You can add PubMed references to your EndNote Library by using the PubMed search tool within EndNote.
Important disadvantage: Note that the search will run differently than searching keywords on the PubMed database and may not get the same results. This is because EndNote cannot recreate how PubMed does "automatic term mapping" which makes the search terms "heart attack" also pull up articles referring to "myocardial infarction" as well. EndNote would simply pull up articles that refer to "heart attack."
These instructions are based on EndNote 20:
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