Hinxton OBO-Edit/Protege 4 workshop Jan 2012: Difference between revisions

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** Macro relations (advanced - see how we're doing for time)
** Macro relations (advanced - see how we're doing for time)
* Working with multiple ontologies
* Working with multiple ontologies
** [[Ontology extensions]] (aka cross-products)
** An introduction to owl:imports
** An introduction to owl:imports
*** Working with owl:imports in P4 (David)
*** Working with owl:imports in P4 (David)

Revision as of 13:05, 22 December 2011

EBI, Courtyard Room. January 30-31 2012

We're looking at running a fairly small, informal training workshop for using Protege 4 for ontology development, especially using it wrt OWL/OBO interconversion and editing in Protege and OBO-Edit simultaneously. It'll be very much a hands-on thing, largely for the benefit of the Gene Ontology developers, but we'd be happy for others to sit in if they were interested.

Tentative Schedule

Day 1

  • Overview and objectives (Chris)
  • An introduction to OWL (Chris)
  • obo to owl and back (David OS)
    • OBO-OWL cheat sheet
    • Anatomy ontology examples
    • Automating multiple classification
    • Automatic error detection
    • OBO-Edit Guide (SKIP THIS - read in advance if you are interested)
    • Quick guide to Protege
    • Introducing the tutorial ontology
  • Converting obo to owl: Basic features of Oort (Chris)
  • Demo of OBO-Edit/P4 dual-editing [David OS]
    • Note: we hope to have a 2.1.1b that makes this even easier
  • P4 tutorial [David OS? Simon and James?]
    • Exercises

Day 2

  • P4 tutorial cont.
  • Practical ontology development using P4/OE
  • Relations Ontology (Chris)
    • Summary of current status
    • Macro relations (advanced - see how we're doing for time)
  • Working with multiple ontologies
    • Ontology extensions (aka cross-products)
    • An introduction to owl:imports
      • Working with owl:imports in P4 (David)
      • Limitation of imports in OE (Chris)
    • Imports vs merging in subsets
      • Extracting ontology subsets: Oort guide, part 2 (Chris/David)
    • Case studies:
      • Drosophila anatomy ontology (David)
      • Cell ontology (Chris)
      • Protein ontology (Chris)
    • Using CL in GO - bp-xp-cl logical definitions
    • Using CHEBI/GOCHE in GO - bp-xp-chebi logical definitions
    • Managing dependencies
      • Ontology "builds" and The OBO Jenkins environment
  • Hands on ontology editing (everyone)
    • Split into groups?
  • Advanced topics (if we have time)
    • Gene associations in OWL (Chris)
  • Discussion
    • GO editors requirements for 2012 (Editors)
      • OBO-Edit
      • Protege 4
      • TermGenie
      • GO-Jenkins

Preliminary list of participants:

Chris Mungall (Berkeley)

Tanya Berardini (TAIR)

Judith Blake (GO, MGI)

Karen Eilbeck (SO, Univ. of Utah)

Rebecca Foulger (GO, EBI)

Midori Harris (PomBase, University of Cambridge)

David Hill (MGI)

Harold Drabkin (MGI)

Jane Lomax (GO, EBI)

David Osumi-Sutherland (FlyBase, University of Cambridge)

Karen Christie (SGD)

Paola Roncaglia (GO, EBI)

James Malone (EBI)

Simon Jupp (EBI)

John Ison (EBI)

Marcus Ennis (CHEBI, EBI)

Emily Dimmer (GOA)

Michael Schroeder (Technische Universität Dresden)

Thomas Wächter (Technische Universität Dresden)

Useful links:

Software and downloads Required

You should have the following installed on your laptop prior to the meeting:

  • Protege4 4.1 recommended. You could also install 4.2alpha side by side
    • Plugins (some of these may be distributed with P4 already):
      • ELK
  • OBO-Edit 2.1
    • Note: we may have a 2.1.1beta ready to try
  • The Oort GUI
  • An svn client

Downloads

Tutorial files will be added here

Meeting Logistics

Accommodation

Name Accommodation 29th 30th 31st Vegetarian (Y/N)
Chris Mungall Campus Y Y - Y Judith Blake Campus Y Y -
David Hill Campus - Y -
Tanya Berardini Campus - Y -
Harold Drabkin Campus Y Y Y
Karen Christie Campus Y Y Y
Karen Eilbeck Campus Y Y Y