Ontology Working Group

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Welcome to the website of the ontology working group for the MGED project, which is charged with developing an ontology for describing samples used in microarray experiments.

What is an Ontology?

From the Stanford Knowledge Systems Lab:
"An ontology is an explicit specification of some topic. For our purposes, it is a formal and declarative representation which includes the vocabulary (or names) for referring to the terms in that subject area and the logical statements that describe what the terms are, how they are related to each other, and how they can or cannot be related to each other. Ontologies therefore provide a vocabulary for representing and communicating knowledge about some topic and a set of relationships that hold among the terms in that vocabulary."

An extensive definition from Tom Gruber.

See also:
Toward Principles for the Design of Ontologies Used for Knowledge Sharing. T. Gruber, 1993
Ontology Development 101: A Guide to Creating Your First Ontology. N. Noy and D. McGuinness
Some Ongoing KBS/Ontology Projects and Groups


MGED Ontology Frequently Asked Questions (FAQ):

Information about the MGED Ontology can be found here.

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 structure queriesw 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.

Read more...


Policies for using the MGED Ontology in MAGE documents:

Policies have been generated for the use of the MGED Ontology in MAGE documents where an OntologyEntry is needed. A document is available with these policies.
A powerpoint presentation on the policies from the Dec. 2003 MAGE Jamboree is now included in the Ontology Presentations section below.
Also available is an example file illustrating the application of these policies. Note that you may need to view source or download in order to see these depending on your browser.

Ontology presentations:


Subscribe to the OWG mail list:

Ontology working group listserv
Subscribe at: Mged-ontologies -- Discussion list for MGED Ontology issues.


Mail Archive:

Here's the new mail archive:View new mail archive
Mail archive (prior to Sept. 16, 2002):View mail archive (prior to 9/16/2002)

Please contact Chris Stoeckert with questions, comments or requests about this site or the working group.

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