Template talk:Taxobox

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Cacopinae and others[edit]

The template: {{Taxonomy/Cacopinae}} is deprecated, and yet a few other taxonomy templates transclude it. [1]I have no idea where to fix this, since the toolserver link [2] doesn't work. — Preceding unsigned comment added by Debresser (talkcontribs) 11 January 2014

This can be fixed by amending the "child taxa" template like this, and then making a null edit on each of the pages that still appears to transclude the deprecated taxon template. --Stemonitis (talk) 08:21, 16 December 2014 (UTC)

Dagger Usage?[edit]

In some taxoboxes, such as the one at Tyrannosaurus, there's a dagger (†) next to a few of the classification names. As someone who isn't familiar with paleontology, I had no idea what this meant, and it took me awhile to figure out that it designated an extinct taxon. It's useful information that non-specialist users would find valuable, so I think we should try to make it more accessible. I can think of two ways to do this:

  1. Dejargonize and simply say "Tyrannosaurus Rex (extinct)"
  2. Link the dagger to something extinction-related, like List of extinct species or Extinction.

Perhaps some more experienced editors could weigh in on which might be a better option? And once a decision is made, maybe we could attract the attention of someone with a bot? Origamidesigner (talk) 01:26, 14 December 2014 (UTC)

Linking to "Extinction" is probably the best option. Abyssal (talk) 02:41, 14 December 2014 (UTC)
Linking it is by far the preferable, and more professional of the options--Kevmin § 03:42, 14 December 2014 (UTC)
There was a recent discussion on this topic at WT:TOL#Extinction daggers in taxoboxes. Several people (including myself) argued that it would be better not to include daggers in the main part of the taxobox at all, but only in lists that include both and extinct and extant taxa, and then only after the symbol has been explained. Linking to anything except is rather easter-egg-y, and will be impenetrable in print, and this particular meaning of that symbol is not widely understood. --Stemonitis (talk) 18:24, 15 December 2014 (UTC)

Foraminifera taxonomy boxes[edit]

I am trying to edit some Foraminifera orders to add the class and make the taxonomy consistent across Wikipedia and tied in to a source. I am trying to add this text to the Order Rotaliida's taxobox, to replace the current taxonomy scheme:

| domain = [[Eukarya]] | regnum = [[SAR supergroup|SAR]] | supergroup = [[Rhizaria]] | phylum = [[Foraminifera]] | classis = [[Globothalamea]]

However, every time I preview I get some weird column spans instead of a taxonomy box. What is going on here?

I also wanted to use a set of code for inserting the citation for this taxonomy, WoRMS use of the Foram DB, but the code does not generate a citation. Maybe this is tied in with the prior error? Can I place this code in the taxonomy box? It should go after the class, as it is specifically a citation for the placement of the order in a Foram class.

{{cite WoRMS |author= Pawlowski, Holzmann, Tyszka|year= 2013|title= Globothalamea|id= 744104|accessdate= January 18, 2015|db=forams}}

Any help would be appreciated.

MicroPaLeo (talk) 21:31, 18 January 2015 (UTC)

