Question: What Is The "Standard" Citation Style/Format In Bioinformatics?
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gravatar for Radek
7.7 years ago by
Radek0
Cambridge, UK
Radek0 wrote:

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?

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ADD COMMENTlink modified 7.7 years ago by Jorge Amigo11k • written 7.7 years ago by Radek0
6
gravatar for Chris Evelo
7.7 years ago by
Chris Evelo9.9k
Maastricht, The Netherlands
Chris Evelo9.9k wrote:

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[?]).

ADD COMMENTlink modified 7.7 years ago • written 7.7 years ago by Chris Evelo9.9k

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.

ADD REPLYlink written 7.7 years ago by David Quigley11k

@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?

ADD REPLYlink written 7.7 years ago by Radek0

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.

ADD REPLYlink written 7.7 years ago by Chris Evelo9.9k

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.

ADD REPLYlink written 7.7 years ago by Chris Evelo9.9k

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).

ADD REPLYlink written 7.7 years ago by David Quigley11k
2
gravatar for Jorge Amigo
7.7 years ago by
Jorge Amigo11k
Santiago de Compostela, Spain
Jorge Amigo11k wrote:

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.

ADD COMMENTlink written 7.7 years ago by Jorge Amigo11k
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