Question: Importing A Large Number Of References From Text
6
gravatar for Chris Miller
6.3 years ago by
Chris Miller17k
Washington University in St. Louis, MO
Chris Miller17k wrote:

Does anyone know of a reference manager that can do some kind of smart auto-import? I've got the text of a paper, with nicely formatted references at the end. What I'd like to do is import all of them into a reference manager as easily as possible.

Ultimately, I'd like the data to end up in Zotero, but once it's in any ref manager, I can export it and move it over easily enough.

Example reference:

Campbell, P.J., Stephens, P.J., Pleasance, E.D., O'Meara, S., Li, H., Santarius, T., Stebbings, L.A., Leroy, C., Edkins, S., Hardy, C., et al.(2008) Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat. Genet. 40:722–729.

There are no DOIs or PMIDs to parse out, just authors, title, year, page #s and journal.

I'm also open to something that can do this programatically (preferably without writing hairy regexen on my own). Using one of the Bio* packages to query pubmed maybe?

reference text pubmed • 2.5k views
ADD COMMENTlink modified 6.2 years ago by Andra Waagmeester3.2k • written 6.3 years ago by Chris Miller17k

FWIW, we're discussing this on FriendFeed too: http://friendfeed.com/the-life-scientists/3b3c2b06/does-anyone-know-of-reference-manager-that-can

ADD REPLYlink modified 2.9 years ago by Istvan Albert ♦♦ 70k • written 6.3 years ago by Chris Miller17k

Does your university have access to scopus?

ADD REPLYlink written 6.3 years ago by Michael Schubert6.6k

It appears that I may have access through the library. Any links showing how it might be used for this sort of thing? (I've never touched scopus before)

ADD REPLYlink written 6.3 years ago by Chris Miller17k

Semi-solution here: http://chrisamiller.com/science/2010/12/13/using-bioruby-to-fetch-citations-from-pubmed/ (via Martin in the above-linked FF thread). I'd still love to hear any real solutions to this problem, that could handle articles that aren't in PubMed Central.

ADD REPLYlink modified 2.9 years ago by Istvan Albert ♦♦ 70k • written 6.3 years ago by Chris Miller17k
5
gravatar for Michael Schubert
6.3 years ago by
Cambridge, UK
Michael Schubert6.6k wrote:

Using Scopus:

  1. Go to the Scopus homepage (you may need to login via your library website) and search for the article you want to extract references from
  2. Scroll down to References, click on "Page" and then "Export", choose your format, done :-)
ADD COMMENTlink written 6.3 years ago by Michael Schubert6.6k

Thanks, Michael. That's a nice clean solution. For those who are interested, there are several alternate solutions discussed in the friendfeed link above.

ADD REPLYlink written 6.3 years ago by Chris Miller17k
1
gravatar for Jorge Amigo
6.2 years ago by
Jorge Amigo9.5k
Santiago de Compostela, Spain
Jorge Amigo9.5k wrote:

the Scopus option would be great... if you have access to Scopus. I know it is a non-free option, but I've been using EndNote for years with magnific results. the integrated search it has is very powerful, since it allows defining any filters you may need, and the database of searcheable resources inside it is just enormous. it even allows integrating your ISI WoK or WoS account and search through it, giving you the option of downloading the associated PDF for a paper and storing it along with the reference itself, all only a couple of clics away. but I understand that you would like to do this programmaticaly, and not 1 by 1, because if not even Zotero would be enough since you could search single references on PubMed (which is freely accessible) and then press the "save to Zotero" icon that appears next to the URL. if so, here are some ideas:

  1. google scholar has a "reference manager" section on its preferences, which allows displaying a "import to" button next to references displayed. currently available formats are bibtex, endnote, refman, refworks and wenxianwang, whatever this last one means.
  2. similarly to Scopus, if you have access to ISI WoK and the paper you are dealing with is indexed there, you should be able to see a "references" section on the right panel, and if you follow the link you would end up with all the references listed. it isn't a one-click-option as in Scopus, but you could browse them individually and download their citations using the "save to" buttons.
  3. I have seen in certain journals (I think they were part of the Springer Verlag editing group) that they have an "export list of refereces" button on the web, which eventually would allow you to download all the references on a particular paper in a useful format (endnote, refworks, ...). I have tested with a paper of mine, and it allows downloading its references for procite, bibtex, endnote, reference manager, pubmed, refworks and bookends.

unfortunately, generally speaking, I've never been able to find out how to do it as anyone would like to. I mean that it would be great if I could copy/paste the references list of a particular paper and that my reference manager would detect them all. I would definitely thank anyone who suggest any viable option... for the non Scopus users ;)

ADD COMMENTlink written 6.2 years ago by Jorge Amigo9.5k
1
gravatar for Andra Waagmeester
6.1 years ago by
Maastricht, the Netherlands
Andra Waagmeester3.2k wrote:

HubMed Citation Finder will be your friend: http://www.hubmed.org/citation.htm

I have tried your example reference. It choked on the ' in O'Meara, but after editing I was able to find: http://www.hubmed.org/display.cgi?uids=18438408

Regards

ADD COMMENTlink written 6.1 years ago by Andra Waagmeester3.2k
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