Scientific Publications
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 Data |
Package |
MAGE-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
Type | BioMaterial | //BioSource/MaterialType_assn/*/@value |
Sample Description | BioMaterial | //BioSource/*/Description/@text |
Sample Project
| BioMaterial | //BioSource/Characteristics_assnlist/*/@value |
Comments | Experiment | //BioSource/*/Description/@text |
Reagents | BioMaterial | //Compound/@name |
Reagent Lot | BioMaterial | //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 Name | Protocol | //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 Date | BioAssay | //Hybridization/*/ProtocolApplication/@activityDate |
Scan Pixel Size | Protocol BioAssay |
Definition: //Protocol/*/Parameter Values: //ImageAcquisition/*/ProtocolApplication/*/ParameterValue The parameters identifier is "Affymetrix.com:Parameter:ScanPixelSize" |
Scan Filter | BioAssay | //Channel/PropertySets_assnlist/*/@value |
Scan Date | BioAssay | //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 Data |
Package |
MAGE-ML XPAth Location |
|---|---|---|
Analysis name |
BioAssay |
//MeasuredBioAssay/@name |
Date |
BioAssay |
//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 type |
BioAssay |
//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 masked |
BioAssayData |
//MeasuredBioAssayData/SummaryStatistics_assnlist/*/@value The name of the parameter is "Number Cells Masked" |
Number outlier cells |
BioAssayData |
//MeasuredBioAssayData/SummaryStatistics_assnlist/*/@value The name of the parameter is "Number Outlier Cells" |
Number cells modified |
BioAssayData |
//MeasuredBioAssayData/SummaryStatistics_assnlist/*/@value The name of the parameter is "Number Cells Modified" |
Rows |
BioAssayData |
//MeasuredBioAssayData/SummaryStatistics_assnlist/*/@value The name of the parameter is "Rows" |
Cols |
BioAssayData |
//MeasuredBioAssayData/SummaryStatistics_assnlist/*/@value The name of the parameter is "Cols" |
Number of cells |
BioAssayData |
//MeasuredBioAssayData/SummaryStatistics_assnlist/*/@value The name of the parameter is "Number of Cells" |
CEL File Entry Data
CEL Entry Data |
Package |
MAGE-ML XPAth Location |
|---|---|---|
X | BioAssayData |
implied by //FeatureDimension/*/Feature_ref/@identifier and stored in //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Y | BioAssayData |
implied by //FeatureDimension/*/Feature_ref/@identifier and stored in //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Intensity | BioAssayData |
//BioDataCube/*/DataExternal (QuantitationType is "MeasuredSignal") |
Stdev | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Number
of pixels used to calculate the intensity value | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Outlier | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Mask | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
CHP File Data
CHP File Data |
Package |
MAGE-ML XPAth Location |
|---|---|---|
Date | BioAssayData | //Transformation/*/ProtocolApplication/@activityDate |
Cols | BioAssayData |
//DerivedBioAssayData/SummaryStatistics_assnlist/*/@value The parameter name is "Cols" |
Rows | BioAssayData |
//DerivedBioAssayData/SummaryStatistics_assnlist/*/@value The parameter name is "Rows" |
Number
of probe sets | BioAssayData |
//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 type | BioAssay |
//DerivedBioAssay/PropertySets_assnlist/*/@value |
CHP File Entry Data For Statistical and PLIER Absolute Analysis
CHP Entry Data |
Package |
MAGE-ML XPAth Location |
|---|---|---|
Probe
set name | BioAssayData |
//BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Pairs | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Pairs
used | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Signal | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "DerivedSignal") |
Detection | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "PresentAbsent") |
p-value | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "PValue") |
CHP File Entry Data For Statistical Comparison Analysis
CHP Entry Data |
Package |
MAGE-ML XPAth Location |
|---|---|---|
Probe
set name | BioAssayData |
//BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Pairs | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Pairs
used | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Signal | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "DerivedSignal") |
Detection | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "PresentAbsent") |
p-value | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "PValue") |
Common
pairs | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Signal
log ratio | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "Ratio") |
Signal
log ratio low | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "Ratio") |
Signal
log ratio high | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "Ratio") |
Change | BioAssayData | //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 Data |
Package |
MAGE-ML XPAth Location |
|---|---|---|
Probe
set name | BioAssayData |
//BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Positive | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Negative | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Pairs | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Pairs
