Searching PubMed Programmatically

Earlier this semester, we taught a workshop on how to use the NCBI Entrez Direct (EDirect) [1] tool to search and compile PubMed and related data from a Unix Shell. EDirect is a great tool and has an approachable learning curve. You may consider using EDirect if, for example, you would like to compile custom bibliographic datasets, perform many searches, or discover related linked data.

All of our workshop materials including code and slides are openly available on GitHub:

Check it out and let us know if you have any questions. We would be happy to help you.


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