Wikipedia talk:Automated taxobox system/Archive 5

quickTax templates
Do Taxonomy/Chordata (quickTax) and Taxonomy/Animalia (quickTax) do anything, or should they be deleted? Plantdrew (talk) 04:55, 14 November 2021 (UTC)
 * They aren't used. I assume they are left over tests from the early days of the automated taxobox. —  Jts1882 &#124; talk 09:29, 14 November 2021 (UTC)

Incertae sedis
How do we show Incertae sedis taxa?Leomk0403 (Don't shout here, Shout here!)  01:25, 7 December 2021 (UTC)
 * see Automated taxobox system/advanced taxonomy. --awkwafaba (📥) 04:53, 7 December 2021 (UTC)

Family for user script
Hello. I wrote a user script, User:Novem Linguae/Scripts/AddTaxobox.js, that adds taxoboxes to articles. Assuming it knows the genus and species from the article title, what is the best way to grab the subfamily, and if that's not found the family, and if that's not found the order, etc? Sometimes the genus doesn't have a category, stub, etc. so it can be useful to crawl back up the tree and then check again, until we find the category and stub needed. Thanks. – Novem Linguae (talk) 09:11, 24 December 2021 (UTC)
 * it's often quite difficult to find the category and/or stub, because they are not readily predictable, given that both are chosen to produce a "reasonable" size of category. You can move up the tree using, or in Lua  . Thus starting from, say, Bellis:
 * If you want a specific rank, say, order, then use (RANK must be lowercase Latin). For example:
 * The problem seems to me that you will have to repeatedly check for the existence of a category and a stub template, and checks for existence are expensive operations, which are limited in number as per mw:Help:Extension:ParserFunctions. Peter coxhead (talk) 09:37, 24 December 2021 (UTC)
 * Awesome. Since it's a user script, I can use the API to get around ifexists limits. I can submit one at a time via mw:API:Expandtemplates. Your info above helps a lot, thanks for the detailed intro. – Novem Linguae (talk) 09:51, 24 December 2021 (UTC)
 * A script can also get the parent of a genus from the taxonomy template. That would be of the form Taxonomy/GENUSNAME, which must exist if the speciesbox is to be added correctly. Then it can get the rank and, if necessary, next parent from the taxonomy template for the parent. —  Jts1882 &#124; talk 09:54, 24 December 2021 (UTC)
 * More specifically you can use this search for genus Giraffa and Taxonomy/Giraffa and then get the parent with regex like . —  Jts1882 &#124; talk 10:14, 24 December 2021 (UTC)
 * Wow, that's denser than I expected. There's like 20 hidden levels in your example. Yeah, grabbing them all in one query and then regex-ing is a great idea. – Novem Linguae (talk) 10:36, 24 December 2021 (UTC)
 * What are you seeing? That linked search should only be returning the wikitext of the template.
 * The default search returns a lot more because it gets the content of the viewed template page, which includes the whole hierarchy as a table , and all the links . —  Jts1882 &#124; talk 10:54, 24 December 2021 (UTC)
 * I was referring the human readable page at Taxonomy/Giraffa. I hadn't tried the API query yet. Thanks for giving sample output above, that's good info. I may end up going with prop=text and regex-ing that, so I can get all the taxa in one go. – Novem Linguae (talk) 13:25, 24 December 2021 (UTC)
 * you can also get all the taxa in one go as a comma-separated list of the form "taxon-rank" with (which was really only designed for debugging). Thus:
 * But you shouldn't need to go all the way up to find a category and stub template. Note also that you need to strip off any qualifier (i.e. any part after a "/") from a taxon name, because it exists only to select one of a set of variant taxonomy templates. Peter coxhead (talk) 16:35, 24 December 2021 (UTC)
 * That's perfect. When querying databases, it's like 1 second round trip, so the less queries the better. I can do that query to get all the taxa I need, then do another query to see if various Template:stub, :Category, and navbox pages exist, then go from there. 2 queries, 2 seconds. Thanks for the ideas. – Novem Linguae (talk) 01:16, 25 December 2021 (UTC)
 * It's working great. Thanks for your help. Happy holidays. – Novem Linguae (talk) 03:29, 25 December 2021 (UTC)
 * More specifically you can use this search for genus Giraffa and Taxonomy/Giraffa and then get the parent with regex like . —  Jts1882 &#124; talk 10:14, 24 December 2021 (UTC)
 * Wow, that's denser than I expected. There's like 20 hidden levels in your example. Yeah, grabbing them all in one query and then regex-ing is a great idea. – Novem Linguae (talk) 10:36, 24 December 2021 (UTC)
 * What are you seeing? That linked search should only be returning the wikitext of the template.
 * The default search returns a lot more because it gets the content of the viewed template page, which includes the whole hierarchy as a table , and all the links . —  Jts1882 &#124; talk 10:54, 24 December 2021 (UTC)
 * I was referring the human readable page at Taxonomy/Giraffa. I hadn't tried the API query yet. Thanks for giving sample output above, that's good info. I may end up going with prop=text and regex-ing that, so I can get all the taxa in one go. – Novem Linguae (talk) 13:25, 24 December 2021 (UTC)
 * you can also get all the taxa in one go as a comma-separated list of the form "taxon-rank" with (which was really only designed for debugging). Thus:
 * But you shouldn't need to go all the way up to find a category and stub template. Note also that you need to strip off any qualifier (i.e. any part after a "/") from a taxon name, because it exists only to select one of a set of variant taxonomy templates. Peter coxhead (talk) 16:35, 24 December 2021 (UTC)
 * That's perfect. When querying databases, it's like 1 second round trip, so the less queries the better. I can do that query to get all the taxa I need, then do another query to see if various Template:stub, :Category, and navbox pages exist, then go from there. 2 queries, 2 seconds. Thanks for the ideas. – Novem Linguae (talk) 01:16, 25 December 2021 (UTC)
 * It's working great. Thanks for your help. Happy holidays. – Novem Linguae (talk) 03:29, 25 December 2021 (UTC)
 * That's perfect. When querying databases, it's like 1 second round trip, so the less queries the better. I can do that query to get all the taxa I need, then do another query to see if various Template:stub, :Category, and navbox pages exist, then go from there. 2 queries, 2 seconds. Thanks for the ideas. – Novem Linguae (talk) 01:16, 25 December 2021 (UTC)
 * It's working great. Thanks for your help. Happy holidays. – Novem Linguae (talk) 03:29, 25 December 2021 (UTC)

30 December 2021 use stats update
30 December 2021 update

Mammal subprojects with articles tagged for both mammals and subproject:

Method: For the most part I use Petscan to search for articles with a talk page banner for a particular Wikiproject and either Taxobox, or any of Automatic taxobox+Speciesbox+(Infraspeciesbox and/or Subspeciesbox (depending on whether botanical/zoological code is relevant)), and record the results. Example search for algae with automatic taxoboxes (search terms are in the Templates&Links tab in Petscan). For viruses, I search for Virusbox rather than the other automatic taxobox templates. For plants, I sum the results for the Plants, Banksia, Carnivorous plants and Hypericaceae projects. "Total" is derived from the Template Transclusion Count tool (https://templatecount.toolforge.org/index.php?lang=en&namespace=10&name=Speciesbox#bottom e.g. results for Speciesbox), and is not actually sum of the results for individual projects (some articles have talk page banners for multiple Wikiprojects, and would be counted twice if rows were summed). I started compiling these stats in April 2017, and have been updating roughly every six months since December 2017. I've kept my method consistent; perhaps I should have included all of the automatic taxobox templates (Hybridbox, Ichnobox, etc.), but I didn't do so at the beginning, and the other templates aren't used in very many articles.

Caveat: The remaining manual taxoboxes in projects with a high percentage of automatic taxoboxes mostly have some kind of "problem". I have periodically reviewed all the manual taxobox articles in projects with less than 141 manual taxoboxes, and chose not to convert them to automatic taxoboxes at that time (however, it has been awhile since my last review, so there probably a few recently included articles I haven't reviewed). "Problems" may include:
 * Fossil taxa; fossil classifications may be derived from multiple sources and present classification on Wikipedia may include mutually incompatible hypotheses. Fossil taxa are often not be linked from extant parent taxa.
 * Synonymy; there is some obvious synonymy issue; e.g., a species is in a genus which redirects (as a synonym) to another genus; maybe the species article needs to be moved or maybe the genus should be reinstated
 * Common names; articles with common name titles may not correspond to taxa, but still have manual taxoboxes. In some cases Paraphyletic group may be appropriate, in others the taxobox should be removed
 * Parasite and pathogens; article on parasites and pathogens may be tagged for the WikiProject of the organisms they infect. Higher level taxonomy templates for the parasites may not yet exist, and the classification presented in manual taxoboxes may not be up to date.

