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Series

I just came across Template:Taxonomy/Saturniiformes which has rank set to "series" and is just below superfamily in rank. There are a few taxonomy templates for plant series (as a rank below subgenus/sectio), e.g. Template:Taxonomy/Banksia ser. Ochraceae. I know manual taxoboxes have |zoodivisio= and |zoosectio= to account for different placement of plant/animal division/section ranks in the taxonomic hierarchy. And there is a numeric value associated with the rank parameters recognized by manual taxoboxes that ensures they display the hierarchy in the right order. I guess the numeric value isn't used by automatic taxoboxes? The order in which ranks are displayed is determined solely by successive parent parameters?

Should there be a "zooseries" rank? Everything seems to be working OK with the plant/animal series templates I've linked above. I guess series isn't checked by Category:Taxonomy templates showing anomalous ranks since it seems like putting series below both superfamily and sectio would be anomalous one way or the other. Plantdrew (talk) 20:40, 31 January 2023 (UTC)

Oops, realized everything is NOT quite working OK. Saturniiformes is italicized by the taxonomy template (which would be correct for the plant rank). Plantdrew (talk) 20:42, 31 January 2023 (UTC)

Series is used inconsistently and isn't checked by Module:Autotaxobox (it's commented out on line 821). It is italicised because of Template:Is italic taxon which italicises series, subseries, and section ranks.
A zooseries rank would make sense if there was a need and it was used consistently. Template:Taxonomy/Saturniiformes is used for families Saturniidae and Lemoniidae in Bombycoidea. However, no other series are used in Bombycoidea and the template was created in 2010 with no source. The parent source doesn't use series and Lemoniidae is no longer recognised. I think it can be deleted after changing Template:Taxonomy/Saturniidae. —  Jts1882 | talk  08:40, 1 February 2023 (UTC)
I've changed the parent on Saturniidae, so Template:Taxonomy/Saturniiformes will be unnecessary when the change propagates. —  Jts1882 | talk  08:48, 1 February 2023 (UTC)
I've reviewed the taxonomy of Lepidoptera and cleared out all the old suprafamiliar taxa (except for a few with articles). The taxonomy template heirarchy follows van Nieukerken et al (2011)[1] at family and above, except for a few new families (which are sourced) and a couple I'm still thinking about whether to move or find an alternative source.—  Jts1882 | talk  18:05, 2 February 2023 (UTC)

References

  1. ^ van Nieukerken, Erik J.; Kaila, Lauri; Kitching, Ian J.; Kristensen, Niels P.; Lees, David C.; Minet, Joël; Mitter, Charles; Mutanen, Marko; Regier, Jerome C.; Simonsen, Thomas J.; Wahlberg, Niklas; Yen, Shen-Horn; Zahiri, Reza; et al. (23 December 2011). Zhang, Zhi-Qiang (ed.). "Order Lepidoptera Linnaeus, 1758" (PDF). Zootaxa. Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. 3148: 212–221.

Forma specialis taxa

I recently created a manual taxobox, which is more-or-less ok, at Puccinia coronata f. sp. avenae. There are more articles at this rank: see Category:Forma specialis taxa. The articles I've looked at use two main approaches to a taxobox:

My recollection is that we discussed adding the rank of form/forma to {{Infraspeciesbox}} and decided not to do so on the grounds that there would be few articles needing it and it would make the template yet more complicated. My preference, I think, is to accept that a forma specialis taxon should use a manual taxobox and revise {{Taxobox}} to accept "forma_specialis" in addition to form/forma so that it can display e.g. "Forma specialis: P. coronata f.sp. avenae".

What do others think? Peter coxhead (talk) 16:34, 24 May 2023 (UTC)

There are a handful of articles on bacteria with different infraspecific ranks. Some are in Category:Pathovars. Bacterial blight of cotton is a pathovar using {{Paraphyletic group}} with custom parameters for the rank. El Tor is a strain, and Escherichia coli NC101 is a serotype, both also using the paraphyletic group template. I think custom rank parameters may be the way to go, perhaps in {{Automatic taxobox}}, since that already has support for custom genus/species/binomials. May also be worth considering whether Wikipedia should even have articles for some of these "taxa". Plantdrew (talk) 19:15, 24 May 2023 (UTC)
Custom rank parameters are implemented in {{Paraphyletic group}} via Jts1882's Module:Biota infobox. It can be driven from a differently named template for clarity, but on reflection, this is the best way forward, since Jts1882 has already done almost all the work needed.
@Jts1882: the custom connecting terms appear in smaller font, which isn't the format we use.
Peter coxhead (talk) 21:48, 24 May 2023 (UTC)
I have now modified Module:Biota infobox so that it doesn't put connecting terms, like "var." or "f.sp." in smaller font. Peter coxhead (talk) 06:36, 25 May 2023 (UTC)
I've created {{Infraspeciesbox special}} as a more obviously titled front-end to Module:Biota infobox for special infraspecific ranks. So far I've not found any problems. Peter coxhead (talk) 08:20, 25 May 2023 (UTC)
I've now converted a few articles to use {{Infraspeciesbox special}}, which can be checked:
I see two issues, which are illustrated by the last example, Puccinia coronata f. sp. avenae:
  • The extra/special rank line in the taxobox just has the epithet, but should be preceded by the abbreviated species name plus connecting term: compare the Variety and Forma specialis rows.
  • The trinomial box should contain only the last (lowest) infraspecific rank – using all four makes it a "quadrinomial" (and is wrong under the ICNafp).
I won't attempt to alter the code for these issues; it needs input from Jts1882. Peter coxhead (talk) 08:48, 25 May 2023 (UTC)
Replies and comments:
  • I'm trying to remember why the |infraspecies_rank1= was left bare in the taxobox rather than including the abbreviate species name. For the strain in El Tor it seems reasonable. Should this be V. cholerae str. El Tor (i.e. the abbreviated trinomial name) or does it need different treatment?
  • The trinomia/quadrinomial point is noted. I was unaware of the ICNafp convention.
  • On using the small text for the connecting terms, I saw this somewhere and thought it a nice convention. It's similar to using small for authorities, in that is makes the different parts of the name clearer, even though its not a convention used much (or at all?) outside Wikipedia. I've no problem with the change, though.
I'll have a look at making the changes when I have time to properly check the results. That bit of code is tricky, not helped by my choice of parameter names, which in retrospect are a bit confusing. —  Jts1882 | talk  09:25, 25 May 2023 (UTC)
I think the trinomial is now correct (no quadrinomial terms). —  Jts1882 | talk  15:25, 25 May 2023 (UTC)
I've made some changes to add abbreviated species names (i.e. G. s.) in infraspecies rows of the taxon hierarchy. Is this as wanted? —  Jts1882 | talk  16:16, 25 May 2023 (UTC)
Looks good to me. I noticed a couple parameters that aren't supported, |species_link= and |type_strain=, although I'm not certain they should be supported.
In the absence of |species_link=, bacterial blight of cotton links to a redirect in the species line (Xanthomonas axonopodis redirects to Citrus canker). In that case the solution is probably to create an article for Xanthomonas axonopodis; citrus canker is pv. citri, so there should be an article for the species that has pathovars infecting citrus, cotton and cassava. And I suspect in most cases where we have an article at the common name (of a disease), the title will refer a particular host, in which case there should probably be an article at the species title with subarticles for f.sp./pv. taxa that infect particular hosts. So |species_link= may not be needed at all.
Xanthomonas campestris pv. campestris had a type strain in the manual taxobox which I've retained, but it doesn't display. Infraspecific ranks aren't governed by the rules of the prokaryote code, although it does have recommendations on how to use them. Given that they aren't subject to the rules of the code, I'm not sure that a designation of a type strain really applies, so |type_strain= may not be needed either. Plantdrew (talk) 16:40, 25 May 2023 (UTC)
@Jts1882: looks good to me too – thanks for the changes.
@Plantdrew: I agree that we should always have a species article for things like f.sp./pv. taxa – and in many cases I suspect that it's better to deal with the subtaxa in that article, rather than creating separate ones. It's not something I interested in working on though – I only got involved because Puccinia coronata f. sp. avenae had been showing up for quite a while in the missing taxobox subcategory of Category:Taxobox cleanup which I monitor regularly, and it finally irritated me enough to try to fix it.
Peter coxhead (talk) 17:10, 25 May 2023 (UTC)

