What Is The "Standard" Citation Style/Format In Bioinformatics?

Question

[Radek]

For example, the Wikipedia entry on the subject mentions "Pechenik Citation Style" described in A Short Guide to Writing about Biology, 6th ed. (2007), by Jan A. Pechenik.

Is there such a standard way to cite sources?

To clarify: The use case is on a site that presents citations to others in the field, so which one would be the easiest for you to use when cutting/pasting?

Answer 1

[Chris Evelo]

I might be wrong, but I don't think there is something like a standard citations style, since all the journals require their own. It might be good to design one for web references. The Pechenik citation might be a good start. There is a quick guide [?]here[?].

But... It is important that there is a standard way to reference a document on the web using a document identifier (DOI), so whenever possible mention at least that DOI or link to it using a dx.doi.org link like this one: http://dx.doi.org/doi:10.1371/journal.pbio.1000472 (click it on your own risk, since I had to use one regardless of content, I chose the first one I could find ;-) ). If you don't have a DOI give a Pubmed ID instead. You can use the DOI instead of the direct link to website, since the DOI is intended to stay functional even if the website moves. In my experience journals are in general happy if you provide them with DOI's or Pubmed ID's even if they don't ask for it.

Taking the two parts together a web citation for that same paper I just mentioned would read like ([?]Kelder et al., 2010[?]).

[David Quigley]

Chris is right: many journals have distinctive citation format. If you use Endnote or another citation software package, this will be taken care of automagically by selecting the correct format and redrawing the citations. Just double-check that the format listed for the journal actually matches the current style required by the journal.

[Radek]

@Chris thanks for the answer, to clarify the format is for presenting citations to others in the field, I am not working on a paper or anything. So if you could choose, which would be the easiest for you to use when cutting/pasting from the web?

[Chris Evelo]

I suppose the answer to that is rather personal. But I think if you use it on the web the Pechenik style is actually quie OK, Although you might want to throw in a javascript that shows the full citation on mouseover.

[Chris Evelo]

I suppose the answer to that is rather personal. But I think if you use it on the web the Pechenik style is actually quite OK, Although you might want to throw in a javascript that shows the full citation on mouseover.

[David Quigley]

Informally, when writing papers and editing drafts with others I just use (Lastname Journal Year) inline until we're ready to write the final draft and don't get the formal full-length citations fixed until we're done editing. For example, I could cite (Churchill Genetics 1994).

Answer 2

[Jorge Amigo]

if you are starting to record references, I would suggest you to consider a reference manager. once stored, the references may be pasted in any desired format (depending on the journal) when needed. as for a starting point, I would go for any of the 3 options listed on this softonic query: EndNote (commercial, very powerful at searching and managing formats), Zotero (free firefox extension, very configurable, allows very easily storage of anything displayed on the browser) or Mendeley Desktop (free, iTunes like interface). once you start saving all your references in any of this softwares, pasting any subset of them in any particular format will be a matter of a couple of clics.