Wikipedia talk:WikiProject Tree of Life/Archive9

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Archives for WT:TOL edit
1 2002-07 – 2003-12 Article names
2 2003-11 – 2004-02 Taxoboxes
3 2004-02 Taxoboxes
4 2004-02 – 2004-08 Bold taxa; taxonomy
5 2004-03 – 2004-04 Taxonomy; photos; range maps
6 2005-04 – 2004-06 Capitalization; authorities; mammals
7 2004-06 – 2004-08 Creationism; parens; common names
8 2004-05 – 2004-08 Templates; †extinct; common names
9 2004-05 – 2004-08 Categories; taxoboxes
10 2004-08 – 2004-12 Categories; authorities; domains; Wikispecies; ranks; G. species; capitalization; Common Names
11 2004-11 – 2005-05 Capitalization; common names; categories; L.; authorities; algae; cultivars
12 2005-03 – 2005-05 Ranks; common names
13 2005-05 – 2005-06 Hybrids; taxobox format; cultivars
14 2005-06 – 2005-07 Categories; food plants; identification; Capitalization
15 2005-07 – 2005-09 Synonyms; types; authorities; status; identification
16 2005-09 – 2005-12 Paleontological ranges; Rosopsida; Taxobox redesign; identification
17 2005-12 – 2006-04 Taxobox redesign; identification; APG; common names; capitalization
18 2006-04 – 2006-10 Categorization; include in references; snakes; range maps; seasonality graph; common names; bioregions; brya;
19 2006-10 – 2007-03 various
20 2007-03 – 2007-06 various

Contents


[edit] MW 1.3 categories

Also new in 1.3 are categories. I was going to suggest we add categories at the order and class level (and perhaps family/genus for large classes) so that we have auto-generated lists of articles.

Unfortunately categories are useless with respect to ToL articles at the moment. Add a category to an article causes the taxobox to be forced into the centre of the page (with lots of whitespace to its right) rather than left right-aligned as it should be.

It would be good to discuss what categories people would find most useful, however I don't think we can use them yet. Pete/Pcb21 (talk) 14:39, 30 May 2004 (UTC)

Looks like the category layout bug in MonoBook has been circumvented by having categories display at the bottom of the page. So, we can go ahead and start to categorize species, if we wish.
I would urge participants to consider common names for categories, for reader-friendliness. For me, I know the taxonomic names of a few families and orders (like Mustelidae), but I would like to browse the Tree of Life with common names, like Category:Weasels. In fact, one could argue that the only reason to use the MW categorization system for the tree of life is to make a common name scaffolding around the strict scientific hierarchy already expressed in the taxoboxes. There doesn't seem to be much point to just replicating the taxonomy in categories like Category:Cupressaceae, is there? People can always browse up and down easily through the taxoboxes.
I realize that there are sticky points in using the common names. There already is a Category:Trees, which does not map easily into taxonomy. Not sure how to resolve this, but I would still urge common categories names. --- hike395 14:53, 10 Jun 2004 (UTC)
Actually, I'm still not certain I want to have categories used for ToL articles. However, if they are, I'd prefer they very closely mimic the taxonomy hierarchy. The point of categories isn't only for navigating up and down the category hierarchy, It's for creating lists and dump off all the children of a certain category. A dump of all the articles in the Category:Mammalia should give every mammal species article, but should also include all the intermediary taxon articles (cetaceans, primates, carnivores, etc).
So that gets us into whether using common names for categories is preferred over scientific. Article names are preferred to be common, when one exists. I'd prefer categories to be just the opposite - always using the scientific name because it will always exist (although it might not be unique and will need to be disambiguated). One of my reasons for this is the ambiguousness surrounding common names. Look at lemur or agouti. Both refer to multiple branches in the ToL. Category:Lemurs and Category:Agoutis would have to include articles that do or don't fall into the category, depending on which definition of those common names you have in your head.
I've removed tree ToL articles from Category:Trees and left in the individual trees. Category:Trees is, as you noted, not appropriate for ToL articles that happen to be be about a kind of tree. - UtherSRG 15:39, 10 Jun 2004 (UTC)

I definately think the Tree of Life, in the categories, should be the scientific names. It'd be excessively silly to splice the two - there is no common name for "Chordata" - yet we'd have a category somewhere below it called "Wolf". Prior to categories, Wiki had no appropriate mechanism by which to display a comprehensive tree of life - there was an indirect tree-of-life via taxoboxes. We should definately use scientific names. We can always create categories in layman's names such as Category:Weasel - for those who are casually browsing. We have the chance to create the largest and most comprehensive Tree of Life on the internet by use of the categories - why ruin the chance with common names? --Oldak Quill 17:29, 10 Jun 2004 (UTC)

I agree with OldakQuill Fuelbottle | Talk 04:11, 13 Jun 2004 (UTC)
I would like to wait until some of the more longer-term ToL contributors weigh in on this issue. However, I will stop deleting the existing categories. There are, however, complications that have not even been brought up yet. What about (to the extreme) Gingko, and other species which are leaves of the ToL but have short, stubby branches? Which category do they go in? - UtherSRG 14:51, 13 Jun 2004 (UTC)
PS to Oldak - The common term for Chordata is chordates. Your point is well taken, though. - UtherSRG 15:26, 13 Jun 2004 (UTC)
There are many extinct members that can be added to the Ginkgo category. Fuelbottle | Talk 18:56, 13 Jun 2004 (UTC)
That's besides the point. I want you to look at the generalities, not the specifics. How should stubby leaves be handled? Should they be put into multiple categories? The uppermost category with branches? Some other configuration? As to Ginkgo, if it has any known relatives, the article and taxobox should be modified to indicate such branchings. As it is, it stands as the sole Species in its entire Division.
These issues need to be discussed. The work you've done may be good, or may need to be removed and redone. The categories you've created are a temptation to other editors to go ahead and add articles to them, which means potentially more ork to be undone or redone. - UtherSRG 21:17, 13 Jun 2004 (UTC)
Weighing in as requested . . . I find it hard to think what's best. I don't see a lot of value in taxonomic categorisation, as it merely duplicates what's already in the taxobox. Or am I misunderstanding their operation?
Otherwise, I can see there might be a case for non-taxonomic categories, like Category:Trees (though I don't greatly like the idea), and/or geographical breakdowns that aren't reflected in the taxoboxes (e.g. Category:Animals of Europe); in such a case, I think the categories should be pretty wide, continent, and kingdom or division rather than order (i.e. Category:Plants of Europe and Category:Animals of Europe rather than, say, Category:Roses of Europe and Category:Rodents of Europe (or for that matter, small areas like e.g. Category:Animals of Bulgaria). Obviously a lot of species, and many more genera, would fit in several categories, e.g. juniper would fit in Category:Plants of Europe, Category:Plants of Asia, Category:Plants of Africa and Category:Plants of North America: tedious to do! - MPF 22:25, 13 Jun 2004 (UTC)
That is one way to do categories. It can run in parallel to the taxonomic categorization. Categories allow scripts to extract articles downward from an arbitrary category (root), through the sub-categories (branches), to all of the articles (leaves). So there is some value in the taxonomic categorization, such as running a script to extract all mamamals or carnivores or etc. - UtherSRG 22:49, 13 Jun 2004 (UTC)
Maybe it could be categorized in ecozones and ecoregions. Fuelbottle | Talk 07:44, 14 Jun 2004 (UTC)