{{Infraspeciesbox special}} has "Trinomial name" linking to Infraspecific name (botany), which is a redirect to Infraspecific name; the redirect should be bypassed (although I don't see much value in having that as a link at all (especially since it's inconsistent; manual taxoboxes for ranks above species and {{Automatic taxobox}} don't have a link like this, it's only for species (as "binomial name") and infraspecies)).

Manual taxoboxes for plant infraspecies also link to Infraspecific name (botany); see e.g. Ulmus × hollandica var. insularum. Manual taxoboxes for animal infraspecies link to trinomen (which redirects to Trinomial nomenclature); see e.g. Onithochiton neglectus neglectus. I'm not sure how related that is to the link in {{Infraspeciesbox special}}; presumably the different links in plants vs. animals with manual taxoboxes is related to the logic that governs the taxobox color, but I just tested {{Infraspeciesbox special}} in an animal article and it linked to Infraspecific name (botany). {{Subspeciesbox}} and {{Infraspeciesbox}} both produce links to "trinomial nomenclature" (see e.g. Kamchatka brown bear and Paeonia daurica subsp. wittmanniana). Plantdrew (talk) 19:42, 26 May 2023 (UTC)

The manual taxoboxes set the link based on the kingdom (see {{taxobox/core}}, line 148), which links to trinomen for animals or to Infraspecific name (botany) for plants and fungi. As I didn't have access to the kingdom, I used the zoological link when using |auto=subspeciesbox and the botanical link when using |auto=infraspeciesbox. The new template {{infraspeciesbox special}} uses the latter. However, I now see that both {{subspeciesbox}} and {{infraspeciesbox}} link to Trinomial nomenclature, the deafult of the switch statement. Perhaps it would be best for all taxoboxes to use that link and remove the kingdom=specific links.
On the parameter comments above, |type_strain= should have been supported, but I hadn't allowed the parameter for the |auto=infraspeciesbox option. It now accepts the parameter with or without the underscore. I've added |species_link= and |species_extinct= and will add |subspecies_link= and |subspecies_extinct= when I find an example to test. As an aside, is parameter |species_link= needed, as there should be redirects for scientific names to common name page titles. —  Jts1882 | talk  07:45, 27 May 2023 (UTC)
Thanks for these updates/fixes. I guess the only justification for |species_link= is that some of us that have different display colours set for redirects, tend to see a redirect in taxobox as a possible error, so it's tidier to have all the links blue. I accept it's a marginal case. Peter coxhead (talk) 10:17, 27 May 2023 (UTC)
Proposal to change parameter names.

Currently the parameters are:

  • |infraspecies_rank1= – name of the taxon
  • |infraspecies_rank1_name= – name of the rank
  • |infraspecies_rank1_abbrev= – abbreviation for separator

I find that confusing as {{para|infraspecies_rank1} can be read as the name of the rank rather than the name of the taxon. So I propose a change to:

  • |infraspecies1_name= – name of the taxon
  • |infraspecies1_rank= – name of the rank
  • |infraspecies1_abbrev= – abbreviation for separator

I can make the code changes leaving the older names, which can be removed later. Or can someone suggest better names? —  Jts1882 | talk  10:01, 27 May 2023 (UTC)

I do agree that the existing parameter names aren't the best, and I prefer the proposed alternatives. It's also more consistent with other parameters to put the number on the first part of the parameter name as in |image_caption= and |image2_caption= or |status_system= and |status2_system= – although these examples suggest that the "1" parameters should have aliases without the "1" for full consistency. Peter coxhead (talk) 10:17, 27 May 2023 (UTC)
I Support the alternative parameter names. Plantdrew (talk) 02:24, 3 June 2023 (UTC)

When I hover over the scientific classification edit link in an automatic taxobox (the pencil icon), the mouseover text merely reads "e" instead of "edit". I don't know if this is intended (if so, it is somewhat confusing). If it isn't intended, could it please be fixed? The problem doesn't occur on {{speciesbox}} (where the mouseover text reads "edit"), but it is also present on {{oobox}}, as far as I can tell. Edward-Woodrow :) [talk] 16:47, 10 June 2023 (UTC)

{{Automatic taxobox}} and {{speciesbox}} both set the mouseover text as a parameter, while {{subspeciesbox}} uses the default in {{Edit taxonomy}}, i.e. "Edit this classification". When discussing the change in the pencil icon, it was suggested we standardise and remove the custom options for the different taxobox templates. I think this is a good idea, using the default "Edit this classification", unless someone has a text suggestion. —  Jts1882 | talk  17:32, 10 June 2023 (UTC)
I've never understood why the mouseover text was a parameter; it goes way back to the creation of the automated taxobox system, so I've just left it when converting to Lua. I strongly agree that it should be removed and a standard text used: "Edit this classification" seems fine to me. Peter coxhead (talk) 08:23, 11 June 2023 (UTC)
I've edit {{Edit taxonomy}} to remove the option for mouseover text and always show "Edit this classification".
However, the |edit link= is still required as it acts as a flag to display the icon in {{taxobox/core}}. An alternative would be to use |parent= as the flag as that is the parameter used to flag the classification hierarchy table. Then the parameter can be removed from the taxobox templates (and the function in the module for automatic taxoboxes). —  Jts1882 | talk  09:13, 11 June 2023 (UTC)
@Peter coxhead: What do you think about eliminateing the |edit link= parameter? —  Jts1882 | talk  15:38, 14 June 2023 (UTC)
@Jts1882: I'm always reluctant to touch {{taxobox/core}} if it can be avoided, but it's odd to have this parameter when it no longer has a real use, so I agree – eliminate it. Peter coxhead (talk) 06:20, 15 June 2023 (UTC)

Infobox class use in preloads

I'm working on a project to remove uses of the infobox class and came across the following pages.

  1. {{Automatic taxobox/editintro/preload}}
  2. {{Automatic taxobox/editintro/preload/?}}
  3. {{Automatic taxobox/editintro/preload/??}}
  4. {{Automatic taxobox/editintro/preload/incertae sedis}}
  5. {{Automatic taxobox/editintro/sameas}}
  6. {{Automatic taxobox/floating intro}}

Can someone give me some insight into what the tables at right are being used for (in each, if necessary)? Izno (talk) 04:12, 15 June 2023 (UTC)

@Izno: when an editor creates a taxonomy template, the first five provide a 'skeleton' to be filled in, appropriate to the kind of taxonomy template. E.g. if you created "Template:Taxonomy/FAMILY/?" (where FAMILY is replaced by the name of a family) the second would be used. The last provides the general introduction you get when creating a taxonomy template. Try clicking on Template:Taxonomy/Nonsense.
Do the tables with explanatory examples need class="infobox biota"? Not that I can see; it's just the format chosen by Smith609 in 2011. Peter coxhead (talk) 06:35, 15 June 2023 (UTC)
(edit conflict)
They are all ancillary templates for the taxobox system and most illustrate part of the taxobox output so use the same classes as the taxobox tables. The use of the infobox class was introduced in 2006 with this edit and the important use is now in {{taxobox/core}}. If the goal is to remove the CSS to templatestyles, is there (or will there be) a generic {{infobox/styles.css}} or should we create a {{taxobox/styles.css}} that can be used in all the taxobox templates? —  Jts1882 | talk  06:45, 15 June 2023 (UTC)
There is already a Module:Infobox/styles.css, yes. It currently lacks the styles found in MediaWiki:Common.css. The objective however is not to call that directly, as doing so will be more work later down the road when I (or maybe some ambitious successor) attempt to change infoboxes to use HTML div rather than table (see also MediaWiki talk:Common.css/to do#Remnants of things). You can start thinking about that now if you want, but this template isn't the only one that would make that difficult right now, and I've been focusing on the easier cases (like the 4k uses in mainspace of the class directly and the non-infobox uses in the template/module spaces). Izno (talk) 18:10, 15 June 2023 (UTC)
most illustrate part of the taxobox output so use the same classes as the taxobox tables This is what I was trying to make sure I understood. Which of the 6 actually do that and which of the 6 are just "consistency with the others"/"pretty styling"? Izno (talk) 18:13, 15 June 2023 (UTC)

30 June 2023 use stats update

30 June 2023 update

Project Auto Manual Total taxa Percentage auto # auto added since 30 December 2022 # manual subtracted
Algae 2105 278 2383 88.3 28 5
Amphibians and Reptiles 22170 219 22389 99.0 1189 12
Animals 10084 2058 12142 83.1 396 186
Arthropods 9908 3424 13332 74.3 859 189
Beetles 22341 15703 38044 58.7 1792 1799
Birds 14291 81 14372 99.4 96 3
Bivalves 1660 34 1694 98.0 16 -1
Cephalopods 1999 568 2567 77.9 30 2
Dinosaurs 1632 1 1633 99.9 14 3
Diptera 13385 2642 16027 83.5 712 185
Fishes 23998 1862 25860 92.8 1880 806
Fungi 9643 5684 15327 62.9 690 113
Gastropods 24442 9750 34192 71.5 1766 1603
Insects 52855 25318 78173 67.6 3428 2676
Lepidoptera 69755 28593 98348 70.9 3427 3459
Mammals 8206 153 8359 98.2 155 31
Marine life 7944 1320 9264 85.8 360 148
Microbiology 6244 6693 12937 48.3 484 434
Palaeontology 14090 3736 17826 79.0 387 60
Plants 78452 964 79416 98.8 2561 1006
Primates 980 0 980 100 -1 0
Protista 170 25 195 87.2 67 -4
Rodents 3120 29 3149 99.1 58 1
Sharks 818 49 867 94.3 14 1
Spiders 9698 0 9698 100 223 0
Tree of Life 82 11 93 88.2 3 0
Turtles 754 1 755 99.9 7 1
Viruses 1714 56 1770 96.8 6 2
Total 364568 93154 457722 79.6 18579 11535

Mammal subprojects with articles tagged for both mammals and subproject:

Project Auto Manual Total taxa Percentage auto
Bats 1597 0 1597 100
Cats 180 0 180 100
Cetaceans 433 0 433 100
Dogs 243 0 243 100
Equine 107 0 107 100


Methods and caveats (copy-pasted from previous update)

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 220 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.

Parrosaurus is the only dinosaur with a manual taxobox, may end up being merged. Solitudo is only turtle now (and not linked from stated parent Testudinidae) but Hoan Kiem turtle had a manual taxobox last time around and IMHO shouldn't have a taxobox of any kind. I don't know what's going on with beetles and Lepidoptera; the total for beetles is down by 7 since last time, and down by 32 for Lepidoptera. Perhaps a bunch of articles on synonyms have been merged, or maybe I made a mistake in my last update. Primates has total articles down by 1. The -1 value for bivalve manual taxoboxes removed means that there is one more article with a manual taxobox than last time. For protists -4 is due to more articles being tagged for the project (many relevant articles are still untagged).

Progress the last 6 months was slower than it has ever been since I started tracking "# manual subtracted" (in June 2021), and is likely slower than it has been since I began these reports in 2017. I had been responsible for a large number of manual subtractions due to my efforts to implement automatic taxoboxes for plants, but plants are almost done now so my contributions have dwindled (although I still am making some efforts to implement automatic taxoboxes in various groups of organisms). Progress on fish had been stalled for awhile but picked back up in the last 6 months.

