1. Building and Refining AraCyc: Data Content, Sources, and Methodologies Kate Dreher TAIR, AraCyc, PMN Carnegie Institution for Science

2.  AraCyc – Arabidopsis Metabolic EnCyclopedia Database of metabolic pathways found in Arabidopsis AraCyc  Accessible from : TAIR – The Arabidopsis Information Resource  www.arabidopsis.org

3.  AraCyc – Arabidopsis Metabolic EnCyclopedia Database of metabolic pathways found in Arabidopsis AraCyc  Accessible from : PMN – Plant Metabolic Network  www.plantcyc.org

4. AraCyc Pathway pages Pathway Enzyme Gene Reaction Compound Evidence Code + Additional curated information

5. AraCyc Pathway pages Classification Summary References Superpathways Pathway variants

6. AraCyc Pathway pages Pathway Enzyme Gene Reaction Compound Evidence Code

7. AraCyc Pathway pages Pathway Enzyme Gene Reaction Compound Evidence Code

8. AraCyc Compound pages AraCyc Compound: CDP-choline Synonyms Appears as Product Classification(s) Molecular Weight / Formula Appears as Reactant

9. AraCyc Pathway pages Pathway Enzyme Gene Reaction Compound Evidence Code

10. AraCyc Enzyme detail pages AraCyc Enzyme: phosphatidyltransferase Multifunctional protein * *

11. AraCyc Enzyme detail pages AraCyc Enzyme: phosphatidyltransferase Reaction Pathway(s) Summary References Inhibitors, Kinetic Parameters, etc.

12. AraCyc Pathway pages Pathway Enzyme Gene Reaction Compound Evidence Code To TAIR...

13. AraCyc 4.5 (released June 2008) Pathways288 Compounds1956 Reactions1723 Citations2279  More detailed information available in the Release Notes

14. PlantCyc 1.0 (released June 2008) Pathways508 Compounds2314 Reactions2277 Citations4208 Species292  www.plantcyc.org

15. Putting AraCyc (and PlantCyc) to use  Reference information Pathways, Genes, Enzymes, Reactions, and Metabolites  Data Analysis (AraCyc) Use the OMICS viewer  Display the results of experiments on an Arabidopsis metabolic map  Study your data or public data sets

16. Putting AraCyc to use Compounds Transcripts or Proteins  Display the results of experiments on an Arabidopsis metabolic map

17. Putting AraCyc (and PlantCyc) to use  Reference information Pathways, Genes, Enzymes, Reactions, and Metabolites  Data Analysis (AraCyc) Use the OMICS viewer  Display the results of experiments on an Arabidopsis metabolic map  Study your data or public data sets Generate new hypotheses  Find metabolic differences in your mutant with “no phenotype”  Identify pathways that are related to your favorite biological process See more at “Advanced Bioinformatic Resources for Arabidopsis”  Thursday, July 24, 7 PM in the Grand Salon  Enzyme discovery Fill “pathway holes” through comparative analyses

18. Putting AraCyc (and PlantCyc) to use Pathway “Hole Filling” ?????? Choline Biosynthesis I AraCyc Spinach Soybean ethanolamine PlantCyc Fill pathway “hole”

19. Curators Metabolic Pathway Databases Data sources and data flow Computational predictions Community submissions Research Community Experimental Data Genes, Proteins, Metabolites Published literature Data repositories

20. Data sources and data flow  Information enters metabolic pathway database in two stages Stage 1: Initial build Stage 2: Updates and improvements  AraCyc 1.0 – Initial Build - 2002

21. Initial AraCyc Build (2002)  7900 Arabidopsis genes annotated to the GO term ‘catalytic activity’  4900 loci in small molecule metabolism 19% of the total genome  Goal: Map these loci to metabolic PATHWAYS  Solution: Use reference database: MetaCyc (460 metabolic pathways) Run PathoLogic program (SRI International) Predict metabolic pathways present in Arabidopsis

22. MetaCyc  Multi-kingdom metabolic pathway database METAbolic EnCYClopedia SRI International (www.metacyc.org)  First released in 1999  All pathways generated by curators extracting information from the scientific literature  Only contains pathways with experimental support  Reference database Used to create SINGLE SPECIES databases... including AraCyc in 2002!

23. Initial AraCyc Build (2002) PathoLogic ANNOTATED GENOME AT1G69370 chorismate mutase prephenate aminotransferase arogenate dehydratase chorismateprephenateL-arogenateL-phenylalanine 5.4.99.5 2.6.1.79 4.2.1.91 Gene calls Gene functions DNA sequences AT1G69370 chorismate mutase MetaCyc AraCyc AT2G27820 arogenate dehydratase

24. PathoLogic Program  Matches input enzymes to reference enzymes Name Enzyme Commission (EC) number  Identifies probable pathways Enzyme coverage Predicted species distribution  Initial AraCyc 1.0 build (2002) PathoLogic inferred over 200 pathways PathoLogic mapped 940 genes to the pathways

25. Validation of a New Database  PathoLogic errs on the side of over-prediction  Curators validate pathways...

26. Validation of a New Database  Curators Find support for predicted pathways  Is the pathway described in Arabidopsis literature?  Are the crucial metabolites described in Arabidopsis literature?  Does the pathway include a unique reaction catalyzed by an Arabidopsis protein?

