The Microarray Gene Expression Data (MGED) society was formed with an initial focus on experiments involving microarray technology. Despite the diversity ofapplications, there are common concepts used and a common need to captureexperimental information in a standardized manner. In building the MGED ontology,it was recognized that it would be impractical to cover all the different types ofexperiments on all the different types of organisms by listing and defining all thetypes of organisms and their properties. Our solution was to create a framework fordescribing microarray experiments with an initial focus on the biological sample andits manipulation. For concepts that are common for many species, we could provide amanageable listing of controlled terms. For concepts that are species-specific or whosevalues cannot be readily listed, we created an ‘OntologyEntry’ concept that referencedan external resource. The MGED ontology is a work in progress that needs additionalinstances and particularly needs constraints to be added. The ontology currentlycovers the experimental sample and design, and we have begun capturing aspects ofthe microarrays themselves as well. The primary application of the ontology will beto develop forms for entering information into databases, and consequently allowingqueries, taking advantage of the structure provided by the ontology. The applicationof an ontology of experimental conditions extends beyond microarray experimentsand, as the scope of MGED includes other aspects of functional genomics, so too willthe MGED ontology.
展开▼