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) 19:53, 30 June 2023 (UTC)

Suggestion for policy regarding lists of synonyms; chronological > alphabetical

Presently, the only guidance I can find regarding the format for a list of synonyms is here, and as a practicing taxonomist, I find the given example runs exactly counter to the convention in all scientific catalogues of names. That is, in catalogues (print catalogues, not databases), synonyms are always given in chronological order, never alphabetical. The example given puts the two names in alphabetical order, rather than chronological. That approach is confusing, to be honest, and not nearly as useful as a chronological listing. This is increasingly important as the list of names gets longer. It is also especially important when one or more of the names in the list of synonyms is OLDER than the name in use for the taxon; this situation in taxonomy is rare, and it is especially noteworthy, but it is only readily visible when the list is chronological. I would like to suggest that Wikipedia should expressly adopt a policy to follow chronological order for lists of synonyms, as there does not presently appear to be any formal policy at all, and in the absence of an existing policy, perhaps establishing one will not be controversial. If necessary, I can raise this topic over at Wikipedia talk:WikiProject Tree of Life, but this seems like the correct place to start the discussion, at least. Dyanega (talk) 18:09, 16 October 2023 (UTC)

  • I too prefer the advantages of the chronological listing of synonyms, and would support changing the format in the example listing, and stating there explicitly that this is the desired format. Esculenta (talk) 18:59, 16 October 2023 (UTC)
@Esculenta:, I haven't paid much attention to how Species Fungorum arranges synonyms. I see there's one view with them alphabetical and another with them chronological (and with homotypic synonyms grouped together). Is the chronological order a recent feature? Is the alphabetical order something that will be maintained or discontinued? Are the chronological views (GSD) available for all species? I'm confused why the record for Anaptychia ciliaris has a link (only) to the alphabetical list and the record for Aspergillus glaucus has a link (only) to the chronological/GSD list (although lists in both arrangements exist for both species and can be found by pasting the appropriate ID into the appropriate URL for a particular arrangement). Plantdrew (talk) 19:56, 16 October 2023 (UTC)
  • I don't really know the details, but it looks like in cases where Species Fungorum get their synonymy data from external Global Species Databases, they get ordered chronologically, with each entry linked. If the synonymy data comes from Index Fungorum, it's in alphabetical order and not linked. I hadn't even noticed before that both arrangements could be had with different URLs, so thanks for pointing that out (I will definitely be linking to the "better" synonymy list from now on). Esculenta (talk) 21:00, 16 October 2023 (UTC)
  • Dyanega This is best raised at Wikipedia talk:WikiProject Tree of Life where the most amount of eyes will see it and will encompass the ICNafp editors as well, rather then possibly missing them.--Kevmin § 19:17, 16 October 2023 (UTC)
  • The example isn't alphabetical OR chronological. I think this would be better to discuss at TOL (while the page is watched by ICNafp editors, I'm not sure that the proposal was made with ICNafp editors in mind; the arrangement of a chronological list would appear un-intuitive if dates are omitted, and synonym lists in plant articles rarely include dates). Plantdrew (talk) 19:40, 16 October 2023 (UTC)
I hadn't realized that botanists omitted the years from synonym lists. That would certainly change the recommended policy based on Kingdom. So, your recommendation is to start a thread on WT:TOL, then? Dyanega (talk) 20:50, 16 October 2023 (UTC)
Yes, this should be at TOL for visibility needs.--Kevmin § 22:00, 16 October 2023 (UTC)
@Dyanega:, botanists do include years in the types of publications I think you're referring to (revisions, monographs, etc.) and do order synonyms chronologically in those publications. Lists of synonyms in Wikipedia articles on plants don't typically include years (and are generally sourced from databases that arrange synonyms alphabetically, and which may not include years (or any publication details) in the view of the synonyms of a particular accepted species (the database may have year/publication details if you click through to the record for a particular synonym). Sorting lists of plant synonyms chronologically would entail significant effort in adding years to the lists before the list could even be re-sorted. For animals, the years would already be present as part of the standard zoological authority citation. Plantdrew (talk) 22:39, 16 October 2023 (UTC)
  • The synonym section in the taxobox often isn't used for a formal list of synonyms, at least for higher taxa. Often or possibly most of the time it's just some of the more common ones. Would this policy encourage putting complete synonym lists in the taxobox? While I prefer chronological order as it provides information on the history, a lot of the commonly used sources are databases that use alphabetical order. —  Jts1882 | talk  06:37, 17 October 2023 (UTC)

New thread has been started, Thanks. Dyanega (talk) 23:49, 16 October 2023 (UTC)

Template deletes?

Is there a way to delete taxonomy templates that are no longer in use? The fungal family Arthopyreniaceae is now considered to be a synonym of Trypetheliaceae, so we no longer need its associated taxonomy template. MeegsC (talk) 21:06, 21 October 2023 (UTC)

Blank the code and add the template to Category:Unnecessary taxonomy templates. Plantdrew (talk) 21:10, 21 October 2023 (UTC)

Small bug with display_parents

In this edit of Arbutus andrachne, |display_parents= had the value as Arbutoideae. The taxobox displays subfamily Arbutoideae, which is 2 parents up from the species. I experimented a little, and it appears that any (?) non-numeric value for |display_parents= results in displaying 2 parents (I tried alphabetic and non-alphanumeric characters). It's not a big deal, but it is strange behavior. Plantdrew (talk) 03:23, 29 November 2023 (UTC)

Looks like the expression (#expr) on line 46 of {{speciesbox}} returns an error when there is not a number and that is passed to the module as value of |display_taxa= instead of the default zero. The tonumber() at line 111 of Module:Autotaxobox returns nil rather than the expected/default zero and that sets displayN to 2 instead of 1, which is the intended default for {{speciesbox}}, whereas in Module:Automated_taxobox |display_taxa= defaults 1, which sets displayN to 2. The fix needs to be in {{speciesbox}} and the expression error. Those parse functions are horrible to deal with. —  Jts1882 | talk  09:04, 29 November 2023 (UTC)

Should clades be included in this template? If so, where?

I recently came across the Wikipedia article for clades, and a lot of Wikipedia articles for the Tree of life are missing this more modern take on taxonomy. I think it should probably be part of a template, but I'm not sure how it should be laid out. It would be great if an editor with more knowledge or official authority on this topic could comment on this. Galactiger (talk) 11:56, 27 December 2023 (UTC)

I'm not sure exactly what you mean. The taxonomy templates accept "clade" as a rank, which is used extensively. See, e.g., the classification at Template: Taxonomy/Dinosauria. Peter coxhead (talk) 12:07, 27 December 2023 (UTC)

New Zealand moth genus Rhathamictis

I've attempted to create a taxonomic template for this genus but for some reason it doesn't seem to be generating correctly. Could someone more knowledgable than me suggest ways in which I can rectify this? Thanks in advance for the assistance. Ambrosia10 (talk) 21:37, 1 January 2024 (UTC)

@Ambrosia10, I just think you had the breaks wrong. Fixed now. YorkshireExpat (talk) 21:50, 1 January 2024 (UTC)
Thanks so much for your help! Much appreciated. Ambrosia10 (talk) 22:07, 1 January 2024 (UTC)

