Taxon and GO

1. Taxon and GO

2. Removal of sensu Old system: larval development (sensu Insecta) def: The process whose specific outcome is the progression of the larva over time, from its formation to the mature structure. As in, but not restricted to Insecta.

3. New system: instar larval development def: The process whose specific outcome is the progression of the larva over time, from its formation to the mature structure. This begins with the newly hatched first-instar larva, through its maturation to the end of the last larval stage

4. GO is species-neutral • The GO can support annotation across all species. • This is good! • Total exclusion of taxon information can • create problems.

5. We have 23802 terms. • Time-sink for users. • Worst for • peripheral • species groups. http://bestblog.mlblogs.com/inside_pitch/images/needle_in_the_haystack_4.jpg

6. Typical User Query: Hello, I'd like to load into our database only GO terms that are relevant for plants. Is there such GO-slim ? If not, is there a way to filter out GO terms that are not applicable for plants? Thanks, -Naama Menda Plant and Animal Genome Meeting 2005: Speaker: Some people think the size of GO makes it hard to handle. Audience: Raucous laughter and shouts of “no really?” Sanger microbial annotation: We need a prokaryote slim or we will not be able to annotate fast enough to meet our targets. (paraphrased)

7. Why is this here? GO language can be quite subtle. membrane of vacuole with cell cycle-independent morphology def: The lipid bilayer surrounding a vacuole that retains the same shape regardless of cell cycle phase. The membrane separates its contents from the cytoplasm of the cell.

8. To an outsider this is like… (8) If the Secretary of State considers it necessary or desirable to do so, he may by regulations prescribe a scale or scales of fees to have effect, for such period as is specified in the regulations, in place of any scale or scales prescribed by the Commission; and, if he does so, references in subsections (3) and (4) to the appropriate scale are to be read as respects that period as references to the appropriate scale prescribed by the Secretary of State. Audit Commission Act 1998 - 1998 CHAPTER 18 - http://www.opsi.gov.uk/acts/acts1998/ukpga_19980018_en_2

9. To an outsider this is like… (8) If the Secretary of State considers it necessary or desirable to do so, he may by regulations prescribe a scale or scales of fees to have effect, for such period as is specified in the regulations, in place of any scale or scales prescribed by the Commission; and, if he does so, references in subsections (3) and (4) to the appropriate scale are to be read as respects that period as references to the appropriate scale prescribed by the Secretary of State. Audit Commission Act 1998 - 1998 CHAPTER 18 - http://www.opsi.gov.uk/acts/acts1998/ukpga_19980018_en_2

10. Seen in context.. membrane of vacuole with cell cycle-independent morphology def: The lipid bilayer surrounding a vacuole that retains the same shape regardless of cell cycle phase. The membrane separates its contents from the cytoplasm of the cell. membrane of vacuole with cell cycle-correlated morphology def: The lipid bilayer surrounding a vacuole, the shape of which correlates with cell cycle phase. The membrane separates its contents from the cytoplasm of the cell.

11. With some inside information… membrane of vacuole with cell cycle-independent morphology def: The lipid bilayer surrounding a vacuole that retains the same shape regardless of cell cycle phase. The membrane separates its contents from the cytoplasm of the cell. membrane of vacuole with cell cycle-correlated morphology def: The lipid bilayer surrounding a vacuole, the shape of which correlates with cell cycle phase. The membrane separates its contents from the cytoplasm of the cell. Plant vacuole membrane Fungal vacuole membrane

12. Metazoan-specific terms Annotation: mps1 mps1 TTK family protein kinase, putative protein threonine/tyrosine kinase gene from Dictyostelium discoideum * IEA * With ZFIN:ZDB-GENE-030123-1 DDB REF:10158 Dictybase IEA annotations for Dicty Error checking !?

13. The Proposed Solution • We can apply taxon information in a rigorous and non-misleading way using relationships: • is_relevant_for • is_only_in • applies_to_all

14. Relevance is_relevant_to

15. Relevance: is_relevant_to • This GO term can be used for annotation of this taxon. • The GO term may not be appropriate for all subgroups of this taxon. • The GO term may not be appropriate for all supergroups of this taxon.