Hello, MicroPaLeo. The taxobox is an example of a Wikipedia Template, {{taxobox}}, which has a large range of possible parameters, but that does not contain 'supergroup'. If the taxon rank you want is not in that template, you can either argue (on the template talk page Template Talk:Taxobox) for adding it to the template, or you can just use 'unranked'. I don't know about the WoRMS: my reading of the template documentation suggests that the 'authority' fields just take text, but I may be wrong. --ColinFine (talk) 22:26, 18 January 2015 (UTC)
Hi Colin, I am using "supergroup" rather than "infrakingdom" because that is what Wikipedia uses for Rhizaria, so I don't think that can be the problem. Unranked would probably work, and I will try that.
I don't understand what you are saying about WoRMS. There is no authority field. MicroPaLeo (talk) 22:31, 18 January 2015 (UTC)
"unranked" does not work, either. MicroPaLeo (talk) 22:38, 18 January 2015 (UTC)
Sorry, MicroPaLeo, this is a complicated area. {{taxobox}} doesn't have parameters 'supergroup', 'infrakingdom', or 'unranked' (my mistake), but it does have 'subregnum', and 'unranked_regnum', 'unranked_phylum' etc. On the other hand, Rhizaria doesn't use that template, but a different one {{automatic taxobox}}, which appears to work very differently. I have not looked into this, but my guess is that this is a more flexible approach that somebody has been working on, but it has not been put in many articles yet. I'm afraid this is an example of the general lack of consistency across Wiipedia. --ColinFine (talk) 00:13, 19 January 2015 (UTC)
@MicroPaLeo: The taxobox, as a tpye of infobox, should succinctly summarize the article and place the taxon into context. Not all higher taxonomic ranks need listing in the taxobox, and in general only the focal taxon should have an authority listed. If there are taxonomic disagreements or conflicting schools of thought, those should be discussed in text, even it means arbitrarily choosing one classification scheme for the Taxobox. If you wish to place a footnote after an authority for taxa that do have fields (e.g. "subregnum_authority), those can be added with a simple <ref> after the Author and Year., e.g. Pawlowski et al. 2013<ref>{{cite WoRMS |author= Pawlowski, Holzmann, Tyszka|year= 2013|title= Globothalamea|id= 744104|accessdate= January 18, 2015|db=forams}}</ref> Hope this helps! --Animalparty-- (talk) 01:19, 19 January 2015 (UTC)
Yes, I did not use the ref tags, just the brackets. MicroPaLeo (talk) 18:55, 19 January 2015 (UTC)

Discussion from Teahouse, can someone here help?[edit]

Thanks, MicroPaLeo (talk) 00:18, 19 January 2015 (UTC)