I have some detailed notes breaking remaining plant manual taxoboxes down by family at User:Plantdrew/Plant automatic taxobox progress. Less detailed notes at User:Plantdrew/Animal automatic taxobox progress that break animals down by phylum, insects and fish by order, and palaeontology and marine life by overlap with other projects. There are a bunch of animal groups with manual taxoboxes in the double digits if anybody is interested in a small task in converting manual taxoboxes to automatic. Plantdrew (talk) 22:14, 30 December 2021 (UTC)


 * What happened with ToL losing so many automatic boxes? Was someone purging the category? --awkwafaba (📥) 02:33, 31 December 2021 (UTC)
 * In the 30_June_2021_use_stats_update there were 129 automatic and 59 manual taxoboxes (total 188) and now it's 74 and 11 (85). All are down so I think you must be right about the category changes. Most (if not all) with automated taxoboxes pages with TOL and another project (e.g. Mammals, Amphibia). The manual taxoboxes include some with multiple projects (e.g. Neokaryotes has TOL, Animal, Plant, Fungi, Algae and Microbiology) and a few orphaned taxa, either because they are uncertainly placed (e.g. Cryptista, which has a taxonomy template since 28 Oct 2021) or things like Ediacaran fossils (Nimbia occlusa, Petalonamae). —  Jts1882 &#124; talk 12:10, 31 December 2021 (UTC)
 * I'm never sure if people are going to want explanations for particular rows. TOL had long had several dozen foraminiferans tagged. I wasn't sure if the Microbiology project should include just bacteria or single celled eukaryotes as well (versus tagging single celled eukaryotes for TOL). Previously unassessed single celled eukaryotes were tagged for Microbiology, before and after 1 January 2019 (net gain of ~2400 articles to Microbiology between my mid 2018 and mid 2019 stats). I think Akwafaba did that? I removed the TOL tag from forams a few months ago and replaced with Microbiology, Marine life, and Palaeontology, as appropriate.
 * The other single row I thought might inspire questions is Cats. All articles were using automatic taxboxes in my last update. Two have been reverted manual. The articles are about populations that were formerly treated as subspecies. I'm not sure how to best handle these cases. There are several other mammal populations with manual taxboxes, mostly bears. Plantdrew (talk) 17:39, 31 December 2021 (UTC)
 * The cats ones are the result of some lumping of cat subspecies by the IUCN Specialist Cat Group. This has left some very well known cats such as the Bengal or Siberian/Amur tiger being regional populations of one subspecies inhabiting the Asian mainland. Similarly the Gulf Coast jaguarundi is no longer a subspecies. We really should have a standard way of handling such populations, which are of importance for conservation and have names with broad public recognition. It can be done using Biota infobox but I don't want to use this template directly in mainspace as it parallels the other taxoboxes, but only in templates like paraphyletic group. The latter could also handle it, but would be a confusing name. Perhaps a template called something like population taxobox or informal group or taxobox misfits would be more appropriate. —  Jts1882 &#124; talk 13:07, 1 January 2022 (UTC)
 * There was a brief discussion at Talk:Barbary_lion. —  Jts1882 &#124; talk 13:11, 1 January 2022 (UTC)
 * I would think any microscopic organism would be included in WP Micro. Even if you get super-strict, you included many domains (bacteria, archaea, viruses in their subproject…) so the project is already paraphyletic.  It’s more like WPs Palaeontology and Marine Life that depend more on other features than taxonomy.  --awkwafaba (📥) 15:05, 1 January 2022 (UTC)

Automatic taxobox support in other language wikipedias
Hi All, I've noticed that in some language wikipedias other than English (I checked German and Czech), automatic taxoboxes appear not to be supported. Two questions: are automatic taxoboxes an English wikipedia-only thing? Do we have plans for making it available for more/all languages? (I speak as a fanboy of automatic taxoboxes.) Ben morphett (talk) 02:28, 31 December 2021 (UTC)
 * The automated taxobox requires a large number of support taxonomy templates. The English wikipedia has at least 80,000 templates. Any Wikipedia can import the relevant templates and modules, but it is difficult. A number of Wikipedias have made the attempt (this list of wikipedias sitelinked to the wikidata item for the template is long), but few seems to have been successful. A quick survey finds:
 * Successful
 * tr: https://tr.wikipedia.org/wiki/Filgiller, https://tr.wikipedia.org/wiki/Memeliler
 * zh: https://zh.wikipedia.org/wiki/%E8%B1%A1
 * sco: https://sco.wikipedia.org/wiki/Afrotheria (but limited use due templates)
 * Implemented but strange machine code errors
 * la: https://la.wikipedia.org/wiki/Abarema, 	https://la.wikipedia.org/wiki/Anopheles
 * Alternative method
 * ru: https://ru.wikipedia.org/wiki/%D0%A1%D0%BB%D0%BE%D0%BD%D0%BE%D0%B2%D1%8B%D0%B5
 * Wikidata. A number of other Wikipedias use Wikidata to automate the classification (Catalan, Hebrew Wikipedias), which has its own problems, but can work for a limited classification for main taxon ranks.
 * There was a recent discussion about how to internationalise the system: Wikipedia_talk:WikiProject_Tree_of_Life. This involved replacing the taxonomy templates with Lua module pages, but would have been harder to edit than the current system, so is now on hold indefinitely. —  Jts1882 &#124; talk 08:06, 31 December 2021 (UTC)
 * Thanks. Ben morphett (talk) 00:48, 1 January 2022 (UTC)
 * I'll just note the irony of the fact that the Latin wikipedia has weird technical problems. You might think Latin would be a no-problems wikipedia for taxoboxes, because after all, clade names are already in Latin.  :-)  Ben morphett (talk) 04:24, 1 January 2022 (UTC)
 * Irony or appropriate? I've done some template archaeology on the Latin wikipedia. It actually has a functioning version of 2011 template, well before the Lua implementation. I found the source of the error in those taxoboxes, which is la:Formula:Taxobox/taxonomy/3. I'm unsure of the correct fix, but noincluding or emptying the template did the trick. It's only used on half a dozen pages, which now work. I think we consider this a living fossil of the pre-Lua automated taxobox. —  Jts1882 &#124; talk 13:20, 1 January 2022 (UTC)

Template:Taxonomy/Gafrarium was created today (for Gafrarium pectinatum), and is the first taxonomy template I've noticed that was first created on another language Wikipedia (zh in this case), and imported to en.wiki. Looking at the creators contributions there are a few others, but most had the en version created within a few days of the zh version. The Gafrarium template was created on zh.wiki four years ago. Plantdrew (talk) 20:35, 1 January 2022 (UTC)

Background
In a taxobox, the automated taxobox system automatically inserts † before the name of an extinct taxon when the taxonomy template for that taxon has yes (or true) – see Tyrannosaurinae for an example, where four lines of taxa have a † based on their taxonomy templates.

Species and lower ranks don't have taxonomy templates (except in a handful of very exceptional cases), so there is no taxonomy template from which to obtain the extinct status. Currently, there are two ways in which the required &dagger; will be inserted:
 * 1) The parent rank, usually the genus, is extinct and is marked as such in its taxonomy template, as for example the speciesbox at Minorcan giant dormouse.
 * 2) The taxobox has extinct with a nonblank value, as for example the speciesbox at Steppe bison.

There are a significant number of taxoboxes for recently extinct species (or lower ranks) that have EX but not NONBLANK_VALUE, so don't have the appropriate &dagger;. An example is [//en.wikipedia.org/w/index.php?title=Stenocarpus_dumbeensis&oldid=1055240264 this version of Stenocarpus dumbeensis].

Proposal
The automated taxobox templates for species and lower ranks should be changed to allow EX to cause &dagger; to appear before the target taxon without the need to set extinct.


 * Would this be inherited by virusbox? The taxobox in Smallpox is a little awkward at the moment, and needs to use '|taxon=' rather than '|parent=' + '|species=' because there's no other way (that I can work out) of marking the species extinct, but not the genus. And of course this necessitates a species level taxonomy template. YorkshireExpat (talk) 17:59, 10 January 2022 (UTC)
 * The smallpox virus is only "EW", extinct in the wild; it still exists in some secure laboratories. I'm not convinced any viruses are truly extinct, but something could be implemented in Virusbox, I suppose. (It's not a change that will be inherited by the way; it will need a small change in all the relevant taxobox templates.) Peter coxhead (talk) 18:23, 10 January 2022 (UTC)


 * Support on the grounds of what people would reasonably expect. When people add EX to a taxobox they would reasonably expect it to indicate that the species is extinct for all taxobox elements, not just for the conservation status. Having to add a separate parameter to mark the species name and bionomial is not intuitive. I can't think of any case where this would cause a problem. —  Jts1882 &#124; talk 18:01, 10 January 2022 (UTC)


 * Support I also cannot think of any situations this could be a problem so long as cats Extinct and Extinct in the Wild are kept as separate entities for classification of status. Cheers Scott Thomson  ( Faendalimas ) talk 17:57, 11 January 2022 (UTC)

Progress
As there have been no objections to date, I've implemented the proposal at Speciesbox/sandbox. You can see it working in the new test case I've added at Template:Speciesbox/testcases. I'll leave it a few more days before making this live, along with the other relevant taxobox templates. Peter coxhead (talk) 17:18, 14 January 2022 (UTC)

