Topics

Here are an initial list of topics that we have thought of for the initial meeting.

• Motivation for ontology in life sciences
• What is an ontology?
• Knowledge representation
• OWL
• RDF
• OBO Format
• Protege
• the OWL API
• OBO-Edit
• OBO-Edit API
• Using ontologies in software; applications of ontologies
• Ontological annotation of data
• Knowledge representation
• Components of an ontology
• Classes and instances
• Syntax, semantics, expressivity and reasoning
• OWL syntaxes
• Relationship of OWL and RDF
• Automated reasoners
• Decideability: what is it and why is it a good thing?
• Formal and informal ontologies
• Upper level ontologies
• Ontology normalisation
• Naming conventions; Labels and identifiers
• OBO Foundry
• Semantic Publishing
• Linked data
• First order logic
• Reasoning with time
• Describing species in an ontology
• the process of building GO
• Definitions: Natural language and logical
• Semantic integration
• Anatomies
• Querying ontologies: SPARQL and SPARQL-DL
• Identity