Not allowed to create new template for new article

Hi, I'm trying to make a taxonomy template for my first article Bubodens, but when I try to create it I get a permission error with "Due to the high impact of editing taxonomy templates, it has been decided to disallow new users to edit them...." How can I get this taxonomy template made for my page? Mojoceratops66 (talk) 08:17, 12 January 2024 (UTC)

@Mojoceratops66: I saw your draft was accepted and created the speciesbox. You can always use the old manual {{taxobox}} system, and someone (like me) will come along and make the automated version. Or ping me and I'll be happy to do it. - UtherSRG (talk) 12:32, 12 January 2024 (UTC)
Thank you!! Mojoceratops66 (talk) 16:21, 12 January 2024 (UTC)
@Mojoceratops66: You can also ping me. Actually, if you just leave an article with a non-functioning automated taxobox (I understand why editors are reluctant to do this), the article will appear in one or more of the subcategories of Category:Taxobox cleanup, which a number of us monitor regularly, and the taxobox will get fixed. After you've been editing a while you will be able to create taxonomy templates. Peter coxhead (talk) 12:40, 12 January 2024 (UTC)

30 December 2023 use stats update

30 December update

Project Auto Manual Total taxa Percentage auto # auto added since 30 June 2023 # manual subtracted
Algae 2163 227 2390 90.5 58 51
Amphibians and Reptiles 22524 206 22730 99.1 354 13
Animals 11167 1158 12325 90.6 1083 900
Arthropods 10774 3067 13841 77.8 866 357
Beetles 24731 13421 38152 64.8 2390 2282
Birds 14358 62 14420 99.6 67 19
Bivalves 1674 32 1706 98.1 14 2
Cephalopods 2009 566 2575 78.0 10 2
Dinosaurs 1643 0 1643 100 11 1
Diptera 14160 2165 16325 86.7 775 477
Fishes 24408 1671 26079 93.6 410 191
Fungi 10655 5171 15826 67.3 1012 513
Gastropods 27510 7224 34734 79.2 3068 2526
Insects 57978 20719 78697 73.7 5123 4599
Lepidoptera 74631 23766 98397 75.8 4876 4827
Mammals 8301 144 8445 98.3 95 9
Marine life 8723 672 9395 92.8 779 648
Microbiology 6971 6030 13001 53.6 727 663
Palaeontology 14779 3474 18253 81.0 689 262
Plants 79920 611 80531 99.2 1468 353
Primates 979 0 979 100 -1 0
Protista 380 80 460 82.6 210 -55
Rodents 3137 28 3165 99.1 17 1
Sharks 829 45 874 94.9 11 4
Spiders 10040 0 10040 100 342 0
Tree of Life 89 6 95 93.7 7 5
Turtles 759 0 759 100 5 1
Viruses 1722 55 1777 96.9 8 1
Total 383888 76708 460596 83.3 19320 16446

Mammal subprojects with articles tagged for both mammals and subproject:

Project Auto Manual Total taxa Percentage auto
Cats 186 0 186 100
Cetaceans 439 0 439 100
Dogs 241 0 241 100
Equine 109 0 109 100
Methods and caveats (copy-pasted from previous update)

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 207 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.

The template for the Bats taskforce was merged into the template for WikiProject Mammals since my last update. I can't track bats separately anymore, but they had been at 100% automatic taxoboxes for a couple years now. WikiProject Protista is slowly being added to more articles; there has been an increase in the number of tagged protist articles with manual taxoboxes. Primates has one less article than it did last time; perhaps a taxon has been lumped and an article merged.

All projects are now over 50% automatic taxoboxes and the majority are now over 90%.

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) 03:10, 31 December 2023 (UTC)

Have you numbers on the number of new manual taxoboxes added, what percentage of all new taxoboxes they make, and the projects still using them? —  Jts1882 | talk  09:18, 18 January 2024 (UTC)
@Jts1882:, there isn't any easy way to get new manual taxoboxes by WikiProject. A PetScan search for articles with taxoboxes sorted by "not at all"/descending shows recently created articles. Of the most recent 20, 7 are moths, 3 fungi, 3 beetles, 2 arthropods, 2 eukaryote incertae sedis, 1 gastropod, 1 insect (Hymenoptera), and 1 (fossil) bird. Single editors (different ones) were responsible for 6 of the moths, 3 beetles, 2 fungi, 2 arthropods and 2 eukaryotes. 8 of the 20 are species and 12 are higher taxa.
82 articles with manual taxoboxes were created between 30 June 2023 and 30 December 2023. Assuming the difference between # auto added and # manual subtracted represents newly created articles (it mostly should), 2874 articles with automatic taxoboxes were created since June 2023. 82+2874=2956. 82 is 2.8% of 2956. Existing articles do occasionally get converted from automatic taxoboxes to manual by editors who want to update the classification without understanding how taxonomy templates work, but that number is negligible.
I guess the take away is that there are a small number of editors creating articles with manual taxoboxes, and they are mostly working in groups where uptake of automatic taxoboxes is relatively low. Groups with low uptake of automatic taxoboxes are going to be missing many taxonomy templates needed to create speciesboxes, but the articles being created with manual taxoboxes are mostly higher taxa, so having taxonomy templates in place probably isn't going to help very much (of the 8 species in the most recent 20, only 1 was in a genus that has an existing taxonomy template). Plantdrew (talk) 16:25, 18 January 2024 (UTC)
7214 articles were created with manual taxoboxes since 10 April 2017, which is when I started tracking stats on automatic taxoboxes. That was a little after automatic taxobox use really started to take off (but well before it was the norm; 13.2% of articles had an automatic taxobox at that point). So less than 10% of articles with manual taxoboxes were created after concerted efforts to use automatic taxoboxes began (obviously there are some articles that were created since 2017 with manual taxoboxes that have now been converted). Plantdrew (talk) 16:58, 18 January 2024 (UTC)
I guess a better date to pick would be 30 August 2018, when the RFC about preferring automatic taxoboxes closed. There are 3970 articles created with manual taxoboxes (and which still have them) since 30 August 2018. Plantdrew (talk) 21:16, 18 January 2024 (UTC)

Aquaterraves‎

Is there any precedent on taxoboxes for 'hypothetical' taxons? I guess they're all hypothetical at some level. YorkshireExpat (talk) 17:03, 13 February 2024 (UTC)