Created my first taxonomy template
Would appreciate it if someone could double check and make sure I did it right. I used Wikidata to get the data for the parent taxa. Template:Taxonomy/Diplocardia. Article diff. I notice the order changed in the diff, from Haplotaxida to Opisthopora. Thanks. – Novem Linguae (talk) 03:44, 26 January 2022 (UTC)
 * Looks good to me, but you would have got a bonus point if you'd have populated the 'refs' field! Adding would make me happy. YorkshireExpat (talk) 06:48, 26 January 2022 (UTC)
 * WoRMS has Crassiclitellata as the order for Lumbricina. The Wikipedia article on Opisthopora doesn't mention Acanthodrilidae as one of the families, while the Oligochaete article doesn't mention order Crassiclitellata. Either the whole taxonomy needs some work or it's following a different taxonomy to WoRMS, which sometimes isn't so up to date for non-marine taxa. —  Jts1882 &#124; talk 07:32, 26 January 2022 (UTC)
 * It's a fair point. I only went for WoRMS as the parent reference was WoRMS. When looking at the reference in a Taxonomy template, I only use it as a reference for the parent, as the parent should have its own reference of course. However, I like WoRMS, as it clearly shows where it is taking its own reference from; in this case this page, which from a quick glance doesn't seem to have views past the familia (and it's all in Latin). And while we're on the subject the two main errors with taxoboxes are not putting the capitalising the rank, and not putting it in Latin, so people usually get 'genus' fine, but 'familia', 'classis' etc are sometimes got wrong. But from your username I would wager you like Latin? YorkshireExpat (talk) 16:18, 26 January 2022 (UTC)
 * Hahaha I wish, that'd be cool to be a Roman. SPQR! Do we need to take any action to reconcile the different orders and suborders mentioned here? Is there an ultimate reference/authority on these things that we can check to make sure we're using the right one? – Novem Linguae (talk) 16:24, 26 January 2022 (UTC)
 * there's no "ultimate reference/authority" for any system of classification – this aspect of taxonomy is a subjective matter. However, to ensure consistency among a set of articles, we have to agree to use one particular system for the article titles and taxoboxes, while mentioning others in the text. Peter coxhead (talk) 16:53, 26 January 2022 (UTC)
 * Wikipedia's annelid classification isn't consistent in following any particular system. And I'm pretty sure there are internal inconsistencies in articles with manual taxoboxes (e.g. a species has a different order than its parent genus shows). Automatic taxoboxes eliminate the potential for internal inconsistencies. Ideally all the annelid automatic taxoboxes should be checkted to ensure they're consistent with a particular system, and manual taxoboxes should be converted to that system. I haven't looked into annelid classifications systems in detail, but WoRMS is likely a good source to follow. Plantdrew (talk) 17:25, 26 January 2022 (UTC)
 * Yes, WoRMS is very good and my first port of call for invertebrates when I don't know an alternative. I know it follows recent classifications for some groups like Gastropods. I made an attempt to understand earthworm taxonomy couple of years ago and found it very confusing. However, looking at my notes, it seems that WoRMS has revised their classification for annelids since then, with Oligochaeta being split into eleven orders instead of five. The Oligochaeta page says the taxonomic source is Schmelz et al (2021) . The records for the additional orders such as Alluroidida were added on 23 Sept 2021. So it looks like their annelid classification is current, although it does contain paraphyletic groups
 * As WoRMS is following a 2021 taxonomic proposal based on a 2020 phylogenetic study, I think it is a good source to follow for the taxonomy. —  Jts1882 &#124; talk 13:28, 27 January 2022 (UTC)

Stilboma genus
Quick follow up question. OK to use CatalogueOfLife.org to flesh out Template:Taxonomy/Stilboma with Stilboma -> Pericalina -> Lebinni -> Lebiinae -> Carabidae? – Novem Linguae (talk) 07:51, 28 January 2022 (UTC)
 * Looking at the taxonbar on the article I might go with Inaturalist here . It has a taxonomy to the subtribe level, and list its source as Carabidae of the World, which I'd have to trust as I don't have a subscription. It agrees with CoL so that should be good too but it's not one I tend to look at. YorkshireExpat (talk) 08:32, 28 January 2022 (UTC)
 * It's hard to assess Carabidae of the World without being able to see any of the taxonomic content. It has an international panel of specialists so seems a serious enterprise. It's not clear when iNaturalist last updated their taxonomy. iNaturalist has some inconsistencies. For instance, iNaturalist has an empty tribe Calleidini in subfamily Lebiinae and a subtribe Calleidina in Lebiini (with content) [is this a iNaturalist error or copied from CotW?].
 * There are some differences in the tribes and subtribes in iNaturalist and CoL. Using the above example, CoL doesn't recognise Calleidini or Calleidina. Instead, genus Calleida and some other Calleidina genera are part of subtribe Agrina. CoL has updates in July 2021 and lists its source as the Carabcat database, which links to Ground Beetles of the World.
 * Overall, I'm unsure if one is more to date than the other or if they represent different taxonomic opinions. Both are closer to each other than the taxonomy we have with the automated taxonomy templates. —  Jts1882 &#124; talk 18:12, 28 January 2022 (UTC)

Refs in taxonomy templates
Quick question. If I am getting taxonomy info from a database website, is it better to include this in the taxonomy template in the |refs= section, or leave |refs= blank? Example: Template:Taxonomy/Heterometopus. Thanks. – Novem Linguae (talk) 21:42, 30 January 2022 (UTC)
 * Please include it. That is what refs is for. Ideally every taxonomy template should have a reference; there isn't any good reason to leave it blank. The reference could be a database website, a book, journal article, etc. With a database, it is a good idea to include an access date in the reference; the database might change its classification in the future. In general, I'd avoid NCBI as a source for classification; they have a disclaimer "NCBI taxonomy database is not an authoritative source for nomenclature or classification...". However, I'm not finding any other sources for alveolate classifications; NCBI may well be the best we can do for alveolates. Plantdrew (talk) 23:05, 30 January 2022 (UTC)
 * Sounds good. Will do from now on. – Novem Linguae (talk) 23:28, 30 January 2022 (UTC)

Converting taxoboxes to speciesboxes
Any objections if, in species articles, I convert a bunch of taxoboxes to speciesboxes? It's technically a cosmetic edit as it is not changing what it displays, but I think this might be outweighed by reducing the maintenance burden of these articles. For example, using a speciesbox instead of a taxobox, if the taxonomy ever changes, articles using speciesbox will be updated automatically instead of requiring manual update. And I believe the reduction in amount of code is also a benefit. Example edit. Thanks. – Novem Linguae (talk) 01:30, 29 January 2022 (UTC)
 * No, I believe this behaviour is positively encouraged! YorkshireExpat (talk) 08:43, 29 January 2022 (UTC)
 * It's encouraged by most editors on most projects under TOL, although there was some opposition from the Gastropod project in the past (I think no longer). However, care should be take not to change the taxonomy shown, unless this is sourced and changed in the rest of the article. Your edit does change the taxa shown in the taxobox, omitting the superfamily Buccinoidea and clade Hypsogastropoda and using the order and subclass as ranks rather than clades. I've added 3 to display the superfamily. WoRMS has Hypsogastropoda as an "alternate representation" so I'm unsure if that should be added. Perhaps can recommend the best solution. —  Jts1882 &#124; talk 09:11, 29 January 2022 (UTC)
 * It's true about the Gastropod project. See this before I changed it. They seem to like that big unranked blob in the middle, and you can't get that with an Automatic taxobox, unless you use 'always display' or something, and even then the formatting won't be the same. YorkshireExpat (talk) 14:49, 29 January 2022 (UTC)

This isn't the best place to get an unbiased answer; most people watching this page aren't against automatic taxoboxes. There was an RFC about this in July 2018: Wikipedia talk:WikiProject_Tree of Life/Archive 41. There was very little opposition, but the most vociferous opposition came from a (no longer very active) editor who worked on gastropods. Prior to 2018, there were a few discussions where there were objections to automatic taxoboxes. A couple editors were against automatic taxoboxes for fungi in 2014 (Wikipedia_talk:WikiProject_Fungi/Archive_9), there are a couple earlier threads in WikiProject Gastropods with the same editor objecting. And there was a editor who worked mostly on crustaceans who was concerned about bugs in early versions of automatic taxoboxes (this editor isn't very active in recent years, but the most recent articles they created used speciesboxes, so I assume they're no longer concerned). There were some major bugs that weren't fixed until mid-2016, and automatic taxoboxes weren't used much before then. One editor started converting reptiles to automatic taxoboxes en masse in fall 2016. I started implementing speciesboxes en masse for plants in spring 2017 (after asking at Wikipedia talk:WikiProject Plants/Archive68). Mammals and birds were largely converted to automatic taxoboxes in 2017 and early 2018. Since the 2018 RFC, automatic taxoboxes have spread across most of the project under TOL (although arthropods and fungi lagged until pretty recently). JoJan has been the most active gastropod editor by far for many years now, and has been using automatic taxoboxes for quite awhile. Some objections to automatic taxoboxes have been addressed by bug fixes; others are no longer being voiced because the editors with those views aren't active anymore.

Gastropods with manual taxoboxes are mostly following a now superseded 2005 classification that didn't assign ranks to many of the groups it recognized. I suppose manual taxoboxes may not have had enough "unranked" parameters early on to display all of the unranked groups for gastropods. However, manual taxoboxes do now (and for many years) have enough "unranked" parameters between subclass and superfamily to accomodate all the groups in the 2005 gastropod classification. The big "unranked blob" for gastropods isn't necessary, but nobody is interested in fixing it while retaining manual taxoboxes. A more recent (2017) classification of gastropods assigns ranks to all groups (although it does have the unusual ranks of "subterclass"). The anti-automatic taxobox gastropod editor supports following the 2017 classification, but hasn't made any serious effort to update manual taxoboxes to follow the more recent classification.

I'm not sure that gastropod taxonomy templates are necessarily following the 2017 classification rather than the 2005 one, but that is relatively easy to fix when articles are using automatic taxoboxes. With no gastropod editors interested in using standard manual taxobox parameters for the "blob", nor in updating manual taxoboxes from the 2005 classification to the 2017, I wouldn't take any potential objections seriously (but somebody should double check that gastropods with automatic taxoboxes are following the 2017 classification). Plantdrew (talk) 23:28, 29 January 2022 (UTC)


 * I am definitely a proponent of the template "speciesbox" instead of the manual taxobox, but only when the template "automatic taxobox" has already been implemented. This means that the taxonomy has been checked with WoRMS, following the 2017 classification, and the text of the article has been updated accordingly. I've been working on gastropods for the last fourteen years and I'm dealing now with the thirth major upgrade of the taxonomy of the Gastropoda, plus all the numerous other changes on a daily basis. The load of work is so enormous, that I have to restrict myself, as far as templates are concerned, only to genera and higher taxa. So if someone would implement the template speciesbox, when there is already a template "automatic taxobox", that would be great help and would be much appreciated. JoJan (talk) 14:40, 30 January 2022 (UTC)
 * Thank you all for the feedback so far. So if I am reading this right:
 * Script assisted conversion from taxobox to speciesbox is OK, but I should program it to skip gastropods.
 * Script assisted conversion from automatic taxobox to speciesbox is OK in any species article, AND there might even be support for a bot to do automatic taxobox to speciesbox in gastropod articles. (idea I can explore if there is support for it)
 * Feel free to correct me if I'm wrong or to expand on these ideas. – Novem Linguae (talk) 15:21, 30 January 2022 (UTC)
 * I think the underlying issue is that when many (?most) editors convert from a manual to an automated taxobox, they want the underlying taxonomy to have consensus. Certainly I do. So script-assisted conversion from Taxobox to Speciesbox is fine if you are sure that the taxonomy templates that will be invoked are based on sound, up-to-date taxonomic sources. Peter coxhead (talk) 16:13, 30 January 2022 (UTC)
 * Hmm. I can't guarantee that. I don't know enough about taxonomic sources yet. Could look at this from an iterative/gradual progress perspective though... a two step process where 1) somebody (me) blindly converts to an automated taxobox, then 2) somebody else comes along and notices an issue and fixes the Template:Taxonomy sub-templates. Up to you guys to determine if iterative is OK, or if you'd prefer a more accurate conversion.
 * About the extent of my skills at the moment is noticing a missing Template:Taxonomy, then creating those based on iNaturalist or WoRMS. I don't really know a lot of websites, which sources are more accurate, how to reconcile conflicting sources, etc. – Novem Linguae (talk) 16:36, 30 January 2022 (UTC)
 * I think is saying convert gastropod species taxoboxes to speciesbox if the genus taxonomy templates and higher taxa taxonomy templates already exist (i.e. the higher taxonomy is set up). He is working on the genus and above taxonomy, keeping them up to date, but doesn't have time to do all the speciesbox conversions himself. This division of labour seems to fit well with what you intend to do. If the genus is missing, then it needs checking against WoRMS, which is presumed to have the latest taxonomy (from Bouchet et al, 2017 or is there an update?). — <span style="font-family:Arial;background:#d6ffe6;border:solid 1px;border-radius:5px;box-shadow:darkcyan 0px 1px 1px;"> Jts1882 &#124; talk 16:33, 30 January 2022 (UTC)

Articles with taxoboxs but without IUCN status
Have noticed that there are a number of articles that have the proper taxobox, but lack the IUCN classification info. Is there an editing banner to alert members to articles that lack this info? --SpiritedMichelle (talk) 02:28, 3 February 2022 (UTC)
 * I'm not sure exactly what you are asking. Are you thinking of a template like IUCN status needed similar to citation needed? I don't think this would be useful as the IUCN redlist only has assessments for around 136,000 species, whereas there are millions of described species. So in most cases the absence of the IUCN status is because they haven't done an assessment. If you know there is a IUCN assesssment and it's not in the taxobox then its easy enough to add. Or you could just add a comment here with links to the assessments in question.
 * Some editors regularly check the new IUCN assessments when they are published and add them to or edit the taxoboxes. It might be possible to do this using a bot. It might also be possible to set up a category for articles with taxoboxes without IUCN assessments when they exist and are recorded on Wikidata. However, I've seen nothing to suggest there are many articles where an existing IUCN conservation is missing. — <span style="font-family:Arial;background:#d6ffe6;border:solid 1px;border-radius:5px;box-shadow:darkcyan 0px 1px 1px;"> Jts1882 &#124; talk 10:00, 3 February 2022 (UTC)
 * One can add Not evaluated to species that are unassessed, but it’s not really encouraged. I like the idea of a maintenance category.  I’m sure there are some that fall through the cracks, and I bet it could find mismatches as well.  --awkwafaba (📥) 12:50, 3 February 2022 (UTC)
 * Some number searches. There are 233,619 pages with speciesbox. There are 55,054 pages with speciesbox and, plus another 5024 using taxobox and 62 using automatic taxobox. That means there are 60-70k IUCN assessments where we don't have articles or have articles without conservation statuses or are missed by my searches. — <span style="font-family:Arial;background:#d6ffe6;border:solid 1px;border-radius:5px;box-shadow:darkcyan 0px 1px 1px;"> Jts1882 &#124; talk 12:56, 3 February 2022 (UTC)
 * I've added a test to speciesbox/sandbox with this edit. If there is no status it looks for an IUCN status for the Wikidata item associated with the page and adds a category if found (i.e. if no status in speciesbox AND status in wikidata item THEN add category ELSE do nothing). To test go to a page with speciesbox and status (e.g. Leopard) and edit to use sandbox with and without the status parameter.
 * Note this is just to flag articles where there may be a missing IUCN status. Wikidata cannot be used to set the status because there is no way of knowing whether Wikidata is using the same species concept and any attempt to handle this using existing wikidata items is reverted regardless of the errors it leaves behind. — <span style="font-family:Arial;background:#d6ffe6;border:solid 1px;border-radius:5px;box-shadow:darkcyan 0px 1px 1px;"> Jts1882 &#124; talk 09:45, 4 February 2022 (UTC)

References in species parameter
I found 93 speciesboxes with a reference in the species parameter. I don't think the parameter should contain the reference. While the taxoboxes work as expected, this means the reference is included as part of the species name and gets added to the species row (within the species span element) and the binomial section (within the bold and italics formatting), although only one links back from the reference list. — <span style="font-family:Arial;background:#d6ffe6;border:solid 1px;border-radius:5px;box-shadow:darkcyan 0px 1px 1px;"> Jts1882 &#124; talk 16:25, 5 February 2022 (UTC)
 * I agree; what would this actually be referencing anyway? They should all be removed. Peter coxhead (talk) 15:45, 6 February 2022 (UTC)

