1. CalbiCyc, Metabolic Pathways at the Candida Genome Database Martha Arnaud arnaudm@genome.stanford.edu

2. Outline Accessing data in the Candida Genome Database (CGD) Gene information in CGD: the Locus Summary page Biochemical pathways at CGD Pathway Prediction and Curation Our favorite PTools customizations / configuration options

3. Introduction to CGD SGD-like resource for Candida albicans CGD started in 2004 All CGD data are freely available to the public Share codebase, tools, and website organization with SGD Manual curation of scientific literature Pathways are just one of the types of data we provide, and they account for a modest fraction of our site usage

4. Accessing data in CGD Quick Search: The main entrance point Search CGD by gene name or keyword Fields searched: - Gene Names - Gene Descriptions - Gene Ontology terms, synonyms, IDs - People (colleagues, authors) - PubMed ID - S. cerevisiae Ortholog or Best Hit - Biochemical pathways

5. Additional tools for accessing data in CGD Advanced Search: Search for genes by properties

6. Uses Textpresso Developed by Wormbase, Caltech Full-text literature search

7. Sequence-related searches and tools BLAST Pattern Match Restriction Map Primers Genome Browser (GMOD’s GBrowse)

8. Community Resources Search for colleagues Browse Candida Labs

9. Bulk Data Downloads Browse list of downloadable files

10. Bulk Data Downloads Browse list of downloadable files Downloads directory on our web site

11. Gene information in CGD CGD focuses on gene-based information Basic gene information is found on the “Locus Summary Page” (LSP) Quick Search is the easiest way to find the LSP for a gene

12. Locus Summary Page LSP summarizes gene information A “hub” that links out to more details

13. Locus Summary Page Gene names, aliases Gene description Mutant phenotypes Gene Ontology Chromosomal location Sequence retrieval Sequence analysis Genome browser Orthologs Pathways

14. Locus Summary Page Gene names, aliases Gene description Mutant phenotypes Gene Ontology Chromosomal location Sequence retrieval Sequence analysis Genome browser Orthologs Pathways

15. Locus Summary Page Gene names, aliases Gene description Mutant phenotypes Gene Ontology Chromosomal location Sequence retrieval Sequence analysis Genome browser Orthologs Pathways

16. Locus Summary Page Gene names, aliases Gene description Mutant phenotypes Gene Ontology Chromosomal location Sequence retrieval Sequence analysis Genome browser Orthologs Pathways

17. Locus Summary Page Gene names, aliases Gene description Mutant phenotypes Gene Ontology Chromosomal location Sequence retrieval Sequence analysis Genome browser Orthologs Pathways!

18. Biochemical Pathways at CGD http://pathway.candidagenome.org/ Search Browse… List… … PTools in “web mode”

19. Biochemical Pathways at CGD Zoom Link out to SGD Curated pathway summary comments References

20. PTools Prediction of pathways for CGD Pathologic pathway database construction: January - April 2007 Pathways released on our public web site: March 2008

21. Two-part curation approach: Step 1. Triage –Literature searches, assemble citation list –Decide to keep or delete pathway –Kept 181, deleted 227, added 15 Step 2. More intensive curation –Pathway modifications –Pathway comments Current statistics: 156 pathways 107 with second-stage curation complete 14 triage and S. cerevisiae comments from SGD 35 triage only (references but, no free-text description) Curation of pathways at CGD

22. Curation of pathways, continued Curation notes Curation challenge: Steep learning curve for the curation tools. The tools are quite different, and the process is distinct, from the usual gene-centric curation we do, curators need to “switch gears” for pathway curation. Found that it was easier to make progress by making a focused “project” out of pathway curation.

23. Multiple routes to customize the function and appearance of the tools: –Menu options –Parameters passed upon PTools web server startup –PTools “init” file –Style sheet –Custom scripts Our favorite configurable Ptools options

24. Some options that we find to be useful: PathoLogic: Specify Reference PGDB SGD had some recent curation that was not yet included in MetaCyc Pathologic allowed us to include the new information in the prediction set!

25. Useful customization options, continued: Pathway Hole Filler can be run without using the operon-related data types Issue command at the lisp prompt before you start the hole filler: (update-nodes '(SSCORE-NODE EVALS-NODE ALN-NODE RANK-NODE))

26. Useful customization options, continued: Gene links within pathway displays link to CGD Locus Summary pages Use -gene-link-db CGD argument when starting web server. Defined link template in the CGD database frame.

27. Useful customization options, continued: Gene links within pathway displays link to CGD Locus Summary pages Use -gene-link-db CGD argument when starting web server. Defined link template in the CGD database frame.

28. Useful customization options, continued: Add custom header and footer Integrated appearance, navigation with the rest of our site Define header and footer in: /ptools-local/html

29. Useful customization options, continued: Customized color of buttons and boxes on the interface Use "CGD Gold" not "EcoCyc Orange” aic-export/htdocs/style.css Relabel “Quick Search” on the interface (because we already have a Quick Search, with different functionality) /ptools-local/ptools-init.dat

30. One more useful customization: Custom-format pathway files, updated weekly Suzanne Paley sent us a Lisp script that we run as a cron job to regenerate the flat-files weekly We then process the flat files to generate an always-current custom-format file, requested by a CGD user

31. Some advice and encouragement on the pathway generation process The process can be very “fiddly.” Hang in there! Helpful user support: ptools-support@ai.sri.com Do not be afraid to ask for help! The process can be complicated, but an active dialogue with the helpful PTools support team makes it all possible

32. Gavin Sherlock, PI Martha Arnaud, Curator Maria Costanzo, Curator Diane Inglis, Curator Marek Skrzypek, Curator Gail Binkley, Database Administrator Stuart Miyasato, Systems Administrator Prachi Shah, Scientific Programmer The Team

33. Peter Karp Suzanne Paley Michelle Green Joe Dale Ron Caspi SGD THANKS For help in getting CGD Pathways up and running Contact us: candida-curator@genome.stanford.edu