CalbiCyc, Metabolic Pathways at the Candida Genome Database
description
Transcript of CalbiCyc, Metabolic Pathways at the Candida Genome Database
![Page 2: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/2.jpg)
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
![Page 3: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/3.jpg)
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
![Page 4: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/4.jpg)
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
![Page 5: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/5.jpg)
Additional tools for accessing data in CGD
Advanced Search:
Search for genes by properties
![Page 6: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/6.jpg)
Uses Textpresso
Developed by
Wormbase, Caltech
Full-text literature search
![Page 7: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/7.jpg)
Sequence-related searches and tools
BLAST
Pattern Match
Restriction Map
Primers
Genome Browser
(GMOD’s GBrowse)
![Page 8: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/8.jpg)
Community Resources
Search for colleagues
Browse Candida Labs
![Page 9: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/9.jpg)
Bulk Data Downloads
Browse list of downloadable files
![Page 10: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/10.jpg)
Bulk Data Downloads
Browse list of downloadable files
Downloads directory
on our web site
![Page 11: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/11.jpg)
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
![Page 12: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/12.jpg)
Locus Summary Page
LSP summarizes gene information
A “hub” that links out to more details
![Page 13: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/13.jpg)
Locus Summary Page
Gene names, aliases
Gene description
Mutant phenotypes
Gene Ontology
Chromosomal location
Sequence retrieval
Sequence analysis
Genome browser
Orthologs
Pathways
![Page 14: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/14.jpg)
Locus Summary Page
Gene names, aliases
Gene description
Mutant phenotypes
Gene Ontology
Chromosomal location
Sequence retrieval
Sequence analysis
Genome browser
Orthologs
Pathways
![Page 15: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/15.jpg)
Locus Summary Page
Gene names, aliases
Gene description
Mutant phenotypes
Gene Ontology
Chromosomal location
Sequence retrieval
Sequence analysis
Genome browser
Orthologs
Pathways
![Page 16: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/16.jpg)
Locus Summary Page
Gene names, aliases
Gene description
Mutant phenotypes
Gene Ontology
Chromosomal location
Sequence retrieval
Sequence analysis
Genome browser
Orthologs
Pathways
![Page 17: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/17.jpg)
Locus Summary Page
Gene names, aliases
Gene description
Mutant phenotypes
Gene Ontology
Chromosomal location
Sequence retrieval
Sequence analysis
Genome browser
Orthologs
Pathways!
![Page 18: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/18.jpg)
Biochemical Pathways at CGD http://pathway.candidagenome.org/
Search
Browse…List…
…
PTools in “web mode”
![Page 19: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/19.jpg)
Biochemical Pathways at CGD
• Zoom
• Link out to SGD
• Curated pathway summary comments
• References
![Page 20: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/20.jpg)
PTools Prediction of pathways for CGD
• Pathologic pathway database construction: January - April 2007
• Pathways released on our public web site: March 2008
![Page 21: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/21.jpg)
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 complete14 triage and S. cerevisiae comments from SGD35 triage only (references but, no free-text description)
Curation of pathways at CGD
![Page 22: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/22.jpg)
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.
![Page 23: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/23.jpg)
• 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
![Page 24: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/24.jpg)
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!
![Page 25: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/25.jpg)
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))
![Page 26: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/26.jpg)
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.
![Page 27: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/27.jpg)
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.
![Page 28: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/28.jpg)
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
![Page 29: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/29.jpg)
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
![Page 30: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/30.jpg)
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
![Page 31: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/31.jpg)
Some advice and encouragement on the pathway generation process
• The process can be very “fiddly.” Hang in there!
• Helpful user support: [email protected]
• 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
![Page 32: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/32.jpg)
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
![Page 33: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/33.jpg)
• Peter Karp• Suzanne Paley• Michelle Green• Joe Dale• Ron Caspi• SGD
THANKS
For help in getting CGD Pathways up and running
Contact us: [email protected]
![Page 34: CalbiCyc, Metabolic Pathways at the Candida Genome Database](https://reader034.fdocuments.net/reader034/viewer/2022051821/568157df550346895dc55f20/html5/thumbnails/34.jpg)