OK, so... is the following correct?
On Sep 17, 2007, at 1:38 PM, Maury Markowitz wrote:
On 9/17/07, Jim Hu jimhu@tamu.edu wrote:
I'm a bit confused. Are cite and ref tags two different things? I recognize ref tags from the Cite.php extension.
This is part of the confusion. There are three different things being discussed, but editors have used the terminology interchangeably, greatly confusing matters.
"FOOTNOTE": a stylistic solution to inserting small amounts of text that would otherwise break up the flow of a statement. Other solutions include the sidebar, callouts, and pop-up text. In the case of the wiki, we don't really have anything that represents these directly.
In the case of a non-paginated wiki page (or most other web pages), it seems to me that it makes more sense to discuss these as ENDNOTES instead of footnotes. Operationally, Cite.php is the main mechanism for putting in endnotes, some of which are references, while others may be free text. The other mechanism being manual editing of the text inline and at the end of a wiki page.
Using Cite, endnotes/footnotes are what gets built around the <references/> tag.
"REFERENCE": any link to another work. in the case of the wiki, we expect these to be the set of resources that are used to build the article.
If I understand this correctly, the reference per se doesn't exist in the display. Reference is a combination of work, expression, and manifestation in WikiCat? I fear that WikiCat and WikiTextrose are much too grandiose for my brain to wrap around.
Handling the reference is a combination of how the endnote and the citation are handled. In some systems (not Cite.php), the reference information is stored in a database or in a non-displaying block on the page (I think that's how Biblio handles it).
When I use EndNote to do references in a word document, the references are in my EndNote database, and only a subset that are cited get applied to a particular document.
With a wiki, one has to figure out whether to store reference information internally or externally. With the current implementation of Cite, it's all internal and it's potentially redundant in ways that make relational db people shrink in horror. For EcoliWiki, I've added my ProcessCite.php extenstion on top of Cite.php and delegated some of the storage to PubMed for that class of references. This is not very useful for fields outside of biology, and doesn't provide good coverage in all areas of biology. But at least every time a user adds <ref name="PMID:number"/>, the endnote looks the same. I also have the ability to store a page of references as a reference library for things not in PubMed, but I don't think this is a good solution as the library gets large.
Is that approach extensible? Maybe this is related to what WikiCat was about, but could Cite/ProcessCite be modified to pull reference info as if it was a interwiki link? i.e. <ref name='WikiCat:PageName/>
"CITATION": a somewhat formal system for including a reference to another work, typically a journal or similar. In the case of the wiki, these
Citation is operationally the inline marker for the reference. Cite.php handles these as superscripted letters or numbers, but alternatives are things like (Doe et al., 2007) or [1]. Using Cite.php, the ref tag is used for citations.
What if Cite.php was modified to append text between ref tags to anything that is provided by the name=x information? This would allow different page ranges for the same source. This would only work if the name=x refers to an external source, not a different instance of the same ref name elsewhere on the page.
But, for example, if we modified Cite to recognize ISBN numbers, one could do <ref name='ISBN:number'>pp 200-210</ref> or something like that.
Or perhaps the ref tag needs more kinds of attributes besides name. What I just wrote above probably breaks backward compatibility horribly. So it would be better to build something like: <ref isbn='number'>pp 200-210</ref>
With more attributes, you could build lists of frequently cited works that are field specific as wiki pages in a reference list namespace, e.g. <ref list='biology' name='Selfish Gene'/>, which would be much more readable than ISBN numbers.
Jim
Now why do I complain they are confused? Well for one, go visit the wiki page on footnotes. Note that the entire article is about references! And where is the REF tag defined? In CITE.PHP!
Maury
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===================================== Jim Hu Associate Professor Dept. of Biochemistry and Biophysics 2128 TAMU Texas A&M Univ. College Station, TX 77843-2128 979-862-4054