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MAGE-ML Data Mapping

This page describes the mappings between data items stored within the Affymetrix data files, GCOS or LIMS systems and the MAGE-ML compliant files generated by the Affymetrix GDAC-Exporter SDK. The MAGE-ML file currently produced by the SDK do not include the DTD version number. Version 1.1 should be assumed.


FILE MAPPING

The MAGE-ML output shall conform to the following mapping between data files data members and the MAGE-ML location.

EXP File Data
Exp File DataPackageMAGE-ML XPath Location
Experiment Name Experiment//Experiment/@name
Probe Array Type ArrayDesign//PhysicalArrayDesign/@name
Probe Array Lot Array//ArrayManufacture/PropertySets_assnlist/NameValueType/@value
Operator Name AuditAndSecurity

BioAssay
BioAssay		//Person/@name
References:
//Hybridization/*/ProtocolApplication/Performers_assnreflist/Person_ref/@identifier
//ImageAcquisition/*/ProtocolApplication/Performers_assnreflist/Person_ref/@identifier
Sample TypeBioMaterial//BioSource/MaterialType_assn/*/@value
Sample DescriptionBioMaterial//BioSource/*/Description/@text
Sample Project BioMaterial//BioSource/Characteristics_assnlist/*/@value
CommentsExperiment//BioSource/*/Description/@text
ReagentsBioMaterial//Compound/@name
Reagent LotBioMaterial//Compound/PropertySets_assnlist/*/@value
Protocol steps
Protocol

BioAssay

Definition:
//Protocol/*/Parameter
Values:
//Hybridization/*/ProtocolApplication/*/ParameterValue/@value

The parameters identifier values are "Affymetrix.com:Parameter:<fluidics protocol name>.HybridizationStep0" thru "Affymetrix.com:Parameter:<fluidics protocol name>.HybridizationStepN-1" where N is the number of steps in the protocol.

Hyb Script NameProtocol//Protocol/@name
Hyb Station
Protocol

BioAssay

Definition:
//Hardware/*/Parameter
Values:
//Hybridization/*/ProtocolApplication/*/HardwareApplication/*/ParameterValue/@value

The parameters identifier is "Affymetrix.com:Parameter:FluidicsStationNumber"

Hyb Position
Protocol

BioAssay

Definition:
//Hardware/*/Parameter
Values:
//Hybridization/*/ProtocolApplication/*/HardwareApplication/*/ParameterValue/@value

The parameters identifier is "Affymetrix.com:Parameter:FluidicsStationPosition"

Hyb DateBioAssay//Hybridization/*/ProtocolApplication/@activityDate
Scan Pixel Size
Protocol

BioAssay

Definition:
//Protocol/*/Parameter
Values:
//ImageAcquisition/*/ProtocolApplication/*/ParameterValue

The parameters identifier is "Affymetrix.com:Parameter:ScanPixelSize"

Scan FilterBioAssay//Channel/PropertySets_assnlist/*/@value
Scan DateBioAssay//ImageAcquisition/*/ProtocolApplication/@activityDate
Scanner ID
Protocol

BioAssay

Definition:
//Hardware/*/Parameter
Values:
//ImageAcquisition/*/ProtocolApplication/*/HardwareApplication/*/ParameterValue/@value

The parameters identifier is "Affymetrix.com:Parameter:ScannerID"

Number of Scans
Protocol

BioAssay

Definition:
//Protocol/*/Parameter
Values:
//ImageAcquisition/*/ProtocolApplication/*/ParameterValue

The parameters identifier is "Affymetrix.com:Parameter:NumberOfScans"

Scanner Type
Protocol

BioAssay

Definition:
//Hardware/*/Parameter
Values:
//ImageAcquisition/*/ProtocolApplication/*/HardwareApplication/*/ParameterValue/@value

The parameters identifier is "Affymetrix.com:Parameter:ScannerType"

CEL File Data
CEL File DataPackageMAGE-ML XPath Location
Analysis name BioAssay//MeasuredBioAssay/@name
DateBioAssay//FeatureExtraction/*/ProtocolApplication/@activityDate
Grid corners
Protocol

BioAssay

Definition:
//Protocol/*/Parameter
Values:
//FeatureExtraction/*/ProtocolApplication/*/ParameterValue/@value