I am yet to be persuaded that there is any particular value in having categories on ToL pages at all. We already have two mature and extensive categorisation and navigation schemes - the taxoboxes and the semi-formalised speecies lists in the text itself. Why would we want to buggerise about inventing categories when there are so many articles that don't even exist at all yet? I'm not actually hostile to categories, I just think that we have real work to do. If and when someone comes up with a compelling reason for categorising the ToL entries (and with a clear and practical proposal for the organisation of the categorisaton scheme, one that doesn't merely reinvent the wheels we already have) then that might be the time to reconsider the idea. That's the nice thing about the wiki software: it has so many features that we can pick and choose which ones are most suited to particular circumstances. We don't have to use everything all the time. Tannin 01:18, 14 Jun 2004 (UTC)

I think that categories should replace the lists in the text as in many articles they are way too large(see for example Asteraceae), so the article can focus on the Genus or Family or whatever it's about instead. For example in the Asteraceae article, the list could be moved to a category while a few of the most common genera could be put in the taxobox and then the last entry there could be a link to "All genera" which would link to the category. Fuelbottle | Talk 01:54, 14 Jun 2004 (UTC)
I can see value in categories that "slice" differently from the taxobox. For instance, how does one find all the ToL articles about trees? or freshwater fish? or even for taxobox entries like beetle? When I went looking for all the beetle articles recently, I had to laboriously thumb through a lot of irrelevant entries in the "links here". I recently acquired a reference on fishes of Nevada (80+ species believe it or not), and I've been debating whether to make a list or a category. A category for the species of a genus seems less useful, since we already expect to have a list (whether long or short, in article or separate) in the genus article.
(I think the above was from user:Stan_Shebs
also weighing in as requested... I haven't had a chance to dig through everything the categories routines can do, but I think it's unlikely that they will do the ToL as well as our existing taxoboxes and lists do (unless we could somehow make them get their information out of the taxobox - maybe by changing the Latin taxon templates somehow?). There are just an awful lot of life forms, and there is nothing that will get them all on one page in a compact form; so a full tree has to be something that can be navigated, to display relevant bite-sized bits of it. Taxoboxes are very sound bites to display, which is why I like them the way they are. Above all we don't want two independent (and therefore inevitably inconsistent) ToLs being read into/out of Wikipedia. On the other hand, categories might have potential to do things that at the moment we can only do laboriously and by hand - like picking up all the disparate things that have a particular common name (trees is a good example). Even better if there would be a way of automatically generating "mammals of Bulgaria"; as a mainly text-based system, Wikipedia is currently weak on that sort of thing. seglea 04:09, 14 Jun 2004 (UTC)
Scientific names are not the clear solution that several contributors appear to think, with taxonomy in such a state of flux. Are birds of prey in Accipitriformes or Ciconiiformes? The former is standard, but Sibley et al propose the latter. I'm always in favour of searching the obvious English word rather than a term that may not be familiar to a layman. I'm a computing ingnoramus, so I can't comment on the technical side. I note that Black-necked Swan is in the Chile category, which i wouldn't have thought was obvious. jimfbleak 05:26, 14 Jun 2004 (UTC)
Standards can be used, when the standard changes it's easy to update Fuelbottle | Talk 07:40, 14 Jun 2004 (UTC)
Ahem. Which standard? The well-recognised international standard that places many birds of prey in Accipitriformes? Or the well-recognised international standard that places them in Falconiformes? Or do you mean the very broadly accepted standard classification scheme that places them all in Ciconiiformes? Even in bird taxonomy (which is simple, unified, and stable by comparison with that of several other branches of the art) we can only talk about "the standard" if we restrict ourselves to one particular locale. (In Australia, for example, the standard is HANZB, but that doesn't apply in France or the UK, and in the US (as I understand it) there are two standards, both official, and neither of them agreeing with the other.) Tannin 13:11, 14 Jun 2004 (UTC)

Here is a summary of what I think. There should be made categories, and the lists over species and genera etc in articles should be moved to categories. One reason for this is, as some users point out in many cases there aren't any standards decided, updating categories can be made in one place instead of in lots of lists in articles as new decisions gets made, which standards to use in wikipedia can be voted over. This is also a problem with taxoboxes, I think the best solution would be if the taxoboxes could use a script to be updated from the categories to ensure consistensy. I think it also would be nice to have all species categorized in some kind of geographical way, as this would make it easy to find which species can be found in different areas. Fuelbottle | Talk 15:20, 14 Jun 2004 (UTC)

That is, let there be categories up to genus, and then add all species articles to the genera categories. If such a scheme were to be used, should suborders, subclasses etc. be used? Fuelbottle | Talk 11:28, 15 Jun 2004 (UTC)
Let's see if I can summarize where we're at. There is disagreement on both if and how categories should be used for ToL pages. Some propose using them to strictly adhere to scientific classification. Some propose using them strictly for common name groupings. Some propose the same, but at a broader, higher level. Some of these proposals are given grudgingly: "If we have to use them, then let's do it this way...." Although we are far from a concensus, the most supported position is to not use categories at all. Since they shouldn't beused until a reasonable agreement can be reached, I will continue to remove the categories from ToL pages and delete the categories. - UtherSRG 11:42, 14 Jun 2004 (UTC)
I removed "Category:Scientific_classification is a tree whose branches end in species" from Wikipedia:Categorization and "For scientific categories, see Category:Plantae." from Category:Botany, similar things might be found more places though. Fuelbottle | Talk 14:20, 14 Jun 2004 (UTC)
I think that is wise, Uther. If we are going to use categories at all, then we should do so in a cooperative way: proposing category schemes here on the talk pages, and throwing ideas around until we achieve a rough consensus. Then we can all pitch in and knock the required changes out in just a few days. This is what we did with the taxobox formatting issue, and the eventual result was one that we are all pretty happy with, and which works very well indeed.

I have to object to the deletion of existing categories by various users - the existance of categories do not adversely affect any user... As such, I do not see why we can have both common-name schemes and scientific classification schemes working side by side? It would please everyone (apart from those who do not want catgories). I would likely work on the scientific scheme - but botanists are likely to have common schemes, as are bird watchers etc. We could also have cladistics - if a user wished to create this. What I am saying is that categories do not and cannot adversely affect anyone - there is absolutely no reason why we can't have mutliple schemes... If someone could justify to me either: a) not having categories OR b) only having one scheme | I will happily concede. If no one can justify either, I will begin creating the scientific scheme. --Oldak Quill 18:19, 14 Jun 2004 (UTC)

Concensus editting means just the opposite. Until we can reach a reasonable agreement on what scheme(s) to use, please do not go adding whatever scheme suits your own individual fancy. I will continue to remove (atthe very least) the taxonomic schemes until the concensus is for some scheme to be put into place. - UtherSRG 18:57, 14 Jun 2004 (UTC)

Moved from Wikipedia talk:Categories for deletion: May I suggest a less hysterical pace of deletion? I am not against the deletion of trivial, empty categories, but they are not the only ones disappearing in this kangaroo court. How about deletion notices on the categories and a waiting period? silsor 14:56, Jun 14, 2004 (UTC)