Hi MicroPaLeo, does this work (and did I get the ranks right)? I had to switch usage to {{Automatic taxobox}} since {{Taxobox}} doesn't seem to support custom ranks as mentioned above. Usage instructions for {{Automatic taxobox}} is in the link, if you are unfamiliar with it. -- OBSIDIANSOUL 01:06, 19 January 2015 (UTC)
Yes, that is correct. I would have left out Retaria, but it works both ways. Now I need to add WoRMS as the citation for the class, preferably in the taxobox. Do you know how to do this? Thanks. MicroPaLeo (talk) 03:44, 19 January 2015 (UTC)
The problem is that every bit of the classification really needs sourcing. Who says that SAR is a Kingdom? There simply is no current consensus as to such "classifications". It would be much better to treat all of these higher levels as unranked clades and then discuss alternatives, with sources, in the text. Peter coxhead (talk) 11:37, 19 January 2015 (UTC)
In every order article? Why? There is no consensus for anything in the forams, but WoRMS is as good as any for a citation of classes. The forams article is the place to discuss, in depth, the current state of forams classification, with the classes versus systems without classes with citations and depth, the class articles can have a moderate discussion of the classes and classification at that level, and something in the orders, but to cite every clade in the order articles and discuss every one when foram orders on Wikipedia have almost no descriptive information is not what a general encyclopedia is about Although a cladist at heart with my own research, my understanding in writing for Wikipedia is that I need sources. I picked WoRMS, as a secondary database compilation used frequently on Wikipedia. But if you have a good source for the unranked clades, I will use that instead of WoRMS. But, no, I am not going to cite every clade in the orders articles. MicroPaLeo (talk) 13:58, 19 January 2015 (UTC)
So am I correct in assuming that you're adding these ranks (Bikonta, Corticata, SAR, and Rhizaria) only to foraminiferan articles to make it consistent with higher classifications? Or are you also revising the articles on other "chromalveolates" to make them all consistent? If the case is the former (i.e. you're only working on Foraminifera), I would agree with Peter. It's better to treat all these higher groups as unranked clades for the moment, since there is far from anything resembling consistency in the articles dealing with "chromalveolates" in Wikipedia and outside sources. The ranks can always be defined later on when it stabilizes. That shouldn't affect anything else on the lower levels (class, order, etc.)-- OBSIDIANSOUL 14:38, 19 January 2015 (UTC)
Same as to Peter, just provide a source. It does not matter that you or I prefer unranked clades, it matters that general knowledge encyclopedias and floras and faunas cite sources for their taxonomies, and not primary sources. MicroPaLeo (talk) 15:23, 19 January 2015 (UTC)
The question is which source to follow. And that can not be easily answered for higher ranks. If you are only revising articles on foraminiferans (which is relatively stable), the higher ranks should accurately reflect the current lack of consensus. SAR for example, can also be treated as Harosa, as the article states. And majority of the articles on protists and higher ranks actually use the Chromalveolata as kingdom scheme (Adl et al., 2005), albeit with significant discussions on other schemes, not SAR as kingdom (Adl et al., 2012). For example Heterokonta, Haptophyta, and Alveolata, and even the article on Eukaryota. Just worried that only partially revising these articles can lead to even more confusion, though {{Automatic taxobox}} itself was created specifically to avoid that kind of thing. Ideally, as Animalparty stated above, articles on lower ranks should only discuss their relationship to their immediate parent taxon, leaving the discussion on higher classifications on their respective articles. So e.g., the discussion on the taxonomy of Rotaliida should really only concern itself with its placement within Globothalamea and so on.
As for your second request "Now I need to add WoRMS as the citation for the class, preferably in the taxobox." - you can't do that, AFAIK, for automatic taxoboxes. And I don't think you should. The citation should be added to text in the body of the article, not the taxobox (because of the limited space).-- OBSIDIANSOUL 15:59, 19 January 2015 (UTC)
No one is working on foram articles on Wikipedia. WoRMS is used on Wikipedia, it is a legitimate secondary source as a citation for the classes. Peter is the one who wants all higher ranks discussed in the classes article, please re-read my first response to him in which I advocate what you say. Taxoboxes on Wikipedia do have the authorities with a citation for it, the automoatic taxobox even offers an argument for it. I just want to use the WoRMS template for it, not rewrite Wikipedia policy. MicroPaLeo (talk) 16:28, 19 January 2015 (UTC)
@MicroPaLeo: that's not what I meant. If you insist on using SAR as a Kingdom, then you should source it. Much better, however, is to stick to unranked clades, which have better consensus at present. Peter coxhead (talk) 20:17, 19 January 2015 (UTC)
I do not insist on anything. Wikipedia uses kingdom and SAR. I did not find a secondary source with unranked clades. If you have one, I am happy to use it. "The problem is that every bit of the classification really needs sourcing." This is where you seem to be saying what you said." (Emphasis in original.) MicroPaLeo (talk) 21:07, 19 January 2015 (UTC)
That's actually the problem. Wikipedia doesn't. Some articles use SAR as the regnum. Some use Chromalveolata. And still others use Rhizaria. The only thing they seem to generally agree on is the order of the ranks, which is what's more or less truly important in phylogeny anyway. Then again, protists are some of the least worked on articles on here. Since I don't usually delve into them, I won't presume to recommend what classification to use. But whatever it is, the important thing is that they be consistent across all related articles.
If you do use WoRMS exclusively for the taxoboxes, all articles of related taxa should also use them. And of course where necessary, taxonomical disputes should be discussed (though that seems to be more or less covered already in articles on the higher taxa).
This is to avoid problems introduced like how Rotaliida currently has SAR as kingdom. But Foraminifera identifies its kingdom as Rhizaria. Same with Retaria. Corticata on the other hand, lists Archaeplastida and Chromalveolata as its supergroups. Despite the Chromalveolata article identifying itself also as a kingdom.
I think what Peter meant was that since there is no consensus as to how to treat these groups, it might be better to leave off naming the ranks in the meantime, same as how plants currently use (unranked) for higher groups to minimize the number of times those articles have to revised while Angiosperm Phylogeny Group is still busy rearranging them. It wouldn't affect the quality of the articles, the order would still be preserved, and it prevents contradictions across articles.-- OBSIDIANSOUL 22:33, 19 January 2015 (UTC)

I am not going to call things unranked without a source that calls them unranked. It is not appropriate for a general resource to use my or your original research for any reason. I can only use an established source, and for taxoboxes it cannot be primary research. Wikipedia calls SAR a kingdom in its taxobox, and attaches a source to this, the automatic taxobox uses kingdom, also. If this is wrong, it can be fixed. MicroPaLeo (talk) 00:26, 20 January 2015 (UTC)

