically placed (spotted or synthesized) on an array e.g. BAC, PAC. The BioSource after any treatment. concrete mage class to hold instances used as the filler for the property has_reason_for_deprecation ontology concrete concrete 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 TestResult is the recorded value of the test outcome. ontology abstract Rating of containment system for the protection of organisms from infectious agents. ontology abstract A physical bioassay is the combination of arrays and biomaterials as in a hybridization. concrete mage concrete Controlled terms for descriptors of failures (as in PCR) associated with reporters. ontology General descriptor of a BioMaterialCharacteristic category. Such as strain or line where the name of the strain or line is encoded in the FactorValue. abstract ontology Organisms or organism parts used as a designed part of the culture (e.g., red blood cells, stromal cells). concrete ontology Controlled terms for descriptors of the type of polymer (RNA, DNA, protein) of the biosequence. concrete ontology Time units not specified in MAGE. concrete Node values allow the organization of the nodes in relation to other nodes produced by mathematical functions such as a clustering algorithm. mage mage A technical manufactured described defect for zones. concrete concrete A perturbational design type is where the organism(s) are treated or manipulated or modified, for example a genetic modification, somatic modification ontology abstract MAGE package for describing the process by which arrays were manufactured. mage ontology concrete The scale (linear, log10, ln, etc) used to represent the value. concrete mage The software application used. concrete mage A parameter is a variable within a protocol. 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. concrete ontology 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 ontology Controlled terms for descriptors of types of hardware. concrete concrete ontology Database of clinical treatment information concrete ontology The version of the MGED Ontology. concrete ontology Factors that relate to properties of the environmental history of the biomaterial, its treatment, or its growth. mage A grouping of bioassay data that has been organized by one or more mathematical functions into nodes. concrete ontology Identifiable resource containing data or external ontologies or controlled vocabularies which has uniquely identifiable records. abstract ontology concrete Units for measuring the intensity of light. The developmental stage of the organism's life cycle during which the biomaterial was extracted. abstract ontology Controlled descriptors for the quality control strategy for an experiment. concrete 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. concrete ontology The target cell type is the cell of primary interest. The biomaterial may be derived from a mixed population of cells although only one cell type is of interest. abstract ontology abstract a plant variety obtained in agriculture in horticulture ontology ontology Primitive data types found in computing languages such as float, boolean, etc. concrete 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. abstract ontology The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.). abstract ontology A DesignElementGroup holds information on Features, Reporters, or CompositeSequences. abstract mage ontology Physical properties of the BioMaterial e. g. mass or height abstract The MAGE package for defining classes for quantitation. mage abstract abstract ontology NormalizationDescription provides details of the normalization strategy for the experiment. A descriptor of the location from which a BioMaterial was obtained, e.g. country, region, grid reference. abstract ontology The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression. abstract ontology mage The machine or instrument used. concrete ontology 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. abstract concrete mage A marking on the surface of the array that can be used to identify the origin of the array. 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 A technical manufacturer described defect for features. mage 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. abstract The effects of different protocols or changes in protocols on experimental results are studied. concrete Database of cell type information. ontology concrete ontology An epidemiological experiment design type is where the biosource history is studied e.g. environmental, clinical and family history. Distance units not specified in MAGE. ontology place_holder Measured values and units. a measurement where the value is independent of other measurements Indicates that one or more BioMaterialCharacteristics have changed during the treatment of a BioMaterial. Non exact synonym: change growth conditions, change environment a measurement where the value is dependent on another measurement concrete mage ontology concrete Database of cell line information. place_holder The genotype of a single chromosome (i.e., the haploid genotype) that is known and relevant to the experiment being performed. ontology abstract Organizations or individuals that may be contacted. mage 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. Version of the MGEDOntology. place_holder ontology concrete Units used for mass measurements. ontology A controlled set of terms to provide a descriptor for the type of protocol. abstract ontology concrete ontology Database of compound information. 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). ontology abstract abstract Water consumed by or enveloping the organism that the biosource is derived from. ontology place_holder ontology Refers to the bedding material present in an animals housing. Volume units not specified in MAGE. ontology place_holder concrete Quantity units not specified in MAGE. ontology 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 The ExperimentDesignType is the high level description for studies such as "time series", "dose response", etc. ontology abstract ontology An antigenic property of a cell (e.g. bacteria, RBC) or virus identified by serological methods place_holder concrete ontology Controlled set of terms for describing the type of values (e.g., Euclidean distance). concrete ontology Used to tell when the BioSample is an extract or not. ontology abstract ReplicateDescription provides details about the type of replication used in the experiment. A representation of a DNA, RNA, or protein sequence. mage concrete Descriptors for protocol parameter types, e.g. compound concentration, media type. concrete The process by which derived BioAssays are created from measured BioAssays and/or derived BioAssays. ontology concrete ontology Units used for time measurements. abstract MAGE package for description of annotations and references to annotations. mage 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 concrete Identifier or name of the individual organism from which the biomaterial was derived. ontology place_holder 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 abstract The temperature that a biosource is exposed to.