Microarray Gene Expression Data (MGED) Society Ontology Working Group (OWG)

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. Please contact Chris Stoeckert (stoeckrt@pcbi.upenn.edu) with questions, comments or requests about this site or the working group.

What's new
Subscribe to the OWG mail list
MGED links
What is an ontology?
Ontology presentations
Ontology editor tools
The MGED Ontology
Ontology resources
Archive of OWG documents

What's new:

Mar. 23, 2002:

The "Builing an ontology" page has been retired as all of the information on that page can now be obtained either on this home page or by following links from the home page.
A new version of the MGED ontology is available (1.3; see "The MGED Ontology" link).

Mar. 17, 2002:

Moved ontology tools to its own section on home page (see Ontology editor tools).
Added a direct link to ontology files at sourceforge (see MGED links).
Thanks to Tim Eyres for these suggestions
Updated Michael Krauthammer's review of clinical sites.

Mar. 11, 2002:

New look for this site. Attempt to better organize information. Updated links and information.
MIAME to MAGE mapping added (see MGED links).
Slides from MGED 4 Ontology Working Group added (see Ontology presentations).
Ontology resources added, concept definitions updated.

Jan. 20, 2002:

A page of microarray descriptions (besides sample or biomaterial) from MAGE requiring inclusion into the MGED ontology.
A new version of the MGED ontology available at the "Building an Ontology" page.
An ontology resource for the Plasmodium parasite added.

Subscribe to the OWG mail list:

Ontology working group listserv
Listserv:	microarray-ontol
Subscribe:	Subscribe me

MGED Links:

MGED home

MGED open source software site: Includes MGED Ontology files.

MIAME: Minimum information about a microarray experiment. This document contains the concepts we are trying to define and structure.

MAGE-OM and ML: Microarray Gene Expression Object Model and Markup Language. Joint submission to the Object Management Group (OMG) from Netgenics, MGED, and Rosetta that contains the data format for the concepts in MIAME.

MIAME to MAGE: The first draft of a document mapping MIAME to MAGE-OM and MGED Ontology by Susanna Sansone. This contains MIAME concepts definition, how its requirements map to the MAGE-OM and where the MGED ontology already exists and where there are descriptions that still require inclusion into the ontology (as also highlighted by Jason Stewart). The MIAME to MAML mapping document is now listed on the OWG document archive page.

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.

Ontology presentations:

Ontology editor tools:

The ontology editors are either open source or licensed for free (at least for academics, let me know if I misrepresented anything). Thanks to Robert Stevens, U. Manchester, for info on Protege and OILed.

GKB-Editor: Generic knowledge base editor from SRI that uses frames and slots.
DAG-EDIT: Editor from the Gene Ontology Consortium.
OILed: OILed is a little editor for creating the OIL and DAML+OIL language. Like GKB and Protege, it has a Frame look and feel, but the option of reasoning support. Oiled is really a toy tool. It is reasonably robust, but not supported in any signficiant fashion. It has a little manual, but one would have to read a little about OIL in order to use some of the features fully. The advantange that OILed has, is that one can create simple DAGS, like GO, all the way to full logic models; and migrate from the former to the latter.
Protege 2000:Protege 2000 is the most widely known and used tool for creating ontologies and knowledge bases.

Products such as those from Rational Rose and Embarcadero can also be used to generate UML models (class diagrams). These are not free.

Last updated April 14, 2002