Workshop Agenda

1. Background and motivation
   • Brief overview of major biological problems BIRN seeks to address [BIRN]
   • Discuss current capabilities and challenges related to ontologies in BIRN [BIRN]
   • How to Build an Ontology [Barry]
2. Tools
   • 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]
     • 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]
3. Content
   • 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]
   • Best practices; lessons learned from other ontology development projects [Barry]
4. Potential Applications: what do we need to get there from here?
   • Integrate multi-scale, multi-modality (images, molecular, functional) data for discovery
   • Computer reasoning with neuroanatomical/spatial component of Neuroscience data