CZ Talk:Citation style

Carried over from Biology/Draft talk, moved momentarily to Citation style, then here. David Tribe 15:03, 31 January 2007 (CST)

The reason for placing this talk dialogue here here was the following comments made at Citation style

I would expect under this title an article about citation styles in "real life". Is there no special namespace here? Andres Luure 05:52, 31 January 2007 (CST) CZ:Citation style? Andres Luure 05:54, 31 January 2007 (CST)

To be cleaned up for clarity David Tribe 22:00, 30 January 2007 (CST)

Formating conventions Version 1.1 biology

• The reference format style started in Horizontal gene transfer is being currently David Tribe 15:07, 31 January 2007 (CST) followed in an attempt at typographical consistency. Books are being cited here by the authors' full name and ISBN numbers are being used to minimize needed detail.
• At some later stage we may well use non abbreviated journal titles for clarity but currently this would expand the size of some articles with many references
• Also possible is use of reference method: <ref name=Smith> giving names to citation when first used David Tribe 20:09, 26 January 2007 (CST)

A proposed new style manual for citation from PloS Biology Slightly modified?

See link to PLoS for their format [1] This is an attempt to create a new reference style model for the future based on PLoS

See link for PLoS Biology format [2]

References ... For all references, list the first five authors We should only give one plus et al. if there are more than two); add "et al." if there are additional authors. You can include a DOI number for the full-text article as an alternative to or in addition to traditional volume and page numbers. Please use the following style for the reference list:

Published Papers

Better 1. Anandalakshmi R et al. (1998) A viral suppressor of gene silencing in plants. Proc Natl Acad Sci U S A 95:13079–13084. Open access

Two authors Published Papers 2. Anandalakshmi R, Defffa J (1998) A viral suppressor of gene silencing in plants. Proc Natl Acad Sci U S A 95:13079–13084. Open access

3. Bernstein E et al. (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409:363–366. PMID 11201747

Accepted Papers Same as above, but "In press" appears instead of the page numbers. Example: Adv Clin Path. In press.

Electronic Journal Articles 4. Loker WM (1996) "Campesinos" and the crisis of modernization in Latin America. Jour Pol Ecol 3. Available: [3]. Accessed 11 August 2006.

Books 5. Bates B (1992) Bargaining for life: A social history of tuberculosis. Philadelphia: University of Pennsylvania Press. 435 p. or 5. Bates B (1992) Bargaining for life: A social history of tuberculosis. ISBN 12345677

Book Chapters 6. Hansen B (1991) New York City epidemics and history for the public. In: Harden VA Risse GB editors. AIDS and the historian. Bethesda: National Institutes of Health. pp. 21–28. Reference Style Model in electronic final form?:

[4]

5. Xie Z et al. (2004) Genetic and functional diversification of small RNA pathways in plants. PloS Biol 2:e104 doi: 10.1371/journal.pbio.0020104.

A variant on the above closer to what Gareth Leng suggested to me: 1. Anandalakshmi R et al. (1998) A viral suppressor of gene silencing in plants. Proc Natl Acad Sci U S A 95:13079–13084. Open access CrossedDavid Tribe 20:13, 30 January 2007 (CST)

Revised reference style proposal

As above

Taking raw PubMed text and PLos izing it, and shortening authors.

RAW start Pubmed:

1: Bernstein E, Caudy AA, Hammond SM, Hannon GJ.

Role for a bidentate ribonuclease in the initiation step of RNA interference.

Nature. 2001 Jan 18;409(6818):363-6. PMID: 11201747 [PubMed - indexed for MEDLINE]

The PubMed to PloS briefened conversion with only deletion and date typing and insertion of et al. Probably suited to a future automatic software algorithm for Pubmed conversion.