Most of my speedy deletes today and recently have been discussed on Wikipedia talk:WikiProject Tree of Life. Quick summary: there is no concensus on if and how to use categories for taxonomic articles, so we're removing categories from ToL articles and deleting the categories so that they are not misused. - UtherSRG 15:17, 14 Jun 2004 (UTC)
This is really ridiculous. The articles I categorized under "Fungi" go under "Fungi" because they are "Fungi", in the same way I might categorize "Table" under "Furniture". You used the rollback feature on all my edits of this morning as if I were some kind of vandal. silsor 21:49, Jun 14, 2004 (UTC)
Rollback is a whole lot faster than editting each article. I'm not accusing you or anyone of being a vandal. Please go to Wikipedia talk:WikiProject Tree of Life for the full discussion of why I'm deleting those categories. - UtherSRG 22:13, 14 Jun 2004 (UTC)
By "we" above (in regards to deleting) you seem to mean "I". What happened to your statement yesterday that you would stop erasing others' work? silsor 22:22, Jun 14, 2004 (UTC)
Also, may I point out that fixing a categorization scheme which you see as "wrong" at some later date requires exactly the same amount of work as waiting until a scheme is made policy, then categorizing the articles? In fact you will have to do less work, since relevant articles will already be grouped together in categories that make sense. This is of course a moot point since there is no more appropriate name for a "fungi" category than Category:Fungi. silsor 22:50, Jun 14, 2004 (UTC)
Do go back and read all of what I wrote on the ToL talk. I'm not going to reply further here. If you want, join the discussion there. No sense being fragmented. - UtherSRG 22:54, 14 Jun 2004 (UTC)
I have read your opinion. Please stop erasing my work. Thanks. silsor 23:14, Jun 14, 2004 (UTC)

Lack of consensus is not actually the same as a mandate to go around deleting content. In fact it would be a good idea to do some experimentation to see how it "feels", and you can't do that without, well, actually creating some categories and putting some articles into them. If the conclusion based on looking at these for a while is that they're undesirable, then at least the category system ensures they'll be easy to find and remove. :-) Several of the comments above are along the lines of "taxobox is all one needs", but it only lists scientific taxa, and competely misses the dozens of other useful ways to organize these articles. Trees are a great example, because tree-ness cuts right across the plant taxa, and is likely of much more interest to the general reader than the lists of obscure species in obscure genera. Stan 05:20, 15 Jun 2004 (UTC)

Experiments can be a good thing. But the word itself implies a certain degree of orderliness and some methodology. That wasn't what was out there that I removed. Some of the questions I raised earlier (above) may be answerable with some experimentation, or it may just take some discussion. Even your example about trees is open for debate - is it worthwhile to place all the tree species in Category:Trees, or should that be reserved for specific individual articles about trees. If we are going to use categories, we need to be working together as a group, rather than each of us choosing and implementing our own categorization schemes. (And yes, it was relatively easy to find and remove what was out there... except for when people didn't want to come here and discuss but went ahead and continued to create as I was deleting.....) - UtherSRG 11:29, 15 Jun 2004 (UTC)
Why can't both categorisation systems work side by side?--Oldak Quill 08:34, 15 Jun 2004 (UTC)
They can. In fact I've left some categories out there. Category:Trees exists and contains unique tree articles. Category:Model organisms contains those articles about organisms used in genomic research. Really, the only one I removed is the one I personally give the most support for - taxonomic categorization. However, I think we have a lot to discuss (and perhaps experiment) before we start implementing it on the scale that had been reached. - UtherSRG 11:29, 15 Jun 2004 (UTC)


From meta: What about a special similar and independent type of categories only for the Tree of Life project that let make a real Tree? It can't be complicated (only make it independent to the other categories and use an other color) and can be very useful I think.

[edit] Categorization schemes

So... let's start listing some categorization models and lay them out on the table for discussion. Here's some schemes that I've seen in our discussion, and some perhaps with a twist:

  • Purely taxonomic in parallel with the taxoboxes - each taxon article would be contained in the category of its containing taxon, and each category would be a subcategory of the taxonomic category above it. This would allow a script to extract all of the article nodes taxonomically descended from an arbitrary root category. (For example, all the mammalian articles, including all the order, family and genus articles.) Other implementations?
If such a scheme should be should it be implemented, should it be as domain > kingdom > phylum > class > order > family > genus or should intermediate ranks like suborder be included? Maybe a mix of both? Fuelbottle | Talk 17:06, 15 Jun 2004 (UTC)
  • Something combining the above two? Probably inevitable in the second case anyway as there aren't common name groupings for all things, especially the microbiota.
  • Both of the above, working in parallel, so that while something might be in Category:Falcons, it would also be in Category:Falco (or perhaps Category:Genus Falco) as well as Category:Kestrels.
I guess that using a names like Category:Genus Falco rather than Category:Falco might be a good idea as it might make it easier to see what kind of category it is. Fuelbottle | Talk 17:31, 15 Jun 2004 (UTC)

Even in listing these possibilities, I see the possibility of improving what we have already. The article Falcon is pointed to from the disambiguation page Falco, even though some of the birds in that genus aren't called falcons (there are kestrels, hobbies, and the merlin). And then there's the family Falconidae which includes Falco and many birds in Falconidaeare also falcons. If the articles were arranged more taxonomically, then the categories could help detail the descendant articles. Or vice versa. - UtherSRG 11:48, 15 Jun 2004 (UTC)

I seem to be the only person advocating common names for ToL categories. Since I am in the distinct minority, I'm happy to yield to whatever system people think is best. -- hike395 04:38, 29 Jun 2004 (UTC)

[edit] categorization redux

I think I've moved firmly into the "pro-category" camp. And, surprisingly perhaps, I find I prefer the possibilities that a "mixed" or "parallel" system of categorization provides a la my last bullet in the section above. If there's anyone at all still interested, can we discuss to what level of refinement we should take the categorizing to?

  • For the taxonomic branch:
    • KPCOFGS/KDCOFGS categories only? (Category:Order Primates would contain Primates and all the articles down to the family level, as well as containing the categories for the families, then each family category contains all the articles from the family down to the genus level, including all of the genus categories, etc.
    • All rankings? Each taxonomic ranking gets its own category, regardless of how intermediate the ranking is. (sub-, infra-, etc.)
  • For the common branch:
    • I suspect the various sub-Projects will make decisions here about how to divide up the common branch categorization
    • Free play on the rest?

Yours in organization - UtherSRG 23:10, 12 Jul 2004 (UTC)

I don't think we need categories for every KPCOFGS that comes along, only those that people naturally think in terms of - to a fair extent, those that coincide with the common branch. For instance, primates would be a good category, but Malacostraca wouldn't. Unstable taxa definitely shouldn't be categories. I think standards here are of limited value, and we should just excercise our judgement on what levels to use. Would that be enough, or am I missing the point?

By the way, please don't use a naming system that prefixes taxa with ranks, which aren't always as stable as the composition! Josh 01:13, 13 Jul 2004 (UTC)

  • I agree with Josh, I think the best we are likely to able to do is to devolve decisions to subprojects, who can pick the best taxa that work for them. However we might be able to offer general guidance on how big categories should be. Less than 10 articles too small, more than 100 too big? Pcb21| Pete 01:26, 13 Jul 2004 (UTC)
Then I suggest we start offering that guidance. Category:Birds and Category:Animals keep getting created and are a mess! Mixtures of common and taxonomic info in the same category. No concept of a larger picture that they are working towards.
My concept for using a rank with a taxa allows that category to be identified as a taxonomic category. I felt this was needed for cases where the taxa name itself would not be sufficient for ths identification, or for where the common and taxonomic naming system may intersect. On second thought, the plural would be used for the common names, and so thre shouldn't be the intersection. Ok then. How about Category:Foo (taxa) for when the category needs to be disambiguated? - UtherSRG 05:45, 13 Jul 2004 (UTC)
I must be asleep. Category:Primates would be a prime (no pun intended) example of my above concern. Should it contain common name articles and categories, taxonomic ones, or both? - UtherSRG 05:55, 13 Jul 2004 (UTC)

I say both, without distinction. We already have the taxoboxes to give an overview of the current taxonomy, so I don't think it's important that the categories reflect that. They can be used for more general things.