The automatic taxobox calls it a kingdom because I inputted it that way, heh.
Anyway, looking at sources, it is actually just referred to as "clade", "group", or "supergroup" not kingdom (including the sources of the SAR supergroup article, e.g. Burki et al., 2007; Hampl et al., 2009; and Archibald, 2009). The name SAR supergroup itself implies that it is informal, as SAR is an acronym (which can be alternatively spelled RAS in some sources), and of course, the "supergroup" part of the name.
Here are all the sources I can scrounge in 20 minutes. All of them call SAR just "clade", "supergroup", "group", "monophyletic megagroup", "assemblage", etc.: Manson's Tropical Diseases, Immunity to Parasitic Infection, Campbell Biology, Genomic Insights into the Biology of Algae, Evolutionary Biology
A more formal treatment under Cavalier-Smith, 2010 names it the subkingdom Harosa. Which incidentally, is the system used by WoRMS (though WoRMS mixes it with older systems). The more comprehensive and newer Adl et al., 2012, on the other hand, formalizes the name to "Sar" (not an acronym), but does not use formal ranks (Sar is a "supergroup").
Note that I am not advocating that it be called one way or another, just that it be consistent across articles. Because again, Wikipedia is actually far more confused when it comes to handling ongoing taxonomic revisions, and what one article uses shouldn't be the sole basis for how we treat it on all subsequent cases. I would actually recommend following Adl et al., 2012 as that seems to be at least semi-official and was created specifically to temporarily stabilize eukaryote higher taxonomy.
The hierarchy of Adl et al., 2012 is identical to your earlier request (Eukarya > Sar > Rhizaria > Retaria > Foraminifera > Globothalamea > Rotaliida). Except that it does not use formal ranks. If you agree to this, I can easily change the automatic taxobox pages in question, and all subsequent automatic taxoboxes will also use the same system. -- OBSIDIANSOUL 02:31, 20 January 2015 (UTC)
Let's see if I got this, use a primary source, discuss every breath I take with you before I take it until you say "breathe," and as long as I agree to do what you demand without your, of course, advocating anything, and also agree to edit 10,000 articles that have been ignored forever, or consider myself denied of you permission to improve foram decriptions on Wikipedia and not one of the anyones allowed to edit your foram articles? MicroPaLeo (talk) 03:38, 20 January 2015 (UTC)
I didn't realize you were perceiving this as hostile and/or personal. It's not. Calm down. Nor am I denying you anything, I already filled your request above. This is an attempt to "finalize" how we treat these taxa, since automatic taxoboxes are automatic. Everything inputted in it will display the same way in different articles. The question is simple: should Sars/SARS be treated as a kingdom (given that sources don't)? And if so, what do we do with other articles that contradict that approach (including multiple foraminiferan articles that use Rhizaria as the kingdom in their taxoboxes)?
As a side note: Adl et al., 2012 is a review/synthesis of previous papers, it's mostly a secondary source. WP:PRIMARY sources are also not forbidden. For taxonomic articles, they are usually preferred to aggregating databases (which are oftentimes out of date). For the purposes of this discussion, all the sources I gave above are secondary, with the exception of the original paper (Burki et al., 2007).
Again, set aside any preconceptions about the discussion above. None of this is hostile. If you don't want to deal with this and just work on foraminiferans (which I have never touched an article of, and know very little about), I can take this to WP:TOL instead and let them hash it over. If anyone cares enough that is. Also note that I'm asking you because you work on these taxa. I don't. I merely came here because you needed help with the taxobox. If that came off as pestering or possessive, that wasn't the intent and I apologize.-- OBSIDIANSOUL 04:47, 20 January 2015 (UTC)

I did not note that I was emotionally uncalm, but as you have moved onto my emotional stability, I stopped reading--a little passive-aggressive and off topic for my tastes. MicroPaLeo (talk) 04:58, 20 January 2015 (UTC)

Sigh. -- OBSIDIANSOUL 05:08, 20 January 2015 (UTC)

IUCN Red List missing[edit]

I'd like to add a hidden cleanup category to this template, but I'd like to get consensus here first. The category would be placed if the taxobox doesn't have anything whatsoever about the IUCN Red List status: any of the normal options, even Data Deficient, would prevent the category from appearing, and we could also have a parameter (e.g. omitiucn=yes) to prevent the category from appearing if we had a good reason to omit the Red List. Basically, the category would be used just to find pages where we haven't addressed Red List status yet. Nyttend (talk) 18:17, 29 January 2015 (UTC)

