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

This site has been moved to http://mged.sourceforge.net/ontologies/index.php for better management and integration with the MAGE effort. Any additions or changes will only be made at the new site. - Nov. 8, 2002.

• What's new
• Subscribe to the OWG mail list Note: The mail list has moved!
• MGED links
• What is an ontology?
• Ontology presentations
• Ontology editor tools
• The MGED Ontology v1.5 Note that DAML and RDFS files can now be obtained from this page via the "namespaces" links.
• Ontology resources
• Archive of OWG documents
• Archive of OWG mail

• A summary of the Onotology Working Group Meeting has been added to the Archive of OWG documents thanks to Helen Parkinson.
• The presentation "The MGED Ontology is an Experimental Ontology," from the 5th Annual Bio-Ontologies meeting (Edmonton, Canada Aug. 2002) has been added to Ontology presentations.
• A picture of the class tree from v1.5 of the MGED ontology is available from a link on the The MGED Ontology v1.5 page thanks to John Matese. Version 1.4 of the ontology has been removed.
• # 27 of vol 1 has been added to the Archive of OWG mail.

• A new version of the MGED ontology (v1.5) has been posted incorporating study design and factors.

• Archive of mail from the microarray-ontol list is now available.
• Additional Ontology Resources added.

• A picture of the biomaterial v1.4 class tree structure has been posted as a link off the MGED Ontology page (thanks to John Matese, Stanford).
• The next Ontology Working Group meeting will take place at ISMB 2002 in Salon 19 at the Shaw Conference Centre on August 7 from 10 - 11 a.m as part of the Birds of a Feather program.

• Meeting of interest: Standards and Ontologies for Functional Genomics conference to be held at Hinxton, 17-20 November 2002.

• A new version of the MGED ontology is posted. Changes include:
  • adding instances for DiseaseState and ClinicalInformation
  • changing CultureCondition to GrowthCondition and making it a subclass of Treatment
  • adding definitions for allele, genotype, and haplotype (making polymorphism part of allele).
  • Organization now has the property of a parent Organization.
  • adding a top class, MGEDontology, that has the property of ID.
• The new MGED ontology was built using OILed 3.4.

• 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).

• 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.

• 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.

• 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.

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.

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

• "The MGED Ontology is an Experimental Ontology,"5th Annual Bio-Ontologies meeting (Edmonton, Canada Aug. 2002)
  
• MGED 4 Ontology Working Group slides (Boston, USA Feb. 2002)
  
• Synopsis of bio-ontologies workshop help at EBI on Dec 5, 2001.
  
• Powerpoint presentation on the MGED OWG from the Fourth Annual Bio-Ontologies meeting (Copenhagen, Denmark, 2001)
  
• MGED 3 Ontology Working Group slides (Palo Alto, March 2001)
  

• 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.