Frequently Asked Questions


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Q1. I don’t see the Interaction Database for my organism of interest on the Agilent server. Is it still possible to perform NLP Network Discovery?

Yes, you can still perform NLP Network Discovery if you create your own Interaction Database by importing pathway files (.owl) for that organism. Follow the steps below to create your organism and import relevant pathway files:

  1. Create new pathway organism : Annotations > Create Pathway Organism.
  2. Import BioPAX (Level 2) pathways: Go to Tools > Import Pathway from File > BioPAX
  3. Select the pathway organism you created from the organism drop-down list in Step 2 of 2 of the Import BioPAX Files process.

You can now perform NLP Network Discovery in relation to your organism.

Q2. Is it possible to create NLP networks using entities and relations from pathways that I imported from WikiPathways?

The entities and relations from WikiPathways do not add to GeneSpring’s Interaction Databases. Hence, these cannot be used for NLP Network Discovery.