1. Building Biomedical Ontologies Jennifer Clark, GO Editorial Office

2. Clark et al., 2005 part_of is_a

3. Clark et al., 2005

4. "encyclopaedia of Flemish children's games“ BRUEGEL

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

8. Domain of Ontology biological process Loggerhead nesting evidence codes NCBI organismal classification

9. is_a part_of develops_from Relationships

10. part_of no necessity necessarily is part necessarily has part necessarily is part and necessarily has part

11. How to define A is_a B A is_a B =def. 1. A and B are names of universals (natural kinds, types) in reality 2.all instances of A are as a matter of biological science also instances of B

13. Easy term request: Please add leucophore differentiation, erythrophore differentiation cyanophore differentiation neuron differentiation

14. cellular process cell differentiation Is_a part_of cell fate cell specification development

15. cell differentiation osteoblast neuron keratinocyte differentiation differentiation differentiation adipocyte garland cell differentiation ‘X cell differentiation’ is_a

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

17. X cell differentiation

18. Differentiation of an x cell.

19. X cell differentiation The process whereby a relatively unspecialized cell acquires specialized features of an x cell. [List characteristics of x cell.]

20. [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

21. [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

22. http://cancerweb.ncl.ac.uk neuron An excitable cell specialised for the transmission of electrical signals over long distances. Neurons receive input from sensory cells or other neurons and send output to muscles or other neurons. Neurons with sensory input are called sensory neurons, neurons with muscle outputs are called motoneurons, neurons that connect only with other neurons are called interneurons. Neurons connect with each other via synapses. Neurons can be the longest cells known, a single axon can be several metres in length. Although signals are usually sent via action potentials, some neurons are nonspiking.excitable celltransmission electricalsignalslongdistancesNeuronsreceivesensorycells outputmusclessensory neuronsmotoneuronsinterneuronssynapsescellssingleaxonmetreslength

23. Stedman's Online Medical Dictionary neuron (noor on) The morphologic and functional unit of the nervous system, consisting of the nerve cell body, the dendrites, and the axon. Syn: neurone Syn: neurocyte, nerve cellneuroneneurocytenerve cell

24. [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 relationship: part_of GO:0048699 ! neurogenesis

25. [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 relationship: part_of GO:0048699 ! neurogenesis intersection_of: is_a GO:0030154 ! cell differentiation intersection_of: has_participant CL:0000540 ! neuron

26. Difficult term request Reconcile plant trichomes and insect trichomes.

27. Plant trichome http://bib18.ulb.ac.be/Botanique_I/ image/6703873062005_trichome_arabidopsis.jpg http://www.innovations-report.de/bilder_neu/40879_szymanski.trichomeLO.jpg http://bib18.ulb.ac.be/Botanique_I/ image/6703873062005_trichome_arabidopsis.jpg

28. Insect trichome http://www.grisda.org/tstandish/images/animalia/arthropoda/Wildtype-D.-melanogaster-EM.jpg

30. If a plant trichome is a hair cell, and an insect trichome is a cell hair, then plant trichome differentiation would be an is_a of hair cell differentiation. And insect trichome formation could be a part_of hair cell differentiation. Becky Foulger 2004-08-04

32. Discussion… 5000 words 25 A4 pages. [ 956691 ] hair/trichome formation https://sourceforge.net/tracker/index.php?func=detail&aid =956691&group_id=36855&atid=440764

33. Difficult term request All the metamorphosis terms should be changed to morphogenesis terms.

34. http://www.kellscraft.com/Butterflies/butter69.jpg

36. Standard structure [i]x development ---[p] x morphogenesis ------[p] x formation ---------[p] y cell differentiation ------[p] x structural organization ---[p] x maturation

37. Standard definitions x development The process whose specific outcome is the progression of the x over time, from its formation to the mature structure. x morphogenesis The process by which the anatomical structures of x are generated and organized. Morphogenesis pertains to the creation of form. x formation The process that gives rise to x. This process pertains to the initial formation of a structure from unspecified parts. x structural organization The process that contributes to creating the structural organization of x. This process pertains to the physical shaping of a rudimentary structure.

