Hinxton OBO-Edit/Protege 4 workshop Jan 2012: Difference between revisions
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* 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 | * An svn client | ||
==== Downloads ==== | |||
You should check out the tutorial | You should check out the tutorial | ||
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svn update | svn update | ||
Note that if you cannot use svn, you can still download the files individually [https://oboformat.googlecode.com/svn/docs/tutorial 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 | |||
===Meeting Logistics=== | ===Meeting Logistics=== |
Revision as of 13:46, 3 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)
- 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
- GO editors requirements for 2012 (Editors)
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 workshop:
- Protege4 4.1 recommended. You could also install 4.2alpha side by side
- Plugins (some of these may be distributed with P4 already):
- ELK
- Plugins (some of these may be distributed with P4 already):
- OBO-Edit 2.1
- Note: we may have a 2.1.1beta ready to try
- The Oort GUI
- An svn client
Downloads
You should check out the tutorial
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
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 |