This FAQ covers how best to link to scientific articles when answering and posting questions on Bio.SE.
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I have created a CSL citation style for the convenience of users. It can be used in Zotero, Papers, Mendeley, and Qiqqa.
It's an author-date style presenting the bibliography as a marked-down bullet list. If the citation contains a DOI, this is used to construct a dx.doi.org link. If there's no DOI, any URL associated with the citation is used. If no URL is found, the item is presented without a link.
The style is demonstrated below, and can be downloaded here (at the top-right of the code display, right-click the <> symbol and save as...).
To use the style from Zotero, you must first install it. Then you just select the items you want to include in the reference list, then right-click and choose 'Create bibliography from selected items'. Next choose the 'Biology.SE' from the list, ensure 'export to clipboard' is chosen, and press OK. Now you can paste the reference list at the end of your post.
Example references
- Carmell MA, Girard A, Kant HJG van de, Bourc’his D, Bestor TH, Rooij DG de, Hannon GJ. 2007. MIWI2 Is Essential for Spermatogenesis and Repression of Transposons in the Mouse Male Germline. Developmental Cell 12: 503–514.
- Castanotto D, Tommasi S, Li M, Li H, Yanow S, Pfeifer GP, Rossi JJ. 2005. Short hairpin RNA-directed cytosine (CpG) methylation of the RASSF1A gene promoter in HeLa cells. Mol Ther 12: 179–183.
- Joshua-Tor L, Hannon GJ. 2010. Ancestral Roles of Small RNAs: An Ago-Centric Perspective. Cold Spring Harbor Perspectives in Biology.
- Kawasaki H, Taira K. 2005. siRNA Induced Transcriptional Gene Silencing in Mammalian Cells. Cell Cycle 4: 442–448.
- Morris KV, Chan SW-L, Jacobsen SE, Looney DJ. 2004. Small Interfering RNA-Induced Transcriptional Gene Silencing in Human Cells. Science 305: 1289 –1292.
- Volpe T, Martienssen RA. 2011. RNA Interference and Heterochromatin Assembly. Cold Spring Harbor Perspectives in Biology 3.
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1$\begingroup$ nice! can't believe I've only just read this. I use Mendeley, and this is a great idea to encourage proper citations in answers. Going to go try it out $\endgroup$ – Luke Jul 19 '12 at 10:07
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$\begingroup$ :) I haven't tried it with Mendeley, so please let me know if anything needs tweaking... $\endgroup$ – Rik Smith-Unna Jul 19 '12 at 16:14
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$\begingroup$ The download link seems to be dead now. $\endgroup$ – fileunderwater May 30 '13 at 21:54
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1$\begingroup$ @fileunderwater sorry about that - have put it on Github and updated the link. $\endgroup$ – Rik Smith-Unna May 30 '13 at 22:00
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How do I use the DOI project to prevent future dead links?
The Digital Object Identifier System (DOI) is a method of linking to digital material (in our case primarily scientific literature). DOI links are advantageous as if the content linked to is deleted at one host in the future, the DOI will automatically resolve to another host without having to change the link.
The DOI number for an article is often included on the abstract page. This should be then appended to the end of the link http://dx.doi.org/.
Example
The article "The tomato genome sequence provides insights into fleshy fruit evolution" from Nature 485, 635–641 (31 May 2012) has a DOI of 10.1038/nature11119 - as given on its abstract page.
The link that should be included in your question/answer should therefore be to:
http://dx.doi.org/10.1038/nature11119
Which is resolved as such.
Usage
This system should be used wherever possible. Users are encouraged to suggest edits to change static links for their appropriate DOI style links.
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$\begingroup$ For those without a subscription would the pubmed ID be an appropriate alternative or should we always resort to the DOI style? $\endgroup$ – bobthejoe May 31 '12 at 22:51
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$\begingroup$ The best that you can do is enough in my opinion so pubmed ID ok in that case if do not have a subscription. $\endgroup$ – Léo Léopold Hertz 준영 Jun 7 '12 at 13:07
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$\begingroup$ You don't need a subscription to see the doi for any journal article. $\endgroup$ – Rik Smith-Unna Jun 8 '12 at 23:01
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$\begingroup$ It's worth mentioning that of course, dx.doi.org is as likely to disappear as any publisher's site. The strength of the doi system is that anyone can host a doi server and to make the switch we could just search and replace all dx.doi.org addresses with the address of the new server. Pubmed etc. don't have that open standard. $\endgroup$ – Rik Smith-Unna Jun 9 '12 at 11:09
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$\begingroup$ I would have thought that if the worst came to the worst the Dev team would be happy to replace every instance of
dx.doi.org/with a new DOI server xD $\endgroup$ – Rory M Jun 9 '12 at 13:02 -
$\begingroup$ Exactly, so it gives us a future-proof system. It would be useful to have some automation for references. I will have a go at a Zotero style. $\endgroup$ – Rik Smith-Unna Jun 9 '12 at 20:26
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$\begingroup$ @RichardSmith Zotero looks great, I think I'll have to give that a try! $\endgroup$ – Rory M Jun 15 '12 at 12:07
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$\begingroup$ Ah, now if only DOIs weren’t also prone to disappearing (happened to me already) … $\endgroup$ – Konrad Rudolph Aug 21 '12 at 9:32
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$\begingroup$ Interesting @KonradRudolph, I've not seen that before. $\endgroup$ – Rik Smith-Unna Sep 16 '12 at 14:16
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$\begingroup$ @Richard Here’s an example. Hard to judge whose fault this is but it seems to be a relatively common problem. $\endgroup$ – Konrad Rudolph Oct 1 '12 at 9:16
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How can I make sure that my use of references is valuable to the community?
When available, provide a link to a PDF that is freely available without subscription.
For many popular articles, a freely available PDF version of an article can be located, e.g. by:
- Searching google for the article title in quotes + filetype:pdf
- Searching google scholar, and when the article you want shows up, click the 'all 3 versions' and see if one is in pdf format
Add the url to the pdf alongside the properly formatted citation, like this; the citation itself links to the doi, followed by a link to a free pdf.
- [ **Carmell MA, Girard A, Kant HJG van de, Bourc’his D, Bestor TH, Rooij
DG de, Hannon GJ**. 2007. MIWI2 Is Essential for Spermatogenesis and Repression
of Transposons in the Mouse Male Germline. Developmental Cell 12: 503–514.]
(http://dx.doi.org/10.1016/j.devcel.2007.03.001)[[free PDF](http://exmaplepdflink.pdf)]
Which looks like this:
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1$\begingroup$ While certainly convenient, I feel that pdfs are dynamic and may drift. I'm personally much more comfortable linking a pmid or the doi. $\endgroup$ – bobthejoe Jun 28 '12 at 9:08
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2$\begingroup$ @bonthejoe The pmid or doi can also be added to the reference. I will adjust the answer. I agree that doi is the 'standard', and i use it in my own database because it reduces error in automated queried (within my database that doesn't have fuzzy matching) but for many without institutional access this is more useful. And having author, year, title, and journal is just as capable of uniquely identifying an article as a doi. $\endgroup$ – Abe Jun 28 '12 at 15:25
