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

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(Software and downloads Required)
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** Plugins:
 
** Plugins:
 
*** [http://code.google.com/p/elk-reasoner/downloads/detail?name=elk-protege-0.2.0.zip&can=2&q= ELK protege plugin]
 
*** [http://code.google.com/p/elk-reasoner/downloads/detail?name=elk-protege-0.2.0.zip&can=2&q= ELK protege plugin]
*** Annotation Search (Protege/Preferences/Plugins/Check for downloads)
+
*** Annotation Search Views (Protege/Preferences/Plugins/Check for downloads)
 
*** Existential Tree (Protege/Preferences/Plugins/Check for downloads)
 
*** Existential Tree (Protege/Preferences/Plugins/Check for downloads)
 
** Setting memory
 
** Setting memory

Revision as of 09:22, 25 January 2012

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)
  • P4 feature walkthrough [Simon]
    • Guided tutorial (allow 2hrs)
  • Converting obo to owl: Basic features of Oort (Chris)
  • Intro to reasoners (Chris)
  • Tutorial examples
    • Within GO examples: occurs_in?

Day 2

  • 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) (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)

Marcus Ennis (CHEBI, EBI) ?

Emily Dimmer (GOA)

Susan Tweedie (FlyBase)

Marta Costa (Virtual FlyBrain)

Suzanna Lewis (Berkeley)

Paul Thomas (USC)

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 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)
      • 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

Food

Monday 30th, Dinner:

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 vegan
Suzanna Lewis Campus (Sat and Wed night in Cam) Y Y Y
Paul Thomas Campus Y Y Y