I am conducting a meta-analysis and searching pertinent articles in PubMed. The typical scenario is to apply a dedicated search string, and then retrieve between 50 and 5000 citations including the abstract.

Citations, abstracts and ancillary details (eg PMID) can be extracted from PubMed but only as text. Some softwares can support data extraction, such as Zotero or Reference Manager, but they are apparently inefficient or costly.

Is there any more suitable alternative, still free?

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    Be careful, mass extraction of data may be against of TOS of the given service.
    – Greg
    Feb 9, 2017 at 11:24
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    If your university library has an bibliometrics division, you could ask for assistance there. They know what is possible, how it has to be done and how not to violate any license agreements. Feb 9, 2017 at 16:03
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    What do you mean that "Citations, abstracts and ancillary details (eg PMID) can be extracted from PubMed but only as text." Other than text, what are you hoping for alternative software to extract? And what exactly is the "inefficient" problem with Zotero? I'm really not clear what you're asking.
    – Tripartio
    Feb 9, 2017 at 19:24
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    Have you checked the FTP dump from NLM? It's not clear what you want other than text but these files are in XML format with tags for different fields. Will that help?
    – syntonicC
    Feb 11, 2017 at 3:17
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    You might try softwarerec reoommendations SE. // A brute force method I have used (but I was working with a smaller set that PubMed) is to bulk download a very large set of PDFs and then hit the folder with FileLocatorLite. Feb 23, 2017 at 5:17

1 Answer 1


Covidence is free for students. Other software includes DistillerSR. All of these will aid with citation management a step up from what can be done with EndNote, Mendeley, Zotero, etc.

Also, I hope you've searched databases beyond PubMed. Great tool, but alone not sufficient for an SR.

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