Mikel Egaña Aranguren, ISMB (Bio-ontologies SIG) 2007

1. Introduction
ODPs
Applying ODPs
Documenting ODPs
Actual applications of ODPs
Conclusion
Acknowledgements
Ontology Design Patterns (ODPs) for
bio-ontologies
Mikel Egaña Aranguren (1), Robert Stevens (1), Erick
Antezana (2)
(1) Manchester university
(2) Flanders Institute for Biotechnology/Ghent university
Bio-ontologies SIG at ISMB 2007
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

2. Introduction
ODPs
Applying ODPs
Documenting ODPs
Actual applications of ODPs
Conclusion
Acknowledgements
Outline
Introduction Documenting ODPs
ODPs Documentation system
What are ODPs? for ODPs
Examples of ODPs Sections of
Advantages of using documentation system
ODPs Actual applications of
Types of ODPs ODPs
Applying ODPs Conclusion
Direct application
Acknowledgements
Application by condition
matching
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

3. Introduction
ODPs
Applying ODPs
Documenting ODPs
Actual applications of ODPs
Conclusion
Acknowledgements
Outline
Introduction Documenting ODPs
ODPs Documentation system
What are ODPs? for ODPs
Examples of ODPs Sections of
Advantages of using documentation system
ODPs Actual applications of
Types of ODPs ODPs
Applying ODPs Conclusion
Direct application
Acknowledgements
Application by condition
matching
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

4. Introduction
ODPs
Applying ODPs
Documenting ODPs
Actual applications of ODPs
Conclusion
Acknowledgements
Outline
Introduction Documenting ODPs
ODPs Documentation system
What are ODPs? for ODPs
Examples of ODPs Sections of
Advantages of using documentation system
ODPs Actual applications of
Types of ODPs ODPs
Applying ODPs Conclusion
Direct application
Acknowledgements
Application by condition
matching
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

5. Introduction
ODPs
Applying ODPs
Documenting ODPs
Actual applications of ODPs
Conclusion
Acknowledgements
Outline
Introduction Documenting ODPs
ODPs Documentation system
What are ODPs? for ODPs
Examples of ODPs Sections of
Advantages of using documentation system
ODPs Actual applications of
Types of ODPs ODPs
Applying ODPs Conclusion
Direct application
Acknowledgements
Application by condition
matching
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

6. Introduction
ODPs
Applying ODPs
Documenting ODPs
Actual applications of ODPs
Conclusion
Acknowledgements
Outline
Introduction Documenting ODPs
ODPs Documentation system
What are ODPs? for ODPs
Examples of ODPs Sections of
Advantages of using documentation system
ODPs Actual applications of
Types of ODPs ODPs
Applying ODPs Conclusion
Direct application
Acknowledgements
Application by condition
matching
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

7. Introduction
ODPs
Applying ODPs
Documenting ODPs
Actual applications of ODPs
Conclusion
Acknowledgements
Outline
Introduction Documenting ODPs
ODPs Documentation system
What are ODPs? for ODPs
Examples of ODPs Sections of
Advantages of using documentation system
ODPs Actual applications of
Types of ODPs ODPs
Applying ODPs Conclusion
Direct application
Acknowledgements
Application by condition
matching
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

8. Introduction
ODPs
Applying ODPs
Documenting ODPs
Actual applications of ODPs
Conclusion
Acknowledgements
Outline
Introduction Documenting ODPs
ODPs Documentation system
What are ODPs? for ODPs
Examples of ODPs Sections of
Advantages of using documentation system
ODPs Actual applications of
Types of ODPs ODPs
Applying ODPs Conclusion
Direct application
Acknowledgements
Application by condition
matching
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

9. Introduction
ODPs
Applying ODPs
Documenting ODPs
Actual applications of ODPs
Conclusion
Acknowledgements
Introduction
Useful bio-ontology: “high resolution” (rich) and rigorous
representation of knowledge domain; more interesting
queries and inferences.
But rich and rigorous modelling is difficult for
bio-ontologists.
All the expressive power of OBO or OWL is not used.
Expressivity only in term labels: useful for humans but
computationally useless.
A solution: ready-made modelling “recipes”: Ontology
Design Patterns (ODPs). Rich and rigorous modelling with
less effort.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