I'm not sure that it will produce the kind of maintenance category you're hoping it would be. The vast majority of species haven't been (and probably never will be) addressed by the IUCN. Other taxoboxes have more specific statuses, such as Western Australia's Declared Rare and Priority Flora List. Unless you can weed these out in a way easier than adding another parameter, the category won't help in the goal of adding the IUCN status to pages that have been assessed but don't have the info yet. It's probably simpler to go through the IUCN list and compare it to articles we have. Rkitko (talk) 18:26, 29 January 2015 (UTC)
If they're not addressed, wouldn't they be Data Deficient? Or even if they're not Data Deficient, couldn't we add a feature that, if activated, would say that the IUCN hasn't addressed the species? If we've chosen to use other lists, e.g. the Declared Rare etc. list, couldn't we add a feature whereby the template doesn't add the cleanup category when another list is used instead? Again, I'm only attempting to ensure that a human has checked the species' conservation status, that Red List status isn't simply forgotten. I'm satisfied as long as a taxobox reflects the IUCN's statements, as long as it notes that they haven't made a statement, or as long as its status is intentionally omitted. Not all of the WA list's potential entries mention their list status in their taxoboxes, either; Eremophila youngii has Priority Four – Rare Taxa status according to the article text, but no mention in the infobox. Nyttend (talk) 19:17, 29 January 2015 (UTC)
There is status = NE (not evaluated), but I've never felt that it's a useful distinction as most species are not evaluated and it would just add unnecessary information to the taxobox. The same would be true for species not evaluated under any of the other systems -- the point is to highlight species of conservation concern. Instead of a category that couldn't distinguish between those articles that shouldn't have a conservation status box because they're not evaluated and those that should but don't yet, a simpler solution is to get someone to scrape the data from IUCN for the species they have evaluated and compare it to the articles we have; if our article has a conservation status that agrees with the current IUCN list, it's removed from the list and the remainder are left for humans to check over. As for Eremophila youngii, WP:SOFIXIT. I just don't see the need or utility of a category for this purpose. Rkitko (talk) 20:01, 29 January 2015 (UTC)
Taxoboxes are often cluttered enough already, and cause layout problems in short articles, so I'm strongly against adding unnecessary information, which "NE" or "data deficient" would be. So I agree with with Rkitko: I don't see the point of such a category. Peter coxhead (talk) 20:10, 29 January 2015 (UTC)
We're already supplying "data deficient" in many articles; click my link for an example. If it's not evaluated, we could replace "Conservation status" with "Conservation status not evaluated", or something to that effect. Your suggestion of scraping their website is good for one-time work, but it won't be enough for articles that get the taxobox added after we use the scrape. Perhaps we could dump such a list on a wikipage, mark each line, have a bot make all the edits once the list's all marked up (it does all the editing work after we humans make the actual decisions; comparable to "Tons of links go to the wrong page" at Wikipedia:Bot requests/Archive 48), and after all those pages are marked with status or not-evaluated, we add the ability to include the category so that future uses are detected and fixed. Final note, I'd be happy to help with evaluating pages from a website scrape, but as I'm not a regular participant here, I don't know how best to implement the WA list. Nyttend (talk) 20:31, 29 January 2015 (UTC)
If I have time, I'm looking at reviving Beastie Bot and doing a full audit of taxobox categories vs IUCN's. (It's been eons since it ran.) A category for articles without status info would not be particularly helpful for that though. —Pengo 21:08, 29 January 2015 (UTC)
Thank you Nyttend, for your initiative on this. But I agree with Pengo that using sensible bots is a more functional and effective way to go than creating categories. --Epipelagic (talk) 08:50, 30 January 2015 (UTC)

Modules[edit]

How might we add a |module= parameter to this template, so that, for example, on Enterobacter aerogenes, the {{Bacterial labs}} template may be embedded? Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 12:30, 2 February 2015 (UTC)

I'm not sure embedding such an infobox is in line with what a Taxobox is for: the content seems more descriptive than taxonomic, more akin to {{Mycomorphbox}} (see e.g. Agaricus bisporus for use). There is a large number of conceivable data we could include in Taxobox for any given taxon (number of chromosomes, genome size, mating system, number of limbs, leaf shape, color, etc), but that we don't for the sake of brevity. --Animalparty-- (talk) 04:40, 18 February 2015 (UTC)
I agree with Animalparty here. Although {{bacterial labs}} is clearly an informative template, I'm doubtful that the taxobox is the place to put it. Taxoboxes are already cluttered. Andy, is there a good reason why it cannot stand alone in an article? Peter coxhead (talk) 09:41, 18 February 2015 (UTC)