The parameter identifiers are:
- Affymetrix.com:Parameter:UpperLeftX
- Affymetrix.com:Parameter:UpperLeftY
- Affymetrix.com:Parameter:UpperRightX
- Affymetrix.com:Parameter:UpperRightY
- Affymetrix.com:Parameter:LowerLeftX
- Affymetrix.com:Parameter:LowerLeftY
- Affymetrix.com:Parameter:LowerRightX
- Affymetrix.com:Parameter:LowerRightY

Probe array typeBioAssay//MeasuredBioAssay/PropertySets_assnlist/*/@value
Cell margin
Protocol

BioAssay

Definition:
//Protocol/*/Parameter
Values:
//FeatureExtraction/*/ProtocolApplication/*/ParameterValue/@value

The parameters identifier is:
- Affymetrix.com:Parameter:CellMargin

Algorithm name
Protocol

BioAssay

Definition:
//Protocol/*/Parameter
Values:
//FeatureExtraction/*/ProtocolApplication/*/ParameterValue/@value

The parameters identifier is:
- Affymetrix.com:Parameter:AlgorithmName

Parameters
Protocol

BioAssay

Definition:
//Protocol/*/Parameter
Values:
//FeatureExtraction/*/ProtocolApplication/*/ParameterValue/@value

The parameters are dependant on the specific algorithm.

Number cells maskedBioAssayData

//MeasuredBioAssayData/SummaryStatistics_assnlist/*/@value

The name of the parameter is "Number Cells Masked"

Number outlier cellsBioAssayData

//MeasuredBioAssayData/SummaryStatistics_assnlist/*/@value

The name of the parameter is "Number Outlier Cells"

Number cells modifiedBioAssayData

//MeasuredBioAssayData/SummaryStatistics_assnlist/*/@value

The name of the parameter is "Number Cells Modified"

RowsBioAssayData

//MeasuredBioAssayData/SummaryStatistics_assnlist/*/@value

The name of the parameter is "Rows"

ColsBioAssayData

//MeasuredBioAssayData/SummaryStatistics_assnlist/*/@value

The name of the parameter is "Cols"

Number of cellsBioAssayData

//MeasuredBioAssayData/SummaryStatistics_assnlist/*/@value

The name of the parameter is "Number of Cells"

CEL File Entry Data
CEL Entry DataPackageMAGE-ML XPath Location
XBioAssayData

implied by //FeatureDimension/*/Feature_ref/@identifier
and stored in //BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")

YBioAssayData

implied by //FeatureDimension/*/Feature_ref/@identifier
and stored in //BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")

IntensityBioAssayData

//BioDataCube/*/DataExternal
(QuantitationType is "MeasuredSignal")

StdevBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
Number of pixels used to calculate the intensity valueBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
OutlierBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
MaskBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")

CHP File Data
CHP File DataPackageMAGE-ML XPath Location
DateBioAssayData//Transformation/*/ProtocolApplication/@activityDate
ColsBioAssayData

//DerivedBioAssayData/SummaryStatistics_assnlist/*/@value

The parameter name is "Cols"

RowsBioAssayData

//DerivedBioAssayData/SummaryStatistics_assnlist/*/@value

The parameter name is "Rows"

Number of probe setsBioAssayData

//DerivedBioAssayData/SummaryStatistics_assnlist/*/@value

The parameter name is "Number of Probe Sets"

Algorithm name
Protocol

BioAssayData

Definition:
//Protocol/*/Parameter
Values:
//Transformation/*/ProtocolApplication/*/ParameterValue/@value

The parameters identifier is "Affymetrix.com:Parameter:AlgorithmName"

Algorithm version
Protocol

BioAssayData

Definition:
//Protocol/*/Parameter
Values:
//Transformation/*/ProtocolApplication/*/ParameterValue/@value

The parameters identifier is "Affymetrix.com:Parameter:AlgorithmVersion"

Params
Protocol

BioAssayData

Definition:
//Protocol/*/Parameter
Values:
//Transformation/*/ProtocolApplication/*/ParameterValue/@value

The parameters are dependant on the specific algorithm.