10. Introduction
ODPs
Applying ODPs
Documenting ODPs
Actual applications of ODPs
Conclusion
Acknowledgements
Introduction
Useful bio-ontology: “high resolution” (rich) and rigorous
representation of knowledge domain; more interesting
queries and inferences.
But rich and rigorous modelling is difficult for
bio-ontologists.
All the expressive power of OBO or OWL is not used.
Expressivity only in term labels: useful for humans but
computationally useless.
A solution: ready-made modelling “recipes”: Ontology
Design Patterns (ODPs). Rich and rigorous modelling with
less effort.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

11. Introduction
ODPs
Applying ODPs
Documenting ODPs
Actual applications of ODPs
Conclusion
Acknowledgements
Introduction
Useful bio-ontology: “high resolution” (rich) and rigorous
representation of knowledge domain; more interesting
queries and inferences.
But rich and rigorous modelling is difficult for
bio-ontologists.
All the expressive power of OBO or OWL is not used.
Expressivity only in term labels: useful for humans but
computationally useless.
A solution: ready-made modelling “recipes”: Ontology
Design Patterns (ODPs). Rich and rigorous modelling with
less effort.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

12. Introduction
ODPs
Applying ODPs
Documenting ODPs
Actual applications of ODPs
Conclusion
Acknowledgements
Introduction
Useful bio-ontology: “high resolution” (rich) and rigorous
representation of knowledge domain; more interesting
queries and inferences.
But rich and rigorous modelling is difficult for
bio-ontologists.
All the expressive power of OBO or OWL is not used.
Expressivity only in term labels: useful for humans but
computationally useless.
A solution: ready-made modelling “recipes”: Ontology
Design Patterns (ODPs). Rich and rigorous modelling with
less effort.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

13. Introduction
ODPs
Applying ODPs
Documenting ODPs
Actual applications of ODPs
Conclusion
Acknowledgements
Introduction
Useful bio-ontology: “high resolution” (rich) and rigorous
representation of knowledge domain; more interesting
queries and inferences.
But rich and rigorous modelling is difficult for
bio-ontologists.
All the expressive power of OBO or OWL is not used.
Expressivity only in term labels: useful for humans but
computationally useless.
A solution: ready-made modelling “recipes”: Ontology
Design Patterns (ODPs). Rich and rigorous modelling with
less effort.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

14. Introduction
ODPs
What are ODPs?
Applying ODPs
Examples of ODPs
Documenting ODPs
Advantages of using ODPs
Actual applications of ODPs
Types of ODPs
Conclusion
Acknowledgements
What are ODPs?
ODPs: known solutions to recurrent modelling problems of
ontology engineering.
Tested in different systems (efficient) and well documented.
Similar idea to design patterns in OOP, but applied to
ontologies.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

15. Introduction
ODPs
What are ODPs?
Applying ODPs
Examples of ODPs
Documenting ODPs
Advantages of using ODPs
Actual applications of ODPs
Types of ODPs
Conclusion
Acknowledgements
What are ODPs?
ODPs: known solutions to recurrent modelling problems of
ontology engineering.
Tested in different systems (efficient) and well documented.
Similar idea to design patterns in OOP, but applied to
ontologies.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

16. Introduction
ODPs
What are ODPs?
Applying ODPs
Examples of ODPs
Documenting ODPs
Advantages of using ODPs
Actual applications of ODPs
Types of ODPs
Conclusion
Acknowledgements
What are ODPs?
ODPs: known solutions to recurrent modelling problems of
ontology engineering.
Tested in different systems (efficient) and well documented.
Similar idea to design patterns in OOP, but applied to
ontologies.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

