Submitting%20pathway%20to%20MetaCyc

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Submitting pathway to MetaCyc

• Ron Caspi

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Why Curate a PGDB?

• A well curated PGDB can serve as a central online
  resource that integrates many types of
  information about an organism
• Novel pathways from organism-specific PGDBs can
  be imported into MetaCyc, where they improve the
  quality of all future PGDBs
• requires modest resources- a part time curator is
  all it takes. A pathway can be researched and
  curated in as little as a day or two, although
  complicated pathways take much longer. Raise
  funding for a curation project!

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What Exactly is Curation?

• Correction of false-positive and false-negative
  predictions
• Incorporation of information from experimental
  literature
• Authoring of comments and citations
• Ongoing updating and refinement of a PGDB
• Gene positions, names, synonyms
• Protein functions, activators, inhibitors,
  reactions catalyzed
• Addition of new pathways, modification of
  existing pathways
• Defining TF binding sites, promoters, control of
  transcription initiation
• Updating database fields

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Overview of Creating a Pathway

• Identify the reactions in the pathway, and look
  up the EC numbers (if applicable)
• Find the individual reactions in the
  PGDB/MetaCyc, and create new reactions if
  necessary. You may need to create new compounds
  as well
• Compose the pathway from the individual reactions
  using the pathway editor
• Add commentary and citations
• Assign the appropriate enzymes, create complexes
  when appropriate.
• Curate full information for enzymes and genes.
• QA make sure that the pathway has an associated
  class, and that every enzyme (and the pathway)
  has an evidence code.

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Run the Consistency Checker

• The Consistency Checker finds data errors and
  inconsistencies that you would have never
  suspected to exist in your PGDB. It is very
  important to run it and fix the errors that it
  finds.
• Running the Consistency Checker is like changing
  the oil in your car!

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Create and Use Author and Organization Frames
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Add Pathway Evidence Codes
Experimental evidence codes IDA inferred from
direct assay IEP inferred from expression
pattern IPI inferred from physical
interaction TAS traceable author statement IGI
inferred from genetic interaction IMP inferred
from mutant phenotype
Evidence Codes Definition http//bioinformatics.
ai.sri.com/evidence-ontology/
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Add Literature References
If a PubMed ID exists enter it in the citation
box. This saves you work, and will provide
hyperlinks to the PubMed abstract pages. If
there is no PubMed ID, use the format Smith89
PubMed references need to be imported manually
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Add Pathway Summaries

• Add any comments that are appropriate for the
  pathway
• Do not add comments about a specific enzyme or
  reaction in here
• Use the CITS button for literature citations
• You can embed web hyperlinks in the text (use the
  Hyperlink button)
• You can refer to other objects in the database by
  generating internal hyperlinks to these objects
• (FRAME button)

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Use Internal Hyperlinks
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Specify Enzyme Complexes
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Use Enzymatic Activity and/or Enzyme Names
Correctly

• In some cases the two names are different
• Example for the enzymes pyruvate kinase I and
  pyruvate kinase II, the enzymatic activity name
  is pyruvate kinase

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Example for a Submitted Pathway
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Submit Your Pathways to MetaCyc

• Right-click on the pathway name, and choose Edit
  - Add pathway to File Export List
• Click on the File menu, and choose Export -
  Selected Pathways to Lisp-Format File
• email the file to biocyc-support_at_ai.sri.com, or
  to any curator.