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Building Biomedical Ontologies

Building Biomedical Ontologies. Jennifer Clark, GO Editorial Office. Clark et al ., 2005. is_a. part_of. Clark et al ., 2005. "encyclopaedia of Flemish children's games“ BRUEGEL. classes GO terms, types, kinds, universals instances annotated gene product attributes,

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Building Biomedical Ontologies

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  1. Building Biomedical Ontologies Jennifer Clark, GO Editorial Office

  2. Clark et al., 2005 is_a part_of

  3. Clark et al., 2005

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

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

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

  7. Relationships • is_a • part_of • develops_from

  8. part_of • no necessity • necessarily is part • necessarily has part • necessarily is part and necessarily has part

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

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

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

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

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

  14. X cell differentiation

  15. X cell differentiation Differentiation of an x cell.

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

  17. [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

  18. [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

  19. http://cancerweb.ncl.ac.uk • neuron • An excitable cell specialised for the transmission of electricalsignals over longdistances. Neuronsreceive input from sensorycells 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 singleaxon can be several metres in length. Although signals are usually sent via action potentials, some neurons are nonspiking.

  20. 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 cell

  21. [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

  22. [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

  23. Difficult term request • Reconcile plant trichomes and insect trichomes.

  24. Plant trichomehttp://bib18.ulb.ac.be/Botanique_I/image/6703873062005_trichome_arabidopsis.jpghttp://www.innovations-report.de/bilder_neu/40879_szymanski.trichomeLO.jpg

  25. Insect trichomehttp://www.grisda.org/tstandish/images/animalia/arthropoda/Wildtype-D.-melanogaster-EM.jpg

  26. 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

  27. 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

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

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

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

  31. 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.

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

  33. 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.

  34. 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.

  35. x morphogenesis starting structure x mature structure gene products act here The process by which the anatomical structures of x are generated and organized. Morphogenesis pertains to the creation of form. x metamorphosis multiple mature structures 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. x starting structure gene products act here

  36. http://www.aardman.com

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

  38. after before

  39. 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

  40. 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

  41. Some more ontology thoughts…

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

  43. molecular function binding tetrapyrrole binding cofactor binding chlorophyll heme coenzyme quinone binding binding binding binding Ontology is_a PSBI PSBI Annotations

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

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