38. morphogenesis terms x morphogenesis The process by which the anatomical structures of x are generated and organized. Morphogenesis pertains to the creation of form.

39. metamorphosis terms 'leg disc metamorphosis' ; GO:0007478 def: The transformation of a leg imaginal disc from a monolayered epithelium in the larvae of holometabolous insects into recognizable adult structures including the leg, coxa and ventral thoracic pleura.

40. Rules Changes can be made to terms: Annotations must still be true afterwards. Name needs changed. Do it. Definition wording needs changed. Do it. Position in the graph needs changed. Do it. Definition meaning needs changed. Obsolete the term.

41. starting structure x mature structure x morphogenesis gene products act here x metamorphosis multiple mature structures gene products act here x starting structure The process by which the anatomical structures of x are generated and organized. Morphogenesis pertains to the creation of form. The transformation of a leg imaginal disc from a monolayered epithelium in the larvae of holometabolous insects into recognizable adult structures including the leg, coxa and ventral thoracic pleura.

42. http://www.aardman.com

43. blob of plasticine Gromit Gromit morphogenesis ‘gene products’ act here Aardman plasticine metamorphosis All the individual characters in the cast of Wallace and Gromit films ‘gene products’ act here huge ball of plasticine Wallace Gromit Killer penguin Shaun the sheep

44. before after

45. Fixed metamorphosis terms leg disc morphogenesis Def: The process by which the anatomical structures derived from the leg disc are generated and organized. Morphogenesis pertains to the creation of form. [description] exact_synonym: leg disc metamorphosis

46. Discussion: 10,000 words 53 A4 pages [ 1228979 ] metamorphosis terms https://sourceforge.net/tracker/index.php?func=detail&aid =1228979&group_id=36855&atid=440764

47. Some more ontology thoughts…

48. Basis in Reality: When building or maintaining an ontology, always think carefully about how classes relate to instances in reality

49. molecular function binding tetrapyrrole bindingcofactor binding chlorophyll heme coenzyme quinone binding binding is_a PSBI Annotations Ontology PSBI

50. superman strength flight x-ray vision leaps over tall buildings in a single bound Catwoman strength, speed, agility and ultra-keen senses of a cat. http://www.uncleodiescollectibles.com/doesnotcompute/2004-10-11/Actor%20Christoper%20Reeve.jpg http://home.austarnet.com.au/davekimble/catwoman.jpg

51. cartoon character super power ontology super sensessuper physical powers x-ray cat super super vision senses leaping strength is_a Annotations Ontology

52. cartoon character super power ontology super sensessuper physical powers x-ray cat super super vision senses leaping strength is_a Catwoman Annotations Ontology Superman

53. cartoon character super power ontology super sensessuper physical powers x-ray cat super super vision senses leaping strength is_a Catwoman’s cat senses Catwoman’s super strength Annotations Ontology Superman’s X-ray vision Superman’s super leaping

54. cartoon character super power ontology super sensessuper physical powers is_a Catwoman’s cat senses Catwoman’s super strength Annotations Ontology Superman’s X-ray vision Superman’s super leaping

55. molecular function binding tetrapyrrole bindingcofactor binding chlorophyll heme coenzyme quinone binding binding is_a PSBI Annotations Ontology PSBI

56. molecular function binding tetrapyrrole bindingcofactor binding chlorophyll heme coenzyme quinone binding binding is_a PSBI’s quinone binding function Annotations Ontology PSBI’s chlorophyll binding function

57. 3 Objectivity: The existence of classes is not dependent on our biological knowledge.

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

59. Task: Annotate molecular function of 10-4, a gene from Drosophila melanogaster

60. molecular function unknown is_a 10-4 Molecular function ontologyAnnotations

61. molecular function unknown is_a 10-4 Molecular function ontologyAnnotations

62. molecular function unknown is_a 10-4 Molecular function ontologyAnnotations

63. With thanks… For slides: Barry Smith David Hill For everything: The Gene Ontology Consortium