Your SlideShare is downloading. ×
0
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Ontology Design Patterns (ODPs) for bio-ontologies
Upcoming SlideShare
Loading in...5
×

Thanks for flagging this SlideShare!

Oops! An error has occurred.

×
Saving this for later? Get the SlideShare app to save on your phone or tablet. Read anywhere, anytime – even offline.
Text the download link to your phone
Standard text messaging rates apply

Ontology Design Patterns (ODPs) for bio-ontologies

795

Published on

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

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

Published in: Education, Technology
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total Views
795
On Slideshare
0
From Embeds
0
Number of Embeds
0
Actions
Shares
0
Downloads
0
Comments
0
Likes
0
Embeds 0
No embeds

Report content
Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
No notes for slide

Transcript

  • 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

×