Ontologies and Databases

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Ontologies and Databases

• Robert Stevens

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From Purgatory.
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To Heaven
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Torment in Bioinformatics
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A Stack of Troubles
Semantics
Structure
Heterogeneity
Syntax
System
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A Smooth Journey on the Semantic Web Underground
from Tim Berners-Lee
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Semantic Web Stack
From Tim Berners-Lee
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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

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Having a GO
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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

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Uniprot Keywords in RDF
rdfcomment
Acetoin Biosynthesis
Protein involved in the synthesis of acetoin
rdftype
owlsameAs
Uniprot Concept
lsiduniprot.orggo45151
After Eric Jain http//www.isb-sib.ch/ejain/rdf/
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Another Level Down
Visualisation and Querying
Graph Model
RDF/XML
Data Sources