Major MAGE-ML Packages:

Protocol Package:

Protocol:

Used to define different protocols (ie: hybridization, extraction, image acquisition, labeling).

BioMaterial Package:

All of the following contain references to appropriate protocols in Protocol Package defining how the sample/extraction/labeled extract was derived.

BioSource:

Used to define source of biomaterial used in experiment.

BioSample:

Used to define samples taken from BioSource--also includes treament information

Extraction:

Used to define extracts taken from BioSample

LabeledExtract:

Used to define labeled extracts

Compound:

Used to define various compounds. For instance, what compound was used to label the extract (ie: biotin)

BioAssayPackage:

This package is used to define chip data. For example, an entire cel file would correspond to a MeasuredBioAssay. A chip image would correspond to a PhysicalBioAssay. These objects mostly provide a way to reference a particular cel file as being associated with a particular chip, or an image file as being associated with a particular chip.

DerivedBioAssay:

A result from a transformation on a MeasuredBioAssay or a DerivedBioAssay (ie: normalization).

MeasuredBioAssay:

Defines the quantitated chip.

PhysicalBioAssay:

Corresponds to the Hybridization table entry in BASE. Can be associated with an image file.

DesignElementPackage:

Describes a chip--names/describes probe sets and specifies locations of probes. Corresponds to the information found in a cdf file or environment. We chose to have this package be a separate file because it is large and is the same for all experiments/samples that use the same type of Affymetrix chip.

CompositeSequence:

Definition/description of a probe set.

Reporter:

Definition/description of a probe. Contains location as well as a reference to the CompositeSequence this Reporter belongs to.

QuantitationType Package:

Used to define various values associated with individual reporters. For us this is only an intensity value.

BioAssayData Package:

The package that contains the data.

BioAssayDimension:

Describes first index into BioDataCube. Corresponds to which chip is referenced by the first index contains references to definitions of those BioAssays in the BioAssay Package.

DesignElementDimension:

Describes which probes indexed by the second index into BioDataCube. Contains references to the definitions of these probes within the DesignElement Package.

QuantitationTypeDimension:

Third index in BioDataCube-which values. Contains references to definitions of what type of value this is as defined in the QuantitationType Package.

Measured BioAssayData:

Defines data. In our case it is a BioDataCube. Contains references to appropriate Dimension definitions from above and also the BioDataCube itself. The BioDataCube either continas the data itself in the form of a DataInternal tag and text corresponding to the values formatted appropriately, or, as in our case, a reference to an external text file that contains the data.