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

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==EBI, Courtyard Room. January 30-31 2012==
+
== 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.
 
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 : Monday Jan 30  ==
 +
 +
=== 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 [http://oboformat.googlecode.com/svn/docs/tutorial/presentations/ tutorial/presentations] directory, which you should have checked out of svn. See the [http://www.geneontology.org/GO.svn.help.shtml GO SVN guide]. If you can't use svn you can get the material [http://www.berkeleybop.org/~cjm/tutorial/ here].
 +
 +
* 9.30-10am : Overview and objectives, basic OWL concepts (30 mins) (Chris)
 +
* 10am-10.30am : obo to owl and back (30 mins) (David OS)
 +
* 10.30am-12.30am : P4 feature walkthrough and exercises (2 hrs) (lead by Simon, exercises lead by Chris)
 +
** Basic editing of subclass hierarchies (15 mins)
 +
** Reasoning with disjoint classes axioms (15 mins)
 +
** Object Properties and restrictions (15 mins)
 +
** DL Queries (15 mins)
 +
** Classification using a reasoner (15 mins)
 +
** class unions and negation (15 mins)
 +
** property chains (15 mins)
 +
** owl:imports and external ontologies (15 mins)
 +
 +
=== Afternoon session 1: Working with OBO and OWL (1:30pm-3pm) ===
 +
 +
In the afternoon we continue with the walkthrough. We will cover dual OE/P4 editing, participants should have OE2.1.1beta4 installed.
  
===Tentative Schedule===
+
* 1.30pm-2pm Reasoners (Chris) (30 mins)
 +
* 2pm-3pm Continuation of walkthrough and exercises (1hr)
 +
** 2pm-2.30pm advanced examples: chebi and disjoint expressions (30 mins)
 +
** 2.30pm - 3pm working with OE and P4 together (30 mins)
  
====Day 1====
+
=== Afternoon session 2: Working with multiple ontologies (3.15pm-5.30pm) ===
  
* Overview and objectives (Chris)
+
Participants should have Oort installed for this session
* An introduction to OWL (Chris)
 
* [http://www.slideshare.net/dosumis/from-obo-to-owl-and-back-building-scalable-ontologies 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====
+
* 3.15-3.45pm [[Oort]] (30 mins) (Chris)
 +
* 3.45pm-4pm [[Ontology_Release_Files_Proposal|GO public release strategy]] (15 mins) (Chris)
 +
* 4pm-4.15pm Reasoner strategy for GO (15 mins) (Chris)
 +
** Current strategy: asserting implied links
 +
** How do we move to dynamic classification?
 +
* 4.15pm-4.30pm [[Relations]] Ontology and [[BFO]] (15 mins) (Chris)
 +
* 4.30pm-5.30pm Introduction to [[Ontology extensions]] (1hr) (Chris)
 +
* 5.30pm - wrap up, make sure everyone has svn set up ready for tomorrow
  
* [[Relations]] Ontology (Chris)
+
== Day 2 : Tuesday Jan 31 ==
** Summary of current status
+
 
* Working with multiple ontologies
+
=== Morning: Practical aspects ===
** [[Ontology extensions]] (aka cross-products)
+
 
** An introduction to owl:imports
+
On day 1 we worked mostly on test ontologies. Everything on day 2 will be on the main GO. Participants should make sure that they have the go ontology svn directory checked out, and have allocated enough memory for Protege.
*** Working with owl:imports in P4 (David)
+
 
*** Limitation of imports in OE (Chris)
+
* Summary of Day 1
 +
* GO strategies for working with multiple ontologies
 +
** GO [[Ontology extensions]] (aka cross-products)
 +
** Which reasoner to use?
 
