"Unless stated otherwise, where multiple SOFT fields are linked to single Tab2MAGE or MAGE-TAB fields they are simply concatenated. Where channel-specific SOFT fields are indicated, all channels should be taken into account; only ch1 fields are listed below. Prefixes in braces are used to indicate which part of the format the information is taken from (i.e. GDS/GSE for SOFT, Hyb/Protocol/Experiment section for Tab2MAGE, or IDF/SDRF for MAGE-TAB)."					
					
"SOFT"	"Tab2MAGE"	"MAGE-TAB"	"MAGE"	"Comment"	"Parsing class (AE GEOImporter)"
					
"[GDS] !Series_sample_id"	"[Hyb] BioSource"	"[SDRF] Source Name"	"BioSource.name"	"maps to [GSE] ^SAMPLE"	"GdsFactorHandler"
"[GDS] !subset_type"	"[Hyb] FactorValue[] header term (titlecased)"	"[IDF] Experimental Factor Type"	"ExperimentalFactor.Category.value"		"GdsFactorHandler"
"[GDS] !subset_description"	"[Hyb] FactorValue[] body term"	"[SDRF] FactorValue[] body term"	"FactorValue.Value.value"		"GdsFactorHandler"
"[GDS] !subset_sample_id"				"mapped to !Series_sample_id"	"GdsFactorHandler"
"[GDS] ^SUBSET"				"no mapping"	"GdsFactorHandler"
"[GDS] ^DATASET"				"no mapping"	"GdsFactorHandler"
					
"[GSE] SERIES"	"[Expt] secondary_accession"	"[IDF] Comment[SecondaryAccession]"	"Experiment.PropertySets.value(name=SecondaryAccession)"		"GeoExperiment"
"[GSE] !Series_title"	"[Expt] name"	"[IDF] Investigation Title"	"Experiment.name"		"GeoExperiment"
					
"[GSE] !Series_summary"	"[Expt] description"	"[IDF] Experiment Description"	"Experiment.Description.text"		"GeoExperiment"
"[GSE] !Series_overall_design"	"[Expt] description"	"[IDF] Experiment Description"	"Experiment.Description.text"		"GeoExperiment"
					
"[GSE] !Series_status = Public on"	"[Expt] geo_release_date"	"[IDF] Comment[GEOReleaseDate]"	"Experiment.PropertySets.value(name=GEOReleaseDate)"		"GeoExperiment"
"[GSE] !Series_submission_date"	"[Expt] submission_date"	"[IDF] Comment[ArrayExpressSubmissionDate]"	"Experiment.PropertySets.value(name=ArrayExpressSubmissionDate)"		"GeoExperiment"
"[GSE] !Series_contact_name"	"[Expt] submitter"	"[IDF] Person Last Name|Person First Name"	"Person.lastName|Person.firstName"		"GeoExperiment"
"[GSE] !Series_contact_email"	"[Expt] submitter_email"	"[IDF] Person Email"	"Person.email"		"GeoExperiment"
					
"[GSE] !Series_contact_laboratory"	"[Expt] organization"	"[IDF] Person Affiliation"	"Person.Affiliation.name"		"GeoExperiment"
"[GSE] !Series_contact_department"	"[Expt] organization"	"[IDF] Person Affiliation"	"Person.Affiliation.name"		"GeoExperiment"
"[GSE] !Series_contact_institute"	"[Expt] organization"	"[IDF] Person Affiliation"	"Person.Affiliation.name"		"GeoExperiment"
"[GSE] !Series_contact_address"	"[Expt] address"	"[IDF] Person Address"	"Person.Affiliation.address"		"GeoExperiment"
"[GSE] !Series_contact_city"	"[Expt] address"	"[IDF] Person Address"	"Person.Affiliation.address"		"GeoExperiment"
"[GSE] !Series_contact_zip/postal_code"	"[Expt] address"	"[IDF] Person Address"	"Person.Affiliation.address"		"GeoExperiment"
"[GSE] !Series_contact_country"	"[Expt] address"	"[IDF] Person Address"	"Person.Affiliation.address"		"GeoExperiment"
					
"[GSE] !Series_pubmed_id"	"[Expt] pubmed_id"	"[IDF] PubMed ID"	"Experiment.Description.BibliographicReference.Accession.accession"		"GeoExperiment"
					
"[GSE] !Sample_supplementary_file"				"Data file archive for download."	"GeoFTP"
					
