5.2 Ontology Languages in Bioinformatics 103
- Rule: a mathematical expression that is added to the model equations
constructed from the set of reactions
MAGE-ML http://www.mged.org
The MicroArray Gene Expression Markup Language is an XML ontology
for microarray data. MAGE-ML aims to create a common data format so
that data can be shared easily between projects (Stoeckert, Jr. et al. 2002).
The predecessor of MAGE-ML is the Gene Expression Markup Language
(GEML), initially developed by Rosetta Inpharmatics (Kohane et al. 2003).
MAGE-ML is a data-exchange syntax for microarray data recently created
by the microarray gene expression data group (MGED) (MAGE-ML 2003).
In order to standardize the information concerning microarray data, MGED
initially introduced the minimal information for the annotation of a microar-
ray experiment (MIAME). MIAME describes the minimum information re-
quired to ensure that microarray data can be easily interpreted and that re-
sults derived from its analysis can be independently verified (Brazma et al.
2001). Practically speaking, MIAME is a checklist of what should be supplied
for publication. MIAME-compliant conceptualization of microarray experi-
ments is then modeled using the UML-based microarray gene expression
object model (MAGE-OM). MAGE-OM is then translated into an XML-based
data format, MAGE-ML, to facilitate the exchange of data (Spellman et al.
2002).
There is a close relationship between the MAGE-ML and MGED ontolo-
gies. The MGED ontology, being developed by the Ontology Working Group
of the MGED ontology project, is providing standard controlled vocabularies
for microarrays. The goal of the MGED ontology is to create a framework of
microarray concepts that reflects the MIAME guidelines and MAGE struc-
ture. Therefore, the MGED ontology project has a practical aim to develop
standards, and to reduce nonuniform usage of annotation in microarray ex-
periments. Concepts for which existing controlled vocabularies and ontolo-
gies can be identified are specified by reference to those external resources,
and no new ontologies will be created. Concepts that are microarray-based
or tractable (such as experimental conditions) are specified within the MGED
ontology. MAGE-ML provides a standard XML format, which supersedes
the MicroArray Markup Language (MAML) format, for reporting microar-
ray data and its associated information.
CellML http://www.cellml.org
The CellML ontology is being developed by Physiome Sciences Inc. in Prince-
ton, New Jersey, in conjunction with the Bioengineering Institute at the Uni-