Tuesday, March 20, 2007

Will DOI cure what ails me?

As I mentioned on my last post, I've been busy reformatting tons of references, adapting something I've written before to satisfy a slightly different format.
Non-scientists, non-scholarly types: It's like writing that 8th grade term paper all over again, times 100. You know, the one where each of your sources for your bibliography had to be on a separate index card, and you had to get your mom to drive you to the Hackettstown Library to search (are you ready now?) the Readers' Guide to Periodical Literature for information on The Manhattan Project. I can't remember why I chose to write a term paper about the A-bomb at the tender age of 14, but a lot of what I read about for that paper still comes up.
But I digress.
The point is that reformatting references is unbelievably mundane work.
There is some computer software out there that's meant to take care of all that for you. The one I had started using is called EndNote. Endnote interfaces with Word, and it's smart enough to know that when you move text around, the numbers of your references will change if the order's been changed. It has templates for bibliographies in many different journals and can (supposedly) instantly reformat your references to a new journal.
Endnote didn't work well for me at all. I was working with a library of a couple hundred references for this review paper back in 2005. Unfortunately, I couldn't figure out a way to make the software format my references according to the specifications of the particular journal. So, once I was sure I was done shuffling text around, I switched my references to text-only and reformatted them manually, and now I'm reformatting once again.
Is there other, better software out there?
The biggest difference between now and when I was in eighth grade is the ease of access to the internet. One of the handiest technologies for keeping track of the scholarly literature is The Digital Object Identifier System, or DOI. DOI is like a homing device for a journal article, so that no matter where the content moves on the web, looking it up using a DOI locates it and retrieves it.
Recently, some Elsevier journals changed their web and old links no longer worked. If I'd set those links to the DOI of the journal article, they'd still be intact. That reminds me; I need to change my research group's "Publications" page so that everything is indexed by DOI.
What I'm wondering is whether there will come a point where DOI will become the universal reference citation standard, including in print. If that happened, I'd never have to worry about whether I should be using bold or italic font, or whether the authors' surnames come first or last, ever again. Just a simple URL would be all I'd need. However, part of me thinks that if journals (or is it the ACS Style Guidepeople?) were ever going to adopt uniform, URL-based standards, they would have done it a few years ago, at the relative "dawn" of the internet age.
What are the barriers to this, if any? Is it a content searching issue?
If you were going to pick a universal reference style, what would it be and why?



At 1:13 PM, Blogger Jonathan said...

It's a good question. Most of the barriers have been removed as far as I can tell - I think it is only a matter of time. The vast majority of scientific, technical and medical articles have DOI's assigned to them now. There's technology like eXtyles refXpress™ that resolves references in almost any format and returns the DOI (you can test it here if you like: http://www.crossref.org/freeTextQuery/ ).

If, for instance, all Publishers implemented this kind of solution into their production process (or better still into their electronic manuscript submission systems) then most references in print and online would have a DOI associated with them. This being the one common element among all the different formats, it would seem likely that DOI would then become the de facto standard reference style.

Most Publishers do have DOI's associated with article references in their online systems, although often the actual DOI is hidden behind a link that says e.g. "Full-text via CrossRef"

One of the barriers to any form of standardisation across journals is the (sometimes fierce!) independance of the Editors of those Journals. Often they have worked hard for years to build an identity for the Journal, looking for the things that set them apart from the rest. I think this is perfectly normal behaviour for well-adjusted Editors! Change comes when it is clearly seen as the right thing to do. Believe it or not, there were Editors that resisted putting their journals online at first - now it's obvious to all that it's a good idea.

DOI is there to be used!

My name is Jonathan Clark and I am the current Chair of the International DOI Federation!

At 1:14 PM, Blogger Edward said...

hi - for managing the bibliography you could try Zotero - http://www.zotero.org/ - and if you want to add DOIs to your bibliography you can use CrossRef's Simplet Text Query - http://www.crossref.org/freeTextQuery/

At 11:17 AM, Anonymous Maxine said...

We at Nature do not recommend use of EndNote in the submitted manuscript. We use a word macro called eXtyles for styling manuscripts, including references, which is not compatible with Endnote macros.

At 10:23 PM, Blogger Colst said...

It wouldn't surprise me if DOIs started to be included in bibliographies, but I can't see it replacing the rest of the reference. Most of the fields aren't necessary to find the article - journal, volume, and page number would do the job if that was the only purpose. That said, it might be nice to see DOI as an additional field.

At 3:18 PM, Blogger Joerg Kurt Wegner said...

Another option to use is

I use it since years, especially because it supports PubMed fetching and several customizable export formats. If you want to create whatsoever output format you can just use one of the HTML templates and export it using your style.

At 3:52 PM, Anonymous Anonymous said...

It's actually quite easy to change the output format in EndNote. You just have to dig through to the correct field, as EndNote allows you to edit output styles for both the bibliography in EndNote itself, as well as the format of references you insert into a document. I think my EndNote library is now up over 1100 entries. I have also never used a DOI for anything, ever, so I can't see it replacing the traditional reference format anytime soon.


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