17. Introduction
ODPs
What are ODPs?
Applying ODPs
Examples of ODPs
Documenting ODPs
Advantages of using ODPs
Actual applications of ODPs
Types of ODPs
Conclusion
Acknowledgements
Example: Value Partition
We want to represent that a parameter can only take
certain values, e.g. regulation can only be positive or
negative.
OWL: Covering and disjoint axioms.
How can we build such structure in the ontology? Using
the ODP Value Partition as a template.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

18. Introduction
ODPs
What are ODPs?
Applying ODPs
Examples of ODPs
Documenting ODPs
Advantages of using ODPs
Actual applications of ODPs
Types of ODPs
Conclusion
Acknowledgements
Example: Value Partition
We want to represent that a parameter can only take
certain values, e.g. regulation can only be positive or
negative.
OWL: Covering and disjoint axioms.
How can we build such structure in the ontology? Using
the ODP Value Partition as a template.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

19. Introduction
ODPs
What are ODPs?
Applying ODPs
Examples of ODPs
Documenting ODPs
Advantages of using ODPs
Actual applications of ODPs
Types of ODPs
Conclusion
Acknowledgements
Example: Value Partition
We want to represent that a parameter can only take
certain values, e.g. regulation can only be positive or
negative.
OWL: Covering and disjoint axioms.
How can we build such structure in the ontology? Using
the ODP Value Partition as a template.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

20. Introduction
ODPs
What are ODPs?
Applying ODPs
Examples of ODPs
Documenting ODPs
Advantages of using ODPs
Actual applications of ODPs
Types of ODPs
Conclusion
Acknowledgements
Example: Value Partition
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

21. Introduction
ODPs
What are ODPs?
Applying ODPs
Examples of ODPs
Documenting ODPs
Advantages of using ODPs
Actual applications of ODPs
Types of ODPs
Conclusion
Acknowledgements
Example: Upper Level Ontology
OBO relations as a result of an upper level.
A series of patterns capturing standard relationships:
Continuant part_of Continuant.
Continuant participates_in Occurent.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

22. Introduction
ODPs
What are ODPs?
Applying ODPs
Examples of ODPs
Documenting ODPs
Advantages of using ODPs
Actual applications of ODPs
Types of ODPs
Conclusion
Acknowledgements
Advantages of using ODPs
Rich and granular Documented modelling.
modelling. Reasoning.
Focused development. Rapid prototyping.
Semantic encapsulation. Alignment.
Tooling. Re-engineering.
Robustness and Comprehension of
modularity. advances in KR.
Good communication.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

23. Introduction
ODPs
What are ODPs?
Applying ODPs
Examples of ODPs
Documenting ODPs
Advantages of using ODPs
Actual applications of ODPs
Types of ODPs
Conclusion
Acknowledgements
Advantages of using ODPs
Rich and granular Documented modelling.
modelling. Reasoning.
Focused development. Rapid prototyping.
Semantic encapsulation. Alignment.
Tooling. Re-engineering.
Robustness and Comprehension of
modularity. advances in KR.
Good communication.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

24. Introduction
ODPs
What are ODPs?
Applying ODPs
Examples of ODPs
Documenting ODPs
Advantages of using ODPs
Actual applications of ODPs
Types of ODPs
Conclusion
Acknowledgements
Advantages of using ODPs
Rich and granular Documented modelling.
modelling. Reasoning.
Focused development. Rapid prototyping.
Semantic encapsulation. Alignment.
Tooling. Re-engineering.
Robustness and Comprehension of
modularity. advances in KR.
Good communication.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

25. Introduction
ODPs
What are ODPs?
Applying ODPs
Examples of ODPs
Documenting ODPs
Advantages of using ODPs
Actual applications of ODPs
Types of ODPs
Conclusion
Acknowledgements
Advantages of using ODPs
Rich and granular Documented modelling.
modelling. Reasoning.
Focused development. Rapid prototyping.
Semantic encapsulation. Alignment.
Tooling. Re-engineering.
Robustness and Comprehension of
modularity. advances in KR.
Good communication.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

