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Principles for Building Biomedical Ontologies

Discover the rules and challenges behind creating effective biomedical ontologies in this insightful talk delivered by Jennifer Clark in 2005. Explore principles like Univocity, Positivity, Objectivity, Single Inheritance, and Intelligibility of Definitions, essential for structuring information in the biomedical domain. Learn how terms, types, and classifications shape our understanding of gene product attributes, tokens, individual particulars, and more. Gain valuable insights into formal ontology construction and information science with a special reference to the biomedical field.

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Principles for Building Biomedical Ontologies

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  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

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