Macs in Chemistry

Insanely Great Science

Scripting PubMed searches

 

PubMed comprises more than 24 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. They also provide a number of programming tools that allow access to the information, E-utilities are a set of server-side programs that provide a stable interface into the Entrez query and database system.

To access these data, a piece of software first posts an E-utility URL to NCBI, then retrieves the results of this posting, after which it processes the data as required. The software can thus use any computer language that can send a URL to the E-utilities server and interpret the XML response; examples of such languages are Perl, Python, Java, and C++.

A while back I wrote a vortex script that helps with these sort of searches if you have multiple terms you want to search. I've updated this script to incorporate the changes requiring api keys to allow multiple requests to the E-utilities api, and I've highlighted where you need to add your own api key in the script. I've also tried to ensure that any query string should be encoded to make it URL safe.

The update is detailed more fully here….

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