Frequently Asked Questions
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:
- Select the pathway entities of interest in the Pathway Viewer
- Right-click over the Pathway Viewer
- Select NLP Network Discovery
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
If the entity already exists in one of the Interaction Databases, GeneSpring prevents you from adding the entity through this process. To add such an entity to the pathway, drag the symbol that represents the desired entity type in the Entity Legend into the Pathway Viewer and type the same term in the Search dialog that opens. Select the appropriate entity from the search results and click OK.
If GeneSpring does not find a match for the 'Synonym' property that you provided you can continue creating this new entity by adding as many properties as possible. For example, Entrez Gene ID, Unigene ID, and other annotations are particularly useful, as they are used for matching during Single Experiment or Multi-Omic Analysis and any of the NLP Networks workflows. The 'Synonym' property is not used for this purpose.
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.
No, it is not possible to make any modifications to an entity after it was added to the Interaction Database.
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.
If the entity of interest is not present in the search result, leave the Search dialog and use the Add entity icon in the Pathway View Toolbar to create the entity with the information you have about this new entity.