26. Introduction
ODPs
What are ODPs?
Applying ODPs
Examples of ODPs
Documenting ODPs
Advantages of using ODPs
Actual applications of ODPs
Types of ODPs
Conclusion
Acknowledgements
Advantages of using ODPs
Rich and granular Documented modelling.
modelling. Reasoning.
Focused development. Rapid prototyping.
Semantic encapsulation. Alignment.
Tooling. Re-engineering.
Robustness and Comprehension of
modularity. advances in KR.
Good communication.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

27. Introduction
ODPs
What are ODPs?
Applying ODPs
Examples of ODPs
Documenting ODPs
Advantages of using ODPs
Actual applications of ODPs
Types of ODPs
Conclusion
Acknowledgements
Advantages of using ODPs
Rich and granular Documented modelling.
modelling. Reasoning.
Focused development. Rapid prototyping.
Semantic encapsulation. Alignment.
Tooling. Re-engineering.
Robustness and Comprehension of
modularity. advances in KR.
Good communication.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

28. Introduction
ODPs
What are ODPs?
Applying ODPs
Examples of ODPs
Documenting ODPs
Advantages of using ODPs
Actual applications of ODPs
Types of ODPs
Conclusion
Acknowledgements
Advantages of using ODPs
Rich and granular Documented modelling.
modelling. Reasoning.
Focused development. Rapid prototyping.
Semantic encapsulation. Alignment.
Tooling. Re-engineering.
Robustness and Comprehension of
modularity. advances in KR.
Good communication.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

29. Introduction
ODPs
What are ODPs?
Applying ODPs
Examples of ODPs
Documenting ODPs
Advantages of using ODPs
Actual applications of ODPs
Types of ODPs
Conclusion
Acknowledgements
Advantages of using ODPs
Rich and granular Documented modelling.
modelling. Reasoning.
Focused development. Rapid prototyping.
Semantic encapsulation. Alignment.
Tooling. Re-engineering.
Robustness and Comprehension of
modularity. advances in KR.
Good communication.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

30. Introduction
ODPs
What are ODPs?
Applying ODPs
Examples of ODPs
Documenting ODPs
Advantages of using ODPs
Actual applications of ODPs
Types of ODPs
Conclusion
Acknowledgements
Advantages of using ODPs
Rich and granular Documented modelling.
modelling. Reasoning.
Focused development. Rapid prototyping.
Semantic encapsulation. Alignment.
Tooling. Re-engineering.
Robustness and Comprehension of
modularity. advances in KR.
Good communication.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

31. Introduction
ODPs
What are ODPs?
Applying ODPs
Examples of ODPs
Documenting ODPs
Advantages of using ODPs
Actual applications of ODPs
Types of ODPs
Conclusion
Acknowledgements
Advantages of using ODPs
Rich and granular Documented modelling.
modelling. Reasoning.
Focused development. Rapid prototyping.
Semantic encapsulation. Alignment.
Tooling. Re-engineering.
Robustness and Comprehension of
modularity. advances in KR.
Good communication.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

32. Introduction
ODPs
What are ODPs?
Applying ODPs
Examples of ODPs
Documenting ODPs
Advantages of using ODPs
Actual applications of ODPs
Types of ODPs
Conclusion
Acknowledgements
Advantages of using ODPs
Rich and granular Documented modelling.
modelling. Reasoning.
Focused development. Rapid prototyping.
Semantic encapsulation. Alignment.
Tooling. Re-engineering.
Robustness and Comprehension of
modularity. advances in KR.
Good communication.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

33. Introduction
ODPs
What are ODPs?
Applying ODPs
Examples of ODPs
Documenting ODPs
Advantages of using ODPs
Actual applications of ODPs
Types of ODPs
Conclusion
Acknowledgements
Advantages of using ODPs
Rich and granular Documented modelling.
modelling. Reasoning.
Focused development. Rapid prototyping.
Semantic encapsulation. Alignment.
Tooling. Re-engineering.
Robustness and Comprehension of
modularity. advances in KR.
Good communication.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

34. Introduction
ODPs
What are ODPs?
Applying ODPs
Examples of ODPs
Documenting ODPs
Advantages of using ODPs
Actual applications of ODPs
Types of ODPs
Conclusion
Acknowledgements
Types of ODPs
Extensional ODPs: Solutions to modelling situations at
the limits of a KR language.
Good practice ODPs: Capturing domain knowledge in
perceived best practice: more modular, efficient and
maintainable ontologies.
Domain Modelling ODPs: Solutions to modelling
situations within the scope of a KR language (“signature
ODPs”).
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

35. Introduction
ODPs
Applying ODPs
Direct application
Documenting ODPs
Application by condition matching
Actual applications of ODPs
Conclusion
Acknowledgements
Direct application
Recreate the structure of the ODP in the ontology “by
hand”.
Protégé wizards:
http://www.co-ode.org/downloads/wizard/
Import (OWL).
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

36. Introduction
ODPs
Applying ODPs
Direct application
Documenting ODPs
Application by condition matching
Actual applications of ODPs
Conclusion
Acknowledgements
Direct application
Recreate the structure of the ODP in the ontology “by
hand”.
Protégé wizards:
http://www.co-ode.org/downloads/wizard/
Import (OWL).
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

37. Introduction
ODPs
Applying ODPs
Direct application
Documenting ODPs
Application by condition matching
Actual applications of ODPs
Conclusion
Acknowledgements
Direct application
Recreate the structure of the ODP in the ontology “by
hand”.
Protégé wizards:
http://www.co-ode.org/downloads/wizard/
Import (OWL).
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

38. Introduction
ODPs
Applying ODPs
Direct application
Documenting ODPs
Application by condition matching
Actual applications of ODPs
Conclusion
Acknowledgements
Application by condition matching: OPL
OPL: Ontology Processing Language.
Syntax for choosing entities in an ontology and adding new
semantics to those entities.
Syntax written in flat files and processed by the OPL
engine: ODPs stored.
http://www.gong.manchester.ac.uk/downloads/
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

39. Introduction
ODPs
Applying ODPs
Direct application
Documenting ODPs
Application by condition matching
Actual applications of ODPs
Conclusion
Acknowledgements
Application by condition matching: OPL
OPL: Ontology Processing Language.
Syntax for choosing entities in an ontology and adding new
semantics to those entities.
Syntax written in flat files and processed by the OPL
engine: ODPs stored.
http://www.gong.manchester.ac.uk/downloads/
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

40. Introduction
ODPs
Applying ODPs
Direct application
Documenting ODPs
Application by condition matching
Actual applications of ODPs
Conclusion
Acknowledgements
Application by condition matching: OPL
OPL: Ontology Processing Language.
Syntax for choosing entities in an ontology and adding new
semantics to those entities.
Syntax written in flat files and processed by the OPL
engine: ODPs stored.
http://www.gong.manchester.ac.uk/downloads/
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

41. Introduction
ODPs
Applying ODPs
Direct application
Documenting ODPs
Application by condition matching
Actual applications of ODPs
Conclusion
Acknowledgements
Application by condition matching: OPL
OPL: Ontology Processing Language.
Syntax for choosing entities in an ontology and adding new
semantics to those entities.
Syntax written in flat files and processed by the OPL
engine: ODPs stored.
http://www.gong.manchester.ac.uk/downloads/
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

42. Introduction
ODPs
Applying ODPs
Direct application
Documenting ODPs
Application by condition matching
Actual applications of ODPs
Conclusion
Acknowledgements
Application by condition matching: OPL
Ontology Processing Language (OPL)
SELECT ?x WHERE ?x label regulation;
ADD ?x equivalentTo (positive or negative);
ADD positive disjointWith negative;
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

43. Introduction
ODPs
Applying ODPs
Documentation system for ODPs
Documenting ODPs
Sections of documentation system
Actual applications of ODPs
Conclusion
Acknowledgements
Documentation system for ODPs
Each ODP is described using some sections.
Alpha version of public catalogue:
www.gong.manchester.ac.uk/
ontologydesignpatterns/
Future implementation directly in OWL.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