Incertae sedis taxonomy template marked as extinct
I'm currently engaged in a possible edit war with about whether or not this taxonomy template should be marked as extinct. I appreciate it maybe doesn't make much sense for incertae sedis to be marked thus, but the taxobox system demands it. Any thoughts? YorkshireExpat (talk) 21:11, 7 February 2022 (UTC)
 * It wasn't an edit war, I didn't notice your first edit and thought I had just copied the "yes" on the extinct parameter from Template:Taxonomy/Eurypterida. But I agree that it is better to discuss this issue here. Super   Ψ   Dro  21:14, 7 February 2022 (UTC)
 * Yes, all friendly :). YorkshireExpat (talk) 21:19, 7 February 2022 (UTC)
 * is there a problem with marking it †? --awkwafaba (📥) 04:01, 8 February 2022 (UTC)
 * The "taxon" is family incertae sedis within order Eurypterida, which is extinct. So logically the template should be marked as extinct. This causes the extinct dagger to be added before incertae sedis in the taxobox. If this is considered slightly confusing, perhaps it should be omitted. But I'm leaning towards marking it extinct so everything below a certain level is marked extinct. — <span style="font-family:Arial;background:#d6ffe6;border:solid 1px;border-radius:5px;box-shadow:darkcyan 0px 1px 1px;"> Jts1882 &#124; talk 08:29, 8 February 2022 (UTC)
 * incertae sedis is still a term though, not a taxon. Sources do not refer to Dorfopterus (the genus I made that template for) as "family incertae sedis", but only as incertae sedis. I added the rank "family" because it's the major taxonomical rank between order and genus. But maybe it'd be better if it only stated "clade". Super   Ψ   Dro  14:24, 8 February 2022 (UTC)
 * Yes, it's a term but it's one that is pretty meaningless without a qualifying rank. The genus Dorfopterus is known to belong to order Eurypterida, it's only incertae sedis at family and other ranks between order and genus. I have a couple of questions:
 * Why is it no longer placed in family Stylonuridae? (e.g. see Kjellesvig-Waering 1966 or IRMNG)
 * Why state family incertae sedis rather than make the parent of the genus the order Eurypterida?
 * It seems the best solution is not to have family incertae sedis at all. It adds nothing. Either omit or give the family. — <span style="font-family:Arial;background:#d6ffe6;border:solid 1px;border-radius:5px;box-shadow:darkcyan 0px 1px 1px;"> Jts1882 &#124; talk 15:03, 8 February 2022 (UTC)
 * 1. Because the genus is too poorly known and more recent sources stopped classifying the genus on the family. See this extinct arthropod catalogue (page 28 exactly). And that second link you gave is wrong in many ways. Stylonuridae wasn't erected in 1979 and Eurypterida's parent Merostomata is defunct.
 * 2. Because that'd give the impression that Dorfopterus is a basal eurypterid rather than just a eurypterid with uncertain classification. This is at least how it is done in other eurypterid articles, see Paraeurypterus and Pentlandopterus, they're basal members of a superfamily not classified in any family because they haven't been labelled as incertae sedis by any researcher. Unlike Dorfopterus. Super   Ψ   Dro  17:00, 8 February 2022 (UTC)
 * The incertae sedis needs to stay, because that's the formal current classification of the genus. I can provide sources if needed. But everything is on the article's classification section already. Super   Ψ   Dro  17:01, 8 February 2022 (UTC)
 * It's a one of these problematic edge cases. On the one hand, whatever family the "incertae sedis" is a placeholder for is clearly extinct because its parent is extinct, which makes it logical to include a †. On the other hand, if incertae sedis is replaced by the translation "of uncertain placement", it seems illogical to have a †. I guess you can regard "Family: †incertae sedis" as meaning "of uncertain placement in an extinct family". Peter coxhead (talk) 22:23, 9 February 2022 (UTC)

What is .../skip and why is it used?
Example: Template:Taxonomy/Testudines/skip. Thanks. – Novem Linguae (talk) 19:36, 8 February 2022 (UTC)
 * It's a means to show different taxa in the taxobox. The usual case is for extant taxa when you don't want to show the full hierarchy that are of relevance for extinct species articles. The usual example is birds, where you don't want to show Theropoda and Dinosauria  for birds like the house sparrow or wren. In this particular case, compare Template:Taxonomy/Testudines/skip with Template:Taxonomy/Testudines. The latter includes the taxa Perichelydia, Mesochelydia, Rhaptochelydia,	Testudinata and Pantestudines between Testudines and Sauria, whereas the skip template jumps (skips) straight to Sauria. There is no need to show intermediate taxa for the common tortoise, but they are important for extinct testudines. — <span style="font-family:Arial;background:#d6ffe6;border:solid 1px;border-radius:5px;box-shadow:darkcyan 0px 1px 1px;"> Jts1882 &#124; talk 08:06, 9 February 2022 (UTC)
 * It’s basically because of stuff like how humans are descended from fish, and if you showed that you’d have phyla within phyla and other nuttiness. That birds are dinosaurs is the tip of the iceberg. --awkwafaba (📥) 13:01, 9 February 2022 (UTC)

Incertae sedis
Was my conversion here from taxobox to speciesbox correct? The order and family are incertae sedis. Did I set up the taxonomy template correctly? Template:Taxonomy/Hypolyssus. Is there a way to incorporate incertae sedis into taxonomy templates, or do you just set the parent in a way that skips the incertae sedis taxa and links it to the next known parent? Thanks. – Novem Linguae (talk) 19:25, 10 February 2022 (UTC)
 * I think you've set is up correctly. There is a way of adding incertae sedis ranks (see discussion two sections up), but I'm unconvinced of the value. If order and family are incertae sedis show the class. — <span style="font-family:Arial;background:#d6ffe6;border:solid 1px;border-radius:5px;box-shadow:darkcyan 0px 1px 1px;"> Jts1882 &#124; talk 20:33, 10 February 2022 (UTC)
 * I would put the order as incertae sedis. I agree that having more than one incertae sedis is silly, but it’s still good to show something there. --awkwafaba (📥) 01:57, 11 February 2022 (UTC)

Relevant discussion at WP:Gastropods
There’s talk about taxobox updates and minor clades at the Gastropod WP. Read it here. --awkwafaba (📥) 13:03, 21 February 2022 (UTC)

User scripts
I've created some user scripts that may be of interest to folks that work with species articles.

1) User:Novem Linguae/Scripts/SpeciesHelper. Sadly I've advertised this one here before and there didn't seem to be much interest. I've put a ton of work into it and it's really good at gnoming species articles. It will look through the bottom 10-20 taxa of a species and pick the lowest, most specific stub and category for the article. It is also quite good at converting Taxobox to Speciesbox (or adding Speciesbox from scratch), and it also adds Taxonbar (with Wikidata ID) and Short description.

2) User:Novem Linguae/Scripts/TemplateTaxonomyAddCite. This one is hot off the press. This is a helper for when you are creating Template:Taxonomy sub pages. It will add useful "search" and "add citation" links, and you can pick from around 8 databases. Feel free to suggest more databases and other tweaks.

Sincerely, – Novem Linguae (talk) 06:22, 30 May 2022 (UTC)

iNaturalist reliability for taxonomy
My impression was that iNaturalist was a realiable source for taxonomy. But I ran across some diffs today of an editor removing iNaturalist with the edit summary "unreliable source". Thoughts? – Novem Linguae (talk) 10:39, 31 May 2022 (UTC)
 * Agree completely. iNaturalist was not created to be a taxonomic authority, and should not be used as one. Esculenta (talk) 10:57, 31 May 2022 (UTC)
 * <ec> Also agree. iNaturalist should not be used as a taxonomic source for Wikipedia as the curators there are only trying to follow existing taxonomic schema and are not always consistent in their approach. They do list one or more external sources for their taxonomy, but it is not clear which one they are using for any given taxa. Further, these sources can be very local or poorly curated themselves. A big problem is the lack of inclusion of any authors names (authorities) accompanying the taxon name. This leads to problems untangling taxonomic homonyms from synonyms. In their defence, although the curators may be volunteer taxonomic editors, there is a method to "flag" a taxon and I have found them to be highly responsive to reviewing taxonomic changes/updates. There are less than 400 curators, whereas the vast majority of iNat users are not curators and unable to change anything on the site. The iNat site does provide curators detailed information on the preferred taxonomic sources to use on iNat (scroll down to "External Taxonomic Authority List" here). Some aspects of the reliability of information on the site are worse than others. The "About" tab is by default just a mirror of Wikipedia, but the listing of common names in the taxonomy section include some names that by their own admission are just newly fabricated by an iNat curator to fill a gap that was thought to be needed (There is a separate debate on the iNat forum on this practice) and the reader cannot determine which common names are legitimate and which were coined on iNat. Loopy30 (talk) 11:52, 31 May 2022 (UTC)
 * I've created several Template:Taxonomy templates cited to iNaturalist. Sounds like that source is unreliable. Any suggestions for a replacement I should use going forward for plants and animals? – Novem Linguae (talk) 13:20, 31 May 2022 (UTC)
 * Kew's Plants of the World (IPNI) is easy, but animals are more varied. The "External Taxonomic Authority List" linked above is pretty good and matches most WP projects (eg. WoRMS for marine invertebrates, ASW for amphibians etc). Loopy30 (talk) 14:16, 31 May 2022 (UTC)
 * @Loopy30 I'd argue that an iNaturalist reference is better than none. They shouldn't remove a reference without replacing it with a better one. As you say it depends what source they are following. I've been doing some work recently on Pyraloidea, and have been following this website. However, because of the way it works you can't link to the taxa (or I can't work out how), but as iNat seems to follow it, why not use that as a proxy, in lieu of something better? YorkshireExpat (talk) 15:38, 31 May 2022 (UTC)
 * I agree that an iNaturalist reference is better than none. Two of the example edits Novem Linguae provided were to Pachnoda tridentata and Sapho ciliata. The only reference now in these two articles is the original description. Both species were originally described in another genus; there is now no reference for the current generic placement. In my opinion, iNat is reliable for the taxonomic hierarchy; not just anybody can edit it, and those who can edit are expected to have some basic taxonomic competence. iNat's taxonomic hierarchy does follow other sources, and it would be much better to cite those other sources directly, but it is not an improvement to remove an iNat reference without replacing it with another source. Plantdrew (talk) 17:01, 31 May 2022 (UTC)
 * I agree that removing the iNaturalist reference and leaving nothing in its place is not helpful editing. If there is some directive that iNaturalist is a blacklisted source then it should be replaced with a citation needed template. If it isn't blacklisted then it should be left or replaced with a better reference. — <span style="font-family:Arial;background:#d6ffe6;border:solid 1px;border-radius:5px;box-shadow:darkcyan 0px 1px 1px;"> Jts1882 &#124; talk 09:08, 1 June 2022 (UTC)
 * Thanks for the info. Besides scientific papers, what websites are considered to have high quality taxonomic databases? I'll try to use those instead of iNaturalist. – Novem Linguae (talk) 10:59, 31 May 2022 (UTC)
 * I'm not a gastropod person, so someone else will have to answer for them, but for fungi, Index Fungorum and MycoBank are the ones to use. Esculenta (talk) 11:10, 31 May 2022 (UTC)
 * For gastropods follow WoRMS, which is kept up to date by the foremost authority on gastropod taxonomy and is favoured by the Gastropod project. For insects it is much more difficult. There don't seem to be good sources covering the large orders. For Scarabaeidae and related beetles, I'd use this, although the googlebooks preview is limited. There are several good sites for Nymphalidae: www.nymphalidae.net, Afrotropical butterflies and Charaxes.be. For bees there is Bees of the World (2000) (available as pdf) but that is a bit dated. There are also several ant websites and the species files sites (see my list). — <span style="font-family:Arial;background:#d6ffe6;border:solid 1px;border-radius:5px;box-shadow:darkcyan 0px 1px 1px;"> Jts1882 &#124; talk 09:19, 1 June 2022 (UTC)

