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Cite.php compatibility

Good grief. This is complicated. To say nothing of its compatibility with Cite.php, which apparently is the way we're going to go with footnoting. Are they compatible? I shudder to think what source text is going to look like in future. This is what a very short paragraph from the article AIDS looks like in the edit box:

In the absence of antiretroviral therapy, progression from HIV infection to AIDS occurs at a [[median]] of between nine to ten years and the median survival time after developing AIDS is only 9.2 months <ref name=Morgan2>{{cite journal | author=Morgan, D., Mahe, C., Mayanja, B., Okongo, J. M., Lubega, R. and Whitworth, J. A. | title=HIV-1 infection in rural Africa: is there a difference in median time to AIDS and survival compared with that in industrialized countries? | journal=AIDS | year=2002 | pages=597-632 | volume=16 | issue=4 | id={{PMID |11873003}}}}</ref>. However, the rate of clinical disease progression varies widely between individuals, from two weeks up to 20 years. Many factors affect the rate of progression. These include factors that influence the body's ability to defend against HIV, including the infected person's genetic inheritance, general immune function <ref name=Clerici>{{cite journal | author=Clerici, M., Balotta, C., Meroni, L., Ferrario, E., Riva, C., Trabattoni, D., Ridolfo, A., Villa, M., Shearer, G.M., Moroni, M. and Galli, M. | title=Type 1 cytokine production and low prevalence of viral isolation correlate with long-term non progression in HIV infection | journal=AIDS Res. Hum. Retroviruses. | year=1996 | pages=1053-1061 | volume=12 | issue=11 | id={{PMID |8827221}}}}</ref><ref name=Morgan>{{cite journal | author=Morgan, D., Mahe, C., Mayanja, B. and Whitworth, J. A. | title=Progression to symptomatic disease in people infected with HIV-1 in rural Uganda: prospective cohort study | journal=BMJ | year=2002 | pages=193-196 | volume=324 | issue=7331 | id={{PMID |11809639}}}}</ref><ref name=Tang>{{cite journal | author=Tang, J. and Kaslow, R. A. | title=The impact of host genetics on HIV infection and disease progression in the era of highly active antiretroviral therapy | journal=AIDS | year=2003 | pages=S51-S60 | volume=17 | issue=Suppl 4 | id={{PMID |15080180}}}}</ref>, access to health care, age and other coexisting infections <ref name=Morgan2>{{cite journal | author=Morgan, D., Mahe, C., Mayanja, B., Okongo, J. M., Lubega, R. and Whitworth, J. A. | title=HIV-1 infection in rural Africa: is there a difference in median time to AIDS and survival compared with that in industrialized countries? | journal=AIDS | year=2002 | pages=597-632 | volume=16 | issue=4 | id={{PMID |11873003}}}}</ref><ref name=Gendelman>{{cite journal | author=Gendelman, H. E., Phelps, W., Feigenbaum, L., Ostrove, J. M., Adachi, A., Howley, P. M., Khoury, G., Ginsberg, H. S. and Martin, M. A. | title=Transactivation of the human immunodeficiency virus long terminal repeat sequences by DNA viruses | journal=Proc. Natl. Acad. Sci. U. S. A. | year=1986 | pages=9759-9763 | volume=83 | issue=24 | id={{PMID |2432602}}}}</ref><ref name=Bentwich>{{cite journal | author=Bentwich, Z., Kalinkovich., A. and Weisman, Z. | title=Immune activation is a dominant factor in the pathogenesis of African AIDS. | journal=Immunol. Today | year=1995 | pages=187-191 | volume=16 | issue=4 | id={{PMID |7734046}}}}</ref>. Different strains of HIV <ref name=Quinones>{{cite journal | author=Quiñones-Mateu, M. E., Mas, A., Lain de Lera, T., Soriano, V., Alcami, J., Lederman, M. M. and Domingo, E. | title=LTR and tat variability of HIV-1 isolates from patients with divergent rates of disease progression | journal=Virus Research | year=1998 | pages=11-20 | volume=57 | issue=1 | id={{PMID |9833881}}}}</ref><ref name=Campbell>{{cite journal | author=Campbell, G. R., Pasquier, E., Watkins, J., Bourgarel-Rey, V., Peyrot, V., Esquieu, D., Barbier, P., de Mareuil, J., Braguer, D., Kaleebu, P., Yirrell, D. L. and Loret E. P. | title=The glutamine-rich region of the HIV-1 Tat protein is involved in T-cell apoptosis | journal=J. Biol. Chem. | year=2004 | pages=48197-48204 | volume=279 | issue=46 | id={{PMID |15331610}}}}</ref> may also cause different rates of clinical disease progression.