44. Introduction
ODPs
Applying ODPs
Documentation system for ODPs
Documenting ODPs
Sections of documentation system
Actual applications of ODPs
Conclusion
Acknowledgements
Documentation system for ODPs
Each ODP is described using some sections.
Alpha version of public catalogue:
www.gong.manchester.ac.uk/
ontologydesignpatterns/
Future implementation directly in OWL.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

45. Introduction
ODPs
Applying ODPs
Documentation system for ODPs
Documenting ODPs
Sections of documentation system
Actual applications of ODPs
Conclusion
Acknowledgements
Documentation system for ODPs
Each ODP is described using some sections.
Alpha version of public catalogue:
www.gong.manchester.ac.uk/
ontologydesignpatterns/
Future implementation directly in OWL.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

46. Introduction
ODPs
Applying ODPs
Documentation system for ODPs
Documenting ODPs
Sections of documentation system
Actual applications of ODPs
Conclusion
Acknowledgements
Sections of documentation system
Name. Elements. Sample.
A.K.A. Structure. Known uses.
URL. Implementation. Related ODPs.
Classification. Result. References.
Motivation. Side effects. Additional
information.
Aim.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

47. Introduction
ODPs
Applying ODPs
Documenting ODPs
Actual applications of ODPs
Conclusion
Acknowledgements
Actual applications of ODPs
Gene Ontology Next Generation workflow.
Normalisation of Gene Ontology’s Molecular Function.
Cell Cycle Ontology.
Galen.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

48. Introduction
ODPs
Applying ODPs
Documenting ODPs
Actual applications of ODPs
Conclusion
Acknowledgements
Actual applications of ODPs
Gene Ontology Next Generation workflow.
Normalisation of Gene Ontology’s Molecular Function.
Cell Cycle Ontology.
Galen.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

49. Introduction
ODPs
Applying ODPs
Documenting ODPs
Actual applications of ODPs
Conclusion
Acknowledgements
Actual applications of ODPs
Gene Ontology Next Generation workflow.
Normalisation of Gene Ontology’s Molecular Function.
Cell Cycle Ontology.
Galen.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

50. Introduction
ODPs
Applying ODPs
Documenting ODPs
Actual applications of ODPs
Conclusion
Acknowledgements
Actual applications of ODPs
Gene Ontology Next Generation workflow.
Normalisation of Gene Ontology’s Molecular Function.
Cell Cycle Ontology.
Galen.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

51. Introduction
ODPs
Applying ODPs
Documenting ODPs
Actual applications of ODPs
Conclusion
Acknowledgements
Conclusion
ODPs make it possible to produce and maintain rich and
rigorous bio-ontologies with less effort.
Issues to solve:
Graphical metalanguage a la UML for ontologies.
Tools for easily creating, storing and sharing ODPs
between bio-ontologists.
Plenty of areas of biological knowledge in need of ODPs.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

52. Introduction
ODPs
Applying ODPs
Documenting ODPs
Actual applications of ODPs
Conclusion
Acknowledgements
Conclusion
ODPs make it possible to produce and maintain rich and
rigorous bio-ontologies with less effort.
Issues to solve:
Graphical metalanguage a la UML for ontologies.
Tools for easily creating, storing and sharing ODPs
between bio-ontologists.
Plenty of areas of biological knowledge in need of ODPs.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

53. Introduction
ODPs
Applying ODPs
Documenting ODPs
Actual applications of ODPs
Conclusion
Acknowledgements
Conclusion
ODPs make it possible to produce and maintain rich and
rigorous bio-ontologies with less effort.
Issues to solve:
Graphical metalanguage a la UML for ontologies.
Tools for easily creating, storing and sharing ODPs
between bio-ontologists.
Plenty of areas of biological knowledge in need of ODPs.
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies

54. Introduction
ODPs
Applying ODPs
Documenting ODPs
Actual applications of ODPs
Conclusion
Acknowledgements
Acknowledgements
Mikel Egaña Aranguren is funded by Manchester University
and EPSRC.
Erick Antezana is funded by EU (FP6, contract number
LSHG-CT-2004-512143).
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana ODPs for bio-ontologies