In particular, I'm thinking of taxa that have fallen out of favor, now used as descriptive groups or being listed for historical interest. These can be interesting, and categories would be a good place for them. But they wouldn't fit in very well if you insisted on separating formal and informal groups. Josh 06:21, 13 Jul 2004 (UTC)

Yes, we already have the taxoboxes. These are a great way to consolidate a bunch of information about the article into a (hopefully) tight little package. It's also a navigational aid. Categories do not work the same as taxoboxes. They serve a different purpose: to consolidate groups of articles into a tight little package. How those articles are grouped, and how the categories are interrelated (the categorization scheme), causes the presented package to take on different meanings. Also, categories are an aid to dumping/offloading (not just navigating) a group of related articles: because categories can have subcategories, a SQL routine or a script can be used to extract all of the articles in a given category tree. This can not at all be done with a taxobox. The taxobox is a purely human-pedia interface. Categories are that too, plus they are also a machine-pedia interface, if implemented with a certain degree of care.
To this end, I want us to be very aware and concerned with the implementation of categories in ToL articles. Dismissing them offhand because we have taxoboxes seems to me to be a narrowminded approach to what we can achieve.
As for discarded taxa - I disagree. They certainly have a place in my schema. Perhaps I'm not drawing a clear enough picture of what I'm envisioning. They would be a leaf in the middle of a branch on the taxonomic tree. For instance, it would be neat to write up an article on the various changes that the classification New World monkeys has undergone in the past few years. Such an article, and any of the discarded taxa, would get categorized under Category:Primates (taxa).
A better example might be Reptilia. Taxonomically, it was lower in rank than a phylum (it makes up a part of the phylum Chordata) and was a class. It would get categorized under Category:Chordata (taxa). However, unlike other classes (say, Amphibia) which would be categorized under their own category (Category:Amphibia (taxa), a subcategory of Category:Chordata (taxa)), there would be no Category:Reptilia (taxa). Anything that would have been included in such a category would get covered by some other taxonomic category.
For categorizing by common groupings, Category:Reptiles would certainly be legitimate. It would likely contain separate subcategories for snakes, lizards, turtles, dinosaurs, etc. Category:Primates might include subcategories each for monkeys and apes, but might include all the rest of the primates directly.
A user wishing to extract a list of all the articles in the 'pedia on reptiles could run a script using Category:Reptiles as the root. A user wishing to extract all of the primates could use either Category:Primates or Category:Primates (taxa), since both would branch down to cover all the primate species. The two lists may be organized differently because the trees are organized differently.
A point was made about the fluidity of taxonomy. This has little to no bearing on how categories are used. If categories are used following any given taxonomy, the connections between categories would have to change - just like the taxoboxes would have to be changed, as well as the classificationlists in articles, etc. In fact, taxoboxes and classification lists would still make up the majority of the changes when a taxonomy changes.
I hope that I've cleared things up. I'm very excited and eager, and I want you all to be this excited. *grins* Chalk it up to a personality trait of "visionary"... - UtherSRG

It's not a simple matter of fluidity. It's not that I mind changing systems, but the idea that there's always one, and only one, currently accepted taxonomy is pure fiction. Reptilia is a case in point. It's not acceptable to clades-only taxonomists, but there's no generally accepted alternative for us to use. Treating Diapsida or Archosauria as a class conflicts with treating Aves as a class, the preeminent standard in ornithology. Besides, some people still argue for paraphyletic taxa. So nobody knows where to place reptiles, and the taxoboxes currently reflect this confusion.

The taxoboxes only give one system, but that's because they aren't flexible enough to reasonably present alternatives - it's a limitation we tolerate because they're still useful, not something desirable. Limiting the categories the same way seems a waste. I really like the idea of them as a more flexible alternative. When there are different versions of the tree, isn't it better for a database readout to include both?

It's easier for me to get excited about something like that than the prospect of simply copying something that creates argument, confusion, and over-simplification when there's no need. Josh 01:11, 14 Jul 2004 (UTC)

Ah! That's not what I expected would be your arguement. It seems that, where taxonomy isn't in any kind of dispute, you agree with my proposed system. It's only at the points of variability in our understanding of evolution and when we attempt to solidify that variability into a rigid system that you seem to have a complaint. That's certainly fair. Let's see if I can be as flexible.
I think that the system I proposed can be utilized to highlight and elucidate these areas of inconsistency. First, a category page can include a description of the category itself, so a category for a minorly disputed taxa can have information about the dispute. For something like the various ways that the avian families are organized differently in the US vs the UK vs ANZ, where each alternative has reasonably equal standing, an article could be placed into multiple cateories. While it would be untenable to have multiple taxoboxes, an article in two or three alternative categories would work. We even have an article explaining the difference between what we used and Sibley-Alquist.
Each point of taxonomic discrepancy may need a different solution. But isn't that already true with how we do taxoboxes? Some of those discrepancies are made clearer by the system we have in place. Other discrepancies ave not been made clearer; perhaps a new system can help.
So get excited! *grins* - UtherSRG 01:52, 14 Jul 2004 (UTC)

I like the basic principles, but I'm not sure on the details. Are you still proposing rank or taxon flags, despite allowing different systems? What about taxonomies nobody believes any more, but are still in common use, like the Cronquist system? And what about common and scientific names - are these supposed to be separate, near-duplicates of each other, or melded together? Josh 03:29, 14 Jul 2004 (UTC)

Nope. No specific rank flags, just a "disambig" flag to denote that the category is a taxon. I don't have any specific proposals about various and competing classification schemas. That should be hashed out by discussion and experimentatioin and concensus - the way we already work out such things. Since ronquist already has an article, probably it should be mentioned on the relevant category pages. I envision the commo and scientific name schemas to be separate but complementary. Look at what I said about Primates above, then look at the classification table on the primate page. Maybe I should implement my system on the primate pages to show as an example. - UtherSRG 07:51, 14 Jul 2004 (UTC)
Going ahead and doing your primates section as an example sounds like a great idea. I've done Category:Cetacea as you know - a simple implementation - one category for all species in the order plus associated non-species articles - making for about 80 articles in the category. This is probably bigger than the average category but doesn't feel too big to me. Then we can link up the primates and cetaceans to do a mammals category to give us a feel for what "big branch" parts of the tree will look like. Pcb21| Pete 08:33, 14 Jul 2004 (UTC)

Well, I was a little sloppy, but I've gotten the dual trees done: Category:Primates for the common route and Category:Primates (taxa) for the taxonomic route. I'm not entirely satisfied with how I have it and plan to tweak it, especially the articles which have multiple taxa categories.... an artifact of an article that represents multiple taxa ranks. - UtherSRG 22:02, 15 Jul 2004 (UTC)

After I added Cockatiel to category:birds I realized I was biting off way more than I can handle. I've always admired the Taxo boxes, but I think categories are needed as well. I've been trying to find what conclusion (if any) you guys had come to. I for one would not be able to find 'birds' under 'Chordate-->Aves' if I was digging down from the top-level categories.
Am I right to conclude from these discussions that there can be two sets of categories, one using the proper KPCOFGS classification and a more general 'common term' tree? I’d really like to contribute to this once I know I’d be working on the right path. : Drhaggis 19:29, 15 Aug 2004 (UTC)

[edit] taxobox_begin documentation

The taxobox_begin,...,taxobox_end syntax needs to be documented somewhere. I think there is a real danger that Wikipedia becomes more and more difficult to use for new users, with all the arcane templates. This documentation belongs in Wikipedia:WikiProject Tree of Life and Wikipedia:Template messages. AxelBoldt 11:06, 3 Aug 2004 (UTC)

