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I'd like to be able to submit a DoI or PubMed ID and find all the papers that cited that paper.

In other words, I need a publicly-available citation graph database that covers papers in PubMed.

The bottom comment on this question refers to a publicly-available citation graph: How do I get a citation dataset with full text articles in PDF format? but does not give any details of where it can be found.

Does anyone know of any such citation databases?

UPDATE: To be clear, I really need a database - not a service like Google Scholar - because I want to do it programmatically for many hundreds of thousands of articles.

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Quick and dirty version: Google Scholar

Type-in the DOI and read the citation count on the field "Cited by". Google Scholar does not filter for quality, so the citation count will include self-published papers, fake publications, etc. Expect some noise.

Better version: Web of Science

Ask your institution's librarian how you can access the Web of Science database and how to use it to retrieve the data that you need. That might require you to walk in daylight to the physical location of your library. Many survived that journey.

  • 1
    Web of Science is generally a good choice but it can sometimes be too narrow in what it includes- many quite reputable publication venues (particularly conference proceedings) are not indexed in Web of Science. Furthermore, this coverage varies across disciplines so that it is not appropriate to compare publications in different disciplines based on Web of Science citation counts. – Brian Borchers Aug 17 '15 at 12:12
  • Thanks. I know about these services, but I really meant "how do I do this programmatically for 100,000 articles" :) I've updated the question to make that clearer. – Richard Aug 17 '15 at 13:32
  • @Richard Web of Science provides downloadable data (that is in part why libraries subscribe to it), usually in the form of spreadsheets. That would suit your purpose. – Cape Code Aug 17 '15 at 13:42
  • Thank you @CapeCode! I'll look into whether this data is downloadable programmatically or only on an individual-article basis. – Richard Aug 17 '15 at 14:24
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    @Richard You might want to look into whether you also have access to Scopus - many institutions pay for both. Scopus is a little broader\less selective & the interface may be easier for what you're trying to do. – Andrew Aug 17 '15 at 16:26
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The graph you are looking for is not easy to get and therefore probably not publicly available for free. Certain firms have specialized in making this data available (e.g. Thomson Reuters "Web of Science, Google Scholar). To protect their asset it seems likely that they will not let you download their databases or query it in such large quantities.

In a way, their business model depends on making this hard to access, for if you could download the whole database, you could offer the same service for a lower price.

Maybe even their terms of use forbid too unstructured or too large queries.

  • 1. This is not an answer to the question but possibly a comment on my answer. 2. the business model depends on how they gather the information and compile it, not giving away your product for free is the basic of every viable commercial company. 3. Anybody is free to start a business of collecting article metrics, serious competition will be welcome by the consumers (our institutions). – Cape Code Aug 17 '15 at 15:09
  • 1) I addressed this in a revision of the answer. 2) The question is: What is the product. Google Scholar is free to use so in a way they are giving that data away for free. 3) Sure, but how is that relevant? – Thomas Kahle Aug 17 '15 at 19:31
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    Obtaining a license for working with a full local copy / download of WoS is possible (though redistribution is not for understandable reasons...). – tsttst Oct 10 '16 at 15:08
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As for doing this programmatically, there are two options. Daniele Rotolo has written an R-script (MedlineR) that will allow to download Web of Science (WoS) information from PMIDs, if your institution provides IP-access to WoS. See: http://www.ncbi.nlm.nih.gov/pubmed/15284107 However, there are some issues with this program - it occassionally crashes after fetching ≈1,000 records.

The other (better) option requires your institution to subscribe to Thomson Reuters Web Services Expanded, which will allow you to use a SOAP API to search WoS and download relevant fields. This also includes cited reference searches. If you can confirm that your institution has such an access, I will be glad to share my own (simple) PHP SOAP call for matching PMID against WoS accession numbers (UT).

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I know of two freely available datasets which might be interesting for you:

For both of them, expect some noise in the extracted citations.

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Europe PMC provides a freely available citation graph for papers indexed in PubMed (I work for Europe PMC). You can access it programmatically using citation module of the Articles RESTful API.

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