Principles for Building Biomedical Ontologies

1. Principles for Building Biomedical Ontologies Talk delivered by Jennifer Clark, GO Editorial Office

2. Clark et al., 2005 is_a part_of

3. Clark et al., 2005

4. Slides and content by: Barry Smith http://ifomis.de Rama Balakrishnan, David Hill, Jennifer Clark. http://www.geneontology.org • formal ontology • information science • special reference to • the bio-medical domain.

5. The Rules • Univocity • Positivity • Objectivity • Single Inheritance • Intelligibility of Definitions • Basis in Reality

6. classes GO terms, types, kinds, universals instances annotated gene product attributes, tokens, individuals, particulars

7. 1 Univocity: Terms should have the same meanings on every occasion of use

8. = bud initiation = bud initiation = bud initiation The Challenge of Univocity: People use the same words to describe different things

9. Bud initiation? How is a computer to distinguish?

10. = bud initiation sensu Metazoa = bud initiation sensu Saccharomyces = bud initiation sensu Viridiplantae Univocity: GO adds “sensu” descriptors to discriminate among organisms

11. The Challenge of Univocity:People call the same thing by different names Taction Tactition Tactile sense ?

12. Univocity: GO uses 1 term and many characterized synonyms Taction Tactition Tactile sense perception of touch ; GO:0050975

13. Univocity in part_of relation • ‘is at times part of’ • antlers part_of red deer • ‘necessarily is_part’ • Seed dormancy part_of seed development • ‘necessarily has_part’ • Plant embryo part_of seed

14. 2 Positivity: The complements of classes are not themselves classes.

15. Vertebrates http://www.cucco.org/CatPictures/Cat%20Nap.jpg

16. non-vertebrates Vertebrates http://www.cucco.org/CatPictures/Cat%20Nap.jpg

17. non-vertebrates Vertebrates http://www.cucco.org/CatPictures/Cat%20Nap.jpg http://www.digibarn.com/collections/systems/canon-cat/Image53.jpg

18. Set of all things non-vertebrates Vertebrates http://www.cucco.org/CatPictures/Cat%20Nap.jpg http://www.digibarn.com/collections/systems/canon-cat/Image53.jpg

19. Set of all organisms Vertebrates http://www.cucco.org/CatPictures/Cat%20Nap.jpg

20. Set of all organisms Invertebrates Vertebrates http://www.cucco.org/CatPictures/Cat%20Nap.jpg

21. Set of all organisms Invertebrates Vertebrates http://www.cucco.org/CatPictures/Cat%20Nap.jpg http://www.artalyst.com/files/userimages/user70/21088058-O.preview.jpg

22. membrane-bound organelle GO:0043227 V. Not a membrane bound organelle Non-membrane bound organelle

23. Non-membrane bound organelles A centrosome is not a membrane bound organelle, but it still may be considered an organelle.

24. 3 Objectivity: The existence of classes is not dependent on our biological knowledge.

25. ‘unlocalised’ ‘unknown’ ‘unclassified’ http://news.bbc.co.uk/1/hi/sci/tech/4501152.stm do not designate biological natural kinds.

26. Task: Annotate molecular function of 10-4, agene from Drosophila melanogaster

27. Molecular function ontology Annotations molecular function molecular function unknown is_a 10-4

28. Molecular function ontology Annotations molecular function molecular function unknown 10-4 is_a

29. Molecular function ontology Annotations molecular function molecular function unknown 10-4 is_a

30. 4 Single Inheritance: No class in a classification hierarchy should have more than one is_a parent on the immediate higher level

31. Clark et al., 2005 is_a part_of

32. Rule of Single Inheritance • no diamonds: C is_a2 B is_a1 A

33. Problems with multiple inheritance B C is_a1 is_a2 A ‘is_a’ no longer univocal (univocal: having only one meaning)

34. Is_a diamond in GO Process behavior is_a locomotory behavior larval behavior larval locomotory behavior

35. behavior behavior of a thing descriptive behavior is_a locomotory behavior larval behavior larval locomotory behavior

36. Is_a diamond in GO Process behavior locomotory behavior larval behavior is_a2 is_a1 larval locomotory behavior

37. 5 Intelligibility of Definitions: The terms used in a definition should be simpler than the term to be defined

38. cellular process cell differentiation cell fate cell Specification development Is_a part_of

39. cell differentiation osteoblast neuron keratinocytedifferentiation differentiation differentiation adipocyte garland cell differentiation differentiation ‘X cell differentiation’ is_a

40. Essence = Genus + Differentiae Genus: differentiation Differentiae: a neuron (or x cell)

41. X cell differentiation

42. X cell differentiation Differentiation of an x cell.

43. Xcell differentiation The process whereby a relatively unspecialized cell acquires specialized features of an xcell. [List characteristics of x cell.]

44. cone cell fate commitment retinal_cone_cell Process ontology Cell Ontology • keratinocyte • keratinocyte differentiation • fat_cell • adipocyte differentiation • dendritic_cell • dendritic cell activation

45. [Term] id: GO:0030182 name: neuron differentiation namespace: biological_process def: "The process whereby a relatively unspecialized cell acquires specialized features of a neuron." [GO:mah] is_a: GO:0030154 ! cell differentiation relationship: part_of GO:0048699 ! neurogenesis

46. [Term] id: CL:0000540 name: neuron def: "The basic cellular unit of nervous tissue. Each neuron consists of a body\, an axon\, and dendrites. Their purpose is to receive\, conduct\, and transmit impulses in the nervous system." [MESH:A.08.663] xref_analog: FBbt:00005106 xref_analog: FBbt:00005146 is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000404 ! electrically signaling cell relationship: develops_from CL:0000031 ! neuroblast

47. [Term] id: GO:0030182 name: neuron differentiation namespace: biological_process def: "The process whereby a relatively unspecialized cell acquires specialized features of a neuron. The basic cellular unit of nervous tissue. Each neuron consists of a body\, an axon\, and dendrites. Their purpose is to receive\, conduct\, and transmit impulses in the nervous system." [MESH:A.08.663, GO:mah] is_a: GO:0030154 ! cell differentiation intersection_of: is_a GO:0030154 ! cell differentiation intersection_of: has_participant CL:0000540 ! neuron

48. Other Ontologies that can be aligned with GO • Chemical ontologies • 3,4-dihydroxy-2-butanone-4-phosphate synthase activity • Anatomy ontologies • metanephros development

49. But Eventually…

50. Building Ontology Improve Collaborate and Learn