You are quite correct! However, even just in the last couple of days there have been some changes. I'd rather wait a little bit longer to see if any further changes come along before publishing the new format formally. Users (readers) shouldn't notice a thing. Die-hard contributors (editors) can take a peek at the taxoboxes on Wikipedia:WikiProject Tree of Life already to see how they are constructed. I'm thinking this weekend or next, depending on if more changes happen. - UtherSRG 11:43, 3 Aug 2004 (UTC)

[edit] Charales

Kranswier

Kranswier
Template:Taxonomy
Kingdom:
Division: Chlorophyta
Class: Charophyceae
Order: Charales
Family
Characeae

Are the Charales considered to be plants ? Some consider algae to be to primitive to be plants. IPNI for instance does not have a genus like Charra in their database so, I am a bit lost on this one. This is what I think I know. Thanks, GerardM 20:30, 4 Aug 2004 (UTC)

According to the Tree of Life [[1]], Charales belong to the Green Plants (= green algae and land plants). JoJan 21:15, 4 Aug 2004 (UTC)

The standard we've been using is that green algae are included among the Plantae - see for instance Chlamydomonas, Volvox. Note the Charales should be placed in the division Charophyta, but it isn't clear what to do with all green algae and adding taxoboxes for some should probably be deferred. Josh 18:15, 8 Aug 2004 (UTC)

[edit] Compacting the taxon lines further, can this be done ?

The taxonlines are dependend on the number of relevant taxons. With the taxobox that I saw on Salmonides there was a seperate message for each taxon. This can be done with a message with two parameters: Taxon and Taxonname it would be like {{Taxobox_entry | taxon = {{Regnum}} | taxonname = [[Animalia]]}}

  • Nesting messages does not work.. alas, having a text, like en: has works great but only for en: ...
  • What alternative is there ? Text does not translate automagically.. :(
  • For the Animalia I have used the latin name as this does translate to other wikipedia where Animal does not.
There is a limit to the number of instances of a template on a single article: 5 instances. Using {{Taxobox_entry | taxon = {{Regnum}} | taxonname = [[Animalia]]}} would limit you to Kingdom, Phylum, Class, Order, and Family before you ran out, if you don't use any finer grades. This is why we had to uncompress the taxobox entry templates. However, we chose to continue to be interwiki compatible. Also, we tend to use [[Animal]]ia to prevent the redirect. Your concern about translation is a tough break.... even if we used the scientific name of a taxon as the article name or a redirect, the scientific name is still usually different in different languages anyway. There is absolutely no reason to compel editors to use one language across all wikis for taxonomy links. Taxonomic names are not latin words. They are latinate words - word with a latin format. However, visit other wikipedias and you'll get other answers. For the interwikis using the Latin alphabet, Primate has the following corresponding interwiki articles: Primat (Danish), Herrentiere (German), Primatoj (Esperanto), Primate (Spanish, French), Primates (Latin, Dutch), Primatas (Portuguese) and Naczelne (Polish). Then add Japanese, Russian and Chinese which don't use the Latin alphabet. - UtherSRG 23:53, 4 Aug 2004 (UTC)

[edit] Rolling out taxobox templates

I'd like to roll out the new template taxobox with a "How to" article on building taxoboxes. I've started it, but i thought it might be a good idea to just start it and post the link here for anyone who wants to craft the "how to" portion, perhaps as a way to learn their workings more. So here it is. - UtherSRG 03:30, 9 Aug 2004 (UTC)

I made a page for copying blank template stuff at User:Yath/tol. There is at least one thing I am not sure about: highlighting of genus/subgenus. In some articles it's ''Genus'' while in others it's '''''Genus'''''. The same goes for the binomial name in text; it's usually (''Genus species'') but sometimes also bold. I am assuming for now that italic only is the correct format. --Yath 21:29, 9 Aug 2004 (UTC)

The current standard for bolding is detailed on this page - the genus name should be bolded whenever the species name is, and any other groups that only contain that species should also be bolded. It's not ideal in my opinion, but after extensive debate has become the standard. Josh 23:37, 9 Aug 2004 (UTC)

After slogging through this discussion from Archive 4, I have gotten some idea of the consensus. I've written them up on User:Yath/tol. Please check it for errors. Also, we should set up a rough draft of this how-to article at something like Wikipedia:WikiProject Tree of Life/Taxobox Usage or something. Either that, or I can just start hacking on UtherSRG's subpage :-) --Yath 00:27, 10 Aug 2004 (UTC)
Hack at will. I've moved my page to the ToL subpage you've aptly named. - UtherSRG 00:46, 10 Aug 2004 (UTC)

Most articles have a modest selection of classification hierarchies, e.g. kingdom, phylum, class, etc. It is possible to create fairly tall taxoboxes if you include every super/sub/infra*phoo. Example: Carpet viper. Should we be conservative and leave out the domain and unnecessary templates? And say so in the instructions? --Yath 06:12, 10 Aug 2004 (UTC)

I guess it would help if I read the main project page. Question answered. --Yath 06:18, 10 Aug 2004 (UTC)
*grins* Looks like Carpet viper needs some mowing... that's some very tall grass. - UtherSRG 11:33, 10 Aug 2004 (UTC)

Questions:

  • When would you put the authority in parentheses?
  • Is it true that the binomial name should be bold and italic when given in the article's opening section? I think most articles don't do this: Wolf, American Robin, Sei Whale. But some articles do.

Yath 19:19, 10 Aug 2004 (UTC)

Authority in parentheses: This is a designation that the type author's original assignment for the species has been changed. For instance, let's say I describe a new critter: Genus1 species1 Uther, 2004. Some bozo comes along and shows I'm wrong and reassigns it: Genus2 species1 (Uther, 2004). - UtherSRG 20:13, 10 Aug 2004 (UTC)
Italics are required. I don't think we ever settled on bold or not bold. - UtherSRG 20:13, 10 Aug 2004 (UTC)
BTW - I think you are doing an excellent job! I'm at work, so I can't make significant mental additions, but I'll work on it when I get home. - UtherSRG 20:37, 10 Aug 2004 (UTC)

[edit] Taxobox update robot

Just finished "modernizing" the taxobox over at Painted Lady. This is not fun (especially for the butterflies, which have around 100 suborders, superfamilies, etc.). It would be nice if we could send a robot to update taxoboxes, or at least have a script that we could copy/paste into. Does anyone on this project have any experience roboting MW or already have some scripting put together? Otherwise I might throw together a perl script to try to automate this to some extent. --Chinasaur 01:16, 10 Aug 2004 (UTC)

I have a program that takes a lot of the grunt work out of updating taxoboxes. It is rather clunky to use, and it only works on HTML-table boxes. I would suggest that if you see a taxobox in HTML table style, you either slap a {{ToLCleanup}} on it or use this program. Whatever you do, don't update any more of those by hand. If you want to look at it, it's here. --Yath 07:54, 11 Aug 2004 (UTC)


[edit] Binominal versus Binomial

While checking the ICZN (International Code of Zoological Nomenclature) 4th ed., Glossary of the ICZN, I stumbled to my surprise on the fact that they only mention the words 'binomen', 'binominal', 'binominal name' and 'Principle of Binominal Nomenclature'. We have been using all the time the words 'binomial' and 'binomial nomenclature'. I think we have a problem worth discussing. JoJan 18:46, 11 Aug 2004 (UTC)

You aren't looking at the ICZN site, you are looking at an Australian governmental site. The glossary is of "selected terms as used and defined in the [ICZN]" . I can't reach the ICZN site just now, but I bet they have binomial in there. - UtherSRG 19:17, 11 Aug 2004 (UTC)
No they have not. Look at [2]. I am quoting from Chapter II, Article 5 : 'Article 5. Names of taxa of ranks in the species-group.-

