Wednesday, March 17, 2010

Biological ontologies


I've postponed really learning about ontologies in bioinformatics for a while now, but circumstances now dictate that I figure it out. It is a little bewildering. As just one example, the current Gene Ontology has the following processes as the top-level categories of "biological processes":


  1. biological adhesion

  2. biological regulation

  3. carbohydrate utilization

  4. carbon utilization

  5. cell killing

  6. cell wall organization or biogenesis

  7. cellular component biogenesis

  8. cellular component organization

  9. cellular process

  10. death

  11. developmental process

  12. establishment of localization

  13. growth

  14. immune system process

  15. localization

  16. locomotion

  17. metabolic process

  18. multi-organism process

  19. multicellular organismal process

  20. nitrogen utilization

  21. phosphorus utilization

  22. pigmentation

  23. reproduction

  24. reproductive process

  25. response to stimulus

  26. rhythmic process

  27. signaling

  28. signaling process

  29. sugar utilization

  30. sulfur utilization

  31. viral reproduction



Most of these are reasonable, some seem odd. Pigmentation? A top-level process?

It reminds me of the fabulous first paragraph of Michel Foucault's "The Order of Things" (in my opinion his best book):


This book first arose out of a passage in Borges, out of the laughter that shattered, as I read the passage, all the familiar landmarks of my thought - our thought, the thought that bears the stamp of our age and our geography - breaking up all the ordered surfaces and all the planes with which we are accustomed to tame the wild profusion of existing things, and continuing long afterwards to disturb and threaten with collapse our age-old distinction between the Same and the Other. This passage quotes a ‘certain Chinese encyclopedia’ in which it is written that ‘animals are divided into: (a) belonging to the Emperor, (b) embalmed, (c) tame, (d) sucking pigs, (e) sirens, (f) fabulous, (g) stray dogs, (h) included in the present classification, (i) frenzied, (j) innumerable, (k) drawn with a very fine camelhair brush, (1) et cetera, (m) having just broken the water pitcher, (n) that from a long way off look like flies’. In the wonderment of this taxonomy, the thing we apprehend in one great leap, the thing that, by means of the fable, is demonstrated as the exotic charm of another system of thought, is the limitation of our own, the stark impossibility of thinking that.

1 comment:

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