Workshop Agenda

Feb 28

1. Background and motivation (9AM-10AM)
   • Brief overview of major biological problems BIRN seeks to address [BIRN]
2. Tools (10AM-Noon)
   • Discussion and presentation of tools used by BIRN (e.g., Bonfire, Mediator) [BIRN]
   • Tutorial on Protégé and some of its more advanced features (examples from other ontology projects) [Stanford]
   • Expressing biological concepts in terms of an ontology [Stanford]
3. Ontology Usage (1PM-5PM)
   • Example scenarios from current cBiO Core 3 projects (sequence data annotation, PaTO) [Stanford]
   • Possible future directions (formal relation ontologies and composed annotations) [Stanford]
   • Image annotation with ontologies [Stanford]

Mar 1

1. Basics of Ontologies (9AM-Noon)
   • 9-10am Discuss current capabilities and challenges related to ontologies in BIRN [BIRN]
   • 10:30-11:30 How to Build an Ontology [Barry]
   • 11:30-noon The Ontology of Spatial Relations [Barry]
2. Content (1PM-3PM)
   • 1-2pm Best practices; lessons learned from other ontology development projects [Barry]
   • 2-5pm Look at ontologies used by BIRN in depth (send out BIRN ontologies for us to review in advance)
     • BIRN Ontologies: An Overview [Barry]
     • The Ontology of Spatial Relations [Barry]
3. Potential Applications: what do we need to get there from here? (3PM-5PM)
   • Integrate multi-scale, multi-modality (images, molecular, functional) data for discovery
   • Computer reasoning with neuroanatomical/spatial component of Neuroscience data