Preferences: PubMed

This dialog box appears when you choose the Tools > Preferences command from the main menu and go to the PubMed tab. It allows you to edit a number of settings that affect the way Publish or Perish deals with queries to PubMed.


This box contains general options relating to the way Publish or Perish issues queries to PubMed.

Option Description
Go to the NCBI web site Click this button to open the NCBI web page in your browser, where you can request an PubMed API key that allows higher data limits.
API key

Enter the PubMed API key that Publish or Perish should use when submitting queries to the PubMed server. You only need this if you expect to exceed the default data allowance that NCBI provides.

Maximum number of results per search Set the maximum number of results that Publish or Perish will request per search. The default value is usually the maximum that the data source allows for API access; you may enter a lower value if you are typically only interested in the most relevant results to your search.
Keep cached results
for <n> days

Enter the number of days to keep the query results from queries. The longer this period, the fewer accesses are required to satisfy repeated queries. Any updates in the query results only become visible after the cache period has expired, so you don't want to make this period too long.


Click this button to reset all fields to their "factory" defaults. This is useful if you have made changes, but decide to start from a known base again.

Note: The API key field is not reset by this command.

Clear cache Click this button to clear the entire results cache. This forces subsequent queries to access PubMed directly, which might be useful after a (suspected) update on PubMed, or if you have reason to believe that the cached results are somehow invalid.