1. Ontology - and Reloaded and Revolutions in Life Science Jie Bao [email_address]

6. Cell? From: Amelia Ireland (2005). GO : the Gene Ontology (Talk)

7. Cell? From: Amelia Ireland (2005). GO : the Gene Ontology (Talk)

8. Cell? From: Amelia Ireland (2005). GO : the Gene Ontology (Talk)

9. Cell? From: Amelia Ireland (2005). GO : the Gene Ontology (Talk)

10. Cell? From: Amelia Ireland (2005). GO : the Gene Ontology (Talk)

11. Cell? From: Amelia Ireland (2005). GO : the Gene Ontology (Talk)

16. This is an ontology

17. Another Ontology

18. Yet Another Ontology

21. Why Ontology What I can do once I have an ontology?

26. More Gradute-advisor conversion Can you give me an example of your knowledge about biological existences ?I assume it is a ontology – the study of existence Let’s Start with GO

27. GO?

28. GO - Gene Ontology Cellular Component Molecular Function Biological Process is NOT an ontology only about Gene This is a typical ontological misunderstanding

29. Cellular Component

30. Molecular Function insulin binding. insulin receptor activity

31. Molecular Function drug transporter activity

32. Biological Process cell division

33. Biological Process Courtship behavior of Homo Sapiens

34. Anatomy of a GO term id: GO:0006094 name: gluconeogenesis namespace: process def: The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol. [http://cancerweb.ncl.ac.uk/omd/index.html] exact_synonym: glucose biosynthesis xref_analog: MetaCyc:GLUCONEO-PWY is_a: GO:0006006 is_a: GO:0006092 unique GO ID term name definition synonym database ref parentage ontology

35. Ontology Structure cell membrane chloroplast mitochondrial chloroplast membrane membrane is-a part-of DAG(directed acyclic graph)

36. What other ontologies in life science There are many! EC, SCOP, CATH, MIPS. MGED… Let’s see some trait ontologies.

37. P henotype (Trait) Ontologies Example: Plant Ontology ( http://www.plantontology.org )

38. Animal Trait Ontology

39. ATO Editor

44. More Gradute-advisor conversion Ontologies are really funny. Could you tell me how useful they are other than helping you to design efficient biological cells? Basically, ontologies help us a lot in design the Matrix. To represent the real world, we need a formalism to do Knowledge Representation.

45. Semantic Web The first prototype of Matrix is based on so called “Semantic Web”

46. Semantic Web

49. DL and OWL

50. DL and OWL(2)

51. Evolution of Web Ontology Languages XML HTML RDFS SHOE OIL DAML-ONT OWL RDF Revision Extend vocabularies Combine vocabularies Extend HTML tags for semantic description Define vocabularies OWL-S SGML DAML-S For Web services 1992 1998 1999 2000 2001 2002 2003 DAML (DAML+OIL)

52. Protégé – Ontology Editor