27. Validation of a New Database  Curators: Remove pathways not found in Arabidopsis  glycogen biosynthesis  C4 photosynthesis  caffeine biosynthesis Edit pathways operating via a different route  Phenylalanine biosynthesis in bacteria vs. Arabidopsis

28. Validation of a New Database AraCyc Pathway: phenylalanine biosynthesis  Edit pathways operating via a different route

29. Completion of a New Database  Curators Add Arabidopsis pathways not present in reference database Add Arabidopsis compounds, reactions, and enzymes not mapped to a pathway Assign evidence codes to pathways and enzymes

30. Assignment of Evidence Codes

31. AraCyc 1.0... and beyond  Information enters metabolic pathway database in two stages Stage 1: Initial build Stage 2: Updates and improvement

32. Database updates and improvements ReleaseAraCyc 1.0AraCyc 4.5AraCyc 5.0 Pathways219288even more!

33. Database updates and improvements  New rounds of computational pathway prediction New TAIR genome releases New MetaCyc releases  New round of PathoLogic prediction

34. Database updates and improvements  New rounds of computational pathway prediction New TAIR genome releases New reference database – PlantCyc  Part of the Plant Metabolic Network  Released in June 2008  Contains plant pathways supported by:  experimental evidence  expert hypothesis ***  Reviewed by an editorial board of biochemists  Will include enzymes from newly sequenced plant genomes and EST collections www.plantcyc.org

35. Database updates and improvements  New rounds of computational pathway prediction Newly predicted pathways undergo pathway validation PathoLogic Program Updated pathway predictions for AraCyc Newest TAIR Genome Annotations Newest Version of PlantCyc See poster: ICAR1404

36. Database updates and improvements  New curator entries Curators search for new information in scientific literature TAIR curators  Assign new functional annotations to metabolic genes AraCyc curators  Manually attach enzymes to pathways  Identify new and updated pathways  Write or revise summaries

37. Database updates and improvements  New community submissions Jamborees  Experts meet individually with curators  Review pathways in specific metabolic domains  Provide useful references and suggest important pathways Curation Booth ******  Open during all poster sessions – Booth #1  Please come (free candy!) TAIR or PMN website

38. Community submissions  TAIR – www.arabidopsis.org

39. Community submissions  TAIR – www.arabidopsis.org

40. Community submissions  PMN – www.plantcyc.org

41. Community submissions  PMN – www.plantcyc.org curator@plantcyc.org

42. Community submissions  PMN Contributor page Your name here! = fame!

43. Acknowledgements Current Curators: - Peifen Zhang (Director and lead curator- metabolism) - Tanya Berardini (lead curator – functional annotation) - David Swarbreck (lead curator – structural annotation) - A. S. Karthikeyan (curator) - Donghui Li (curator) Recent Past Curators: - Christophe Tissier (curator) - Hartmut Foerster (curator) Tech Team Members: - Bob Muller (Manager) - Larry Ploetz (Sys. Administrator) - Raymond Chetty - Anjo Chi - Vanessa Kirkup - Cynthia Lee - Tom Meyer - Shanker Singh - Chris Wilks Metabolic Pathway Software: - Peter Karp and SRI group (NIH) TAIR, AraCyc, and the PMN Eva Huala (Director and Co-PI) Sue Rhee (PI and Co-PI)

44. Thank you... www.arabidopsis.org curator@arabidopsis.org www.arabidopsis.org/biocyc curator@arabidopsis.org www.plantcyc.org curator@plantcyc.org Please visit us at the Curation Booth!

45. Curation workflow identify a pathway find details of reactions find details of enzymes data entry structure of substrates enzymes EC number kinetic parameters inhibitors / activators coding gene reactions draw pathway diagram

46. Database maintenance and improvement Single Species Databases Multi-species reference database AraCyc 4.5 RiceCyc PoplarCyc PlantCyc Genome AnnotationPathoLogic PredictionManual Pathway Curation ++ Refine existing databases *PlantCyc* AraCyc 5.0 RiceCyc PoplarCyc

47. Database maintenance and improvement Single Species Databases Multi-species reference database PlantCyc Genome AnnotationPathoLogic PredictionManual Pathway Curation ++ AraCyc 5.0 RiceCyc PoplarCyc MaizeCyc and more *PlantCyc*

48. Database maintenance and improvement Single Species Databases Multi-species reference database PlantCyc Genome AnnotationPathoLogic PredictionManual Pathway Curation ++ AraCyc 10.0 RiceCyc PoplarCyc MaizeCyc and more *PlantCyc*

49. Database maintenance and improvement Single Species Databases Multi-species reference database AraCyc 4.5 RiceCyc PoplarCyc PlantCyc Genome AnnotationPathoLogic PredictionManual Pathway Curation ++ Refine existing databases *PlantCyc* AraCyc 5.0 RiceCyc PoplarCyc

50. Database maintenance and improvement Single Species Databases Multi-species reference database PlantCyc Genome AnnotationPathoLogic PredictionManual Pathway Curation ++ AraCyc 5.0 RiceCyc PoplarCyc MaizeCyc and more *PlantCyc*

51. Database maintenance and improvement Single Species Databases Multi-species reference database PlantCyc Genome AnnotationPathoLogic PredictionManual Pathway Curation ++ AraCyc 10.0 RiceCyc PoplarCyc MaizeCyc and more *PlantCyc*

52. Database maintenance and improvement Build NEW databases Single Species Databases Multi-species reference database AraCyc 4.5 RiceCyc PoplarCyc PlantCyc Genome AnnotationPathoLogic PredictionManual Pathway Curation ++