1. Ontologies and Databases
Robert Stevens

2. From Purgatory….

3. To Heaven……

4. Torment in Bioinformatics

5. A Stack of Troubles
Semantics
Structure
Heterogeneity
Syntax
System

6. A Smooth Journey on the Semantic Web Underground
from Tim Berners-Lee

7. Semantic Web Stack
From Tim Berners-Lee

8. A Shared Understanding
Semantic Understanding perhaps the most trouble
(Computer science) ontology – a technique for representing the things and relationships between things in our world
Overcoming vocabulary problems: Same word different understandings; Different terms, same understandings
To compare understandings in different resources, need a common understanding

9. Having a GO

10. Making Usage Consistent
GO (and other ontologies) provide a common understanding of a domain
Primary useage is for describing functional attributes of gene products
Ensuring consistent usage by users is another level of trouble
Checking consistency is necessary to optimise integration and discovery

11. Uniprot Keywords in RDF
rdf:comment
Acetoin Biosynthesis
Protein involved in the synthesis of acetoin
rdf:type
owl:sameAs
Uniprot Concept
lsid:uniprot.org:go:45151
After Eric Jain

12. Visualisation and Querying
Another Level Down
Visualisation and Querying
Graph Model
RDF/XML
Data Sources