MAGE package for bioassay. 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). A methodological experiment design type investigates differences caused by application of protocols, hardware, software and bioassay relationships, e.g. quality control, replicates, loop. Units of measure. Units used for distance measurements. Properties of the biomaterial before treated in any manner for the purposes of the experiment. 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. 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. The factors in the study that are experimental parameters or regarded as influencing the experimental results. Mass units not specified in MAGE. Uniform Resource Identifier Compounds that are used for labeling extracts. Controlled set of descriptors for indicating the specific type of a Feature, Reporter, or CompositeSequence. The MAGE package for describing the elements located on the array. Defects associated with features or zones such as those that are missing or moved. The technology type or platform of the reporters on the array. A descriptor that indicates the type of the fiducial such as chrome border of an Affymetrix array or a laser ablation mark. 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. A treatment is the process or action by which a biomaterial is created from an input biomaterial. The individual to contact regarding something provided such as a biomaterial. Descriptors of biosequence based on the Sequence Ontology (SO) project. class to hold instances used as the filler for the property has_cancer_site Controlled descriptors for the normalization strategy used for the experiment. A descriptor used in cancer biology to describe abnormalities of tumor cells. E.g. an instance from NCI Thesaurus. The humidity that the biosource is exposed to. Database of strain, line, cultivar or ecotype information. The descriptions associated with the Experiment package of MAGE 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. An array group is a physical platform that contains one or more arrays that are separately addressable or a virtual grouping of arrays. Database of geographic locations. A type of relationship applicable to mammals to describe the genetic relatedness of the individual under study. E.g. brother or mother. the organism part in which additional tumors are identified remote from the primary site the organism part in which the tumor originated Anatomical location(s) of disease. The effects of different investigators, laboratories, or organizations on experimental results are studied. Database of phenotype information BioAssayData refers to the data files including images generated from one or more BioAssays. Controlled terms for descriptors of the warnings associated with reporters. A theoretical biosequence type is an abstraction used for annotation design of elements, e.g. gene, intron. 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. Database of targeted cell type information. The concentration range of the organism. A protocol which yields a dataset(s) from which biological conclusions can be derived. E.g. clustering (not normalization or averaging). Units used for temperature measurements. The identifier for the established culture of a metazoan cell if one was used as a biomaterial. Controlled terms for descriptors for the type of control design element. 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. Observation will record the macroscopic examination of the biomaterial. Technology-based grouping of features representing individual locations on the array. A description of the conditions the organism has been exposed to that are not one of the variables under study. A bioassay is an abstract class representing physical and computational groupings of biomaterials and arrays. An ontology developed by the Microarray Gene Expression Data (MGED) Society to provide descriptors required for MAGE v.1 documents. 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. Relevant aspects of genetic preconditions or family member's clinical history. The photoperiod and type (e.g., natural, restricted wavelength) of light exposure. Units used for concentration measurements. User is a way to id a person in a database The MAGE package for protocols. Database of taxonomic information. class to hold instances used as the filler for the property has_result 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. An atomic action is a single step process on the biomaterial, e.g. mix by inversion, wait, add The current clinical treatment(s) of the patient from which the biosource is derived. A drug, solvent, chemical, etc., with a property that can be measured such as concentration. a biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler class to hold instances used as the filler for the property has_measurement_type A node is an individual component of BioAssayDataCluster that groups design elements, quantitation types, and BioAssays together. A node may contain other nodes. Description of the material placed on a feature (spot). All protocols which involve treatment of a biomaterial or an array during the course of a microarray experiment. Database of codes for clinical findings. The BioSource is the original source material before any treatment events. The term was deleted from the MGED CoreOntology. 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. Version of the MGED Ontology. Controlled terms for descriptors of types of array substrates. The point from which measurements of age were taken. The effects of different hardware, types of hardware, or models of hardware on experimental results are studied. 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). The stage premortem or postmortem at which the sample was processed for extraction of biomaterials. Database for sequence annotation information. 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. Concentration units not specified in MAGE. External (to the MGED ontology) controlled vocabulary or ontology that can be referred such as ICD-9 or Gene Ontology. QualityControlDescription provides details of the quality control aspects of the experiment. MAGE package for measurement. Complex actions are composed of multiple steps (as opposed to AtomicAction) e.g. mRNA labeling, protein purification. Database of terms for observations such as 'abnormal coat', 'skin pigment abnormality' describing macroscopic examinations. 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. class to hold instances used as the filler for the property has_reason_for_deprecation 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. TestResult is the recorded value of the test outcome. Rating of containment system for the protection of organisms from infectious agents. A physical bioassay is the combination of arrays and biomaterials as in a hybridization. Controlled terms for descriptors of failures (as in PCR) associated with reporters. General descriptor of a BioMaterialCharacteristic category. Such as strain or line where the name of the strain or line is encoded in the FactorValue. Organisms or organism parts used as a designed part of the culture (e.g., red blood cells, stromal cells). Controlled terms for descriptors of the type of polymer (RNA, DNA, protein) of the biosequence. Time units not specified in MAGE. Node values allow the organization of the nodes in relation to other nodes produced by mathematical functions such as a clustering algorithm. A technical manufactured described defect for zones. A perturbational design type is where the organism(s) are treated or manipulated or modified, for example a genetic modification, somatic modification MAGE package for describing the process by which arrays were manufactured. The scale (linear, log10, ln, etc) used to represent the value. The software application used. 