GO slim overhaul (completed 2009): Difference between revisions

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'''Terms:'''
'''Terms:'''


# cellular component assembly
# cellular component assembly ; GO:0022607
# anatomical structure formation involved in morphogenesis
# anatomical structure formation involved in morphogenesis ; GO:0048646
# cell adhesion (look at multicellular organism adhesion later)
# cell adhesion ; GO:0007155
#*  look at multicellular organism adhesion later
#* look at "biological regulation" 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)
#* look at cell killing later (may be picked up if we include multicellular organismal process although this is a bit broad)

Revision as of 09:27, 21 February 2010

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
  5. ribonucleoprotien complex assembly
  6. cell wall organization or biogenesis
  7. extracellular matrix organization
  8. membrane organization
  9. chromosome organization
  10. cytoskeletal organization
  11. mitosis
  12. cell adhesion
  13. aging
  14. signal transduction
  15. cell-cell signalling
  16. cell cycle
  17. cell death
  18. cell division
  19. growth
  20. cell proliferation
  21. cell wall org & biogenesis
    • later - cell junction org, cell projecgtion org
  22. cell differentiation
  23. cell morphogenesis
  24. cell motility
  25. homeostatic process
  26. vesicle-mediated transport
  27. nucleocytoplasmic transport
  28. transmembrane transport
  29. macromolecular complex assembly
  30. plasma membrane organization ?
  31. chromosome organization
  32. cytoskeleton organization
  33. mitochondrion organization
  34. extracellular matrix organization
  35. cell junction organization
  36. cell motility
  37. pigmentation
  38. reproduction
  39. transposition
  40. immune system process
  41. locomotion
  42. biosynthetic process
  43. catabolic process
  44. DNA metabolic process
  45. transcription
  46. generation of precursor metabolites and energy
  47. cellular amino acid and derivative metabolic process
  48. nucleobase, nucleoside and nucleotide metabolic process
  49. cofactor metabolic process
  50. photosynthesis
  51. small molecule metabolic process ; GO:0044281
  52. sulfur metabolic process
  53. secondary metabolic process
  54. vitamin metabolic process* (need this?)
  55. carbohydrate metabolic process
  56. lipid metabolic process
  57. translation
  58. protein folding
  59. protein modification process
  60. protein maturation
  61. symbiosis, encompassing mutualism through
  62. developmental maturation (might be able remove this one)
  63. anatomical structure development ; GO:0048856
  64. embryonic development ; GO:0009790
  65. circulatory system process ; GO:0003013
  66. neurological system process ; GO:0050877
    • (note: we'll probably need some other system processes here)
  67. 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?