MAGE Ontology Entries |
Class Name | Association Name | Cardinality | Description |
ArrayGroup | substrateType | 0..1 | Commonly, 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. |
BibliographicReference | parameters | 1..N | Criteria that can be used to look up the reference in a repository. |
BioMaterial | materialType | 1 | The type of material used, i.e. rna, dna, lipid, phosphoprotein, etc. |
BioSample | type | 1 | The Type attribute describes the role the BioSample holds in the treatment hierarchy. This type can be an extract. |
BioSequence | ontologyEntries | 0..N | Ontology entries referring to common values associated with BioSequences, such as gene names, go ids, etc. |
BioSequence | polymerType | 1 | A choice of protein, RNA, or DNA. |
BioSequence | species | 0..1 | The organism from which this sequence was obtained. |
BioSequence | type | 1 | The type of biosequence, i.e. gene, exon, UniGene cluster, fragment, BAC, EST, etc. |
BioSource | characteristics | 0..N | Innate properties of the biosource, such as genotype, cultivar, tissuetype, celltype, ploidy, etc. |
Compound | merckIndex | 0..1 | The Merck Index of this Compound. |
Contact | roles | 0..N | |
DatabaseEntry | type | 0..1 | The type of record (e.g. a protein in SwissProt, or a yeast strain in SGD). |
DerivedBioAssay | type | 0..1 | The derivation type, for instance collapsed spot replicate, ratio, avarged intensity, bioassay replicates, etc. |
Description | annotations | 0..N | Allows specification of ontology entries related to the instance being described. |
DesignElement | controlType | 0..1 | If the design element represents a control, the type of control it is (normalization, deletion, negative, positive, etc.) |
DesignElementGroup | species | 0..1 | The organism from which the biosequences of this group are from. |
DesignElementGroup | types | 0..N | The 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. |
ExperimentDesign | types | 0..N | Classifical of an experiment. For example 'normal vs. diseased', 'treated vs. untreated', 'time course', 'tiling', etc. |
ExperimentalFactor | category | 0..1 | The category of an ExperimentalFactor could be biological (time, [glucose]) or a methodological factor (differing cDNA prepartion protocols). |
FeatureDefect | defectType | 1 | Indicates the type of defect (e.g a missing feature or a moved feature). |
FeatureGroup | featureShape | 0..1 | The expected shape of the feature on the array: circular, oval, square, etc. |
FeatureGroup | technologyType | 0..1 | The 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. |
Fiducial | fiducialType | 0..1 | A descriptive string that indicates the type of a fiducial (e.g. the chrome border on an Affymetrix array, a laser ablation mark). |
Hardware | type | 0..1 | The type of a piece of Hardware. Examples include: scanner, wash station... |
Image | format | 1 | The file format of the image typically a TIF or a JPEG. |
NodeValue | dataType | 0..1 | The data type of the any element. |
NodeValue | scale | 0..1 | The scale (linear, log10, ln, etc.) of the value. |
Parameter | dataType | 0..1 | The type of data generated by the parameter i.e. Boolean, float, etc... |
PhysicalArrayDesign | surfaceType | 0..1 | The type of surface from a controlled vocabulary that would include terms such as non-absorptive, absorptive, etc. |
Protocol | type | 0..1 | The type of a Protocol, a user should provide/use a recommended vocabulary. Examples of types include: RNA extraction, array washing, etc... |
QuantitationType | dataType | 1 | The specific type for the quantitations. From a controlled vocabulary of {float, int, boolean, etc.} |
QuantitationType | scale | 1 | Indication of how to interpret the value. From a suggested vocabulary of {LINEAR | LN | LOG2 |LOG10 | FOLD_CHANGE | OTHER} |
Reporter | failTypes | 0..N | If 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.) |
Reporter | warningType | 0..1 | Similar to failType but indicates a warning rather than a failure. |
Software | type | 0..1 | The type of a piece of Software. Examples include: feature extractor... |
Treatment | action | 1 | The event that occurred (e.g. grow, wait, add, etc...). The actions should be a reccommended vocabulary |
ZoneDefect | defectType | 1 | Indicates the type of defect (e.g a missing zone or a moved zone). |