Function-process links

1. Function-process links Conclusions of the electron transport working group.

2. biosynthetic process UDP-glucose metabolic process colanic acid biosynthetic process UTP:glucose-1-phosphate uridylyltransferase activity α-D-glucose 1-phosphate + UTP -> UDP-D-glucose + diphosphate galactose metabolic process carbohydrate catabolic process response to desiccation glucose metabolic process hp hp hp hp hp hp hp Process Function

3. Lysine biosynthesis pathways

4. Process lysine biosynthesis is_a lysine biosynthesis 7? is_a is_a is_a is_a is_a is_a lysine biosynthesis 1 lysine biosynthesis 3 lysine biosynthesis 5 lysine biosynthesis 4 lysine biosynthesis 2 lysine biosynthesis 6 Function

5. Process Lysine Biosynthesis = has_part new GO term Shared function? Function existing GO term Non-shared function

6. Process Lysine Biosynthesis Process B = has_part new GO term Shared function? Function existing GO term Non-shared function

7. Process Lysine Biosynthesis Process B Process C = has_part new GO term Shared function? Function existing GO term Non-shared function

8. Process Lysine Biosynthesis Relationship explosion Process B Process C (or Editorial office explosion) Function

9. Where do pathways start and end? process 2 A B C D process 1 process 3

10. Use cases • Can we slim from function up to process? • Can we infer annotations to process from those to function?

11. Process has_part polyamine biosynthesis urea cycle has_function Function arginosuccinate synthase activity has_function but only as part_of polyamine biosynthesis has_function but only as part_of urea cycle Gene products Gene product y Gene product x

12. Process has_part polyamine biosynthesis urea cycle has_function Function ? Gene products Gene product y Gene product x

13. Process has_part polyamine biosynthesis urea cycle has_function Function has_part cannot be used for slimming. No Gene products Gene product y Gene product x

14. Can we infer annotations to process from those to function? • No. There is too much variation in process details, • and too many functions are shared.

15. So what can we do?

16. Process phosphorylation part_of Function kinase activity We can make relationships between single step processes and their respective functions.

17. Process glucose transport part_of Function glucose transporter activity We can make any obvious relationship where part_of holds, and this will allow useful slimming.

18. We can mine the other links from pathway databases and make non-curated sometimes_part_of links.

19. sometimes_part_of What does this buy us? Very full coverage of function-process links. No manual link curation. What work does it involve? We maintain the mapping files e.g. reactome2go. We write the mining scripts.

20. Acknowledgements Michelle Gwinn-Giglio Debbie Siegele Ingrid Keseler Harold Drabkin Jennifer Deegan Chris Mungall Peifen Zhang

23. Part_of Car part_of? wheel http://www.treehugger.com/ e-zip-2008-trailz-hybrid-electric-bike.jpg

24. Part_of Car part_of? car wheel http://www.classicnation.com/pictures/images/ car_shows/goodguys_columbus/ goodguys-columbus-car-show-047.jpg

25. has_part wheel has_part car http://www.aa1car.com/library/wheel_missing.jpg

26. Process: Travel from New York to California (by car)

27. Process: Travel from New York to California via Minnesota (Google maps)

28. Process: Travel from New York to California via Oklahoma

29. Process: Travel from New York to California via Iowa

30. Travel from New York to California is_a is_a is_a Travel from New York to California via Iowa Travel from New York to California via Minnesota Travel from New York to California via Oklahoma

31. Travel from New York to California Process is_a is_a is_a Travel from New York to California via Minnesota Travel from New York to California via Iowa Travel from New York to California via Oklahoma sometimes _has_part sometimes _has_part sometimes _has_part Travel from Wisconsin to Minnesota Travel from Missouri to Oklahoma Travel from Iowa to Nebraska Function

32. Do the sub-process share any functions?

33. Function: get in the car. http://www.ozbadge.com/sitebuildercontent/sitebuilderpictures/wapol1911ford.jpg

34. Travel from New York to California Process is_a is_a is_a Travel from New York to California via Minnesota Travel from New York to California via Iowa Travel from New York to California via Oklahoma has_part has_part has_part Get in car Function

35. Travel from New York to California Process is_a is_a is_a Travel from New York to California via Minnesota Travel from New York to California via Iowa Travel from New York to California via Oklahoma Any part_of children? Function

38. Photosynthetic electron transport chain http://genomics.energy.gov/gallery/gtl/originals/422.jpg

39. Anoxygenic Oxygenic http://thumbs.dreamstime.com/ thumb_55/1145821933432C7c.jpg Green plants + Algae + Cyanobacteria http://www.emc.maricopa.edu/faculty/farabee/BIOBK/84150f.jpg Other photosynthetic bacteria http://genomicsgtl.energy.gov/benefits/hfromh2o.shtml

40. process terms photosynthetic electron transport chain (psth) is_a is_a anoxygenic psth oxygenic psth part_of part_of has part has part H2S -> NADPH + S H2O -> O2 + NADPH light- harvesting Function terms Option 1

41. process terms photosynthetic electron transport chain (psth) part_of part_of part_of H2S -> NADPH + S H2O -> O2 + NADPH light- harvesting Function terms Option 2

42. - no photosynthetic functions - No annotations for function But…

44. arginine • biosynthetic • process polyamine biosynthesis arginosuccinate synthase activityCatalysis of the reaction: ATP + L-citrulline + L-aspartate = AMP +diphosphate + (N(omega)-L-arginino)succinate urea cycle hp hp hp Process Function

45. Arginine and proline metabolism Glutamate metabolism Nitrogen metabolism carbamoyl-phosphate synthase activityCatalysis of a reaction that results in the formation of carbamoyl phosphate. Urea cycle and metabolism of amino groups hp hp hp hp Process Function