Exhibit A

1. Bernstein E et al. (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature. 409:363-6. PMID 11201747

Automated PMID

But using link to algorithm engin provided by Gareth , that is [5]

{{cite journal |author=Bernstein E, Caudy A, Hammond S, Hannon G |title=Role for a bidentate ribonuclease in the initiation step of RNA interference |journal=Nature |volume=409 |issue=6818 |pages=363-6 |year=2001 |id=PMID 11201747}} {{cite journal |author=Bernstein E ''et al.''|title=Role for a bidentate ribonuclease in the initiation step of RNA interference |journal=Nature |volume=409 |pages=363-6 |year=2001 |id=PMID 11201747}}

Gives: Exhibit B

Bernstein E, Caudy A, Hammond S, Hannon G (2001). "Role for a bidentate ribonuclease in the initiation step of RNA interference". Nature 409 (6818): 363-6. PMID 11201747.

Exhibit C

Bernstein E et al. (2001). "Role for a bidentate ribonuclease in the initiation step of RNA interference". Nature 409: 363-6. PMID 11201747.

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Formal reference biology style proposal

I propose (float the conjecture) that all the three exhibits are, A, B, C acceptable, and that if any one is chosen that it must be used consistently

I prefer Exhibit A. Its about as easy as the B and C to do. It fits with using PLOS as a style manual better

Thus the guideline proposed is: "Follow PLoS Biology as closely as practical but allow briefer author lists (e.g. exhibit A) and where appropriate for reader clarity full journal titles. Technical articles will not need full titles but more general,introductory or more topical articles will need full journal titles. Adopt citation styles that that fit this guideline which can created by easy manual editing of raw PubMed text output. " David Tribe 21:24, 30 January 2007 (CST)

This proposal is for further comment and draws on (Gareth Leng's?) bolded comments just below, which were bolded by David Tribe 20:29, 30 January 2007 (CST)

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Couple of comments 1) Most style manuals propose that non English words be italicized' except when they are incorporated into normal use - thus in vivo but vice versa. Thus it would be et al - but this is something for CZ-wide style to decide. 2) PubMed citations give the page range as 13079-84. 3) Ideally I'd like to see a simple way of importing from PubMed directly into CZ style, that way, as we check we can copy edit too. Please see this [6] - Not perfect but easily edited. I guess using a template like this has the advantage that reference templates can later be changed to implement a future style change en masse? 4) Books are a problem, and there's a case for giving authors names in full I guess.Follow PLos for Style 5) There's a case for putting some journal titles in full in some articles - Sci Am is fine in a scholarly list but for an introductory article perha[ps Scientific American would be better. 6) So think we may need slightly different guidelines depending on the intended readership??

Accepted David Tribe 20:29, 30 January 2007 (CST)

Well done for taking this on. I do think it's important to get this consistent; I don't mind what convention is adopted, but think it's important we have one. Gareth Leng 06:59, 30 January 2007 (CST)

I've previously been following you with bold vol numbers. Ital Journal titles.

Amazingly, the WP MOS has inconsistent references in its own (Physics type ) type style manual!

The advantage of PloS with minimal change is

1. The Style Manual is almost already done. 2. Minimal key work for italics and bold. Needs a few more full stops and commas than Ive been using so far. The less keywork the easier to get followers to follow. Glad to see that a retreat from yor suggest is pragmatically possible.

I'm now going to propose (see above) that we follow PLos with some minimal changes and allow ISBN and PMIDs and doi to enable shorter citations and see what the response is David Tribe 20:03, 30 January 2007 (CST)

We can use all this grinding work Biology as a testing ground and precedent for style and process.David Tribe 20:13, 30 January 2007 (CST)

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One of the reasons for the style that I used [in preceding biology article and exhibits B and C above] was that it mirrored the product of the WP journal reference template, and many of the better WP articles used this template throughout. I guess it should be possible for our technical citizens to alter the output of this template in any we we want? If so the PubMed citation tool indicated above could very efficiently drop references into any chosen style. So - query, is it pssible to change the reference template to give the output you prefer (which is fine by me, BTW)?Gareth Leng 09:26, 31 January 2007 (CST)