Q2. How can I import pathways from BioCyc in GeneSpring?

Submitted by maria_2 on Thu, 2013-05-30 16:04

To import pathways from BioCyc (www.biocyc.org) in GeneSpring, follow these steps:

Q7. I was able to import pathways earlier. However, if I try to import pathways now, I am asked to download the organism’s Interaction Database. Is there a way to skip this?

Submitted by bandana on Thu, 2012-02-16 20:52

Only GPML and BioPax Level 3 pathways can be imported into GeneSpring without the organism’s Interaction Database. However, to import and work with any other file format, the common as well as the organism specific Interaction Databases are required.

Q6. GeneSpring indicates that it has found duplicate pathways. What are my options to resolve these duplicates?

Submitted by bandana on Thu, 2012-02-16 20:50

When importing pathways in the GPML format, GeneSpring identifies duplicate pathways based on pathway name, organism and pathway provider. If duplicate pathways are found, the Resolve Duplicates dialog gives you the choice to

  • rename any of the pathways identified as duplicate and import them,
  • overwrite the existing pathway with the new pathway,
  • ignore duplicate pathways and not import them at all.

 

Q5. If I delete pathways from Update Pathway dialog, will it delete pathways from my experiment as well?

Submitted by bandana on Thu, 2012-02-16 20:48

Yes, deleting a pathway in the Update Pathway dialog will delete the pathway from any experiment it is saved in, as it is permanently deleted from the GeneSpring database.

Q4. How can I update pathways?

Submitted by bandana on Thu, 2012-02-16 20:39

Every time you update an Interaction Database in GeneSpring, the Update Pathways dialog opens automatically. This dialog allows you to choose which of the pathways that you previously imported into GeneSpring (non-GPML format only) you would like to update or delete based on the new information recorded in the updated Interaction Database. For each pathway the Update Pathways dialog displays updated entities and obsolete entities.

Q3. Which pathway files can be imported into GeneSpring?

Submitted by bandana on Thu, 2012-02-16 20:35

GeneSpring supports the import of pathways from the WikiPathways portal (directly in GeneSpring or as GPML files that were previously downloaded from the portal, also see Q1. How can I import pathways from WikiPathways in GeneSpring?). You can also import pathways from BioCyc directly in GeneSpring (see Q2.

Q1. How can I import pathways from WikiPathways in GeneSpring?

Submitted by bandana on Thu, 2012-02-16 20:30

To import pathways from WikiPathways, follow these steps:

  • Go to Tools > Import pathways from WikiPathways
  • Select the organism for which you wish to download the pathways
  • The drop-down list consists of the organisms for which pathways are available for download from the WikiPathways portal (www.wikipathways.org)

If you have downloaded pathways from WikiPathways in the GPML format outside GeneSpring, then you can import these pathways by following these steps:

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