A newbie finding that in an edit box will end up running screaming in the opposite direction faster than you could say Jesus H. Tapdancing Christ. ENCEPHALON 16:29, 12 February 2006 (UTC)

At least you won't need to block him then :-). Seriously: question here is: is it a problem caused by cite journal template or is it a problem inherent with that Cite.php? How would that page source look without using cite journal? The text would look cluttered too, wouldn't it? Just some thoughts. Make a variant of the same above with manually subst'ed cite journal (it cannot be substed because it uses qif, which cannot be substed). Would that look any better (i.e. not make the newbie running? At least cite journal can be used without Cite.php. --Adrian Buehlmann 16:45, 12 February 2006 (UTC)

Hey there. I was thinking the same thing when I clicked save—is the bigger problem with cite.php or cite journal? Well, if we didn't use cite.php, all the refs (the full citations) would be at the bottom, in the actual references section. The only thing in the text would be the {{ref}} bits. So yeah, the real issue is that cite.php requires the entire reference to be placed in the text. Using {{journal reference}} or {{cite journal}} together with cite.php, however, will makes matters worse, and leads to disasters like the above (assuming cite journal works with cite.php, that is; I haven't bothered to test it because I know now there's no way I'll use the combination). I think it basically boils down to not using a combination, as was done in AIDS. If one uses cite.php, I think just typing out the reference is the only way to go (minimises words). Thanks for your interest. ENCEPHALON 17:22, 12 February 2006 (UTC)

I've reformatted the wikisource of the intro of AIDS. Take a look at http://en.wikipedia.org/w/index.php?title=AIDS&action=edit&section=0. --Adrian Buehlmann 17:26, 12 February 2006 (UTC)

Yeah, saw that. So we don't need to keep the thing in a line [1]. I suppose the same is probably true for {{cite journal}}? Still, I think I'll probably use cite.php without any other templates though; I'm used to writing refs and can do it without a "prompter" template. Plus the text will be shorter without the addition of the extra words. ENCEPHALON 17:33, 12 February 2006 (UTC)

Yes. No need to keep everything inline. You can insert newlines at several places without disturbing the result (Just ask me on my talk if you are uncertain, I will help you). This holds true also for the template calls. The advantage of usig cite journal is that you can change the formatting of all references in one place. On the old {{Journal reference}} (uses uppercase params), there was recently a change to make the volume bold. With the template, you can make such a thing with a finger tip. I mean, Encyclopedia Brittannica certainly has all references looking the same, do they? We can do this here too. That's one of the reasons for using {{cite journal}}. --Adrian Buehlmann 17:51, 12 February 2006 (UTC)

I'm tempted to ask Aevar (the parser hook's author) to add a feature to cite.php which allows you to specify a "silent" usage the first time you define a ref if you want to. THen you can refer to it by name everywhere else. This way, only the empty ref tags would be needed in the body text itself. -Splash^talk 19:15, 12 February 2006 (UTC)

(resetting indent). Splash, I'm interested to understand your idea. But I didn't. Could you give an example of what you mean? --Adrian Buehlmann 20:33, 12 February 2006 (UTC)

Amend cite.php so that it has something like the following construct:

<ref name="id" silent="silent">yadda yadda</ref>

This will create the ref so that it can be referred to by name in future but would not result in actual usage of it in the article. You would then use the normal syntax whenever you want to cite the ref:

SoandSo said "yadda yadd"<ref name="id" />

The point is that you could then have all the refs defined in bulk at some point in the article with "silent" set on all of them, rather than having the horrific wikisyntax that Encephalon points out above. This behaviour would closely model that which we already have with {{ref}} and {{note}} but would still get to take advantage of collecting all the descriptions of the refs up in one place. It would need someone to change Mediawiki though. -Splash^talk 21:29, 12 February 2006 (UTC)

This has already been raised, in the context of converting existing lists of references. See here for ongoing discussion.

Actually, I rather prefer having the reference in the text where it is actually used, because at least you have the reference next to the text it is supposed to be supporting. My personal opinion is that wikitext should have a lot more line-feeds anyway: there's no need to have huge paragraphs because—like HTML—they get joined up in the output anyway. If you create your source wikitext with each sentence starting on a new line, then you can add your references in on a per-sentence basis and it all gets much easier to read. This also has the added bonus that Diffs become much easier to read because the unit for comparing gets much smaller. So your example from earlier should look more like:

In the absence of antiretroviral therapy,
progression from HIV infection to AIDS occurs at a [[median]] of between nine to ten years and the median survival time after developing AIDS is only 9.2 months
<ref name=Morgan2>{{cite journal
 | author=Morgan, D., Mahe, C., Mayanja, B., Okongo, J. M., Lubega, R. and Whitworth, J. A.
 | title=HIV-1 infection in rural Africa: is there a difference in median time to AIDS and survival compared with that in industrialized countries?
 | journal=AIDS
 | year=2002
 | pages=597-632
 | volume=16 | issue=4
 | id={{PMID |11873003}}
 }}</ref>.
However, the rate of clinical disease progression varies widely between individuals, from two weeks up to 20 years.
Many factors affect the rate of progression.
These include factors that influence the body's ability to defend against HIV, including the infected person's genetic inheritance, general immune function
<ref name=Clerici>{{cite journal
 | author=Clerici, M., Balotta, C., Meroni, L., Ferrario, E., Riva, C., Trabattoni, D., Ridolfo, A., Villa, M., Shearer, G.M., Moroni, M. and Galli, M.
 | title=Type 1 cytokine production and low prevalence of viral isolation correlate with long-term non progression in HIV infection
 | journal=AIDS Res. Hum. Retroviruses.
 | year=1996
 | pages=1053-1061 | volume=12 | issue=11
 | id={{PMID |8827221}}
 }}</ref>
<ref name=Morgan>{{cite journal
 | author=Morgan, D., Mahe, C., Mayanja, B. and Whitworth, J. A.
 | title=Progression to symptomatic disease in people infected with HIV-1 in rural Uganda: prospective cohort study
 | journal=BMJ
 | year=2002 | pages=193-196 | volume=324 | issue=7331
 | id={{PMID |11809639}}
 }}</ref>
<ref name=Tang>{{cite journal
 | author=Tang, J. and Kaslow, R. A.
 | title=The impact of host genetics on HIV infection and disease progression in the era of highly active antiretroviral therapy
 | journal=AIDS
 | year=2003 | pages=S51-S60 | volume=17 | issue=Suppl 4
 | id={{PMID |15080180}}
 }}</ref>,
access to health care, age and other coexisting infections
<ref name=Morgan2>{{cite journal
 | author=Morgan, D., Mahe, C., Mayanja, B., Okongo, J. M., Lubega, R. and Whitworth, J. A.
 | title=HIV-1 infection in rural Africa: is there a difference in median time to AIDS and survival compared with that in industrialized countries?
 | journal=AIDS
 | year=2002 | pages=597-632 | volume=16 | issue=4
 | id={{PMID |11873003}}
 }}</ref>
<ref name=Gendelman>{{cite journal
 | author=Gendelman, H. E., Phelps, W., Feigenbaum, L., Ostrove, J. M., Adachi, A., Howley, P. M., Khoury, G., Ginsberg, H. S. and Martin, M. A.
 | title=Transactivation of the human immunodeficiency virus long terminal repeat sequences by DNA viruses
 | journal=Proc. Natl. Acad. Sci. U. S. A.
 | year=1986 | pages=9759-9763 | volume=83 | issue=24
 | id={{PMID |2432602}}
 }}</ref><ref name=Bentwich>{{cite journal
 | author=Bentwich, Z., Kalinkovich., A. and Weisman, Z.
 | title=Immune activation is a dominant factor in the pathogenesis of African AIDS.
 | journal=Immunol. Today
 | year=1995 | pages=187-191 | volume=16 | issue=4
 | id={{PMID |7734046}}
 }}</ref>.
Different strains of HIV
<ref name=Quinones>{{cite journal
 | author=Quiñones-Mateu, M. E., Mas, A., Lain de Lera, T., Soriano, V., Alcami, J., Lederman, M. M. and Domingo, E.
 | title=LTR and tat variability of HIV-1 isolates from patients with divergent rates of disease progression
 | journal=Virus Research
 | year=1998
 | pages=11-20 | volume=57 | issue=1
 | id={{PMID |9833881}}
}}</ref>
<ref name=Campbell>{{cite journal
 | author=Campbell, G. R., Pasquier, E., Watkins, J., Bourgarel-Rey, V., Peyrot, V., Esquieu, D., Barbier, P., de Mareuil, J., Braguer, D., Kaleebu, P., Yirrell, D. L. and Loret E. P.
 | title=The glutamine-rich region of the HIV-1 Tat protein is involved in T-cell apoptosis
 | journal=J. Biol. Chem.
 | year=2004
 | pages=48197-48204 | volume=279 | issue=46
 | id={{PMID |15331610}}
 }}</ref>
may also cause different rates of clinical disease progression.