"[GSE] ^SAMPLE"	"[Hyb] BioSource"	"[SDRF] Source Name"	"BioSource.name"		"GeoProtocol"
"[GSE] !Sample_treatment_protocol_ch1"	"[Prot] text"	"[IDF] Protocol Description"	"Protocol.text"		"GeoProtocol"
"[GSE] !Sample_extract_protocol_ch1"	"[Prot] text"	"[IDF] Protocol Description"	"Protocol.text"		"GeoProtocol"
"[GSE] !Sample_label_protocol_ch1"	"[Prot] text"	"[IDF] Protocol Description"	"Protocol.text"		"GeoProtocol"
"[GSE] !Sample_hyb_protocol_ch1"	"[Prot] text"	"[IDF] Protocol Description"	"Protocol.text"		"GeoProtocol"
"[GSE] !Sample_scan_protocol_ch1"	"[Prot] text"	"[IDF] Protocol Description"	"Protocol.text"		"GeoProtocol"
"[GSE] !Sample_growth_protocol_ch1"	"[Prot] text"	"[IDF] Protocol Description"	"Protocol.text"		"GeoProtocol"
					
"[GSE] !Sample_channel_count"				"not mapped (used internally during parsing though)"	"HybridizationHandler"
"[GSE] !Sample_series_id"				"not mapped (used internally, also can be concat with sample_id for Names etc.)"	"HybridizationHandler"
"[GSE] !Sample_title"				"not mapped"	"HybridizationHandler"
"[GSE] !Sample_organism_ch1"	"[Hyb] BioMaterialCharacteristics[Organism]"	"[SDRF] Characteristics[Organism"	"BioSource.Characteristics.value(category=Organism)"		"HybridizationHandler"
"[GSE] !Sample_supplementary_file"	"[Hyb] File[raw]"	"[SDRF] Array Data File"	"recoded in MAGE BioAssayData"	"Exact position depends on file extension (CEL=raw, CHP=norm, EXP=exp)"	"HybridizationHandler"
"[GSE] !Sample_supplementary_file"	"[Hyb] File[normalized]"	"[SDRF] Derived Array Data File"	"recoded in MAGE BioAssayData"	"Exact position depends on file extension (CEL=raw, CHP=norm, EXP=exp)"	"HybridizationHandler"
"[GSE] !Sample_supplementary_file"	"[Hyb] File[exp]"	"[SDRF] Comment[EXP]"	"recoded in MAGE (various packges)"	"Exact position depends on file extension (CEL=raw, CHP=norm, EXP=exp)"	"HybridizationHandler"
"[GSE] !Sample_platform_id"	"[Hyb] Array[accession]"	"[SDRF] Array Design REF"	"Array.name"	"mapped to AE accessions"	"HybridizationHandler"
"[GSE] !Sample_table_begin"	"[Hyb] File[normalized]"	"[SDRF] Derived Array Data File"	"recoded in MAGE BioAssayData"	"output as normalized .txt file"	"HybridizationHandler"
"[GSE] !Sample_table_end"	"[Hyb] File[normalized]"	"[SDRF] Derived Array Data File"	"recoded in MAGE BioAssayData"	"output as normalized .txt file"	"HybridizationHandler"
					
"[GSE] !Sample_description"	"[Hyb] BioSource Description"	"[SDRF] Description"	"BioSource.Description.text"		"MaterialHandler"
"[GSE] !Sample_molecule_ch1"	"[Hyb] Extract Material"	"[SDRF] Material Type"	"BioMaterial.MaterialType.value"		"MaterialHandler"
					
"All the following are used for text mining to get sample characteristics (details are beyond the scope of this document):"					
"[GSE] !Series_title"	"[Hyb] BioMaterialCharacteristics[]"	"[SDRF] Characteristics[]"	"BioSource.Characteristics.value"		"annotate_gse.pl"
"[GSE] !Series_summary"	"[Hyb] BioMaterialCharacteristics[]"	"[SDRF] Characteristics[]"	"BioSource.Characteristics.value"		"annotate_gse.pl"
"[GSE] !Series_type"	"[Hyb] BioMaterialCharacteristics[]"	"[SDRF] Characteristics[]"	"BioSource.Characteristics.value"		"annotate_gse.pl"
"[GSE] !Series_overall_design"	"[Hyb] BioMaterialCharacteristics[]"	"[SDRF] Characteristics[]"	"BioSource.Characteristics.value"		"annotate_gse.pl"
"[GSE] !Sample_title"	"[Hyb] BioMaterialCharacteristics[]"	"[SDRF] Characteristics[]"	"BioSource.Characteristics.value"		"annotate_gse.pl"
"[GSE] !Sample_description"	"[Hyb] BioMaterialCharacteristics[]"	"[SDRF] Characteristics[]"	"BioSource.Characteristics.value"		"annotate_gse.pl"
"[GSE] !Sample_source_name_ch1"	"[Hyb] BioMaterialCharacteristics[]"	"[SDRF] Characteristics[]"	"BioSource.Characteristics.value"		"annotate_gse.pl"
"[GSE] !Sample_characteristics_ch1"	"[Hyb] BioMaterialCharacteristics[]"	"[SDRF] Characteristics[]"	"BioSource.Characteristics.value"		"annotate_gse.pl"