There is precedent; see e.g. Eocyte hypothesis and Articulata hypothesis (there's relevant discussion going on at Template_talk:Taxonbar#Further_discussion, with the newly created Wikidata item taxon hypothesis (Q124477390) stemming from that). I'm not sure that the precedent needs to be followed if something is really framed as a hypothesis (i.e., we might consider removing those taxoboxes).
It gets more complicated with Tactopoda and Antennopoda, which are framed as "proposed clades", but which represent mutually exclusive hypotheses regarding the relationship of tardigrades, arthropods and onychophorans.
Avifilopluma is another weird one. It was the last article tagged for WikiProject Dinosaurs to get an automatic taxobox. It is the clade of feathered animals, with feathers not being precisely defined, and it not being clear exactly which taxa would be included. Plantdrew (talk) 18:06, 13 February 2024 (UTC)
Ok, will leave alone for the moment. Thanks. YorkshireExpat (talk) 08:38, 14 February 2024 (UTC)
There are articles for Columbaves, Inopinaves and Aequorlitornithes (all from Prum et al, 2015), as well as Columbea and Passerea (from Jarvis et al 2014). Gruimorphae also has one, as do the more questionable Otidae and Gruae. While I think it is useful to have short articles clearly defining these proposals, perhaps the Neoaves article could be expanded discuss the alternative arrangements, which are currently shown in he cladograms. I think this new proposal certainly should be covered. —  Jts1882 | talk  10:37, 14 February 2024 (UTC)

Any interest in adding automatic links to wikispecies, commons categories and galleries, and wikidata at the bottom of our taxboxes to improve integration with our sister projects? Compare hr:Dracaena aethiopica / en:Dracaena aethiopica. Coded in hr:Template:Taksokvir (note the four tracking categories). Ponor (talk) 11:43, 17 April 2024 (UTC)

We use {{taxonbar}} to link to various taxon IDs, including wikidata, wikispecies, etc. All of the IDs are stored at Wikidata. We could consider adding commons and gallery to the taxonbar. @Tom.Reding and Jts1882: thoughts on this? - UtherSRG (talk) 12:21, 17 April 2024 (UTC)
I was thinking of a more prominent place. {{Taxonbar}}, to me, is something that experienced editors might need, it's not very friendly to our readers. It's also not shown to >2/3 of them Ponor (talk) 12:41, 17 April 2024 (UTC)
Instead of duplicating the effect in the taxobox, we can perhaps work to make the taxonbar available on mobile. - UtherSRG (talk) 14:46, 17 April 2024 (UTC)
Unfortunate side-effects to that would include:
  1. people complaining about WP:OVERLINKING
  2. people removing {{Commons}}, {{Commons category}}, etc., due to the presence of a link in {{Taxonbar}}
I don't agree with this behavior, but it happens relatively often.   ~ Tom.Reding (talk ⋅dgaf)  15:09, 17 April 2024 (UTC)
I'm not against an unobtrusive addition at the bottom of the taxobox. However, as an infobox, the taxobox is supposed to summarize information on the taxon, so it is probably better for links to other resources to be elsewhere.
There was a previous discussion about including wikispecies and commons in the taxonbar or only using the templates {{Commons category}} and {{Wikispecies}} to avoid redundancy. In the end the status quo was kept (with Wikispecies in the taxonbar). I'm not adverse to adding the commons gallery or commons category.
The taxonbar doesn't appear on mobile because it uses Navbox, which is not allowed on mobile view for some reason (possibly because you can't collapse large navboxes or they are condised too large for downloading on phones). I believe there were some proposed changes aimed at making a mobile compliant navbox. @Tom.Reding: do you know anything on this? It would certainly be possible to make an alternative output for the taxonbar without using navbox, although this may go against decisions made elsewhere for such content (e.g. authority control). —  Jts1882 | talk  15:03, 17 April 2024 (UTC)
Mobile & style issues are sort of a black box to me. My impression is that there's a desire, and some work being done, to, at some point, make navboxes viewable on mobile, but I don't keep up with that at all. I don't know of another navbox-like utility (not that I've looked for one). If there were a flag or something in Lua that would designate a user's device as mobile or non-mobile, then an alternate method could be used (even something dumb like an un/ordered list, assuming consensus, etc., etc.).   ~ Tom.Reding (talk ⋅dgaf)  15:22, 17 April 2024 (UTC)
There is no way of detecting the skin in Lua. It can only be done in JS or CSS. Without Wikimedia support, this means any solution must use CSS, which can be customised for different skins (including the mobile one, Minerva). I'm not sure how Navboxes are blocked in Mobile view, but I assume it's server side, as the HTML code for navbox is not on the page (although strangely their templatestyles is). An alternative output could mimick the navbox styles and hav different displays for mobile and desktop (or narrow and wide screen).
An alternative output from taxonbar shouldn't be too difficult. I did some experimenting in the module sandbox some time ago, using horizontal and vertical lists, with collapsible options. However, it would be good to find out what Wikimedia plans are for navboxes and mobile. —  Jts1882 | talk  07:39, 18 April 2024 (UTC)

Taxonbar appears to be overpopulated, uncurated, containing numerous links to, from a reader's perspective, low-quality sites (database dumps); on mobile devices this would be one half of the screen full of some links. On the other hand, I know that a link to the commons category/gallery will take me to moderately well-curated images of the species, which are made and heavily used by us. Since our articles don't have more than a picture of two, and many readers probably want to see more, I am still not convinced that adding a wikispecies link and one or two commons links would be a bad idea, as unobtrusive as we want it to be. While the taxobox is intended to summarize information on the taxon (meaning: classification), we already deviate from this by incorporating images, statuses, and range maps. Should this be discussed anywhere else? Can we BOLDly add it and wait for the avalanche? — Preceding unsigned comment added by Ponor (talk • contribs)

