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Representing the ChEBI ontology in OWL

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Janna Hastings
Janna Hastings

Presented at the EBI Industry Programme Ontology tutorial.

Tecnología
1 de 22
The ChEBI ontology and OWL Industry Programme Ontology Tutorial European Bioinformatics Institute 13 October 2010 Janna Hastings EBI Chemoinformatics and Metabolism
Overview ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],ChEBI ontology 20.10.10
Introduction to ChEBI ,[object Object],[object Object],[object Object],[object Object],[object Object],ChEBI ontology 20.10.10
ChEBI ontology 4/26/2010 A ChEBI entry page
ChEBI ontology ChEBI ontology 20.10.10 ,[object Object],[object Object],[object Object],[object Object],( R ) -adrenaline
ChEBI ontology 20.10.10 Molecular structure ontology
ChEBI ontology 20.10.10 Role ontology
ChEBI internal ontology architecture ChEBI ontology 20.10.10 Oracle database
A ChEBI entity in OBO format ,[object Object],ChEBI ontology 20.10.10
Expressing ChEBI in OWL ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],ChEBI ontology 20.10.10
ChEBI in OWL: Relationship patterns ,[object Object],[object Object],[object Object],[object Object],[object Object],ChEBI ontology 20.10.10
ChEBI in OWL: Metadata ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],ChEBI ontology 20.10.10
A ChEBI entity in OWL format ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],ChEBI ontology 20.10.10
ChEBI in OWL: Editing and reasoning ,[object Object],[object Object],[object Object],[object Object],ChEBI ontology 20.10.10
Chemical structures and OWL ,[object Object],ChEBI ontology 20.10.10 caffeine Molecules consist of atoms connected by bonds single bond double bond Carbon atom Hydrogen atom Nitrogen atom Oxygen atom
Structure-based classification ,[object Object],carboxylic acid cyclic molecule if molecule has part some carboxy group if molecule has property cyclic, i.e. a self-connected cyclic path exists through the molecule’s atoms
OWL representation Without internal structure, all parts must be explicitly asserted (which leads to a combinatorial explosion for larger molecules) But the internal structure of complex molecules cannot be encoded in OWL ontology axioms due to their cycles does not have a model in the shape of a tree
Description Graphs ,[object Object],[object Object],[object Object],[object Object]
Rules ,[object Object],[object Object],[object Object],[object Object],[object Object]
Chemical description graphs + Rules defined to detect cycles and parts Reasoning results: able to perform classification (but scalability a concern)
Acknowledgements ,[object Object],[object Object],[object Object],[object Object],ChEBI ontology 20.10.10
Thank you for your attention

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Representing the ChEBI ontology in OWL

  • 1. The ChEBI ontology and OWL Industry Programme Ontology Tutorial European Bioinformatics Institute 13 October 2010 Janna Hastings EBI Chemoinformatics and Metabolism
  • 2.
  • 3.
  • 4. ChEBI ontology 4/26/2010 A ChEBI entry page
  • 5.
  • 6. ChEBI ontology 20.10.10 Molecular structure ontology
  • 7. ChEBI ontology 20.10.10 Role ontology
  • 8. ChEBI internal ontology architecture ChEBI ontology 20.10.10 Oracle database
  • 9.
  • 10.
  • 11.
  • 12.
  • 13.
  • 14.
  • 15.
  • 16.
  • 17. OWL representation Without internal structure, all parts must be explicitly asserted (which leads to a combinatorial explosion for larger molecules) But the internal structure of complex molecules cannot be encoded in OWL ontology axioms due to their cycles does not have a model in the shape of a tree
  • 18.
  • 19.
  • 20. Chemical description graphs + Rules defined to detect cycles and parts Reasoning results: able to perform classification (but scalability a concern)
  • 21.
  • 22. Thank you for your attention