MAGE Ontology Entries
Class NameAssociation NameCardinalityDescription
ArrayGroupsubstrateType0..1Commonly, arrays will be spotted on 1x3 glass microscope slides but there is nothing that says this must be the case. This association is for scanners to inform them on the possible different formats of slides that can contain arrays.
BibliographicReferenceparameters1..NCriteria that can be used to look up the reference in a repository.
BioMaterialmaterialType1The type of material used, i.e. rna, dna, lipid, phosphoprotein, etc.
BioSampletype1The Type attribute describes the role the BioSample holds in the treatment hierarchy. This type can be an extract.
BioSequenceontologyEntries0..NOntology entries referring to common values associated with BioSequences, such as gene names, go ids, etc.
BioSequencepolymerType1A choice of protein, RNA, or DNA.
BioSequencespecies0..1The organism from which this sequence was obtained.
BioSequencetype1The type of biosequence, i.e. gene, exon, UniGene cluster, fragment, BAC, EST, etc.
BioSourcecharacteristics0..NInnate properties of the biosource, such as genotype, cultivar, tissuetype, celltype, ploidy, etc.
CompoundmerckIndex0..1The Merck Index of this Compound.
Contactroles0..N 
DatabaseEntrytype0..1The type of record (e.g. a protein in SwissProt, or a yeast strain in SGD).
DerivedBioAssaytype0..1The derivation type, for instance collapsed spot replicate, ratio, avarged intensity, bioassay replicates, etc.
Descriptionannotations0..NAllows specification of ontology entries related to the instance being described.
DesignElementcontrolType0..1If the design element represents a control, the type of control it is (normalization, deletion, negative, positive, etc.)
DesignElementGroupspecies0..1The organism from which the biosequences of this group are from.
DesignElementGrouptypes0..NThe specific type of a feature, reporter, or composite. A composite type might be a gene while a reporter type might be a cDNA clone or an oligo.
ExperimentDesigntypes0..NClassifical of an experiment. For example 'normal vs. diseased', 'treated vs. untreated', 'time course', 'tiling', etc.
ExperimentalFactorcategory0..1The category of an ExperimentalFactor could be biological (time, [glucose]) or a methodological factor (differing cDNA prepartion protocols).
FeatureDefectdefectType1Indicates the type of defect (e.g a missing feature or a moved feature).
FeatureGroupfeatureShape0..1The expected shape of the feature on the array: circular, oval, square, etc.
FeatureGrouptechnologyType0..1The technology type of this design. By specifying a technology type, higher level analysis can use appropriate algorithms to compare the results from multiple arrays. The technology type may be spotted cDNA or in situ photolithography.
FiducialfiducialType0..1A descriptive string that indicates the type of a fiducial (e.g. the chrome border on an Affymetrix array, a laser ablation mark).
Hardwaretype0..1The type of a piece of Hardware. Examples include: scanner, wash station...
Imageformat1The file format of the image typically a TIF or a JPEG.
NodeValuedataType0..1The data type of the any element.
NodeValuescale0..1The scale (linear, log10, ln, etc.) of the value.
ParameterdataType0..1The type of data generated by the parameter i.e. Boolean, float, etc...
PhysicalArrayDesignsurfaceType0..1The type of surface from a controlled vocabulary that would include terms such as non-absorptive, absorptive, etc.
Protocoltype0..1The type of a Protocol, a user should provide/use a recommended vocabulary. Examples of types include: RNA extraction, array washing, etc...
QuantitationTypedataType1The specific type for the quantitations. From a controlled vocabulary of {float, int, boolean, etc.}
QuantitationTypescale1Indication of how to interpret the value. From a suggested vocabulary of {LINEAR | LN | LOG2 |LOG10 | FOLD_CHANGE | OTHER}
ReporterfailTypes0..NIf at some time the reporter is determined to be failed this indicts the failure (doesn't report on what it was intended to report on, etc.)
ReporterwarningType0..1Similar to failType but indicates a warning rather than a failure.
Softwaretype0..1The type of a piece of Software. Examples include: feature extractor...
Treatmentaction1The event that occurred (e.g. grow, wait, add, etc...). The actions should be a reccommended vocabulary
ZoneDefectdefectType1Indicates the type of defect (e.g a missing zone or a moved zone).