CalbiCyc, Metabolic Pathways at the Candida Genome Database

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CalbiCyc, Metabolic Pathways at the Candida
Genome Database

• Martha Arnaud
• arnaudm_at_genome.stanford.edu

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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

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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

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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

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Additional tools for accessing data in CGD

• Advanced Search
• Search for genes by properties

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Full-text literature search
Uses Textpresso Developed by Wormbase,
Caltech
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Sequence-related searches and tools
BLAST Pattern Match Restriction
Map Primers Genome Browser (GMODs GBrowse)
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Community Resources
Search for colleagues Browse Candida Labs
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Bulk Data Downloads
Browse list of downloadable files
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Bulk Data Downloads
Browse list of downloadable files
Downloads directory on our web site
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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
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Locus Summary Page
LSP summarizes gene information A hub that
links out to more details
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Locus Summary Page

• Gene names, aliases
• Gene description
• Mutant phenotypes
• Gene Ontology
• Chromosomal location
• Sequence retrieval
• Sequence analysis
• Genome browser
• Orthologs
• Pathways

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Locus Summary Page

• Gene names, aliases
• Gene description
• Mutant phenotypes
• Gene Ontology
• Chromosomal location
• Sequence retrieval
• Sequence analysis
• Genome browser
• Orthologs
• Pathways

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Locus Summary Page

• Gene names, aliases
• Gene description
• Mutant phenotypes
• Gene Ontology
• Chromosomal location
• Sequence retrieval
• Sequence analysis
• Genome browser
• Orthologs
• Pathways

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Locus Summary Page

• Gene names, aliases
• Gene description
• Mutant phenotypes
• Gene Ontology
• Chromosomal location
• Sequence retrieval
• Sequence analysis
• Genome browser
• Orthologs
• Pathways

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Locus Summary Page

• Gene names, aliases
• Gene description
• Mutant phenotypes
• Gene Ontology
• Chromosomal location
• Sequence retrieval
• Sequence analysis
• Genome browser
• Orthologs
• Pathways!

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Biochemical Pathways at CGD http//pathway.candid
agenome.org/

Search
List
Browse
PTools in web mode
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Biochemical Pathways at CGD

• Zoom
• Link out to SGD
• Curated pathway summary comments
• References

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PTools Prediction of pathways for CGD

• Pathologic pathway database construction
  January - April 2007
• Pathways released on our public web site March
  2008

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Curation of pathways at CGD

• 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)

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Curation of pathways, continuedCuration 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.

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Our favorite configurable Ptools options

• 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

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Some options that we find to be
usefulPathoLogic 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!
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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))

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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.
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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.
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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
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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
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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

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Some advice and encouragement on the pathway
generation process

• The process can be very fiddly. Hang in
  there!
• Helpful user support ptools-support_at_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

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The Team

• 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

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For help in getting CGD Pathways up and running
THANKS

• Peter Karp
• Suzanne Paley
• Michelle Green
• Joe Dale
• Ron Caspi
• SGD

Contact us candida-curator_at_genome.stanford.edu
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