Workshop Agenda

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  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