(a) Principle of Binominal Nomenclature.- The scientific name of a species, and not of a taxon of any other rank, is a combination of two names (a binomen), the first being the generic name and the second the specific epithet; the specific epithet must always begin with a lower-case letter. ' JoJan 20:13, 11 Aug 2004 (UTC)

Fascinating. Still, I can't reach ICZN, and your quote is from the DRAFT 4th edition, not the final. Google hits seem to be more in favor of "binominal", primarily from *ZN related sites, while in favor of "binomial" from *.edu sites. Further, the seemingly defunct www.biosis.org lists *both* in its glossary. However, Google gives 10800 hits for "binomial nomenclature" (which is listed in www.Dictionary.com) and only 361 for "binominal nomenclature", and even recommends using "binomial" as a replacement for "binominal". Again I say: Fascinating. I wonder when this split occured. I think we should keep steady on the course for using "binomial" throughout. - UtherSRG 21:04, 11 Aug 2004 (UTC)

Fascinating indeed. The site I first cited Glossary of the ICZN, takes its data from the ICZN 4th edition. I have a print-out of this glossary always at my side when editing a page. That's how I stumbled on this 'anomaly'. Now that the new taxobox templates are rolling out, a small change in your template could do the trick (if a consensus can be reached which word to use). I admit, the words 'binomial' as well as 'binominal' are in the dictionary. On the other hand 'binominal' seems more logical, if you take the Latin origin 'binomen' into account. Look at the word 'nominal' as in 'nominal value' : there is no such word as nominial. And 'nominal' is also derived from the Latin word 'nomen" (= name). Therefore 'binomial' seems like an aberration, even if it is accepted by dictionaries. JoJan 21:44, 11 Aug 2004 (UTC)
Ahhh.. but ther IS such a word as "nomial" (oddly, it's a noun). See http://www.onelook.com Mackerm 22:24, 11 Aug 2004 (UTC)

It looks like the difference is that binomial is from the French word nom. Far from being an aberration, though, it's the original term and more in line with other compounds like polynomial and multinomial. It looks like binominal is a Latin re-synthesis, and I don't think we should concern ourselves much with it. Josh

[edit] Slow down!

As taxoboxes are rapidly being converted to use templates, many other changes seem to be creeping in. These include breaking of piped links, introduction of semi-standard taxa of intermediate ranks, and occasionally a notable departure from the classification being used for the group in question. I appreciate the conversion is difficult, but it is not more important to roll this out than to preserve what we have so far. Please, be careful! And, is it really now preferred to use bulleted rather than indented lists in the subdivision box? Josh 23:14, 11 Aug 2004 (UTC)

Some of the things you've been cleaning up (such as the prokaryote domain business on bacillus) are caused by misinformation on the Taxobox Usage usage page, which is mostly written by me. I've corrected one thing but I'm sure there are other problems with it.
Incidentally, I would prefer indented lists. There is nothing written on any ToL project page about it, yet. --Yath 23:34, 11 Aug 2004 (UTC)
Except, Sometimes it is convenient to represent more than one level of classification in the subdivision list. In that case the lower level groups may moved over to the right by prefixing them with   markers—usually three the first level, and then one to three more for each subsequent one.
Josh - can you point me to some of the pages you have objections to?
Indented is the preferred. It was in the original, and is in the new: Wikipedia:WikiProject_Tree_of_Life/Taxobox_Usage#Non-species_footer - UtherSRG 00:35, 12 Aug 2004 (UTC)

Most examples are small. Hymenostome suddently picked up a domain, changed the phylum from Ciliophora to Ciliate, and switched from an indented to a bulleted list. Ciliate was similar, and the image was removed. The classification on Proteobacteria was greatly improved, but no attempt was made to link to our current articles, and as a result many bacteria were orphaned. These are not so serious, but if they happen quickly amid a flurry of other changes, they are hard to spot. More important are changes which are quickly copied everywhere, like the prokaryote domain or the use of the semi-standard subkingdom Metazoa and a bunch of other intermediate ranks on insect species pages. Plus, the changes to bulleted lists, which are more difficult to reverse. Note I'm not saying we should stop changing to templates, or that people aren't doing good work. I'm just calling for more caution, because it's hard to fix problems when they spread so quickly.

Btw, I notice that the new taxoboxes don't seem to use the Taxobox_end_placement macro, and instead absorb this into Taxobox_section_subdivision. This wasn't discussed above, and I think it's a bad idea. Josh 04:31, 12 Aug 2004 (UTC)

Is there some reason Taxobox_section_subdivision includes </table></td></tr>? Perhaps that should be removed. Then we'd have to update a lot of pages quickly... --Yath 08:41, 12 Aug 2004 (UTC)

About 350 pages by now, which gives some idea of how overzealous the conversion's been. At this point, I think we have to use a script to repair them. It'll only get worse... Josh 09:02, 12 Aug 2004 (UTC)

If someone can point me to a 'bot how-to, I can make that fix. - UtherSRG 11:32, 12 Aug 2004 (UTC)
And looking at those specific pages, I see that it's Azyhd who you are complainging about. I've have tried repeatedly to get him to conform more, to only a small amount of success. I believe he does not read talk:ToL, so you'll have to post a message on his talk page. Maybe if more people tell him he's out of line he'll listen. - UtherSRG 11:37, 12 Aug 2004 (UTC)

My impression was that he's simply been one of the more enthusiastic converters, rather than someone uniquely out of line. Either way, I've pointed him here. Josh 12:01, 12 Aug 2004 (UTC)

[edit] Modifying Taxobox_section_subdivision

Taxobox_section_subdivision includes </td></tr></table>, and is inconsistent with the taxobox template scheme. It would be nice to remove that part, and insert Taxobox_end_placement on each page that uses Taboxo_section_subdivision. Unfortunately, this will disrupt the pages' format for as long as it takes to modify all of the pages that are involved.

  • If you insert Taxobox_end_placement prior to changing Taxobox_section subdivision, the lower part of the box floats over to the left: User:Yath/sandbox1
  • If you modify Taxobox_section_subdivision before inserting Taxobox_end_placement, the entire article gets sucked into the box: User:Yath/sandbox2

I am proposing a temporary modification to Taxobox_section_subdivision, which will look not-too-horrible both before and after Taxobox_end_placement placed above it. The procedure would go something like this:

  1. Specially modify Taxobox_section_subdivision. Pages using it will look like this: User:Yath/sandbox3 (Not including the blue box at the top!).
  2. Add Taxobox_end_placement to all infolved pages. Perhaps using a bot. Note that this will not change the appearance of the pages. They still look like this.
  3. Finally, change Taxobox_section_subdivision to the final version, without those closing tags. This makes the pages look nice again.

See the source of User:Yath/sandbox3 for the exact modification. It's clearly demarcated by HTML comments. --Yath 23:47, 12 Aug 2004 (UTC)

I think this is a good idea, even without a bot. The broken taxoboxes aren't that much of a problem, and if five people do ten pages a day, we can restore them within a week - much sooner if people show the same zeal in fixing as they did in creating. Josh
I am going ahead with this (sorry for not saying anything :-] ) and the bot should be done 5-6 hours after this timestamp... unless I speed it up --Yath 07:25, 14 Aug 2004 (UTC)

Now that that's done, {{Taxobox_end_placement}} always follows {{Taxobox_begin_placement}}> --Yath 10:51, 14 Aug 2004 (UTC)

Taxoboxes look funny : see for instance Agave. Something wrong with the template ? JoJan 15:09, 14 Aug 2004 (UTC)

It looks like Yath's bot (excellent work with that, btw) skipped a handful of pages. I've fixed them. Incidentally, it seems like there are many pages that have nothing on them, save the taxobox. Josh

[edit] Templates upon templates

The "lots of templates in a series make a taxobox" method was adopted essentially because no other way would work - essentially there could be no truly generic template because optional elements would be required.

