Sonny Software

Recently I have started creating new references by dragging a .pdf file into an empty reference, tick the "import reference from Pubmed...", "rename" and "move to attachment folder".

Now it all works very well (if there's a DOI obviously), but the only problem is that when this new reference is created an empty one is created as well. If I create 10 new references using this method, I end up with 10 of the correct ones, but also 10 empty ones that I will have to delete manually.

Is there any way to do this more efficiently? Maybe include a "make reference from .pdf file" menu or something like that?

As always - thanks for a great program - I really like version 10 a lot

You're doing it wrong. You drag the pdf onto the list view and it creates the new reference for you. It won't remove any reference you created (empty or not).

Jon
Sonny Software

When I drop the icon from a pdf file containing a doi onto the list view, it invariably asks if I want the file to be attached to the selected record. Presumably if no record were selected, it might ask if I want to create a new reference. However, I have not been able to figure out how to unselect a record without selecting another one.

If Bookends can identify the doi, you'll see a checkbox called

Import reference from PubMed and then attach

If you don't see this, it means either

1. You don't have "Check to see if the reference is available form PubMed" enabled in preferences, or

2. Bookends can't find the doi in the pdf, or

3. The reference isn't on PubMed.

Jon
Sonny Software

So you're saying that it shouldn't matter if a reference is selected or not; if the preference is set and the article is listed on pubmed, I should always see the option to "import reference from Pubmed and then attach" if bookends can decode the doi from the pdf.

I've tried this with several articles from well-known medical journals, which have the doi prominently displayed on the front page and findable (at least with Preview), but without success.

Perhaps you could send me a pdf that is known to work.

Thanks for your help.

Henry

Sure. Contact me directly and I'll send you one. I just tried a download from Immunity, and that worked, so you might try that.

Jon
Sonny Software

P.S. Several well known journals, like PNAS and JEM, don't provide the dois in format that be found. I've dealt with the publisher, and they are not interested in a "software issue".

We've been able to work around the problems with PNAS pdf files, and in the next Bookends update you'll be able to attach these and have Bookends retrieve the citation information automatically. Still working on JEM...

Jon
Sonny Software

Thank you for the help!

Henry

The next Bookends update will be able to work with pdfs from more journals, including J Exp Med. If you have examples of pdfs from other journals where Bookends doesn't pick up the doi, you can send them to me and I'll see if it can be remedied.

Jon
Sonny Software

Would it be possible to do this with JSTOR articles too?

Shayne

I haven't looked into that, but I'd think it's unlikely. Do pdfs downloaded from JSTOR include doi's?

Jon
Sonny Software

Jon wrote:I haven't looked into that, but I'd think it's unlikely. Do pdfs downloaded from JSTOR include doi's?

I don't see them in any articles that I use (all in philosophy). I do see, however, that several publishers/repositories do include them (at least in the cases I've examined):

-Cambridge Journals (e.g., Medieval Philosophy and Theology)
-Oxford Journals (e.g., Mind)
-Springer (e.g., Synthese)
-Informaworld (e.g., British Journal for the History of Philosophy)

Perhaps there's a way to make these work, or do they already, since there are probably science journals published by these vendors?

If it would help, I can send you sample PDFs.

Hi,

You can send me one pdf and I'll look.

But getting the doi is just the beginning. JSTOR must be able to retrieve references by doi. Can it?

Jon
Sonny Software

Jon wrote:But getting the doi is just the beginning. JSTOR must be able to retrieve references by doi. Can it?

Sorry, I wasn't at all clear. I ran together two different ideas without differentiating. That's why mind-reading would be so useful.

JSTOR doesn't show any DOI on articles, as far as I can tell, although I don't have a lot of recent JSTOR articles. (Newer philosophy articles are stored at the journal publishers; JSTOR only has older stuff, and I don't know when DOI's started to become commonplace.) So I was dismissing the possibility of using JSTOR via DOI info.

I was suggesting that the other publishers (Cambridge, Oxford, Informaworld, Springer) be set up to use the DOI info that they include in their articles.

JDB

Hi,

I see. But what is the PubMed equivalent, then, that would allow you to look up the reference information (author, title, etc.) based on the doi and get it back in an intelligible form?

Jon
Sonny Software