Q5. How can I find out if an entity that I would like to add to my pathway already exists in one of the GeneSpring Interaction Databases?
To find out if an entity is already present in an Interaction Database, drag the symbol that represents the desired entity type in the Entity Legend into the Pathway Viewer and type the term by which this entity is most commonly referred to in the Search dialog that opens. The search results will display all the matching entities GeneSpring found in the Interaction Databases.
If the search result contains the entity you would like to add to the pathway, select the corresponding row and click OK.
Q4. Is it possible to modify an entity (change the name, add annotation information, aliases, etc.) after it was added to the Interaction Database?
No, it is not possible to make any modifications to an entity after it was added to the Interaction Database.
Q3. Is it possible to query the pathways created using the 'Create New Pathway' feature in future during Single Experiment or Multi-Omic Analysis?
Yes, you can query such pathways. They are identified as Hand created pathways in Step 1 of 4 of an SEA or MOA and can be selected under Curated pathways.
Q2. What are the mandatory requirements when adding new entities to a pathway?
When adding a new entity to a pathway with the Add entity icon, either while creating a new pathway or during one of the NLP Networks workflows, the only required property is 'Synonym'. GeneSpring uses this property to search the appropriate Interaction Databases for a match
Q1. Can I use entities from existing pathways for NLP Network Discovery?
Yes, GeneSpring allows you to run NLP Network Discovery on entities that were selected in the Pathway Viewer or the Heatmap table of an open pathway list. This workflow will result in a new pathway. The identified interactions will not be added to the existing pathway. To use this feature, follow these steps:
