OBI tutorial 2011 ICBO

Schedule
All slides and related documents for presentations and hands-on tutorials can be found on:

https://obi.svn.sourceforge.net/svnroot/obi/trunk/docs/presentations/OBI%20tutorial%20July%202011%20ICBO/

12:30 pm Presentations (20 min for each presentation)

1) Overview and high level classes of OBI (Bjoern)

'''OBI applications '''

2) How to extend an existing database (Bjoern, IEDB) 3) How to design a data submission form (Jie, EuPathDB) 4) How to develop an interoperable representation of research resources (Carlo, eagle-i)

5) ISA tools and annotation of functional genomics experiments (Phillipe)

6) How to link to OBI within an existing ontology development project (Marcus, ECO)

2:30pm BioBreak

2:45pm Hands On Session (25 min for each topic including 10 min brief introduction)

1) Add individual classes to OBI (OWL, restrictions, Protege) (Bjoern) 2) Add multiple classes to OBI using spreadsheets (QTT, Carlo)

3) Import external terms into OBI and create community views (MIREOT and OntoFox-View, Oliver and Jie)

Reading Material

 * Modeling biomedical experimental processes with OBI. J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S7. [Full Text]


 * MIREOT: the Minimum Information to Reference an External Ontology Term. International Conference on Biomedical Ontology (ICBO) Buffalo, New York (July 2009) [PDF]


 * QTT: Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates [PDF]


 * Ontology Driven Data Collection for EuPathDB. International Conference on Biomedical Ontology (ICBO) Buffalo, New York (July 2011) [PDF]

OBI Check out
check out latest version of OBI svn co http://obi.svn.sourceforge.net/svnroot/obi/trunk/src/ontology/

Details for SVN see http://obi-ontology.org/page/General_introduction#SVN

Recommended software installations
Ideally complete these steps before the workshop.

http://protege.stanford.edu/download/protege/4.1/installanywhere/Web_Installers/
 * Download Protégé 4.1 Release Candidate 5 at:


 * Follow the instruction to install Protégé posted on the same page


 * Load the checked out version of OBI from the file, or load from the url: http://purl.obolibrary.org/obo/obi.owl


 * If the OBI classes are displayed labeled as IDs rather than human readable text
 * 1) Make sure that under the "View" menu, "Render by label is checked"
 * 2) Click 'File' menu and choose 'Preferences...':
 * 3) In the 'Renderer' tab, click on the 'Annotations ...' button, add 'en, en-US, !' in the languages column.


 * If you encounter speed difficulties with reasoning (> 5 minutes)
 * 1) In the reasoner tab "initialization", choose only "class members" and under "Displayed inferences" choose only "unsatisfiable classes", "equivalent classes" and "superclasses".  No instance reasoning is done, but for most OBI development this isn't necessary. These settings can make a particularly big difference when using Hermit as the reasoner.

Other Information
obi-developer : List for discussion regarding the development of OBI. [mailto:obi-developer@lists.sourceforge.net email obi-developer] obi-users : List for general discussion on using OBI. [mailto:obi-users@googlegroups.com email obi-users] http://sourceforge.net/tracker/?group_id=177891&atid=886178
 * Join OBI mailing list:
 * Submit new terms to OBI via tracker: