Getting a handle on references

So every scientific journal has its own style of referencing the past papers, books and resources that you want to cite in your manuscript. I suspect that part of the reason for this is so that if you want to resubmit your paper to a different journal after it has been turned down because the reviewers were all ignorant (for what other reason could there be?) you are forced to jump through hoops reformatting everything. This ensures that you know your place as the editor's bitch.

Software like EndNote and Reference Manager claim to make the process easier but I find that, inevitably, the output styles that ship with citation software include templates for journals like Contemporary Accounting Research and Advances in Polymer Technology but not Bioinformatics or any of the BMC titles (to be fair, I just checked and EndNote does actually carry these styles now. Not so six months ago, though).

Anyway, the two main ways of referencing works in text (at least in biomedical journals) look like so:

• Harvard style - "thus we can conclude that protein interaction networks are scale-free (Stew, 2003)"
• Vancouver style - "as evidenced in our previous analyses of overrepresented GO terms in microarray experiments (2)"
  

There are also myriad formatting issues in the actual references section - what gets put in bold, do the names of the authors come before the name of the paper etc.: you might not think that this is all that important, but sometimes the backend systems at publishers rely on you having properly formatted your references to automatically fetch crossref links and so on for the electronic version of your paper.

Personally, I find the Harvard style (citing a reference by including the surname of the primary author and the year that the paper came out) infuriating. It's the style of choice for OUP's Bioinformatics. It's not so bad when everything is hyperlinked on screen, but if you print out a long paper with lots of references you then have to waste time trying to find the actual citation at the back of your huge sheaf of paper. It's also quite intrusive, especially when more than one source is cited mid-sentence. The flow of the text gets broken by this big bracketed list of frankly meaningless names and numbers.

It's high time we all switched to the Vancouver style, I say. Also, there are two further developments that could make life easier.

The first: little explanations below selected citations in the references section. Sometimes you see this in Nature Reviews, not sure if it has cropped up anywhere else:

i.e.

31. Kanduri, C. et al. Functional association of CTCF with the insulator upstream of the H19 gene is parent of origin-specific and methylation-sensitive. Curr. Biol. 10, 853−856 (2000).
This paper shows that CTCF binding is methylation sensitive and provides important mechanistic insights into how cells distinguish between maternal and paternal alleles.
(..)
36. Dean, W. et al. (..) 13734−13738 (2001)
37. De Baun, M. R et al. (..) 156−160 (2003)
References 34−37 show that in vitro culturing of embryos can lead to epigenetic defects in animals and that this might also have a role in humans.

A little bit of commentary goes a long way, making it much easier to cull references from papers. Think back to the last time that you were reading about a new aspect or technology that you weren't familiar with and remember how difficult is was to pick out the seminal references from which to learn more...

Secondly, I don't see why references can't be grouped by the section of the manuscript that first mentions them; in theory Vancouver style references are already in the order of their appearance. Simply throw in "Background", "Methods" and "Discussion" headers into the references section and immediately we can see, for example, which papers are most closely related to the one being read (cited in the background section) and which are more distantly related (cited in the discussion).