Ontology Working Group

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What's new:

March 31, 2010: October 23, 2009:
  • A list of mapped terms between the MGED ontology and the OBO foundry ontologies (PATO, SO, and UO) has been posted on the MGED ontology website.
October 1, 2009:
  • Updated mapping file about a list of MO terms that were deprecated in MO version 1.3.1.1 since they were mapped to the Sequence Ontology (SO) terms.
  • Mapped terms between the MGED ontology and the ontology for Biomedical Investigations (OBI) have been posted on the MGED ontology website. Mapping have been reviewed by several people.
September 22, 2009:
  • A list of mapped terms between the MGED ontology and the Experimental Factor ontology (EFO) has been posted on the MGED ontology website.
  • Mapped terms between the MGED ontology and the ontology for Biomedical Investigations (OBI) have been posted on the MGED ontology website for review.
February 22, 2007:
  • Version 1.3.1.1 of the MGED Ontology has been posted. In addition to a new owl file and an update of notes (for 1.3.1), the main web page for the ontology now shows the latest MO version (1.3.1.1 instead of 1.2.0). A link is also now provided under "Alternate views of the MGED Ontology" to a static view of the class hierarchy.
November 22, 2006:
  • Version 1.3.1 of the MGED Ontology has been posted along with notes. Signficant changes include the use of annotation properties for identifiers, deprecation, and synonyms. Also enumerated lists have been replaced by classes and instances. These changes were made to make MO more application friendly. Many thanks to Trish Whetzel for putting in all the changes. Also many thanks to Gilberto Fragoso and Kjell Petersen for their time on the developing/reviewing the Deprecation Policy and others for their time with the Refactoring in general.
  • Have also added a pointer to the six presentations from the MGED Ontology Workshop held at MGED9 (Seatlle, WA, USA, Sept. 2006).
June 21, 2006:
  • Replaced the owl file at http://mged.sourceforge.net/ontologies/MGEDOntology.owl with version 1.3.0.1. Changes are in http://mged.sourceforge.net/ontologies/MOv1.3.0-Notes.txt. Also added a link to the MGED Ontology page at http://mged.sourceforge.net/ontologies/MGEDontology.php for MOv1.3.0.1 owl docs.
May 6, 2006:
  • Version 1.3 of MO is now available as an OWL file at http://mged.sourceforge.net/ontologies/MGEDOntology.owl. Notes for changes in v1.3 are at http://mged.sourceforge.net/ontologies/MOv1.3.0-Notes.txt. The html page at http://mged.sourceforge.net/ontologies/MGEDontology.phpis still for v1.2.
Apr 13, 2006:
  • An article on the MGED Ontology has been published in Bioinformatics (Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P, Sansone SA, Taylor C, White J, Stoeckert CJ Jr. 2006 The MGED Ontology; a resource for semantics-based description of microarray experiments. Bioinformatics 22:866-73.)
  • A FAQ on the MGED Ontology has been posted. A link is provide from the Ontology Working group home page.
Feb. 4, 2006:
  • Added file of notes from conference call on MO refactoring - http://mged.sourceforge.net/ontologies/MORefactoringCallNotes.
Nov. 28, 2005:
  • Added link to MGED Ontology page to mapping file at the SONG site for MO and SO terms.
Apr. 15, 2005:
  • Replaced owl and daml files with correct 1.2 versions, somehow managed to get them mixed up with older ones. Sorry about that - Chris..
Apr. 4, 2005:
  • Posted new version of the MGED Ontology (v1.2) along with OWL, DAML and notes file. This is the final version to be developed in Oiled with a switch to Protege and OWL becoming the primary format.
Dec. 8, 2004:
  • Posted OWL version of the MGED Ontology.
Sept. 14, 2004:
  • Posted presentations from the MGED Ontology Workshop at MGED7 (Toronto, Canada).
Sept. 6, 2004:
  • Posted MO1.1.9 and updated notes file to list changes plus pending issues and those still under discussion. Thanks to the VOW group and especially to Trish Whetzel for adding changes 1.1.9 and generating notes.
June 2, 2004:
  • Ontology Tools developed at the MAGE Jamboree will be available shortly.
April 4, 2004:
  • Posted MO 1.1.8 which includes 6 bug fixes noted in the notes files
March 22, 2004:
  • Updated the files for coding the MGED Ontology in MAGE and added a powerpoint presentation on this topic from the December 2003 MAGE Jamboree in Hinxton. These are all found on the Home Page.
March 12, 2004:
  • Added a notes file to document any changes to MO 1.1.7. A link is provided from the MGED Ontology
March 2, 2004:
  • Version 1.1.7 of the MGED Ontology has been reposted. The new version fixes lost associations and missing definitions plus some minor adjustments.
January 25, 2004:
  • Version 1.1.7 of the MGED Ontology has (finally) been posted! This represents the FINAL stable version of the MGED Core Ontology that can be coded to. We will still be adding instances taking care that they will not affect the usage of any present terms. Any structural changes such as classes, properties, and axioms will not be made to the MGEDCoreOntology, however, we will use the MGEDExtendedOntology cafor this purpose. Many thanks to the many people who have contributed to this effort.
November 11, 2003:
  • Policies for using the MGED Ontology in MAGE documents have been updated to reflect the new method of referencing OntologyEntry in MAGE. These are available from the OWG home page along with the ling annotation example that has also ben updated and validated.
  • A tracker on sourceforge is now avaialble for new terms proposed for the MGED Ontology - see http://sourceforge.net/tracker/?atid=603031&group_id=16076&func=browse
October 22, 2003:
  • Policies for using the MGED Ontology in MAGE documents have been posted on the OWG home page along with 2 examples and the associated powerpoint presentation from MGED6.
September 1, 2003:
  • A new version of the MGED Ontology is posted, v1.1.6. This is very close to being the official stable version!
July 7, 2003:
  • A link has been added to the MGED Ontology html page for an alternate view of the ontology using the NCI DTS Browser prvoding a much needed class view. Thanks to Gilberto Fragoso.
June 22, 2003:
  • At long last, posted version 1.1.5 of the MGED Ontology resulting from the May Penn Ontology Workshop 4 and follow up discussions. A link to changes is found at the ontology along with usual daml and rdfs files.
May 5, 2003:
  • Posted a new version (1.1.4) of the MGED Ontology. Primarily bug fixes and new instances. Thanks to Trish for generating this and the list of changes to 1.1.4..
April 6, 2003:
  • Finally posted the summary for the Penn Ontology Workshop 3. Thanks to Helen P. for writing it, sorry to take so long to post it.
March 9, 2003:
  • Posted a new version of the MGED Ontology from the Ontology Workshop at Penn March 3-5. Note that I cleaned up the namespace issue. Summary to be posted shortly.
February 13, 2003:
  • Posted an updated version of the MGED Ontology. This contains the remaining results from the last workshop (Helen's version 7 in place of version 3) and some follow-ups.
January 19, 2003:
  • Posted a new version of the MGED Ontology. The new ontology is the result of a workshop at the University of Pennsylvania.
  • There will be a Working Group meeting to discuss the new ontology on Feb. 16, 2003 in Denver, Colorado after the morning session of Microarrays and Functional Genomics meeting organized by MGED and Science magazine as part of the annual AAAS meeting.
December 9, 2002:
  • Added the MGED Core Ontology. The last version (1.6) of the MGED Ontology is also provided.
  • A position statement for the MGED Ontology Working Group has been posted indicating the need to work with the MAGE group and develop a core stabe ontology.
  • A presentation has been posted on the MGED ontology given at the recent Standards and Ontologies for Functional Genomics meeting.
November 8, 2002:
  • The web site has moved here!
  • Version 1.6 of the MGED Ontology has been posted.
  • The Ontology Resources page has a couple changes. The "General" category at the end of "Ontology resources for different species" has been promoted so that you know its there and can jump directly there from the top. The SRS description of Medline has been added that defines the different fields.
September 20, 2002:
  • The list serv has moved to Sourceforge to take advantage of better mail management and a browseable archive.
August 26, 2002:
  • 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.
August 7, 2002:
  • A new version of the MGED ontology (v1.5) has been posted incorporating study design and factors.
July 16, 2002:
  • Archive of mail from the microarray-ontol list is now available.
  • Additional Ontology Resources added.
June 6, 2002:
  • 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.
June 2, 2002: Apr. 28, 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.
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.
Please contact Chris Stoeckert with questions, comments or requests about this site or the working group.

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