Used | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Pairs
in Avg | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Pos
Fraction | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "Ratio") |
Log
Avg | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Pos/Neg | BioAssayData | //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 Data |
Package |
MAGE-ML XPAth Location |
|---|---|---|
Probe
set name | BioAssayData |
//BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Positive | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Negative | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Pairs | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Pairs
Used | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Pairs
in Avg | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Pos
Fraction | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "Ratio") |
Log
Avg | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Pos/Neg | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "Ratio") |
Avg
Diff | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "DerivedSignal") |
Abs
Call | BioAssayData | //BioDataCube/*/DataExternal (QuantitationType is "PresentAbsent") |
Inc |
BioAssayData |
//BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Dec |
BioAssayData |
//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/Dec |
BioAssayData |
//BioDataCube/*/DataExternal (QuantitationType is "Ratio") |
DPos-DNeg
Ratio |
BioAssayData |
//BioDataCube/*/DataExternal (QuantitationType is "Ratio") |
Log
Avg Ratio |
BioAssayData |
//BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Diff
Call |
BioAssayData |
//BioDataCube/*/DataExternal (QuantitationType is "PresentAbsent") |
Avg
Diff Change |
BioAssayData |
//BioDataCube/*/DataExternal (QuantitationType is "SpecializedQuantitationType") |
Baseline
is Absent |
BioAssayData |
//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 Element |
Package |
MAGE-ML XPAth Location |
|---|---|---|
Array
Structure |
ArrayDesign 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 Set |
DesignElement |
//ReporterCompositeMap |
Probes per Probe
Pair |
DesignElement |
//FeatureReporterMap |
| ProbeSets |
ArrayDesign 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
Pairs |
DesignElement |
//Reporter |
Probes |
ArrayDesign |
//FeatureGroup/Features_assnlist/Feature |
PM/MM Relationship |
ArrayDesign ArrayDesign DesignElement | //Feature/ControlFeatures_assnreflist/Feature_ref //FeatureGroup/Features_assnlist/Feature //FeatureInformation/MismatchInformation_assnlist/* |
CDF File Array Data
Structure Element |
Package |
MAGE-ML XPAth Location |
|---|---|---|
Probe
Array Name |
ArrayDesign |
//PhysicalArrayDesign/@name |
Rows |
ArrayDesign |
//ZoneLayout/@numFeaturesPerCol |
Cols |
ArrayDesign |
//ZoneLayout/@numFeaturesPerRow |
Number of cells |
ArrayDesign |
//PhysicalArrayDesign/@numberOfFeatures |
Cell location |
ArrayDesign |
//Feature/*/FeatureLocation |
Cell type |
ArrayDesign | //Feature/ControlType_assn/*/@value The value is either "PM" or "MM" |
Probe
set name |
DesignElement |
//CompositeSequence/@name |
Subtitution position |
DesignElement |
//FeatureInformation/*/MismatchInformation/@startCoord |
Probe base at substitution
position |
DesignElement | //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 Information |
Package |
MAGE-ML XPAth Location |
|---|---|---|
Sample
Name |
BioMaterial |
//BioSource/@name |
Sample Attribute
Template Name |
BioMaterial |
//BioSource/PropertySets_assnlist/NameValueType[@name="Sample
Template Name"] |
Sample
Attribute Template Name-Value |
BioMaterial |
//BioSource/PropertySets_assnlist/NameValueType |
Sample Type |
BioMaterial |
//BioSource/MaterialType_assn/*/@value |
Sample Description |
BioMaterial |
//BioSource/*/Description/@text |
Sample Project
|
BioMaterial |
//BioSource/Characteristics_assnlist/*/@value |
Comments |
Experiment |
//BioSource/*/Description/@text |
Reagents |
BioMaterial |
//Compound/@name |
Reagent Lot |
BioMaterial |
//Compound/PropertySets_assnlist/*/@value |
Experiment Information
Experiment Information |
Package |
MAGE-ML XPAth Location |
|---|---|---|
Experiment
Name |
Experiment |
//Experiment/@name |
Experiment Attribute
Template Name |
Experiment |
//Experiment/PropertySets_assnlist/NameValueType[@name="Experiment
Template Name"] |
Experiment
Attribute Template Name-Value |
Experiment |
//Experiment/PropertySets_assnlist/NameValueType |
Probe Array Type
|
ArrayDesign |
//PhysicalArrayDesign/@name |
Probe Array Lot
|
Array |
//ArrayManufacture/PropertySets_assnlist/NameValueType/@value |
Hybridization Information
Experiment Information |
Package |
MAGE-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 Name |
Protocol |
//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 Date |
BioAssay |
//Hybridization/*/ProtocolApplication/@activityDate |
Scan Information
Experiment Information |
Package |
MAGE-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 Filter |
BioAssay |
//Channel/PropertySets_assnlist/*/@value |
Scan Date |
BioAssay |
//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" |