Alright, I'm looking for a replacement for iNaturalist when I make taxonomy templates. I may be making a lot of taxonomy templates and I don't want to use controversial sources. I found WikiProject Tree of Life, and Catalogue of Life is at the top of the list. Any objections to Catalogue of Life? – Novem Linguae (talk) 22:00, 5 June 2022 (UTC)
 * CoL has previously had a large number of errors, although I haven't investigated it recently. I don't think any of the "all taxa" databases (i.e., CoL, GBIF, EOL, NCBI) are really of sufficient quality to use for taxonomy templates (although NCBI may be the only game in town for some protozoan groups). Different databases (or individual published taxonomic revisions) should be consulted for different groups of organisms.Plantdrew (talk) 00:34, 6 June 2022 (UTC)
 * So I guess I should use the databases at WikiProject Tree of Life, minus the "General taxonomy" section? – Novem Linguae (talk) 00:56, 6 June 2022 (UTC)
 * I think there are two answers here. Many taxonomy templates (possibly most?) don't have references so the global/aggregate databases are better than nothing, especially if it doesn't seem controversial. However, if you are trying to tidy up the taxonomy of a group it would be best for find a good source for that group. Given this can be difficult, it's something worth asking about and discussing here. This would also mean we could improve the list of recommended sources.
 * It's also worth noting that CoL has a list of its taxonomic sources. The source for ground beetles Carabcat database says "All data from CarabCat concerning species-group names (...) can also be accessed through the Catalogue of Life", so in such cases CoL might be acceptable if easier to link to the appropriate data, Some databases, including Carabcat and the Pyraloidea database mentioned above, aren't link friendly. In fact, the FAQS section on Carabcat actually says "The Catalogue of Life is the best place for searching on all binomina, including synonyms, original combinations, and outdated combinations". Carabcat is a tricky database to use and you can't (or I can't) link the results, so this is a good example where CoL could be used. — <span style="font-family:Arial;background:#d6ffe6;border:solid 1px;border-radius:5px;box-shadow:darkcyan 0px 1px 1px;"> Jts1882 &#124; talk 07:13, 6 June 2022 (UTC)
 * Thanks for the feedback. I don't plan to edit taxonomy templates, just create them, so that when I convert taxobox to speciesbox, the speciesbox works. – Novem Linguae (talk) 07:59, 6 June 2022 (UTC)

On Catalogue of Life as a reliable source
Following the above discussion, I've been looking a bit more into CoL and its sourcing. The short answer is that it's a mixed bag, reliable for some taxa and less so for others. I've tried to divide it into categories. Overall, I think that CoL can be a reliable source, but that it depends on the taxon. In many cases the sources can and should be cited directly, but in some direct links are not possible. It needs to be decided on a case by case basis and is a useful tool to find alternatives. Anyway, I thought I'd share what I'd found in case it helps anyone. — <span style="font-family:Arial;background:#d6ffe6;border:solid 1px;border-radius:5px;box-shadow:darkcyan 0px 1px 1px;"> Jts1882 &#124; talk 16:47, 9 June 2022 (UTC)
 * The sources for reptiles and fish are Reptile Database and Fishbase. These are both reliable sources and recommended by their Wikipedia projects. However there is no reason not to use these databases directly. Other databases in this category are WCVP (WCSP), World Plants and World Ferns that provide much of the plant data, plus WSC for spiders and WoRMS for various marine invertebrates.
 * The source for mammals and birds is ITIS, which itself is a bit mixed. ITIS uses MSW3 for mammals so is nearly two decades old. Birds are variable, with many taxa using old sources, but some quite up to date, e.g. trogons follow IOC 12.1 (2022). I don't think CoL should be used for these taxa and using ITIS directly should be on a case by case basis.
 * Other taxa, especially large insect groups use a variety of sources for different parts. I looked a Coleoptera in some detail.
 * As mentioned above, CoL uses CarabCat for caraboid beetles. The database is well-maintained and up to date, but it is tricky to use and needs a multi-step process. Moreover, there is no way of linking the results. In their FAQ they recommend using CoL for most purposes. This is an example where CoL is a suitable reliable source. One quirk is that Caraboidea is placed as order incertae sedis in Insecta, rather than within Coleoptera.
 * For Scarabaeoidea (scarab beetles) CoL uses the World Scarabaeidae Database, which isn't available elsewhere. It seems up-to-date.
 * A number of other beetle groups have their own specialist sources for their CoL entries: Buprestoidea Jewel beetles at the online version of The World of Jewel Beetles; Staphyliniformia (rove beetles, clown beetles & water scavenger beetles) at StaphBase; Curculionoidea (weevils) at WTaxa, with more specialist databases for Brentidae (Straight-snouted weevils) and Entiminae (Broad-nosed weevils); Cerambycidae (longhorn beetles, timber beetles) at TITAN; and tribe Sepidiini (toktokkies) at the World catalogue of the tribe Sepidiini. I don't know how reliable or up to date (a couple look older) these sources are but CoL might be a convenient way of citing them if there are no alternatives. Perhaps the Catalogue of Life citation template can be modified to indicate the source.
 * Other beetle groups are covered by ITIS and many others have no data source listed.


 * That's a pretty complicated work instruction. If picking sources for taxonomy templates is this hard, I may just stop making them. Correct me if I'm wrong, but the vibe I'm getting from this conversation is that it's better not to have a taxonomy template than to have one with a mediocre or poor source. – Novem Linguae (talk) 18:36, 9 June 2022 (UTC)
 * I don't think that's true to be honest. A poor reference is better than none and an automatic taxobox is better than a manual one. YorkshireExpat (talk) 17:04, 30 June 2022 (UTC)
 * Agreed. Automated taxoboxes are much better for maintaining a system and any reference is better than none. At least it makes it clear where the information comes from. Others can find better sources and make appropriate changes.
 * The above was certainly not intended as a work instruction. It's my musings on how CoL is sourced. Unfortunately, although inevitably given the intended scope, CoL sourcing is uneven. Some parts are very good and others poor. After spending time going through the beetle sourcing I noticed a little checkbox which would have saved me a lot of time. Select "info" next to the search box in the CoL taxon browse and the tree shows the sources used next to the taxon in orange. Some have specialist sources, ranging from large (WoRMS, Fishbase, Reptile database) to small (on just the tribe Sepidiini), others use ITIS, and others don't say. So in many cases CoL is reliable and up to date. Given many taxonomy templates have no reference at all, I'd say is preferable to use CoL for taxonomy templates than nothing at all. It can also be used as a resource to get a more specialised source. — <span style="font-family:Arial;background:#d6ffe6;border:solid 1px;border-radius:5px;box-shadow:darkcyan 0px 1px 1px;"> Jts1882 &#124; talk 07:53, 1 July 2022 (UTC)

30 June 2022 use stats update
30 June 2022 update

Mammal subprojects with articles tagged for both mammals and subproject:

Method: For the most part I use Petscan to search for articles with a talk page banner for a particular Wikiproject and either Taxobox, or any of Automatic taxobox+Speciesbox+(Infraspeciesbox and/or Subspeciesbox (depending on whether botanical/zoological code is relevant)), and record the results. Example search for algae with automatic taxoboxes (search terms are in the Templates&Links tab in Petscan). For viruses, I search for Virusbox rather than the other automatic taxobox templates. For plants, I sum the results for the Plants, Banksia, Carnivorous plants and Hypericaceae projects. "Total" is derived from the Template Transclusion Count tool (https://templatecount.toolforge.org/index.php?lang=en&namespace=10&name=Speciesbox#bottom e.g. results for Speciesbox), and is not actually sum of the results for individual projects (some articles have talk page banners for multiple Wikiprojects, and would be counted twice if rows were summed). I started compiling these stats in April 2017, and have been updating roughly every six months since December 2017. I've kept my method consistent; perhaps I should have included all of the automatic taxobox templates (Hybridbox, Ichnobox, etc.), but I didn't do so at the beginning, and the other templates aren't used in very many articles.