However when I have extra knowledge, such as when I describing a species of cetacean, I don't have requirements for optional elements (I always have an image, range map, author, date, and a known number of taxa). This enables me to get back to the heart of the idea of templates - just listing the data without worrying about ordering/presentation. I have changed Gray Whale as an example (you'll need to look at the wikitext). The two new templates "cetacea_taxobox_head" and "cetacea_taxobox" call the generic ToL taxoboxes behind the scenes.

From the selfish perspective of the cetaceans project, this suits my means a lot better - verbiage in the article wikitext is at a minimum. However I thought I should check if there are any wider implications - e.g. wrt internationalization that you guys could warn be about before I go spreading across the other 70 odd species articles. Pcb21| Pete 00:53, 14 Aug 2004 (UTC)

Note that doing things like {{template_name | blah = {{insert_blah_value_from_this_other_template}} }} is still broken - so I can't quite yet reach template nirvana - but I believe devs are thinking about this issue. Pcb21| Pete 00:53, 14 Aug 2004 (UTC)
My initial impression is that custom macros for different groups are a bad idea. The result would be that someone moving from one taxon to another would have to familiarize themselves with a different standard each time. Surely a little extra wikitext is worth making things as accessible as possible? Josh 01:39, 14 Aug 2004 (UTC)
My problem with this is what if someone wants to add some information not handled well by your template? They would either have to do something really hacky (and thus also would have to know your template prety well) or they would have to redo the entire table in a more flexible format. I think the taxobox template, especially if it is adjusted to allow both HTML and wiki-table markup to be shotgunned in, is flexible enough while still providing some streamlining. --Chinasaur 04:16, 16 Aug 2004 (UTC)
To my mind, the great benefit of templates is not just making it faster to author new articles, but more importantly the ability to change every current article in the project space consistently from one spot. On this front, I think the only further advantage offered by a separate cetacean template and not already offered in the general taxobox templates is the ability to reorder different parts of the template in the vertical organization, like if you suddenly decided that all cetacean range maps should be at the top of the taxobox. These sorts of rearrangements seem unlikely (a more experienced ToLer can say how often this occurs). --Chinasaur 04:45, 16 Aug 2004 (UTC)
Because the specific whale template is implemented in terms of the general taxobox template, you can still change every article in one place. (If your hypothetical change to the general template breaks the cetacea template, then it will break articles implementing it directly.) I view the advantages mainly as presenting the information as data with the minimum specified about the presentation - the general template can't do this. It also more intuitive.
However I think Josh's point is a very good one - it creates a barrier to entry to those already familiar with the general syntax. I am not sure whether the gain because the template is intuitive is sufficient to override this concern. Pcb21| Pete 08:11, 16 Aug 2004 (UTC)
I think you missed my point. I recognize that the whale template is implemented in terms of the general templates. My point was that the one advantage the separate whale template gives you (from the perspective of rapid global changes from a single location) is if we wanted to reorder the sections of the taxobox. For example, if we suddenly decided it was vital to have range maps at the top (rather than the bottom) of all taxoboxes, it would be a lot nicer to change a handful of group specific templates than to change every single article. But I don't have any sense for how frequent these taxobox gross rearrangements will be. --Chinasaur 05:30, 17 Aug 2004 (UTC)
I really don't follow you. Let us suppose we have 70 articles that have a range map and use the taxobox templates directly, and 70 articles that use the cetacean template. The general taxobox is rigid about placement - if we wanted to move the range map we would have to change every article using the taxobox templates (basically changing the order the templates are used). However to update the cetacean we would only have to update one page - the cetacea template page.
I.e. the cetacea template is providing exactly the flexibility you are asking for! Pcb21| Pete 08:30, 17 Aug 2004 (UTC)
Yup, that's what I said in the first place. If you look at my original pair of posts above, with separate signatures, the first one is basically saying what I think the drawback of the whale template is (the inflexibility in non-standard additions), and the second is saying what I think the benefit is (the ease of rearrangement of the general templates). I was trying to be thorough by pointing out both sides of the argument, as I saw them. Sorry it wasn't clear. The upshot is that you have to weigh the drawback and the benefit; I don't think the benefit is very substantial because I don't think the general templates ever need to be rearranged, but I could be wrong.

They don't very often. More important would be cases where the high level section of the taxonomy changes - these templates would save us from doing an extensive search and replace. However, I don't think Pete's considered exactly how many new templates would be needed. Even for the Cetacea, his template only applies to species; there'd have to be others for genera and families. Spread that across the board, and you have exactly the situation the split templates were designed to prevent. Josh

Right, I only planned to have them for species. (Indeed that still means really you want two templates, because some species are in classified in a superfamily, and some are not).
I think the shortest possible conclusion of what we've been trying to say is that this template would be useful if you wanted to make some change to all cetacean species articles, but not useful if you wanted to make a change to just one article (it would require hacking).
The latter type of change happens if the taxonomy of the Order changes (e.g. some subfamilies were introduced or something). I guess I am gambling on that not happening very often - the taxonomy is reasonably well understood already at this point in the tree
However I do think it is quite likely that we will make "prettiness" changes e.g. as the MediaWiki software develops. (You might well ask why? - but history has proved that tboxes change style quite a lot! These stylistic changes will affect all articles.
Thus my reading was that the benefits will be reaped fairly often, but the drawbacks not, making it worthwhile. Pcb21| Pete 15:56, 19 Aug 2004 (UTC)

I think I understand Josh's point: for many higher taxonomy changes a species or genera specific template could save you some time. I think I also see what Pete means that for some taxonomy changes, like addition of subfamily branches within your template group, the template would have to be hacked/split and probably wouldn't save you time. Putting these points together, it seems the issue is whether the new taxonomy involves branching or just renaming/rearranging. If there's new branches within your template group, then the existing species template won't save you time. Overall it seems too complicated and arbitrary to try to use the species templates to deal with these changes (also what Josh said I think). On the issue of "prettiness" changes, I would think most of these would be things that could be changed on the general templates, not the species template.

After all this debating, things haven't really changed much. My take is that the species specific template doesn't afford you the benefits that in my mind the templates are really great for. Nevertheless, it's certainly more convenient for you to be able to use them in your editing. But then again, it is less convenient for newbies who want to edit the cetacea pages. All arguments we've heard before. The only thought I have left is if you really wanted them as a handy template, but wanted to avoid confusing newbies, you could use the {{subst:taxobox_cetacea etc.} construction; it wouldn't be a whole lot better than cut and paste, but it's all I can think of. --Chinasaur 16:49, 19 Aug 2004 (UTC)

Well yes I am not going to use them - there is no support for it. However, I just wanted to disagree with "less convenient for newbies who want to edit the cetacea pages". The general taxobox looks complicated, the specific one does not, ergo the specific is easier for newbies. Pcb21| Pete 09:11, 23 Aug 2004 (UTC)

[edit] Update of the Angiosperm Phylogeny Group

For those of you interested in botany, I have made a Word-document of this important update. I have made it available for you to download at the following address : [[3]]. It will remain there for 30 days. JoJan 09:08, 15 Aug 2004 (UTC)

That folder appears to be empty. Yahoo! Briefcase apparently doesn't allow public access to user folders. Is it uploadable to Wikipedia? Also if you have a Yahoo! account, you could upload it to your equivalent Geocities page which is publicly accessible. Thanks! Pcb21| Pete 12:02, 15 Aug 2004 (UTC)
You're quite right. My mistake. I have put it now on a special page in Wikipedia. But wikifying this long file was no small beer. You can find it here Wikipedia_Tree_of_Life/Update_of_the_Angiosperm_Phylogeny_Group.Since the original file was given as 'free content' I don't think there will be any problem with copyright. JoJan 19:48, 15 Aug 2004 (UTC)

[edit] HTML vs. Wiki vs. Taxobox Templates

I don't quite understand what seems to be resistance to template based taxoboxes. Using the templates means that we can easily switch the underlying code just by changing the template pages, so if UtherSRG (or should we say a majority of the project members?) decides at some point that Wiki is better than HTML (or anything is better than anything else), it can be switched over with minimal effort.