Summary statistics BioAssayData

//DerivedBioAssayData/SummaryStatistics_assnlist/*/@value

Included, for Statistical and PLIER results, are background, noise, rows, cols, number of probe sets and RawQ

Probe array typeBioAssay//DerivedBioAssay/PropertySets_assnlist/*/@value

CHP File Entry Data For Statistical and PLIER Absolute Analysis
CHP Entry DataPackageMAGE-ML XPAth Location
Probe set nameBioAssayData

//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")

PairsBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
Pairs used BioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
SignalBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "DerivedSignal")
DetectionBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "PresentAbsent")
p-valueBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "PValue")

CHP File Entry Data For Statistical Comparison Analysis
CHP Entry DataPackageMAGE-ML XPAth Location
Probe set nameBioAssayData

//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")

PairsBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
Pairs used BioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
SignalBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "DerivedSignal")
DetectionBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "PresentAbsent")
p-valueBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "PValue")
Common pairs BioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
Signal log ratioBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "Ratio")
Signal log ratio lowBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "Ratio")
Signal log ratio highBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "Ratio")
ChangeBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "PresentAbsent")
Change p-value BioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "PValue")

CHP File Entry Data For MAS 4 Absolute Analysis
CHP Entry DataPackageMAGE-ML XPAth Location
Probe set nameBioAssayData

//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")

PositiveBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
NegativeBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
PairsBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
Pairs Used BioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
Pairs in AvgBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
Pos Fraction BioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "Ratio")
Log Avg BioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
Pos/NegBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "Ratio")
Avg Diff BioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "DerivedSignal")
Abs Call BioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "PresentAbsent")

CHP File Entry Data For MAS 4 Comparison Analysis
CHP Entry DataPackageMAGE-ML XPAth Location
Probe set nameBioAssayData

//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")

PositiveBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
NegativeBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
PairsBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
Pairs Used BioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
Pairs in AvgBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
Pos Fraction BioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "Ratio")
Log Avg BioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
Pos/NegBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "Ratio")
Avg Diff BioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "DerivedSignal")
Abs Call BioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "PresentAbsent")
IncBioAssayData

//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")

DecBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
Inc Ratio BioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "Ratio")
Dec Ratio BioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "Ratio")
Pos Change BioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
Neg Change BioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
Inc/DecBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "Ratio")
DPos-DNeg Ratio BioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "Ratio")
Log Avg RatioBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
Diff Call BioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "PresentAbsent")
Avg Diff ChangeBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
Baseline is AbsentBioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")
Fold Change BioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "Ratio")
Sort Score BioAssayData//BioDataCube/*/DataExternal
(QuantitationType is "SpecializedQuantitationType")

CDF File Array Structure
Structure ElementPackageMAGE-ML XPath Location
Array StructureArrayDesign
ArrayDesign
DesignElement

//ReporterGroups_assnreflist /*
//CompositeGroups_assnreflist/*
//CompositeSequence

The probe set names are stored in the "name" attribute in the //CompositeSequence location.

Probe Pairs per Probe SetDesignElement//ReporterCompositeMap
Probes per Probe PairDesignElement//FeatureReporterMap
ProbeSetsArrayDesign
ArrayDesign
DesignElement		//CompositeGroup[@identifier="Affymetrix.com:CompositeGroup:ProbeSets.<probe array type>"] where <probe array type> is the name of the probe array type.
//ReporterGroup
//CompositeSequence
Probe PairsDesignElement//Reporter
ProbesArrayDesign//FeatureGroup/Features_assnlist/Feature
PM/MM RelationshipArrayDesign
ArrayDesign
DesignElement		//Feature/ControlFeatures_assnreflist/Feature_ref
//FeatureGroup/Features_assnlist/Feature
//FeatureInformation/MismatchInformation_assnlist/*

CDF File Array Data
Structure ElementPackageMAGE-ML XPath Location
Probe Array NameArrayDesign//PhysicalArrayDesign/@name
RowsArrayDesign//ZoneLayout/@numFeaturesPerCol
ColsArrayDesign//ZoneLayout/@numFeaturesPerRow
Number of cellsArrayDesign//PhysicalArrayDesign/@numberOfFeatures
Cell locationArrayDesign//Feature/*/FeatureLocation
Cell typeArrayDesign

//Feature/ControlType_assn/*/@value

The value is either "PM" or "MM"

Probe set nameDesignElement//CompositeSequence/@name
Subtitution positionDesignElement//FeatureInformation/*/MismatchInformation/@startCoord
Probe base at substitution positionDesignElement//FeatureInformation/*/MismatchInformation/@newSequence

LIMS/GCOS MAPPINGS

The MAGE-ML output shall conform to the following mapping between LIMS or GCOS data and the MAGE-ML location. The mappings for CEL, CHP and CDF files stored within the LIMS or GCOS system as identical as those in a non-LIMS system. Please refer to the FILE MAPPING section above for the mapping information for those files.

