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November 28, 2011

Turning DOIs into formatted citations

Today two new content types were added to dx.doi.org resolution for CrossRef DOIs. These allow anyone to retrieve DOI bibliographic metadata as formatted bibliographic entries. To perform the formatting we're using the citation style language processor, citeproc-js which supports a shed load of citation styles and locales. In fact, all the styles and locales found in the CSL repositories, including many common styles such as bibtex, apa, ieee, harvard, vancouver and chicago are supported.

First off, if you'd like to try citation formatting without using content negotiation, there's a simple web UI that allows input of a DOI, style and locale selection.

If you're more into accessing the web via your favorite programming language, have a look at these content negotiation curl examples. To make a request for the new "text/bibliography" content type:

$ curl -LH "Accept: text/bibliography; style=bibtex" http://dx.doi.org/10.1038/nrd842

@article{Atkins_Gershell_2002, title={From the analyst's couch: Selective anticancer drugs}, volume={1}, DOI={10.1038/nrd842}, number={7}, journal={Nature Reviews Drug Discovery}, author={Atkins, Joshua H. and Gershell, Leland J.}, year={2002}, month={Jul}, pages={491-492}}

A locale can be specified with the "locale" content type parameter, like this:

$ curl -LH "Accept: text/bibliography; style=mla; locale=fr-FR" http://dx.doi.org/10.1038/nrd842

Atkins, Joshua H., et Leland J. Gershell. « From the analyst's couch: Selective anticancer drugs ». Nature Reviews Drug Discovery 1.7 (2002): 491-492.

You may want to process metadata through CSL yourself. For this use case, there's another new content type, "application/citeproc+json" that returns metadata in a citeproc-friendly JSON form:

$ curl -LH "Accept: application/citeproc+json" http://dx.doi.org/10.1038/nrd842

{"volume":"1","issue":"7","DOI":"10.1038/nrd842","title":"From the analyst's couch: Selective anticancer drugs","container-title":"Nature Reviews Drug Discovery","issued":{"date-parts":[[2002,7]]},"author":[{"family":"Atkins","given":"Joshua H."},{"family":"Gershell","given":"Leland J."}],"page":"491-492","type":"article-journal"}

Finally, to retrieve lists of supported styles and locales, either hit these URLs:

or check out the CSL style and locale repositories.

There's one big caveat to all this. The CSL processor will do its best with CrossRef metadata which can unfortunately be quite patchy at times. There may be pieces of metadata missing, inaccurate metadata or even metadata items stored under the wrong field, all resulting in odd-looking formatted citations. Most of the time, though, it works.

March 20, 2009

Citation Typing Ontology

I was happy to read David Shotton's recent Learned Publishing article, Semantic Publishing: The Coming Revolution in scientific journal publishing, and see that he and his team have drafted a Citation Typing Ontology.*

Anybody who has seen me speak at conferences knows that I often like to proselytize about the concept of the "typed link", a notion that hypertext pioneer, Randy Trigg, discussed extensively in his 1983 Ph.D. thesis.. Basically, Trigg points out something that should be fairly obvious- a citation (i.e. "a link") is not always a "vote" in favor of the thing being cited.

In fact, there are all sorts of reasons that an author might want to cite something. They might be elaborating on the item cited, they might be critiquing the item cited, they might even be trying to refute the item cited (For an exhaustive and entertaining survey of the use and abuse of citations in the humanities, Anthony Grafton's, The Footnote: A Curious History, is a rich source of examples)

Unfortunately, the naive assumption that a citation is tantamount to a vote of confidence has become inshrined in everything from the way in which we measure scholarly reputation, to the way in which we fund universities and the way in which search engines rank their results. The distorting affect of this assumption is profound. If nothing else, it leads to a perverse situation in which people will often discuss books, articles, and blog postings that they disagree with without actually citing the relevant content, just so that they can avoid inadvertently conferring "wuffie" on the item being discussed. This can't be right.

Having said that, there has been a half-hearted attempt to introduce a gross level of link typology with the introduction of the "nofollow" link attribute- an initiative started by Google in order to try to address the increasing problem of "Spamdexing". But this is a pretty ham-fisted form of link typing- particularly in the way it is implemented by the Wikipedia where CrossRef DOI links to formally published scholarly literature have a "nofollow" attribute attached to them but, inexplicably, items with a PMID are not so hobbled (view the HTML source of this page, for example). Essentially, this means that, the Wikipedia is a black-hole of reputation. That is, it absorbs reputation (through links too the Wikipedia), but it doesn't let reputation back out again. Hell, I feel dirty for even linking to it here ;-).

Anyway, scholarly publishers should certainly read Shotton's article because it is full of good, and practical ideas about what can can be done with today's technology in order to help us move beyond the "digital incunabula" that the industry is currently churning out. The sample semantic article that Shotton's team created is inspirational and I particularly encourage people to look at the source file for the ontology-enhanced bibliography which reveals just how much more useful metadata can be associated with the humble citation.

And now I wonder whether CiteULike, Connotea, 2Collab or Zotero will consider adding support for the CItation Typing Ontology into their respective services?


* Disclosure:

a) I am on the editorial board of Learned Publishing
b) CrossRef has consulted with David Shotton on the subject of semantically enhancing journal articles

December 3, 2008

Ubiquity commands for CrossRef services

So the other day Noel O'Boyle made me feel guilty when he pinged me and asked about the possibility using one of the CrossRef APIs for creating a Ubiquity extension. You see, I had played with the idea myself and had not gotten around to doing much about it. This seemed inexcusable- particularly given how easy it is to build such extensions using the API we developed for the WordPress and Moveable Type plugins that we announced earlier in the year. So I dug up my half-finished code, cleaned it up a bit and have posted the results.

Note that the back-end that supports the plugins has been moved to more stable machines and the index is now being automatically updated with journal and conference proceeding deposits (sorry, no books yet).

Also note that we are hoping that others will look at the code for the WordPress, Moveable Type and Ubiquity plugins and create more such extensions. If you do, please let us know about them at citation-plugin@crossref.org.

February 9, 2008

CrossRef Citation Plugin (for WordPress)

OK, after a number of delays due to everything from indexing slowness to router problems, I'm happy to say that the first public beta of our WordPress citation plugin is available for download via SourceForge. A Movable Type version is in the works.

And congratulations to Trey at OpenHelix who became laudably impatient, found the SourceForge entry for the plugin back on February 8th and seems to have been testing it since. He has a nice description of how it works (along with screenshots), so I won't repeat the effort here.

Having said that, I do include the text of the README after the jump. Please have a look at it before you install, because it might save you some mystification.

Continue reading "CrossRef Citation Plugin (for WordPress)" »

January 15, 2008

CLADDIER Final Report

I just ran across the final report from the CLADDIER project. CLADDIER comes from the JISC and stands for "CITATION, LOCATION, And DEPOSITION IN DISCIPLINE & INSTITUTIONAL REPOSITORIES". I suspect JISC has an entire department dedicated to creating impossible acronyms (the JISC Acronym Preparation Executive?)

Anyhoo- the report describes a distributed citation location and updating service based on the linkback mechanism that is widely used in the blogging community.

I think this is an interesting approach and is one that I talked about briefly (PDF) at the UKSG's Measure for Measure seminar last June. I think that, like most proponents of p2p distributed architectures, they massively underestimate the problem of trust in the network. They fully knowledge the problem of linkback spam, but their hand-wavy-solution(tm) of using whitelists just means the system effectively becomes semi-centralized again (you have to have trusted keepers of the whitelists).

And of course I was mildly exasperated by the report's characterization of one of the perceived "disadvantages" of the CrossRef architectural model being a :

"Centralised service hosting a large persistent store – with the need for a (possibly commercial) business model to justify providing the service."

Though DOI registries like Bowker and Nielsen Bookdata are commercial, CrossRef, the organization that services the industry that the JISC is concerned with, is *not* a commercial service.

Also if you replaced the phrase "justify providing" with the word "sustain", the sentence wouldn't sound like such a "disadvantage."

But aside from these quibbles, the report makes an interesting (if technical) read.

October 15, 2007

NLM Blog Citation Guidelines

I've just returned from Frankfurt Book fair and noticed that there has been some recent popular interest in the The NLM Style Guide for Authors, Editors and Publishers recommendations concerning citing blogs.

Which reminds me of an issue that has periodically been raised here at CrossRef- should we be doing something to try and provide a service for reliably citing more ephemeral content such as blogs, wikis, etc.?

Continue reading "NLM Blog Citation Guidelines" »

September 19, 2007

Style Guides Recommend DOI strings

A couple of recent posts - from Scott Memorial Library at Jefferson University and IFST at Univ of Delaware- note that the AMA and APA style guides now recommend using a DOI, if one is assigned, in a journal article citation.

A citation in the APA style with a DOI would be:

Conley, D., Pfeiffera, K. M., & Velez, M. (2007). Explaining sibling differences in achievement and behavioral outcomes: The importance of within- and between-family factors. Social Science Research36(3), 1087-1104. doi:10.1016/j.ssresearch.2006.09.002

In the AMA style a reference would be:

Kitajima TS, Kawashima SA, Watanabe Y. The conserved kinetochore protein shugoshin protects centromeric cohesion during meiosis. Nature. 2004;427(6974):510-517. doi:10.1038/nature02312

This is great news. I haven't looked at the full style guides but it's not clear if information is given about linking DOIs via http://dx.doi.org/

Continue reading "Style Guides Recommend DOI strings" »