Back in the old days, we did try putting those links in the taxobox. It got shot down. This is why Tom said what he did above. Those were the arguements against. - UtherSRG (talk) 13:04, 22 April 2024 (UTC)
Taxonbar links are curated to some extent. We've decided not to include databases published by governments of non-English speaking countries. And there are many Wikidata properties for taxonomic databases that aren't included in taxonbars (where there has never been any discussion to include or exclude them).
I'm against including (potentially) 4 links to Wikispecies in desktop view. Currently links appear in the desktop sidebar, in the taxonbar, and via {{Wikispecies}} (if present). A link the in the taxobox would be a fourth. Sidebar and taxonbar links don't appear in mobile view. It would be good to enable links to Wikispecies and Commons in mobile in some way aside from {{Wikispecies}} and {{Commons}}. Plantdrew (talk) 19:51, 22 April 2024 (UTC)
I concur, PD.
Let's see if I can sum up. There's a desire for links to Wikispecies/CommonsCats/CommonsGal/Wikidata to be available to mobile users, if they exist. Taxonbar is where these are already present in desktop, but is suppressed in mobile, as is the sidebar where some of these links are present in desktop. Links to CC, CG and WS should be listed on WD, if they exist. So it seems that only a link to WD would suffice, though providing all four would ease the burden on the user to click through WD to get to the others.
This seems to be our list of current options, though they weren't all stated above:
  1. Add these links as originally requested to the Taxobox system.
  2. Add these links as originally requested to the Taxobox system, but have them appear only for mobile users; so CSS or JS changes
  3. Tweak the CSS or JS (or ?) so that the Taxonbar appears on mobile
  4. Tweak the CSS or JS (or ?) so that the Taxonbar appears on mobile, but in a limited form with just WS/CC/CG/WD, if available.
Option 1 is ruled out by history. It's a good ask, but I don't think it will ever see traction. All the rest, as far as I can figure, need someone who can tweak the CSS or JS so that the good magic happens. Do we need to poke elsewhere for CSS/JS/? support on this? - UtherSRG (talk) 00:38, 23 April 2024 (UTC)
Another option is to create a simple template that displays a box with the wikimedia links that only displays on mobile. If could be floated right below the taxobox or placed at the bottom of the page instead of the taxonbar. The taxobox or taxonbar templates could be used to place it automatically. It can be given a class so that it will only be shown in mobile (the CSS would be set using templatestyles). —  Jts1882 | talk  07:03, 23 April 2024 (UTC)
A summary of relevant differences between desktop and mobile views (mostly redundant with above discussion).
  • Template {{taxonbar}} is only shown in desktop, so mobile views don't get information that is exclusive to taxonbar.
  • In desktop, Wikispecies is shown in sidebar, taxonbar (if other identifiers) and in template {{Wikispecies}} or {{Wikispecies-inline}} (if present).
  • In mobile, Wikispecies is only shown if template {{Wikispecies}} or {{Wikispecies-inline}} is on the page.
  • In desktop, the Commons gallery or category is shown in the sidebar and in in template {{Commons}} or {{Commons-inline}} or {{Commons category}}
  • In mobile, Commons gallery or category is only shown if template {{Commons}} or {{Commons-inline}} or {{Commons category}} is only page.
  • Normally only one of the Commons gallery or category is linked. Both the sidebar and the commons templates show the gallery if it exists and the category if there is no gallery. Both can be linked if {{Commons category}} is also added.
In short, mobile users need the wikispecies and commons templates if they are to see wikimedia links. Some numbers:
In short, only about 10% of the pages on taxa have the wikimedia link templates. I thought it would be higher. A taxobox or taxonbar solution is easier than adding the wikimedia templates.—  Jts1882 | talk  09:04, 23 April 2024 (UTC)

30 June 2024 use stats update

30 June update

Project Auto Manual Total taxa Percentage auto # auto added since 30 December 2023 # manual subtracted
Algae 2280 160 2440 93.4 117 67
Amphibians and Reptiles 22711 199 22910 99.1 187 7
Animals 11596 915 12511 92.7 429 243
Arthropods 11355 2719 14074 80.7 581 348
Beetles 26514 11994 38508 68.9 1783 1427
Birds 14405 48 14453 99.7 47 14
Bivalves 1696 28 1724 98.4 22 4
Cephalopods 2020 558 2578 78.4 11 8
Dinosaurs 1624 0 1624 100 -19 0
Diptera 15081 1565 16646 90.6 921 600
Extinction 796 31 827 96.3 NA NA
Fishes 25302 960 26262 96.3 894 711
Fungi 12194 3932 16126 75.6 1539 1239
Gastropods 32419 2972 35391 91.6 4909 4252
Insects 61302 18450 79752 76.9 3324 2269
Lepidoptera 83659 14801 98460 85.0 9028 8965
Mammals 8401 124 8525 98.5 100 20
Marine life 8990 527 9517 94.4 267 145
Microbiology 7675 5393 13068 58.7 704 637
Palaeontology 15506 3198 18704 82.9 727 276
Plants 81558 188 81746 99.8 1638 423
Primates 983 0 983 100 4 0
Protista 778 150 928 83.8 398 -70
Rodents 3161 25 3186 99.2 24 3
Sharks 833 38 871 95.6 4 7
Spiders 10110 0 10110 100 70 0
Tree of Life 100 0 100 100 11 6
Turtles 760 0 760 100 1 0
Viruses 1736 55 1791 96.9 14 0
Total 407991 57001 464992 87.7 24103 19707

Mammal subprojects with articles tagged for both mammals and subproject:

Project Auto Manual Total taxa Percentage auto
Cats 185 0 185 100
Cetaceans 445 0 445 100
Dogs 241 0 241 100
Equine 109 0 109 100
Methods and caveats (copy-pasted from previous update)

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 207 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've added WikiProject Extinction to the table this time. WikiProject Protista continues to have tags added to existing articles, with a net increase in the number of tagged articles with a manual taxobox. WikiProject Dinosaurs recently merged a bunch of largely redundant articles for nodes in a cladogram, resulting in a net decrease in the number of articles tagged for that project. Plantdrew (talk) 17:12, 30 June 2024 (UTC)

Thanks for doing these updates. Good to see progress. Did you include {{WikiProject Cacti}} in with the Plants totals? It doesn't look like that template automatically adds it to the parent WP like the other plants subprojects. awkwafaba (📥) 19:01, 1 July 2024 (UTC)
@Awkwafaba:, I did not include WikiProject Cacti in the totals. However, for the past several years, I've been running the "Taxon pages not tagged in WP ToL clade projects" query on your user page to ensure all taxobox articles are tagged for a project immediately before I start compiling an update of these numbers (and in general I run your query every couple of weeks, but haven't made it a priority to tag redirects). I did pick up several cacti articles and added WikiProject Plants tags before I started this update. None of the plant subprojects get picked up in a Petscan search for {{WikiProject Plants}}, so I have always done a separate search for Banksia/Carnivorous plants/Hypericaceae and added those results to the results for Plants when presenting these numbers (the other 3 subprojects aside from Cacti do contribute to the numbers reported in the assessment table for WikiProject Plants). Plantdrew (talk) 20:07, 1 July 2024 (UTC)

Automatic child taxa?

I don't really know how else to title this. I'm one of the editors on a wiki which focuses on recording fictional species made for a large collaborative speculative evolution project, and at some point for much the same reason you all did, we came up with an automated taxonomy system to reduce the pain of updating taxonomy for hundreds, even thousands of species. However, ours works a bit different from Wikipedia's, storing all taxonomy data in a centralized place--a JSON file. As all the data is in one place, it also allowed us to also be able to easily reverse the direction and display, for instance, all descendant taxa as well.

Looking at how Wikipedia does taxonomy, I noticed that there are places where it would make sense to automatically generate a list of descendant taxa. Most notably, the subdivision section of the automatic taxobox, and perhaps various other lists of genera and species around the wiki. I can't imagine pages like the list of Asteraceae genera being anything short of a nightmare to update and maintain, assuming its reputation among botanists is earned, and I could see it being worse for decently large mid-level taxa that are in a state of flux due to several new studies being published.