Furthermore, as UtherSRG says, the underlying template implementation is of no concern to the enduser unless he/she is doing something pretty nonstandard with the taxobox. Anyone Wiki-literate enough to understand Wiki tables should understand templates well enough to use them too. I for one, understand templates better than tables; templates are inherently more transparent in implementation (since you can go to the template page and see what's being substituted) than Wiki table translations going on in the dark interworkings of MW (okay, it's open source but who's going to bother to go look at the code).

There is one valid issue here, which is that if one wants to do something non-standard within the taxobox, then our current templates are not conducive to Wiki table markup but do allow HTML markup. This is because (I assume) the wikiserver backend doesn't realize that Wiki-table markup is markup at all unless it is within the {| |} closures. The upshot is that HTML is allowed within Wiki markup tables, but Wiki markup will die within HTML tables You can see this from the examples below:

<!-- This will work -->
{| border="1"
|-
| Hello
|-
| World
</tr><tr><td>!!!</td>
|}
Hello
World
!!! 
<!- This will not work in MW1.3 -->
<table border="1">
<tr>
<td>Hello</td>
</tr><tr>
<td>World</td>
|-
| !!!
</td></tr>
</table>

|- | !!!

Hello
World

So this might be a good reason to convert the taxobox templates into Wiki table markup; that way either HTML or wiki markup could be included with template taxoboxes for non-standard info. Once again because of the dark innerworkings of MW, I wouldn't normally even be sure that this would work at all, let alone solve the problem, but since Angela tells us that Wiki table markup is okay within templates for other wikis, it should be okay here. In fact, I would expect that just changing the opening and closing <table></table> tags in the templates to {| |} would enable Wiki table markup within our templates even if we didn't bother to convert the rest of the template (whether that's a good idea is debateable).

As a final point, and I believe Yath will agree, using the template tags makes robot-assisted correction of the entire project space easier than if the tables are left in HTML or, especially, Wiki format. The template tags are easier to parse and more specific than plain HTML or Wiki, thus a taxorobot will not mix up the taxobox with an unrelated table in an article, and will not mix up the <tr> of the placement section with that for another section. Of course, due to the earlier prevalence of other formats, Yath has already written a parser for HTML and Wiki taxoboxes, but template use will still allow more stable parsing in the future.

I see no overriding argument against templates, and will continue efforts on conversion unless more counterarguments are presented.

P.S. Apologies if any of the points made here are obvious or already available elsewhere; I just called like I saw it as things came to me. On the other hand, some of these points are relevant to MetaWikis if not already made, but I'm not really active on those sites, so I wouldn't know where to put them or if they've already been stated. Someone more cosmopolitan is welcome to copy my comments to a meta wiki if they are at all relevant. --Chinasaur 22:58, 15 Aug 2004 (UTC)

As Chinasaur has stated above, template taxoboxes are a good choice. I have not observed any resistance to them; perhaps I am not looking in the right places? At any rate, the helper program wikitool is better now, and can also handle wiki-style taxobox-tables. Looking at what-links-to Templage:Regnum, there are several hundred to do. I urge people to try this program as I likely will not have the endurance to convert all of these myself. P.S. I do not know whether the program can be used in MS Windows. --Yath 03:31, 16 Aug 2004 (UTC)

Yes the bulk of opinion has been pro templates. The main complaint against them is that they are hardly intuitive - ideally a complete beginner is supposed to be able to wade into a wikipage and instinctively understand how to edit it. That is clearly not possible with taxobox templates. Pcb21| Pete 08:01, 16 Aug 2004 (UTC)

Chinasaur, some of your points have been raised and countered/accepted before, and as Pete has pointed out, we're genreally pro-template. It just took us a while to get there, and the fact that the initial MW 1.3 version templates were barely functional was a significant factor. (They still have lots of improvements to make....) However, I disagree that Wiki markup is easier to use than HTML is. HTML tags are names or mnemonics - there is some clue as to what the tag will do in its name. Wiki markup is pure symbol gobbledy-gook - there's nothing inherent or contextual about it that gives the user any help in deciphering what it does or how to use it. The ability to add unconventional portions to a taxobox via new code is, IMHO, not a benefit but a bug: standardized templates should be just that, standardized. Additions should be implemented via the WikiProject that set that standard. As for the allowability of wiki in HTML vs HTML in wiki, I'd say you should post that as a bug to sourceforge. Either should work, or neither should. - UtherSRG 11:57, 16 Aug 2004 (UTC)

I didn't mean to suggest that I favor Wiki markup; I prefer HTML as well, but that's not really the discussion I want to get into. I also agree with you about the MW1.3 templates being not quite adequate. But moving along: The important question is whether people should be able to add non-standard stuff into a template-based taxobox. I think the answer is going to have to be yes; there's too many idiosyncracies and inconsistencies in taxonomy for the template to be 100% canonical. The best we can do is try to educate people on how to make non-standard insertions into the taxobox in a way that won't break if the template is changed. Anyway, that's my opinion, although I recognize it's debateable.
It's a separate issue whether HTML or WikiML should be favored for making non-standard additions. HTML insertions will always be possible since ultimately MW is just translating the WikiML and the Templates into HTML. I think it makes most sense to allow WikiML also, and from I believe this would be easy to implement with our current templates (as I described above; maybe I'll test this on a sandbox version of the templates). --Chinasaur 18:55, 16 Aug 2004 (UTC)

The templates aren't 100% canonical - they're divided into sections which can be used or omitted as necessary, and some of them have several different versions. If a custom mod is needed in one place, it may be needed elsewhere, and so should probably be added to the set of available templates. Whether HTML or WikiML should be favoured is still a separate issue, though. Josh

Okay, good point, so then basically we can deprecate any hacky non-standard insertions to the taxoboxes? In which case the HTML/WikiML underlying code is insignificant as far as I can tell. The HTML hacks within WikiML tables (works) vs. WikiML hacks within HTML tables (don't work) was the only distinction between the two implementations I could think of, and if we don't want hacks, then it doesn't seem to matter. I will still do a sandbox test of the simple {| |} replacement of the outer table tags in our templates and report on the results. --Chinasaur 05:34, 17 Aug 2004 (UTC)
So, the upshot is that WikiML table elements broken up across several templates do not work at all. I'm not sure whether this was obvious to everyone else, but for some reason something Angela said in Archive8 made me think that this would work. Now I see she that when she said WikiML tables are the standard in other wikis, she did not mean a standard for taxoboxes. End results:
  1. Taxobox templates must be written in HTML tables
  2. Thus, HTML hacks can never be prohibited in taxoboxes
  3. WikiML hacks will never work in taxoboxes
  4. Perhaps this is something no one cared about in the first place and was entirely based on my misunderstanding of Angela, but anyway that's the upshot and hopefully this is a dead subject.

--Chinasaur 14:04, 19 Aug 2004 (UTC)