Caveat: The remaining manual taxoboxes in projects with a high percentage of automatic taxoboxes mostly have some kind of "problem". I have periodically reviewed all the manual taxobox articles in projects with less than 235 manual taxoboxes, and chose not to convert them to automatic taxoboxes at that time (however, it has been awhile since my last review, so there probably a few recently included articles I haven't reviewed). "Problems" may include:
 * Fossil taxa; fossil classifications may be derived from multiple sources and present classification on Wikipedia may include mutually incompatible hypotheses. Fossil taxa are often not be linked from extant parent taxa.
 * Synonymy; there is some obvious synonymy issue; e.g., a species is in a genus which redirects (as a synonym) to another genus; maybe the species article needs to be moved or maybe the genus should be reinstated
 * Common names; articles with common name titles may not correspond to taxa, but still have manual taxoboxes. In some cases Paraphyletic group may be appropriate, in others the taxobox should be removed
 * Parasite and pathogens; article on parasites and pathogens may be tagged for the WikiProject of the organisms they infect. Higher level taxonomy templates for the parasites may not yet exist, and the classification presented in manual taxoboxes may not be up to date.

I have some detailed notes breaking remaining plant manual taxoboxes down by family at User:Plantdrew/Plant automatic taxobox progress. Less detailed notes at User:Plantdrew/Animal automatic taxobox progress that break animals down by phylum, insects and fish by order, and palaeontology and marine life by overlap with other projects. There are a bunch of animal groups with manual taxoboxes in the double digits if anybody is interested in a small task in converting manual taxoboxes to automatic. The single turtle article with a manual taxobox is Acleistochelys, which is placed in a tribe that isn't mentioned anywhere else on Wikipedia. Plantdrew (talk) 15:34, 30 June 2022 (UTC)


 * Interesting to see that Dinosaurs is down to five. And my area of concern, Cats, is at zero. Thanks for the update! SilverTiger12 (talk) 17:09, 1 July 2022 (UTC)

Template-protected edit request on 14 July 2022
I think that maybe the clade dinosauria-found in the classification/hierarchy box of this page-should be change to be listed as a super-order as opposed to clade, because I think that the word clade being easily overlooked and thus the information associated with it (but that just me), also I can not assess sandbox (due to me not being logged in) to show you and for that I am sorry.169.1.154.245 (talk) 13:13, 14 July 2022 (UTC) I have dyslexia 😂 169.1.154.245 (talk) 13:13, 14 July 2022 (UTC)
 * Red information icon with gradient background.svg Not done for now: please establish a consensus for this alteration before using the template. Per Dinosaur classification, most dinosaur paleontologists have advocated a shift away from traditional, ranked Linnaean taxonomy in favor of rankless phylogenetic systems, so it's not at all clear to me that Linnean taxonomial terms should be used here. * Pppery * <sub style="color:#800000">it has begun...  14:18, 14 July 2022 (UTC)

Guidance on changing a taxonomy
Trying to help recently, I realized there's no straightforward guidance on how to revise a taxonomic hierarchy. So I've drafted some at Automated taxobox system/changing a taxonomy. Please feel free to revise or comment here. : I'd particularly welcome it if you could look over the draft, as you do more work on taxoboxes these days than anyone else, I think. Peter coxhead (talk) 17:50, 16 November 2022 (UTC)
 * I'm not sure that "At this point, |link=Xidae at "Template:Taxonomy/Xidae" can be revised to |link=Xidae|Xinae." is good advice. While it is the quickest way to get the updated taxonomy to display, if the old taxonomy template isn't going to be deleted, it is likely to be confusing to anybody who views it in the future. For step 3, "Find all taxonomy templates" could do with instructions on how to find them ("What links here" or Jts1882's taxonomy browser). Plantdrew (talk) 21:30, 16 November 2022 (UTC)
 * I have expanded this part a bit; "What links here" doesn't work usually because it shows all the descendants not just the children. It would be good if could add info about how to get his taxonomy browser working. Peter coxhead (talk) 19:20, 17 November 2022 (UTC)
 * Thanks for taking on this task. I think it would benefit from an explanation of why taxonomy templates should not be moved. All other templates that I can think of are capable of being moved, even if it takes some additional editing of related pages. I have set up plenty of redirects to and from taxonomy templates, and they appear to work fine. – Jonesey95 (talk) 22:22, 16 November 2022 (UTC)
 * it's partly because it can create undesirable effects for editors of taxoboxes. Suppose "Template:Taxonomy/Xidae" is actually a redirect to "Template:Taxonomy/Xinae". Then if an editor puts Xidae in an automatic taxobox, the page will actually show "Subfamily: Xinae" in the taxobox, preceded by whatever family "Template:Taxonomy/Xinae" has as its parent, which will surely puzzle many editors. It creates a variant of the WP:EASTEREGG problem.
 * Also, the difference from 'normal' templates is that the automated taxobox system generates the template name. If you put Z in an automatic taxobox, the system generates the name "Template:Taxonomy/Y" and then looks for it, because it expects the taxon name and the taxonomy template name to match. Redirecting "Template:Taxonomy/Y" to "Template:Taxonomy/Z" means that checks on the consistency and correct formatting of taxonomy templates are by-passed, which is undesirable. Categories like Category:Taxonomy templates with name and link text not matching which track inconsistencies don't work with redirects.
 * I don't really want to go into all this on the page I've been constructing. Peter coxhead (talk) 19:20, 17 November 2022 (UTC)

Show children feature
Would it be at all possible to alter the autotaxobox system so that a taxobox could be set to show all of its immediate children? I.e. a genus taxobox showing all speciesboxes using it as the genus. I think it could be very useful, but if it won't work, just say so. --SilverTiger12 (talk) 21:10, 16 November 2022 (UTC)
 * This was attempted when automatic taxoboxes were first being developed, but it didn't work. There is a script, User:Jts1882/taxonomybrowser.js you can install which makes it possible to browse the tree of taxonomy templates (but since species don't have individual taxonomy templates, it won't show species). Plantdrew (talk) 21:26, 16 November 2022 (UTC)
 * That would require the children to be in the taxonomy templates or the use javascript to find them (as in my taxonomy browser). While the former would be possible I don't think it would work well. The subdivision sections of taxoboxes get edited regularly. If this was removed to the taxonomy templates it would be more obscure (discouraging newer editors). Taxonomy templates have few watchers so this would also allow more errors to go unnoticed. — <span style="font-family:Arial;background:#d6ffe6;border:solid 1px;border-radius:5px;box-shadow:darkcyan 0px 1px 1px;"> Jts1882 &#124; talk 08:17, 17 November 2022 (UTC)
 * I have a version of the taxonomy browser that gets speciesboxes, but it may not capture all cases and its a bit buggy. I've put a version at User:Jts1882/taxonomybrowser2.js. The old version will continue to run as before. To install add the following to common or skin javascript file (e.g. User:YourName/common.js)
 * At genus level it will get the species boxes. If there are subgenera (e.g. Mus) or sections (e.g. Poa) it gets all speciesboxes for the genus and only works if the genus is the immediate parent. Let me know if there are problems. — <span style="font-family:Arial;background:#d6ffe6;border:solid 1px;border-radius:5px;box-shadow:darkcyan 0px 1px 1px;"> Jts1882 &#124; talk 17:34, 17 November 2022 (UTC)
 * one reason it doesn't work at many taxonomic levels is that the taxonomy templates do not represent straightforward trees, but networks, because of things like skip taxonomy templates, which mean that the children of a taxon can be at very different levels in the taxonomic hierarchy. Thus the children of Sauropsida include the class Reptilia immediately below it as well as the clade Archosauria, which is 11 levels below it in the full hierarchy, but has a skip taxonomy template (Template:Taxonomy/Archosauria/skip) that omits them. There are also incertae sedis "taxa", which effectively create gaps. Most bird articles have taxoboxes that lead to Template:Taxonomy/Aves/skip (the skips prevent all the dinosaur clades showing, and allow "Class Aves" not to clash with "Class Reptilia"). In addition to the expected two infraclasses, Neognathae and Palaeognathae, its immediate children include "Order: incertae sedis" (as well as two oogenera).
 * one reason it doesn't work at many taxonomic levels is that the taxonomy templates do not represent straightforward trees, but networks, because of things like skip taxonomy templates, which mean that the children of a taxon can be at very different levels in the taxonomic hierarchy. Thus the children of Sauropsida include the class Reptilia immediately below it as well as the clade Archosauria, which is 11 levels below it in the full hierarchy, but has a skip taxonomy template (Template:Taxonomy/Archosauria/skip) that omits them. There are also incertae sedis "taxa", which effectively create gaps. Most bird articles have taxoboxes that lead to Template:Taxonomy/Aves/skip (the skips prevent all the dinosaur clades showing, and allow "Class Aves" not to clash with "Class Reptilia"). In addition to the expected two infraclasses, Neognathae and Palaeognathae, its immediate children include "Order: incertae sedis" (as well as two oogenera).


 * Another problem is that major ranks, like families, are often not divided into an exhaustive set of minor ranks, like subfamilies, at least in consistent sources. So the child taxa of a family may be a mixture of subfamilies and genera. Right now if you look at the immediate children of the family Ericaceae, there are 9 subfamilies and 29 genera.


