Hinxton OBO-Edit/Protege 4 workshop Jan 2012

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Revision as of 22:06, 26 January 2012 by Cjm (talk | contribs) (Day 1)

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Introduction

Location: 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.

Day 1

Morning: Introduction to OWL and Protege (9.30am-12.30)

The first morning will include a brief background and introduction before getting started with a progressive walkthrough of OWL concepts and corresponding Protege 4 operations. The participants should have Protege installed and open on their laptops so they can work through the examples as we go along. The slides and documents are in the tutorial/presentations directory, which you should have checked out of svn.

  • Overview and objectives, basic OWL concepts (30 mins) (Chris)
  • obo to owl and back (30 mins) (David OS)
  • P4 feature walkthrough and exercises (2 hrs) (lead by Simon, exercises lead by Chris)
    • Basic editing of subclass hierarchies
    • Reasoning with disjoint classes axioms
    • Object Properties and restrictions
    • DL Queries
    • Classification using a reasoner
    • class unions and negation
    • property chains
    • owl:imports and external ontologies

Afternoon session 1: Working with OBO and OWL (1:30-3pm)

  • Reasoners (Chris) (30 mins)
  • Continuation of walkthrough and exercises (30 mins))
    • advanced examples: chebi and disjoint expressions
    • working with OE and P4 together

Afternoon session 1: Working with multiple ontologies (3.30pm-5.30pm)

  • Oort (30 mins) (Chris)
  • Reasoner strategy for GO (30 mins) (Chris)
  • owl:imports (30 mins) (Simon)
  • Relations Ontology and BFO (30 mins) (Chris)

Day 2

  • 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
        • Target plugins for improvement: E.g. OntoGraf?
      • TermGenie
      • GO-Jenkins

Preliminary list of participants:

Chris Mungall (Berkeley) (V)

Tanya Berardini (TAIR)

Judith Blake (GO, MGI)

Karen Eilbeck (SO, Univ. of Utah) (Vegan)

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)

Emily Dimmer (GOA)

Susan Tweedie (FlyBase)

Marta Costa (Virtual FlyBrain)

Suzanna Lewis (Berkeley)

Paul Thomas (USC)

Useful links:


Software and downloads Required

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

  • Protege4 4.1 recommended. You could also install 4.2alpha side by side
    • Plugins:
      • ELK protege plugin
      • Annotation Search Views (Protege/Preferences/Plugins/Check for downloads) - once installed: views/misc views/annotation search
      • Existential Tree (Protege/Preferences/Plugins/Check for downloads)
    • Setting memory
    • Getting OwlViz to work
      • Protege -> Preferences -> General Options
      • Dot Application Path - set this to the same path you set up for your Graphviz Editor in OE (check your settings)
      • for me (on my Mac), this is /Applications/Graphviz.app/Contents/MacOS/dot
  • OBO-Edit 2.1
    • Note: we may have a 2.1.1beta ready to try
  • The Oort GUI
  • An svn client; see Apache Subversion for subversion software


Downloads

  • Amelia's guide for SVN access to GO svn files SVN help

You should check out the tutorial files, which are arranged in separate directories:

 svn co https://oboformat.googlecode.com/svn/docs/tutorial

When you get to Hinxton you'll make sure you're up to date:

 cd tutorial
 svn update

Note that if you cannot use svn, you can still download the files individually click here to navigate - however, it's strongly recommended you get a working svn client installed before the meeting.

SVN clients:

  • Command line (linux/mac): The standard client is just called "svn" - type this on the command line to see if you have it
  • Windows users: Tortoise recommended
  • Mac users (who prefer GUIs): Smart SVN pro

Reading List

Read / refresh yourself before workshop:

  • Cross-Product Extensions of the Gene Ontology Journal of Biomedical Informatics 2010. Christopher J. Mungall and Michael Bada and Tanya Z. Berardini and Jennifer Deegan and Amelia Ireland and Midori A. Harris and David P. Hill and Jane Lomax
    • Note: the formatting is a little screwed up in the html version - download the pdf
    • Familiarity with this will help for the session on working with multiple ontologies

Additional material:

  • OWL2-primer (ADVANCED)
    • Note: if you read this you should select "manchester syntax" as the display option (software developers choose "functional syntax")
    • You can ignore: 4.7, 4.8 (datatypes), 5.4, 6.3 (keys), all of section 7 (datatypes), section 9

Meeting Logistics

Travel

  • Directions to the Wellcome Trust Genome campus are available here


  • From London Heathrow airport
    • Take the Heathrow Express train to London Paddington Station (20 mins)
    • Take a short Underground tube ride to London Kings Cross Station (20 mins)
    • Take a train to Cambridge Station (50 mins)
    • Pick up a taxi to Hinxton (20 mins)


  • From London Gatwick airport
    • Take the Gatwick Express train to London Victoria Station (40 mins)
    • Take a short Underground tube ride to London Kings Cross Station (10 mins)
    • Take a train to Cambridge Station (50 mins)
    • Pick up a taxi to Hinxton (20 mins)
  • For train (and tube) times see here
  • If you require taxis from/to London airports, please email Tracy in panda_admin BY MONDAY 23RD JANUARY.


Accommodation

Details of the Hinxton rooms are here: http://www.wtconference.org.uk/bedrooms.aspx


Food

Monday 30th, Dinner:

  • Curry in Cambridge (TBC)
Name Accommodation Sun 29th Mon 30th Tues 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 - (staying w/ Terry)
Karen Christie Campus Y Y Y
Karen Eilbeck Campus Y Y Y vegan
Suzanna Lewis Campus (Sat night in Cam) Y Y Y
Paul Thomas Campus Y Y Y