Sample Information
Sample InformationPackageMAGE-ML XPath Location
Sample NameBioMaterial//BioSource/@name
Sample Attribute Template NameBioMaterial//BioSource/PropertySets_assnlist/NameValueType[@name="Sample Template Name"]
Sample Attribute Template Name-ValueBioMaterial//BioSource/PropertySets_assnlist/NameValueType
Sample TypeBioMaterial//BioSource/MaterialType_assn/*/@value
Sample DescriptionBioMaterial//BioSource/*/Description/@text
Sample Project BioMaterial//BioSource/Characteristics_assnlist/*/@value
CommentsExperiment//BioSource/*/Description/@text
ReagentsBioMaterial//Compound/@name
Reagent LotBioMaterial//Compound/PropertySets_assnlist/*/@value

Experiment Information
Experiment InformationPackageMAGE-ML XPath Location
Experiment NameExperiment//Experiment/@name
Experiment Attribute Template NameExperiment//Experiment/PropertySets_assnlist/NameValueType[@name="Experiment Template Name"]
Experiment Attribute Template Name-ValueExperiment//Experiment/PropertySets_assnlist/NameValueType
Probe Array Type ArrayDesign//PhysicalArrayDesign/@name
Probe Array Lot Array//ArrayManufacture/PropertySets_assnlist/NameValueType/@value

Hybridization Information
Experiment InformationPackageMAGE-ML XPath Location
Hybridization Operator Name AuditAndSecurity

BioAssay		//Person/@name
References:
//Hybridization/*/ProtocolApplication/Performers_assnreflist/Person_ref/@identifier
Protocol steps
Protocol

BioAssay

Definition:
//Protocol/*/Parameter
Values:
//Hybridization/*/ProtocolApplication/*/ParameterValue/@value

The parameters identifier values are "Affymetrix.com:Parameter:<fluidics protocol name>.HybridizationStep0" thru "Affymetrix.com:Parameter:<fluidics protocol name>.HybridizationStepN-1" where N is the number of steps in the protocol.

Hyb Script NameProtocol//Protocol/@name
Hyb Station
Protocol

BioAssay

Definition:
//Hardware/*/Parameter
Values:
//Hybridization/*/ProtocolApplication/*/HardwareApplication/*/ParameterValue/@value

The parameters identifier is "Affymetrix.com:Parameter:FluidicsStationNumber"

Hyb Position
Protocol

BioAssay

Definition:
//Hardware/*/Parameter
Values:
//Hybridization/*/ProtocolApplication/*/HardwareApplication/*/ParameterValue/@value

The parameters identifier is "Affymetrix.com:Parameter:FluidicsStationPosition"

Hyb DateBioAssay//Hybridization/*/ProtocolApplication/@activityDate

Scan Information
Experiment InformationPackageMAGE-ML XPath Location
Scan Operator Name AuditAndSecurity

BioAssay		//Person/@name
References:
//ImageAcquisition/*/ProtocolApplication/Performers_assnreflist/Person_ref/@identifier
Scan Pixel Size
Protocol

BioAssay

Definition:
//Protocol/*/Parameter
Values:
//ImageAcquisition/*/ProtocolApplication/*/ParameterValue

The parameters identifier is "Affymetrix.com:Parameter:ScanPixelSize"

Scan FilterBioAssay//Channel/PropertySets_assnlist/*/@value
Scan DateBioAssay//ImageAcquisition/*/ProtocolApplication/@activityDate
Scanner ID
Protocol

BioAssay

Definition:
//Hardware/*/Parameter
Values:
//ImageAcquisition/*/ProtocolApplication/*/HardwareApplication/*/ParameterValue/@value

The parameters identifier is "Affymetrix.com:Parameter:ScannerID"

Number of Scans
Protocol

BioAssay

Definition:
//Protocol/*/Parameter
Values:
//ImageAcquisition/*/ProtocolApplication/*/ParameterValue

The parameters identifier is "Affymetrix.com:Parameter:NumberOfScans"

Scanner Type
Protocol

BioAssay

Definition:
//Hardware/*/Parameter
Values:
//ImageAcquisition/*/ProtocolApplication/*/HardwareApplication/*/ParameterValue/@value

The parameters identifier is "Affymetrix.com:Parameter:ScannerType"
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