I think that the current system Wikipedia is using might make generating lists of child taxa impractical, but on the other hand, I wonder if the changes needed to support it would actually be considered worthwhile to those involved in this wikiproject. I know that for the aforementioned wiki I'm part of, this also made it much easier to browse taxonomy in general because readers and editors alike could reliably access related and descendant taxa from anywhere. And while editing is moderated on our wiki so we haven't had need for this, I can't help but imagine it would make it a bit easier to spot and fix vandalism as well because it would be plainly visible from higher taxa (which one might be more likely to view in some cases). Any thoughts on the idea? Disgustedorite (talk) 21:24, 20 July 2024 (UTC)

@Disgustedorite:, when automatic taxoboxes were first being developed (ca. 2011), there was an attempt to include automatic child taxa that was eventually abandoned. I don't know the details about why it didn't work.
There is a script (User:Jts1882/taxonomybrowser.js) that allows you to see the taxonomy in a tree view, with children.
However, not all articles are using automatic taxoboxes (~88% are using them, but that still leaves 50,000+ articles with manual taxoboxes). And Wikipedia doesn't have articles for every genus, let alone every species. Plantdrew (talk) 22:44, 20 July 2024 (UTC)
On our wiki we actually manually update some lower taxa on a species by species basis while the higher taxa are what is automated, since for a collaborative speculative evolution project with nearly 10 times as many species as there are dinosaurs and upwards of 200 more added every year, the frequency at which those are defined and updated can make dinosaur researchers jealous.
I just skimmed the source code of the taxonomy browser and...well, I suppose the processing impact doesn't matter that much when it's run on your own machine, lol. I will say using the search API and taking advantage of taxonomy being stored exclusively within the template namespace is pretty smart. Our strategy was to index child taxa and then search that index taxon by taxon, though having far fewer species than have been described in real life (and not actually having a page for every member of a genus of insects) gives us the advantage of not needing to actually maintain an index by hand (we have few enough taxa that it's economical to index it over again every time).
If I were to take a guess, I can see that Wikipedia has no extensions like Semantic MediaWiki (understandable given its current state), Cargo (I wouldn't use it either), or even DynamicPageList3 (performance hell), which leaves the search API and checking each and every result as basically the only option, which, even if it was possible in a module, I could imagine hitting memory limits fast. On our wiki, we're looking into making a sort of poor man's Semantic MediaWiki using an autonomous bot that records and indexes information about pages in various dedicated JSON files...but a bot-dependent system wouldn't fly here, right?
Although, Wikipedia does have CategoryTree, which I think is what our wiki attempted to use for taxonomy browsing...in 2007, when there were only a few hundred species. But in any case, using the various different parameters of its parser function, it might be possible to twist it into something like a poor man's DPL3 by having each taxonomy template page automatically be added to a category like "child taxon of Parentsnameidae" and then using several instances of the CategoryTree parser function (or just one that's been quite heavily altered by the lua script after it was generated, if that's possible) to display it. But that's also a lot of potential categories... Disgustedorite (talk) 00:33, 21 July 2024 (UTC)
While I agree it would be nice to have automatic child taxa, it really isn't practical for Wikipedia. Wikipedia has to be open for everyone to edit, which is why we have the template system over centralised JSON or Lua module methods, and NPOV means we have to be able to show alternative taxonomies over one agreed system.
The taxonomy browser was developed as a tool to manage the taxonomy templates. It picks up the parent-child relationship of templates, which most of the time is a taxonomic relationship but gets more confusing where there are alternative taxonomies. And any JS additions have to be opt-in. For a Wiki that could impose one taxonomy with a centralised JSON source, a JS addition to the taxobox would be possible.  —  Jts1882 | talk  10:37, 21 July 2024 (UTC)

Template/Taxonomy for something about which very little is known?

I've recently been updating things to the automated system, and today I dealt with Mawsonites. It's a genus defined by a fossil from hundreds of millions of years ago, and apparently there's not even a remote consensus about what it is (jellyfish? trace fossil? microbial colony? etc. etc. etc.). There was no {{taxonomy}} template for it, so I created Template:Taxonomy/Mawsonites, but ran into a couple things that I'm not sure I did correctly, and don't know how to "really" handle.

1. The existing {{taxobox}} listed it as in Animalia, then incertae sedis from there down to the genus itself. I put the existing "Animalia/incertae sedis" claim in the new taxonomy template. However, some of the theorized possibilities listed in the main article for the genus are not actually animals. Should its parent perhaps be set to {{Taxonomy/Incertae sedis/Life}} instead? I should note here that some of the theorized possibilities aren't even organisms, e.g. "mud volcano or other sedimentary structure", but the article reads like those theories are now thought to be very unlikely.

2. I wasn't sure what to do about the taxonomy template's "extinct" field. I guess at least the species is almost certainly extinct, since we apparently haven't kept finding these things, but the genus? Again, I'd guess extinct, but... what if it's just some jellyfish (I know that's not a genus, but that doesn't mean that its genus would necessarily be extinct)? Or even some weird mark left by a jellyfish? But as far as I can see from the documentation, "extinct" is just yes/no; I'm not sure if it's appropriate or even possible to instead set it to "probably" or "unknown" or whatever.

For what it's worth, I'm thinking "Incertae sedis/Life" and "extinct=yes", but instead of making it that way, I decided to just keep things as close as possible to the way they were in the pre-automated article, and raise my questions here. - Rwv37 (talk) 18:21, 9 September 2024 (UTC)

@Rwv37:, "Animalia/incertae sedis" seems appropriate. The Paleobiology Database lists the parent as Metazoa (i.e. Animalia) citing a 2004 paper. The 2004 paper actually discusses Mawsonites in the context of "medusoids". "Medusoids" does appear in quotation marks in the paper, suggesting that the authors are hedging their bets a bit; i.e., they are discussing fossils that have been classified as medusoids, but aren't definitively taking a position on whether the fossils mentioned are or are not actually medusoids. The source currently in the article for the statement "jellyfish (although this is considered unlikely)" actually says "not considered by Glaessner (1979) to be undoubtedly a jellyfish", which is not at all the same thing as "considered unlikely to be a jellyfish".
Based on what I've seen I think you could set the parent template to be Template:Taxonomy/Scyphozoa/? (questionably a jellyfish), but "Animalia/incertae sedis" works as well. The non-animal hypotheses for Mawsonites don't seem to be well supported.
For taxa known from fossils, you can pretty safely set "extinct=yes". If a genus is known from fossils as well as extant species a quick check on a search engine should turn up sources discussing the extant species. The absence of a † in a manual taxobox shouldn't be taken to indicate that extinct status is uncertain for a taxon that the article describes as being known from fossils. Plantdrew (talk) 21:10, 9 September 2024 (UTC)

Edit request 9 September 2024

Hello, please apply this fix to the module in production. Od1n (talk) 18:22, 9 September 2024 (UTC)

 Completed. P.I. Ellsworth , ed. put'er there 20:19, 9 September 2024 (UTC)
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