16. membrane of vacuole with cell cycle -independent morphology is_relevant_for Arabidopsis membrane of vacuole with cell cycle- correlated morphology is_relevant_for Saccharomyces

17. Relevance relationships • Added by curators. • Inferred from annotations.

18. Relevance - Propagation • Propagates up the GO. • Propagates up the taxon hierarchy.

19. Therefore: Danio is_relevant_for rerio Danio is_relevant_for rerio hatching from chorion Relevance

20. Therefore: Danio May be used for rerio annotation of Danio May be used for rerio annotation of hatching from chorion Relevance

21. hatching from chorion is_relevant_for (some subgroups of) hatching from chorion is_relevant_for Relevance cellular organisms; Eukaryota; Fungi/Metazoa group; Metazoa; Eumetazoa; Bilateria; Coelomata; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Actinopterygii; Actinopteri; Neopterygii; Teleostei; Elopocephala; Clupeocephala; Otocephala; Ostariophysi; Otophysi; Cypriniphysi; Cypriniformes; Cyprinoidea; Cyprinidae; Rasborinae; Danio

22. hatching from chorion May be used for annotation of (some subgroups of) May be used for annotation of hatching from chorion Relevance cellular organisms; Eukaryota; Fungi/Metazoa group; Metazoa; Eumetazoa; Bilateria; Coelomata; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Actinopterygii; Actinopteri; Neopterygii; Teleostei; Elopocephala; Clupeocephala; Otocephala; Ostariophysi; Otophysi; Cypriniphysi; Cypriniformes; Cyprinoidea; Cyprinidae; Rasborinae; Danio

23. Specificity is_only_in

24. Specificity – is_only_in • The GO term never applies to species outside of this taxon. (The GO terms may apply to only some subtaxa of the taxon, and not all.)

25. Viridiplantae http://www.seaweed.ie/algae/images/hydrodictyon2.jpg http://www.blackburn.gov.uk/server.php?show=conMediaFile.7355 green plants and algae

26. http://www.blackburn.gov.uk/server.php?show=conMediaFile.7355http://www.blackburn.gov.uk/server.php?show=conMediaFile.7355 Leaf development never occurs outside of Viridiplantae. Not all subtaxa of Viridiplantae make leaves. http://www.seaweed.ie/algae/images/hydrodictyon2.jpg

27. formally… GO term: leaf development relationship: is_only_in taxon: Viridiplantae Leaf development never occurs outside of Viridiplantae. (Not all subtaxa of Viridiplantae make leaves.)

28. Specificity - is_only_in • Added manually by curators as they develop the graph.

29. Specificity - is_only_in • Propagates down the GO. • Propagates up the taxon hierarchy. GO Taxon

30. Viridiplantae is_only_in Therefore: Viridiplantae is_only_in Specificity - is_only_in

31. never occurs outside Viridiplantae Therefore: Viridiplantae never occurs outside Specificity - is_only_in

32. Therefore: leaf development is_only_in leaf development is_only_in Specificity - is_only_in Cellular organisms Eukaryota Viridiplantae

33. Therefore: leaf development never occurs outside of never occurs outside of leaf development Specificity - is_only_in Cellular organisms Eukaryota Viridiplantae

34. What about convergent evolution? http://www.dcn.davis.ca.us/go/platypus/images/platygeo.jpg http://homepage.mac.com/wildlifeweb/bird/mallard/mallard_male_image_11tfk.jpg

35. Assumptions- beak development • These beaks were produced by convergent evolution • The two beak development processes are the same.

36. one beak development term • is_relevant_for Anas platyrhynchos (mallard) • is_relevant_for Ornithorhynchus anatinus (Platypus) • is_only_in Amniota (or vertebrata if that is easier)

37. Validity applies_to_all

38. Validity – applies_to_all The GO term applies to all subtaxa of a given taxon. (The GO term may also apply to species outside of the taxon.)

39. Validity – applies_to_all Homoiothermy is exhibited by all subtaxa of the taxon Mammalia. http://www.thermalconsultancy.com/ http://coolcosmos.ipac.caltech.edu/image_galleries/ir_zoo/coldwarm.html

40. Validity – applies_to_all Homoiothermy is absent in many of the taxonomic groups outside of Mammalia. http://coolcosmos.ipac.caltech.edu/image_galleries/ir_zoo/coldwarm.html

41. Validity – applies_to_all with some exceptions… Homoiothermy is also present in birds, tuna fish, and honey bees. Bee Hive http://www.beebehavior.com/

42. formally… GO term: homoiothermy relationship: applies_to_all taxon: Mammalia Homoiothermy is found in all subtaxa of the taxon Mammalia. (Homoiothermy is also found outside of the taxon Mammalia.)

43. GO Taxon Validity • Propagates up the GO. • Propagates down the taxon hierarchy.

44. Mammalia applies_to_all Mammalia applies_to_all Validity

45. All of these GO terms also apply to all mammals. They can also apply to taxonomic groups outside of mammalia. This process occurs in all mammals. Validity

46. The GO term homoiothermy applies_to_all mammals. Therefore the GO term homoiothermy applies_to_all types of mammals. Validity

47. Validity – applies_to_all • Added manually by curators

48. Cave fish Not all fish carry out eye development processes. http://www.petpig.com/fish/fish/blind_cave_fish1.jpg

49. fish

50. eye development applies_to_all fish ?