How to programmatically get references/citations of an article?
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7.9 years ago
samad.lotia ▴ 20

I have a list of articles, including their PubMed IDs. I would like to programmatically retrieve the citations of a given article through a web service.

PubMed comes close, but only gives me a list of articles that cite a given article. (This is the opposite direction I want to go.) It can also give me a list of related articles, but this isn't what I'm interested in.

Thomson Reuters' Web of Science website comes close, but when I try to use their web service, I get this error: "The Web Service (version 2.0) has been retired permanently." Moreover, when I try to look at their web services page, I get a 404.

literature mining articles • 3.0k views
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did you get "Thomson Reuters' Web of Science" working? I cant get passed the authentication version error as well

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7.9 years ago
5heikki 10k

Sounds like a job for Entrez Direct

In the documentation there are some citation examples. If your list is big, then you probably need to write a small while read line script.

edit. Do you mean something like references of this?

esearch -db pubmed -query 24987404 | elink -related -name pubmed_pubmed_refs | efetch -mode text

..

            <Link>
                <Name>pubmed_pubmed_refs</Name>
                <Menu>References for PMC Articles</Menu>
                <Description>Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.</Description>
                <DbTo>pubmed</DbTo>
            </Link>

..
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In my question above, I mention "PubMed", but I meant to write "Entrez Direct". From my understanding, Entrez Direct does not give me the list of references of a given article. It gives me related articles and articles that were cite a given article, neither of which is what is needed.

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I edited the answer.

einfo -db pubmed

AFAIK prints everything you can connect to a PubMed ID

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