Table 1

A spreadsheet representation of the investigation design graph shown in Figure 1.

Sample ID

Characteristics [Organism]

Characteristics [OrganismPart]

Protocol REF

Hybridization ID

ArrayDesign REF

ArrayData URI

Protocol REF

DerivedArrayData Matrix URI

liver 1

Homo sapiens

liver

P-XMPL-1

hyb 1

HG_U95A

Data1.cel

P-XMPL-2

FGDM.txt

kidney 1

Homo sapiens

kidney

P-XMPL-1

hyb 2

HG_U95A

Data2.cel

P-XMPL-2

FGDM.txt

brain 1

Homo sapiens

brain

P-XMPL-1

hyb 3

HG_U95A

Data3.cel

P-XMPL-2

FGDM.txt

Each initial sample has a Sample ID (the first column in the spreadsheet) and Characteristics – Organism (genus and species) and OrganismPart (the second and third columns). The terms used to annotate the characteristics can be obtained from the MGED Ontology [26], another suitable source of controlled vocabulary terms, or provided as user defined terms. The fourth column gives a reference to a relevant protocol, while the fifth gives the IDs of the three hybridizations performed. The reference to the array design type (HG_U95A) is given as a hybridization property, which is followed by the data file names, a reference to the data normalization protocol and the normalized data file.

Rayner et al. BMC Bioinformatics 2006 7:489   doi:10.1186/1471-2105-7-489