…which is a lot less scary, if no less complicated. The article you cite is probably one of the more densely-referenced articles, and one wonders whether newbies who "run screaming" at the sight of so much citation would be better off testing their feet in a less complicated article . HTH HAND —Phil | Talk 09:52, 14 February 2006 (UTC)

I completely agree that any citation templates should be written with linebreaks. Much easier to read and edit. However, I feel that it is much more editor-friendly to put the citations at the bottom in the reference list. The reason I say this is that the text just reads much more easily if you see something like:

 this causes the '''[[color]] of [[food]]''' to influence the [[perception|perceived]] flavor,
 in anything from [[confectionery|fruit gums]] to [[wine]]{{ref|colorflavor}}.  For this reason, ...

instead of something like:

 in anything from [[confectionery|fruit gums]] to [[wine]]
 <ref name="colorflavor">{{cite journal
 | author=Jeannine Delwiche
 | title= The impact of perceptual interactions on perceived flavor
 | journal= Food Quality and Preference
 | year=2004
 | volume=15
 | pages=137–146 }}</ref>.  For this reason, ...

Not only is it easier to follow the flow of the sentence while editing, but the diffs are -much- easier to read when someone changes something! --Slashme 10:52, 14 February 2006 (UTC)

While line breaks make it a bit easier to follow, if there was the option of having a silent define section, as Splash has suggested, you could define relevant references at the beginning of the section in which it is used. This would make it neater, easier for people to edit the text (which IMO is more important than the references), place the references close to the text to which it refers, and would be familiar for anyone who has used programming languages. Example:

 ==Animal food==

 <ref name="cat" silent=1>{{cite journal
 | author= Felix
 | title= Why dry cat food is worse
 | journal= Cats & Dogs
 | year=2004
 | volume=3
 | pages=555–666 }}</ref>

  <ref name="dog" silent=1>{{cite journal
 | author=Rover
 ...
 | pages=137–146 }}</ref>

 Cats prefer dry animal food <ref name="cat" />, whereas dogs prefer cats as food <ref name="dog" />

 ==Cattle fodder==
 ...

Spaully 21:45, 23 February 2006 (UTC)