Ontology Position Statement:
The primary purpose of the MGED Ontology is to provide standard terms for the annotation of microarray experiments. These terms will enable structured queries of elements of the experiments. Furthermore, the terms will also enable unambiguous descriptions of how the experiment was performed. The terms will be provided in the form of an ontology which means that the terms will be organized into classes with properties and will be defined. A standard ontology format will be used. For descriptions of biological material (biomaterial) and certain treatments used in the experiment, terms may come from external resources that are specified in the Ontology. Software programs utilizing the Ontology are expected to generate forms for annotation,populate databases directly, or generate files in the established MAGE-ML format. Thus, the Ontology will be used directly by investigators annotating their microarray experiments as well as by software and database developers and therefore will be developed with these very practical applications in mind.
As the terms encoded in the Ontology ultimately will be placed in a MAGE-ML document, to facilitate this process it is important that the efforts of the MAGE and Ontology working groups are coordinated where there is overlap. Ontology classes will strive to maintain the same names and relationships where appropriate to MAGE classes. For instance, 'Experiment' is used because of MAGE in place of 'Study' even though 'Experiment' is not ideal as it interpreted in multiple ways including the distinction from observational studies. As the MAGE effort moves forward and requires terms to describe elements of microarray experiment, the Ontology group should be consulted so as not to duplicate efforts and to use the Ontology to establish terms of choice.
The Ontology is expected to continually grow especially as new applications of microarray technology arise that require descriptive terms. For software programming efforts a fixed Ontology is desired so that usage need not be constantly revised. In order to meet both needs, a core MGED Ontology will be established that will not change. A second layer of the Ontology, the extended MGED Ontology, will contain all additional terms that must be logically consistent with the core Ontology. This approach follows the successful model of the Protein Data Bank and the core mmCIF dictionary approved by the IUCr and exchange mmCIF dictionary.
The core MGED ontology will made to work seamlessly with the published MAGE 1.0 schema and will be completed no later than Sept. 3, 2003 so that it can be presented and voted on at the MGED 6 meeting. To achieve this goal, a series of MGED Ontology Jamborees will be held in the same spirit as the MAGE programming jamborees. The extended MGED ontology will be developed in conjunction with MAGE efforts to develop MAGE 2.0.
The MGED Ontology is one of several ongoing efforts to represent the domains of genomics and proteomics. A
global open biological ontologies effort (GOBO) is underway to collect freely-available ontologies that use a
standard format and are orthogonal in their coverage. The MGED Ontology will participate in this effort through
the provision of terms for experimental conditions. Furthermore, to advance the use of freely available
ontologies as part of the GOBO mission, the MGED Ontology will only include reference to freely available