Minimal Information About Microarray Experiments (MIAME):

The boundaries between MIAME concepts, the MIAME-compliant MAGE-OM and the MGED ontology- that try to define and structure the MIAME concepts- is neither well defined nor easy to understand.

In order to provide some help, these pages contain explanatory documentation for the MIAME concepts, how its requirements map to the MAGE-OM and where a MGED ontology inclusion is required.

At the present time the MGED ontology covers only experimental sample (BioMaterial). Work is in progress. Microarray descriptions that still require inclusion into the ontology are specified.

MIAME	Description	MGED Ontology	MAGE-Object Model	When applicable	Notes	Allowed values
1. Array design	The layout or conceptual description of array that can be implemented as one or more physical arrays. The array design specification consists of the description of the common features of the array as the whole, and the description of each array design elements (e.g., each spot). MIAME distinguishes between three levels of array design elements: feature (the location on the array), reporter (the nucleotide sequence present in a particular location on the array), and composite sequence (a set of reporters used collectively to measure an expression of a particular gene)		ArrayDesign_package	When an array design is novel and cannot refer to manufacturer	Array design should be provided by the array providers and manufactures, in which case the user will only need to reference an existing design
1.1. Array related information	Description of the array as the whole
Array design name	Given name for the array design, that helps to identify a design between others (e.g: EMBL yeast 12K ver1.1)		Name is an attribute of ArrayDesign_package	When an array design is novel and cannot refer to manufacturer	Should be consistent with the design name given for the array copy in the Experiment design	Design name, number of features, version (e.g: EMBL yeast 12K ver1.1)
Platform type	The technology type used to place the biological sequence on the array	MGED controlled vocabulary to be developed for FeatureGroup TechnologyType	TechnologyType is an association with FeatureGroup, class of ArrayDesign_package	When an array design is novel and cannot refer to manufacturer		in situ synthesized, spotted cDNA, etc
Surface and coating specification	Type of surface and name for the type of coating used	MGED controlled vocabulary to be developed for PhysicalArrayDesign SurfaceType	SurfaceType is an association with PhysicalArrayDesign, a class of ArrayDesign_package OntologyEntry class in Description_package	When an array design is novel and cannot refer to manufacturer	Should be consistent with TechnologyType	SurfaceType = glass, membrane, etc name of coating type (e.g. amino silane)
Array dimensions	The physical dimension of the array support (e.g. of slide)	MGED controlled vocabulary to be developed for ArrayGroup Substrate type	Width and Length are attributes of ArrayGroup, class of Array_package	When an array design is novel and cannot refer to manufacturer		width, length
Number of elements on the array	The number of features on the array		NumberOfFeatures is an attribute of ArrayDesign, class of Array_package	When an array design is novel and cannot refer to manufacturer		number of elements
Production protocol	A description of how the array was manufactured	MGED controlled vocabulary to be developed for Protocol type, Hardware and Software type	Protocol_package ProtocolApplication is an association with ArrayManufacture, class of Array_package	When an array design is novel and cannot refer to manufacturer	Should be consistent with Feature Location and Zone	Protocol= description, printing hardware, printing software
Provider	The primary contact (manufacturer) for the information on the array design		DesignProvider as an association with ArrayDesign, class of ArrayDesign_package	Always		Contact details of manufacturer
1.2. Reporter related information	Information on the nucleotide sequence present in a particular location on the array
1.2.1.For each reporter type
Reporter type	Physical nature of the reporter (e.g. PCR product, synthesized oligonucleotide)	MGED controlled vocabulary to be developed for DesignElementGroup type	Types is an association with DesignElementGroup, class of Array_package	When an array design is novel and cannot refer to manufacturer	Should be consistent with TechnologyType	Types= empty, PCR, synthesized oligonucleotide, plasmid, colony, etc
Single or double stranded	Whether the reporter sequences are single or double stranded	MGED controlled vocabulary to be developed for DesignElementGroup type	Types is an association with DesignElementGroup, class of Array_package	When an array design is novel and cannot refer to manufacturer	Should be consistent with element Type	Types= single, double
1.2.2. For each reporter
Reporter sequence information	The nucleotide sequence information for reporter: sequence accession number (from DDBJ/EMBL/GenBank), the sequence itself (if known) or a reference sequences (e.g. for oligonucleotides) and PCR primers pair information (if relevant)	MGED controlled vocabulary to be developed for DatabaseEntry	ImmobilizedCharacteristics is an association with Reporter, class of DesignElement_pakage DatabaseEntry is a class of Description_package	When elements are NOT composite and when array design is novel and cannot refer to manufacturer	Should be consistent with element type and clone	sequence annotation, sequence, sequence accession number, PCR primer pair
Reporter approximate length	The approximate length of the reporter’s sequence			When the exact reporter sequence is NOT known		Number of bases
Clone information	For each reporter, the identity of the clone along with information on the clone provider, the date obtained, and availability	MGED controlled vocabulary to be developed for DatabaseEntry type	ImmobilizedCharacteristics is an association with Reporter, class of DesignElement_pakage BioMaterial Is associated with ManufactureLIMS, class of Array_package OntologyEntry, associated to Biosource a class in BioMaterial_package DatabaseEntry is a class of Description_package	When elements are obtained from clones and when an array design is novel and cannot refer to manufacturer	Should be consistent with element type	clone ID,