 * So many taxoboxes which contained automatically generated children would be a mess. Peter coxhead (talk) 19:03, 17 November 2022 (UTC)

Help needed
Can anyone explain why the status system in our Xanthoparmelia metastrigosa article is showing as "unrecognised"? The system (NSWBCA) is listed as a valid one on the Conservation status page. MeegsC (talk) 22:34, 13 December 2022 (UTC)
 * Hmm odd, its showing correctly for me at this point.-- Kev min  § 23:39, 13 December 2022 (UTC)
 * A mention of NSWBCA was added to Conservation status in June 2021. I don't think support for the status system was actually implemented in taxoboxes (there was a somewhat recent discussion somewhere about potentially adding taxobox support for more status systems that didn't really end up going anywhere. I think that discussion was prior to June 2021 (maybe sometime in 2020?)). Prior to that discussion, I had tried to keep Category:Taxoboxes with an unrecognised status system empty (mostly by moving statuses in unsupported status systems out of the taxobox and into the body of the article). I've since let the unrecognised status system accumulate articles in hopes that it may indicate what systems should have support added. By "support", I mean that the taxobox would recognize an abbreviation/acronym for a status system and would link to an article about the system, as well as (potentially) producing a graphic illustrating the status categories under a particular system. Plantdrew (talk) 04:10, 14 December 2022 (UTC)
 * , it shows correctly, but keeps showing up on our project's cleanup listing as needing to be fixed. MeegsC (talk) 08:25, 14 December 2022 (UTC)
 * , using the IUCN codes is obviously preferable – but only if the IUCN actually includes an assessment for the species. And most fungi and flora aren't included. MeegsC (talk) 08:31, 14 December 2022 (UTC)
 * The taxobox system doesn't (or didn't) support the NSWBCA system. I've added basic support to expand the codes and link to the page on the BCA act (someone should add the conservation statuses mentioned in the act: EN, VU, CR, EX and EW from my quick reading). I'm not sure which cleanup listing it was showing in, but has it gone? — <span style="font-family:Arial;background:#d6ffe6;border:solid 1px;border-radius:5px;box-shadow:darkcyan 0px 1px 1px;"> Jts1882 &#124; talk 09:16, 14 December 2022 (UTC)
 * Thanks ! Your changes appear to have removed the article from the (hidden) category it was in, so I'm assuming that the next time the cleanup listing runs (i.e. next Tuesday), it will have been marked as resolved. MeegsC (talk) 11:05, 14 December 2022 (UTC)

30 December 2022 use stats update
30 December 2022 update

Mammal subprojects with articles tagged for both mammals and subproject:

Method: For the most part I use Petscan to search for articles with a talk page banner for a particular Wikiproject and either Taxobox, or any of Automatic taxobox+Speciesbox+(Infraspeciesbox and/or Subspeciesbox (depending on whether botanical/zoological code is relevant)), and record the results. Example search for algae with automatic taxoboxes (search terms are in the Templates&Links tab in Petscan). For viruses, I search for Virusbox rather than the other automatic taxobox templates. For plants, I sum the results for the Plants, Banksia, Carnivorous plants and Hypericaceae projects. "Total" is derived from the Template Transclusion Count tool (https://templatecount.toolforge.org/index.php?lang=en&namespace=10&name=Speciesbox#bottom e.g. results for Speciesbox), and is not actually sum of the results for individual projects (some articles have talk page banners for multiple Wikiprojects, and would be counted twice if rows were summed). I started compiling these stats in April 2017, and have been updating roughly every six months since December 2017. I've kept my method consistent; perhaps I should have included all of the automatic taxobox templates (Hybridbox, Ichnobox, etc.), but I didn't do so at the beginning, and the other templates aren't used in very many articles.

Caveat: The remaining manual taxoboxes in projects with a high percentage of automatic taxoboxes mostly have some kind of "problem". I have periodically reviewed all the manual taxobox articles in projects with less than 235 manual taxoboxes, and chose not to convert them to automatic taxoboxes at that time (however, it has been awhile since my last review, so there probably a few recently included articles I haven't reviewed). "Problems" may include:
 * Fossil taxa; fossil classifications may be derived from multiple sources and present classification on Wikipedia may include mutually incompatible hypotheses. Fossil taxa are often not be linked from extant parent taxa.
 * Synonymy; there is some obvious synonymy issue; e.g., a species is in a genus which redirects (as a synonym) to another genus; maybe the species article needs to be moved or maybe the genus should be reinstated
 * Common names; articles with common name titles may not correspond to taxa, but still have manual taxoboxes. In some cases Paraphyletic group may be appropriate, in others the taxobox should be removed
 * Parasite and pathogens; article on parasites and pathogens may be tagged for the WikiProject of the organisms they infect. Higher level taxonomy templates for the parasites may not yet exist, and the classification presented in manual taxoboxes may not be up to date.

I grabbed the raw numbers on 30 December, but didn't get around to doing the math right away. Petscan has been failing a lot (and for several months now) with the searches I run for this, so I wanted to grab the numbers when I had the opportunity.

WikiProject Protista is new and doesn't have very many of the articles that would be in scope tagged yet. Most protist articles are currently tagged for WikiProject Microbiology; a substantial number of articles tagged for WikiProject Algae could be considered protists, as well as a few articles tagged for WikiProject Fungi. I suspect that as a group, articles for protists have the lowest uptake of automatic taxoboxes.

I have some detailed notes breaking remaining plant manual taxoboxes down by family at User:Plantdrew/Plant automatic taxobox progress. Less detailed notes at User:Plantdrew/Animal automatic taxobox progress that break animals down by phylum, and insects and fishes by order. Plantdrew (talk) 03:15, 5 January 2023 (UTC)
 * Wow,	8653 conversions in Lepidoptera. I've been making an effort with Crustaceans recently and only made a small dent in the numbers. Are these being done with a tool? I vaguely remember someone mentioning a script for adding speciesboxes, but forget the editors name. — <span style="font-family:Arial;background:#d6ffe6;border:solid 1px;border-radius:5px;box-shadow:darkcyan 0px 1px 1px;"> Jts1882 &#124; talk 16:31, 5 January 2023 (UTC)
 * , the tool/script is User:William Avery/taxoboxalyzer. User:Scorpions13256 has been using the tool a lot and I think is responsible for the vast majority of the conversions in Lepidoptera and Gastropods over the last 6 months. There were also 7k Lepidoptera were converted between June and December 2021, and 10k between December 2021 and June 2022. Plantdrew (talk) 17:54, 5 January 2023 (UTC)
 * Thanks, I'll have a look at that. It did remind me of a conversion template I'd started working on and forgotten about. I've set it up at convert taxobox. To use simply replace the first line of the manual taxobox  with   and it will substitute the code for the appropriate speciesbox or automatic taxobox. For speciesbox it uses genus and species after stripping wikitext formatting; for automatic taxobox is runs down the possible taxa and uses the lowest ranked taxon along with its authority. Unnecessary parameters are deleted as used in the conversion, but any extras not handled are left at the bottom of the parameter list. This means a taxobox with several parent authorities will keep parameters like ordo_authority when used in a family taxobox. These will need manual conversion to parent_authority. I've run a number of conversions today and it seems to be reliable, so I don't expect it to clutter your maintenance categories. — <span style="font-family:Arial;background:#d6ffe6;border:solid 1px;border-radius:5px;box-shadow:darkcyan 0px 1px 1px;"> Jts1882 &#124; talk 15:18, 7 January 2023 (UTC)


 * I'm rather curious about those negative numbers, and those four remaining dinosaurs with manual taxoboxes. All in all, though, it looks like the autotaxobox system is continuing to replace the manual system at a somewhat-steady rate. SilverTiger12 (talk) 22:35, 5 January 2023 (UTC)
 * . Negative numbers under "# manual subtracted" represent a net increase in manual taxoboxes; e.g. there are two more shark articles using manual taxoboxes than there were six months ago (there is an editor has been creating articles for fossil shark genera that aren't placed to a family, and the genera aren't mentioned in any article for a higher taxon; I'd prefer to see these articles de-orphaned before replacing the manual taxobox with an automatic one). I know the -1 for turtles is due to a manual taxobox being added to Hoan Kiem turtle, which probably shouldn't have a taxobox at all (and which didn't have a taxobox 6 months ago). The -2 for viruses is due to new articles with manual taxoboxes being created for virus "taxa" that aren't recognized by the ICTV (I don't remember specifically what those articles are).


 * Negative numbers under "# auto added" represent a net decrease in articles with automatic taxoboxes; I would guess the -1 for rodents represents a species being lumped, with a former article (with an automatic taxobox) being turned into a redirect, and the -1 for Tree of Life represents a TOL banner being replaced with a banner for a more specific WikiProject.


 * Remaining dinosaurs are Stegopodus (ichnogenus, should use Ichnobox?), Megalosaurus dunkeri (dubious species, genus maybe should be Altispinax?), Macrodontophion (dubious genus, of uncertain placement, once thought to be a dinosaur) and Avifilopluma (proposed clade for feathered animals, I'm not sure that it is generally recognized currently). Plantdrew (talk) 23:12, 5 January 2023 (UTC)