MAGE-TAB version 1.0 mapping document.
--------------------------------------

This document gives a mapping from MAGE-TAB row and column headings to
MAGE object attributes.

IDF
===
MAGE-TAB	MAGE
--------	----
Investigation Title	Experiment.name
Experimental Design	ExperimentDesign.types.value
Experimental Factor Type	ExperimentalFactor.category.value
Experimental Factor Type Term Source REF	ExperimentalFactor.category.OntologyReference.Database.name
Experimental Factor Name (Unique)	ExperimentalFactor.name
Person Last Name	Person.lastName
Person First Name	Person.firstName
Person Email	Person.email
Person Phone	Person.phone
Person Address	Person.address
Person Affiliation	Person.affiliation.Organization
Person Roles	Contact.roles.value
Quality Control Types	ExperimentDesign.qualityControlDescription.annotations.value
Replicate Types	ExperimentDesign.replicateDescription.annotations.value
Normalization Types	ExperimentDesign.normalizationDescription.annotations.value
Date of Experiment	arbitrary date: should be specified or removed
Public Release Date	Experiment.PropertySets.value
PubMed ID	Experiment.descriptions.bibliographicReferences.accessions.accession	#resolved by adding database identifier
Publication DOI	Experiment.descriptions.bibliographicReferences.accessions.accession	#resolved by adding database identifier
Publication Author List	Experiment.descriptions.bibliographicReferences.authors
Publication Title	Experiment.descriptions.bibliographicReferences.title
Publication Status	Experiment.descriptions.bibliographicReferences.parameters.value
Experiment Description	Experiment.Descriptions.text
Protocol Name	Protocol.title	and Protocol.name
Protocol Type	Protocol.type.value
Protocol Type Term Source REF	Protocol.type.ontologyReference.database.name
Protocol Description	Protocol.text
Protocol Parameters	Protocol.parameterTypes.name
SDRF File	file_name	#container sheet for the SDRF; required along with IDF for valid MAGE-ML
Term Source	Database.name
Term Source File	Database.URI
Term Source Version	Database.version

SDRF
====
MAGE-TAB	MAGE
--------	----
Source Name	BioSource.name
Characteristics [Ontology class]	BioMaterial.characteristics.value
Term Source REF	Refers to Term Source from IDF; user_defined if blank
Provider	BioSource.sourceContact.name
MaterialType 	BioMaterial.materialType.value
Term Source REF	Refers to Term Source from IDF; user_defined if blank
Description	BioMaterial.descriptions.text
Comment [name of NVT]	implementation specific, prefered use as NVT
Protocol REF	Refers to Protocol Name from IDF; BioMaterial.treatments.protocolApplications.protocol.name
Parameter Value [Reference to Protocol Parameter]	ProtocolApplication.parameterValues.value
Performer	ProtocolApplication.performers.name
Date	ProtocolApplication.activityDate
Sample Name	BioSample.name; BioSample.type = 'not_extract' or null (refer to Source for other mappings)
Extract Name	BioSample.name; requires BioSample.type = 'extract'
LabeledExtract Name	LabeledExtract.name
Label	LabeledExtract.labels.name
Protocol REF	Protocol for hybridization; Hybridization.protocolApplications.protocol.name
Hybridization Name	Hybridization.name
ArrayDesign REF	ArrayDesign.name; reference to ADF
Protocol REF	Protocol for scanning; ImageAcquisition.protocolApplications.protocol.name
Scan Name	ImageAcquisition.name
Image File	Image.URI
Protocol REF	Protocol for FeatureExtraction; FeatureExtraction.protocolApplications.protocol.name
ArrayData File	MeasuredBioAssayData.bioDataValues.dataExternal.filenameURI (eg. CEL/CHP file)
Protocol REF	Protocol for Normalization/; DerivedBioAssay.protocolApplications.protocol.name
Normalization Name	DerivedBioAssay.name
DerivedArrayData File	DerivedBioAssayData.bioDataValues.dataExternal.filenameURI
DerivedArrayData Matrix	DerivedBioAssayData.bioDataValues.dataExternal.filenameURI
FactorValue [ExperimentalFactor name]	one of:
	FactorValue.measurement.value
	FactorValue.value.category
Term Source REF	FactorValue.value.ontologyReference.database.name
Unit [subclass of Unit, eg MassUnit, TimeUnit]	FactorValue.measurement.value.unit.nameCV
Term Source REF	There is no direct mapping in MAGEv1.1; to reference an external ontology. Use FactorValue.value.ontologyReference.database.name.