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. 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. Controlled terms for descriptors of types of hardware. Database of clinical treatment information The version of the MGED Ontology. Factors that relate to properties of the environmental history of the biomaterial, its treatment, or its growth. A grouping of bioassay data that has been organized by one or more mathematical functions into nodes. Identifiable resource containing data or external ontologies or controlled vocabularies which has uniquely identifiable records. Units for measuring the intensity of light. The developmental stage of the organism's life cycle during which the biomaterial was extracted. Controlled descriptors for the quality control strategy for an experiment. 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. 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. a plant variety obtained in agriculture in horticulture Primitive data types found in computing languages such as float, boolean, etc. 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. The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.). A DesignElementGroup holds information on Features, Reporters, or CompositeSequences. Physical properties of the BioMaterial e. g. mass or height The MAGE package for defining classes for quantitation. 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. The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression. The machine or instrument used. 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. 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. A technical manufacturer described defect for features. The effects of different protocols or changes in protocols on experimental results are studied. Database of cell type information. 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. 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 Database of cell line information. The genotype of a single chromosome (i.e., the haploid genotype) that is known and relevant to the experiment being performed. Organizations or individuals that may be contacted. 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. Units used for mass measurements. A controlled set of terms to provide a descriptor for the type of protocol. 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). Water consumed by or enveloping the organism that the biosource is derived from. Refers to the bedding material present in an animals housing. Volume units not specified in MAGE. Quantity units not specified in MAGE. Controlled set of descriptors for the type of database record such as a protein record (in SWISS-PROT) or a gene object (in SGD). The ExperimentDesignType is the high level description for studies such as "time series", "dose response", etc. Controlled set of terms for describing the type of values (e.g., Euclidean distance). Used to tell when the BioSample is an extract or not. ReplicateDescription provides details about the type of replication used in the experiment. Descriptors for protocol parameter types, e.g. compound concentration, media type. A representation of a DNA, RNA, or protein sequence. The process by which derived BioAssays are created from measured BioAssays and/or derived BioAssays. Units used for time measurements. MAGE package for description of annotations and references to annotations. 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. Identifier or name of the individual organism from which the biomaterial was derived. 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. The temperature that a biosource is exposed to. MAGE package for contacts including organizations and people. Design elements are reporters, features, and composite elements as defined by MAGE. Database of histology 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. The organization (e.g. company, hospital) to contact to obtain or purchase something. Method and type of preserving the organism or biosource (i.e. keeping it in stasis). 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). Units used for volume measurements. Controlled terms for descriptors of the role of contact, e.g. submitter, biosource_provider. Database of disease state information. Description of the source of the nucleic acid used to generate labeled material for the microarray experiment. 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. Tests and results for pathogens infecting organism from which the biosource is derived a result which can not be interpreted as positive or negative false or no true or yes Version of the MGEDOntology. 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. MAGE package for BioAssayData. Database of tumor grading information Member of the biosource's family. The BioMaterial's (i.e., the patient's) medical record as background information relevant to the experiment. Factors that relate to properties of the biomaterial, its treatment, or its growth. MAGE package for biological sequences (biosequence). 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. Microscopic morphology of tissues. Procedures used during treatment. The type of method used to preserve (keep in stasis) the organism or biosource. 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 An assay performed on a biomaterial for the purposes of determining one or more biomaterial characteristics e.g. clinical chemistry. Controlled terms for descriptors for coating of the substrate. Other units are those types not specified in MAGE such as lumens, radioactivity, etc. Database of organism part information. A bibliographic reference is a published citation in a journal, book, other format e.g. web resource Controlled terms that provide descriptors for the type of software. The value of an ExperimentFactor. Units for measuring decay of a radioactive isotope over time. A factor category describes factors which are under test in the experiment and allowable factor categories can be BioMaterialCharacteristics, Compound (names, concentrations) and Action etc. E.g. in an experiment where leukemia types are compared the factor categories are ALL and AML. Class to hold deprecated instances and classes. the term has been subsumed into a more general term The term name was changed to one more appropriate to the intent of the definition. the term has been decomposed into more specific terms Controlled terms for how the sequence features were determined (e.g., experimental, computational, etc.) Controlled terms for descriptors of the type of publication such as those used by Medline (review, book, etc.). A BioAssay that is created by the transformation of measured or derived BioAssays. Units used for quantity measurements. Controlled terms for descriptors of the image file format (TIFF, JPEG, GIF, etc.) Descriptions pertaining to the array. 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. Documentation of the set of steps taken in a procedure.