[BioNLP] Citation information

Dazhi Jiao dazhi.jiao at gmail.com
Wed Oct 21 08:07:49 EDT 2009

This blog post is about getting citation information from scopus and
web of X. I've never tested it myself, but it seems promising.



Dazhi Jiao
PhD Candidate in Chemical Informatics
Indiana University School of Informatics

On Mon, Oct 19, 2009 at 1:40 PM, Heather Piwowar <hpiwowar at gmail.com> wrote:
> Three ideas for getting citation information:
> 1.
> Publish Or Perish is software that extracts and analyzes citation
> information from Google Scholar:
> http://www.harzing.com/pop.htm
> 2.
> Many bibliometrics scholars do their data collection by manually saving web
> pages containing citation result listings from ISI Web of Science (not
> free), Scopus (not free) or Google Scholar (free) and then write scripts to
> extract the info from them.  The manual saving of full web pages actually
> doesn't take as long as you might think, and can be done while you watch
> your favourite videos :)
> I have code I'd be happy to share if you are interested.
> 3.
> Another GREAT and underused source of citation information, depending on
> your needs, is PubMed Central.
> Free, open, programmatic access to lists of all PubMed papers cited by any
> paper in PubMed Central.  Admittedly this limits the set in two ways (the
> cited papers need to have a PubMed ID, and the citing papers need to be in
> PubMed Central), but it can nonetheless be sufficient for many projects.
> Especially true as the number of papers in PubMed Central continues to
> rise.  It also sets you up to filter the lists in all sorts of powerful
> ways, using the other Entrez tools.
> eLink is the key to programmatic access for citations:
> http://www.ncbi.nlm.nih.gov/corehtml/query/static/elink_help.html
> http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html#UserSystemRequirements
> For example, this URL returns a list of all five PubMed Central IDs that
> cite PubMed article ID 17375194 :
> http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=17375194&db=pmc
> This is the same list you see on the lower right "Cited by" list on the main
> PubMed page for the article:
> http://www.ncbi.nlm.nih.gov/pubmed/17375194
> I've done quite a bit of this sort of PubMed Central data extraction in
> Python.  I've been using an updated version of the EUtils python library and
> have some home-spun code as well (to be open source, but I haven't posted it
> yet).  If you are interested in more info or the code I've been using, let
> me know and I'd be glad to help (though with a bit of lag time, since I'm in
> the midst of moving to Vancouver Canada this week and am surrounded by
> moving boxes! )
> Hope that helps someone.
> Heather Piwowar
> doctoral candidate
> Dept of Biomedical Informatics
> University of Pittsburgh
> _______________________________________________
> BioNLP mailing list
> BioNLP at lists.ccs.neu.edu
> https://lists.ccs.neu.edu/bin/listinfo/bionlp
> The BioNLP website: http://www.bionlp.org

More information about the BioNLP mailing list