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Useful items from this FAQ will eventually be integrated into the main user's guide, but this page can be a useful place to check in if your question isn't in the guide at the moment...
- My ontology has way too many roots! Why? - There 3 major causes for this problem:
- Cross products - Are there many cross products in this ontology? In a perfectly non-redundant ontology, all cross-product terms will appear to be roots unless the reasoner is turned on. When the reasoner is enabled, the cross-product terms will be placed in the graph correctly. The internal editors version of the Sequence Ontology works this way, for example. If this is the problem, turn on the reasoner.
- Transitivity - By default, OBO-Edit doesn't show non-transitive relationships in the Ontology Editor. If a term is connected to its parents only by non-transitive links, it will appear to be an orphan. To solve this problem, first check to make sure that all transitive relationships are really marked as transitive relationships. If there are still orphans after you've done that, the ideal course would be to edit your ontology and guarantee that all terms have a complete is_a path to the root (otherwise your ontology is technically incorrect). If you're happy with a broken ontology and just want to change the display, open the Global Filters plugin. Select the Link Filter that contains the condition "Link Self NOT Is Transitive" and delete that condition.
- Old Filters - You've accidentally left a filter on from the previous session - I've done this many times!