** Imports vs merging in subsets
 
** Imports vs merging in subsets
 
*** Extracting ontology subsets: Oort guide, part 2 (Chris/David)
 
*** Extracting ontology subsets: Oort guide, part 2 (Chris/David)
Line 32: Line 60:
 
*** Drosophila anatomy ontology (David)
 
*** Drosophila anatomy ontology (David)
 
*** Cell ontology (Chris)
 
*** Cell ontology (Chris)
*** Protein ontology (Chris)
 
** Using CL in GO - [[XP:biological_process_xp_cell|bp-xp-cl logical definitions]]
 
** Using CHEBI/GOCHE in GO - [[XP:biological_process_xp_chebi|bp-xp-chebi logical definitions]]
 
 
** Managing dependencies
 
** Managing dependencies
*** Ontology "builds" and The OBO Jenkins environment
+
*** Ontology "builds" and the [http://ladle.lbl.gov:8080 OBO Jenkins environment]
* Hands on ontology editing (everyone)
+
** GO Taxon Constraints
** Split into groups?
+
* Timeline for switching GO to SVN
* Advanced topics (if we have time)
+
 
** Gene associations in OWL (Chris)
+
=== Afternoon session 1: Hands on session ===
* Discussion
+
 
** GO editors requirements for 2012 (Editors)
+
* Hands on ontology hackathon (everyone)
*** OBO-Edit
+
 
*** Protege 4
+
Split into groups. Some will work on specific areas of the ontology. Others will work on GO strategy and advanced topics
*** TermGenie
+
 
*** GO-Jenkins
+
* Possible groups (to be decided on the day)
 +
** signaling
 +
** taxon constraints
 +
** relations ontology
 +
** development, cell and anatomy logical definitions
 +
** modeling genes and gene associations in OWL
 +
** chebi
 +
** SO
 +
 
 +
=== Afternoon session 2: Discussion and requirements ===
 +
 
 +
* Report back from working groups
 +
* Requirements gathering
 +
** Strategy for OE
 +
** P4 plugins wishlist
 +
* Open discussion
  
===Preliminary list of participants:===
+
== List of participants ==
  
 
Chris Mungall (Berkeley) (V)
 
Chris Mungall (Berkeley) (V)
Line 79: Line 119:
  
 
John Ison (EBI)
 
John Ison (EBI)
 
Marcus Ennis (CHEBI, EBI) ?
 
  
 
Emily Dimmer (GOA)
 
Emily Dimmer (GOA)
Line 91: Line 129:
  
 
Paul Thomas (USC)
 
Paul Thomas (USC)
 
Michael Schroeder (Technische Universität Dresden)
 
 
Thomas Wächter (Technische Universität Dresden)
 
  
 
===Useful links:===
 
===Useful links:===
Line 118: Line 152:
 
*** for me (on my Mac), this is /Applications/Graphviz.app/Contents/MacOS/dot
 
*** for me (on my Mac), this is /Applications/Graphviz.app/Contents/MacOS/dot
 
* OBO-Edit 2.1
 
* OBO-Edit 2.1
** Note: we may have a 2.1.1beta ready to try
+
** [http://oboedit.org/test_release/2.1.1-b4/ 2.1. beta4] is recommended
 
* The [http://code.google.com/p/owltools/wiki/OBOReleaseManagerGUIDocumentation Oort GUI]
 
* The [http://code.google.com/p/owltools/wiki/OBOReleaseManagerGUIDocumentation Oort GUI]
 
* An svn client; see [http://subversion.apache.org/ Apache Subversion] for subversion software
 
* An svn client; see [http://subversion.apache.org/ Apache Subversion] for subversion software
  
 
==== Downloads ====
 
  
 
* Amelia's guide for SVN access to GO svn files [http://www.geneontology.org/GO.svn.help.shtml SVN help]
 
* Amelia's guide for SVN access to GO svn files [http://www.geneontology.org/GO.svn.help.shtml SVN help]
Line 195: Line 227:
 
! Name
 
! Name
 
! Accommodation
 
! Accommodation
! 29th
+
! Sun 29th
! 30th
+
! Mon 30th
! 31st
+
! Tues 31st
 
! Vegetarian (Y/N)
 
! Vegetarian (Y/N)
 
|-
 
|-
Line 229: Line 261:
 
| Y
 
| Y
 
| Y
 
| Y
| Y
+
| - (staying w/ Terry)
 
|-
 
|-
 
|Karen Christie
 
|Karen Christie
Line 245: Line 277:
 
|-
 
|-
 
|Suzanna Lewis
 
|Suzanna Lewis
|Campus (Sat and Wed night in Cam)
+
|Campus (Sat night in Cam)
 
| Y
 
| Y
 
| Y
 
| Y
Line 260: Line 292:
  
 
Monday 30th, Dinner:
 
Monday 30th, Dinner:
* http://www.al-casbah.com/ or curry (TBC)
+
* Curry in Cambridge (TBC)
  
 
[[Category:Ontology]]
 
[[Category:Ontology]]
 
[[Category:Meetings]]
 
[[Category:Meetings]]
 +
[[Category:Protege]]

Latest revision as of 13:28, 12 April 2014

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 : Monday Jan 30

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. See the GO SVN guide. If you can't use svn you can get the material here.

  • 9.30-10am : Overview and objectives, basic OWL concepts (30 mins) (Chris)
  • 10am-10.30am : obo to owl and back (30 mins) (David OS)
  • 10.30am-12.30am : P4 feature walkthrough and exercises (2 hrs) (lead by Simon, exercises lead by Chris)
    • Basic editing of subclass hierarchies (15 mins)
    • Reasoning with disjoint classes axioms (15 mins)
    • Object Properties and restrictions (15 mins)
    • DL Queries (15 mins)
    • Classification using a reasoner (15 mins)
    • class unions and negation (15 mins)
    • property chains (15 mins)
    • owl:imports and external ontologies (15 mins)

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

In the afternoon we continue with the walkthrough. We will cover dual OE/P4 editing, participants should have OE2.1.1beta4 installed.

  • 1.30pm-2pm Reasoners (Chris) (30 mins)
  • 2pm-3pm Continuation of walkthrough and exercises (1hr)
    • 2pm-2.30pm advanced examples: chebi and disjoint expressions (30 mins)
    • 2.30pm - 3pm working with OE and P4 together (30 mins)

Afternoon session 2: Working with multiple ontologies (3.15pm-5.30pm)

Participants should have Oort installed for this session

  • 3.15-3.45pm Oort (30 mins) (Chris)
  • 3.45pm-4pm GO public release strategy (15 mins) (Chris)
  • 4pm-4.15pm Reasoner strategy for GO (15 mins) (Chris)
    • Current strategy: asserting implied links
    • How do we move to dynamic classification?
  • 4.15pm-4.30pm Relations Ontology and BFO (15 mins) (Chris)
  • 4.30pm-5.30pm Introduction to Ontology extensions (1hr) (Chris)
  • 5.30pm - wrap up, make sure everyone has svn set up ready for tomorrow

Day 2 : Tuesday Jan 31

Morning: Practical aspects

On day 1 we worked mostly on test ontologies. Everything on day 2 will be on the main GO. Participants should make sure that they have the go ontology svn directory checked out, and have allocated enough memory for Protege.

  • Summary of Day 1
  • GO strategies for working with multiple ontologies
    • GO Ontology extensions (aka cross-products)
    • Which reasoner to use?
    • Imports vs merging in subsets
      • Extracting ontology subsets: Oort guide, part 2 (Chris/David)
    • Case studies:
      • Drosophila anatomy ontology (David)
      • Cell ontology (Chris)
    • Managing dependencies
    • GO Taxon Constraints
  • Timeline for switching GO to SVN

Afternoon session 1: Hands on session

  • Hands on ontology hackathon (everyone)

Split into groups. Some will work on specific areas of the ontology. Others will work on GO strategy and advanced topics

  • Possible groups (to be decided on the day)
    • signaling
    • taxon constraints
    • relations ontology
    • development, cell and anatomy logical definitions
    • modeling genes and gene associations in OWL
    • chebi
    • SO

Afternoon session 2: Discussion and requirements

  • Report back from working groups
  • Requirements gathering
    • Strategy for OE
    • P4 plugins wishlist
  • Open discussion

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
  • The Oort GUI
  • An svn client; see Apache Subversion for subversion software


  • 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