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Slow or "hung" at startup
After launching Phenex, Java can sometimes be a little slow to start up. If you're running Java 6 or later, you should see a splash screen image shortly after launching. This is followed by a panel informing you that Phenex is checking for ontology updates. If you have not run Phenex before, your computer needs to be online in order for Phenex to download the required ontologies. If you have run Phenex before, Phenex will check for the availability of a newer version of each ontology and download it if necessary. It is okay to work offline if Phenex has previously had a chance to download the ontologies. Phenex performs a check for ontology updates each time it is launched.
Removing Corrupted Ontology Files
Local copies of ontology files can become corrupted, causing Phenex to display a warning about "dangling" terms on start-up. Note that the warning about danglers can also indicate a valid ontology change related to merging of terms from a recent ontology update.
To remove local copies of ontologies from your Phenex directory, delete all files within the “Ontology Cache” folder on your computer. This folder can be found within the Phenex settings folder.
Phenex will then download new copies of the ontology files on startup.