Ontologies and Databases Robert Stevens

From Purgatory….

To Heaven……

Torment in Bioinformatics

A Stack of Troubles Semantics Structure Heterogeneity Syntax System

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

Semantic Web Stack From Tim Berners-Lee

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

Having a GO

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

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 http://www.isb-sib.ch/~ejain/rdf/

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