GO slim overhaul (completed 2009)

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We plan to completely revise the generic GO slim, and in the process come up with some guidelines for developing slims. This project began in Sept 2009.

Personnel

Jane, Val

Notes

  • Ideally want three "generic" slims:
    • truly generic slim for all species (probably very high level indeed)
    • slim for multi-cellular organisms
    • slim for single-celled organisms
  • could also do eukaryotic vs. prokaryotic
  • Other considerations
    • Email with specific queries about terms included and omitted from current (as of June 2009 page creation, actual last update much earlier)
    • Mailing list thread with Val's criteria for term selection Amelia comment:Most of this might be automatable, the hardest part of automatation will be to identify "biologically relevent terms". may be necessary to look at "extermal sources of terms"
    • Can we avoid "other X" terms? They're confusing and hard to handle.
    • Try to make slims is_a complete

Tangentially related: Does anyone know of a web-based slimming tool which shows the number of gene products which are annotated, but not to any term in your slim, and the number which are not annotated to any GO term (i.e root node annotations)? (question from Val)

Linda suggested:

  1. slim for metagenomics
  2. Collecting purpose made slims

Meetings

Terms:

  1. cellular component assembly ; GO:0022607
  2. anatomical structure formation involved in morphogenesis ; GO:0048646
  3. cell adhesion ; GO:0007155
    • look at multicellular organism adhesion later
    • look at "biological regulation" later
    • look at cell killing later (may be picked up if we include multicellular organismal process although this is a bit broad)
  4. protein complex assembly ; GO:0006461
  5. ribonucleoprotein complex assembly ; GO:0022618
  6. cell wall organization or biogenesis ; GO:0071554
  7. extracellular matrix organization ; GO:0030198
  8. membrane organization ; GO:0061024
  9. chromosome organization ; GO:0051276
  10. cytoskeletal organization ; GO:0007010
  11. mitosis ; GO:0007067
  12. aging ; GO:0007568
  13. signal transduction ; GO:0007165
  14. cell-cell signalling ; GO:0007267
  15. cell cycle ; GO:0007049
  16. cell death ; GO:0008219
  17. cell division ; GO:0051301
  18. growth ; GO:0040007
  19. cell proliferation ; GO:0008283
  20. cell wall organization or biogenesis ; GO:0071554
    • later - cell junction org, cell projecgtion org
  21. cell differentiation ; GO:0030154
  22. cell morphogenesis ; GO:0000902
  23. cell motility ; GO:0048870
  24. homeostatic process ; GO:0042592
  25. vesicle-mediated transport ; GO:0016192
  26. nucleocytoplasmic transport ; GO:0005487
  27. transmembrane transport ; GO:0055085
  28. macromolecular complex assembly ; GO:0065003
  29. plasma membrane organization ; GO:0007009 ?
  30. chromosome organization ; GO:0051276
  31. cytoskeleton organization ; GO:0007010
  32. mitochondrion organization ; GO:0007005
  33. extracellular matrix organization ; GO:0030198
  34. cell junction organization ; GO:0034330
  35. pigmentation ; GO:0043473
  36. reproduction ; GO:0000003
  37. transposition ; GO:0032196
  38. immune system process ; GO:0002376
  39. locomotion ; GO:0040011
  40. biosynthetic process ; GO:0009058
  41. catabolic process ; GO:0009056
  42. DNA metabolic process ; GO:0006259
  43. transcription ; GO:0061018
  44. generation of precursor metabolites and energy ; GO:0006091
  45. cellular amino acid and derivative metabolic process ; GO:0006519
  46. cellular nucleobase, nucleoside and nucleotide metabolic process ; GO:0034655
  47. cofactor metabolic process ; GO:0051186
  48. photosynthesis ; GO:0015979
  49. small molecule metabolic process ; GO:0044281
  50. sulfur metabolic process ; GO:0006790
  51. secondary metabolic process ; GO:0019748
  52. vitamin metabolic process ; GO:0006766 * (need this?)
  53. carbohydrate metabolic process ; GO:0005975
  54. lipid metabolic process ; GO:0006629
  55. translation ; GO:0006412
  56. protein folding ; GO:0006457
  57. protein modification process ; GO:0006464
  58. protein maturation ; GO:0051604
  59. symbiosis, encompassing mutualism through parasitism; GO:0044403
  60. developmental maturation ; GO:0021700 (might be able remove this one)
  61. anatomical structure development ; GO:0048856
  62. embryonic development ; GO:0009790
  63. circulatory system process ; GO:0003013
  64. neurological system process ; GO:0050877
    • (note: we'll probably need some other system processes here)
  65. response to stress ; GO:0006950

Meeting Dates:

  • 21 August
  • 8 Sept
  • 7 Oct
  • 25 Nov
  • 21 Jan
  • 2 Feb

TODO:

Val to translate list of slim terms to ids to check bucket terms

(when we choose terms we should also consider IEA annotations as will give a better idea of how many gene products are likely to be to a term when "annotation complete")

  • Need to re-check how annotations are allocated to this slim when regulates is made non-transitive in map2slim (new in GO moose).

Issues to consider

  1. How will this slim be maintained to ensure it keeps in line with ontology rearrangements? Yearly revision? More frequent?
  2. What other slims should we maintain in the GO file: cellular v/s multicellular v/s multi-organism? Euk v/s prok?
  3. Mapping over different relations for map2slim - regulates?