SRI International Bioinformatics 1 Submitting pathway to MetaCyc Ron Caspi.

SRI International Bioinformatics1

Submitting pathway to MetaCyc

Ron Caspi

2 SRI International Bioinformatics

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!


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


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.


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!


Create and Use Author and Organization Frames


Add Pathway Evidence Codes

Evidence Codes Definition: http://bioinformatics.ai.sri.com/evidence-ontology/

Experimental evidence codes:

IDA: inferred from direct assayIEP: inferred from expression patternIPI: inferred from physical interactionTAS: traceable author statementIGI: inferred from genetic interactionIMP: inferred from mutant phenotype


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 importedmanually


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)


Use Internal Hyperlinks


Specify Enzyme Complexes


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”


Example for a Submitted Pathway


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 [email protected], or to any curator.

SRI International Bioinformatics 1 Submitting pathway to MetaCyc Ron Caspi.

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