User talk:Awkwafaba/Archive 9

El Tor
Hello. You seem to keep reverting my changes at El Tor. The page is currently asking for a taxobox. As taxoboxes currently stand there does not seem to be way of representing the taxobox as you wish to see it (presumably if you knew how to do it, you would be more positive in your editing and simply do it). Therefore I have added a taxobox that is not incorrect, i.e. a speciesbox representing the species that the strain discussed on the page is part of.

Please take a look at the following template:

The strains of E. coli represented in the template either do not have a taxobox, or have one at the species level. Please choose what you would like to see at El Tor and do that. I see you are busy in real life, so will give you a week or so, and then will put back the taxobox I put in previously. Thanks. YorkshireExpat (talk) 08:26, 17 October 2021 (UTC)
 * taxoboxes should show the taxon discussed in the article, not the parent article. El Tor is not a species, Vibrio cholerae is a separate article.  Look at Bacillus cereus biovar anthracis.  Look at Subspeciesbox and infraspeciesbox.  These templates are used on thousands of pages for varieties, strains, and other infraspecific taxa.  For viruses, you can use virusbox.  There is no reason to put the wrong taxon in the taxobox.  If those strains of E. coli have a taxobox for the parent, they are wrong too.  I would change it myself, but I don’t often get to use a desktop much, and putting in a full taxobox is difficult on a tablet, so I use the missing-taxobox template and pass the buck.  Thanks for sticking with this, though.  I appreciate your work on all these taxa articles.  Cheers. --awkwafaba (📥) 12:43, 17 October 2021 (UTC)
 * Thanks for this. However, I'm not sure there is a good solution in here. Bacillus cereus biovar anthracis uses a manual taxobox using the 'varietas' parameter, where for El Tor what you need is 'serotype' and 'strain'. Also, I much prefer using automatic taxobox types. infraspeciesbox is for botanical taxa, and Subspeciesbox only goes to subspecies level (I'll admit to not fully understanding the links between subspecies, strain and serotype). virusbox is clearly for viruses. Maybe we need a bacteriabox ? YorkshireExpat (talk) 14:56, 17 October 2021 (UTC)
 * what would the last few lines of such a taxobox look like? Like this?


 * With, I asume, no equivalent of the trinomial box you get with a subspecies or variety. Should there be a line for the serotype as well? Peter coxhead (talk) 15:24, 17 October 2021 (UTC)
 * See also, as another example, the taxobox at Cantaloupe. Would it be like this, with "serotype" instead of "subspecies" and "strain" instead of "variety", but with the values not italicized? Peter coxhead (talk) 15:31, 17 October 2021 (UTC)
 * Or from a quick read on the subject maybe serogroup would be better than serotype.


 * Maybe there's somewhere better to have this conversation where people who know what they're on about could see it? YorkshireExpat (talk) 15:52, 17 October 2021 (UTC)
 * WP:WikiProject Microbiology? Peter coxhead (talk) 18:04, 17 October 2021 (UTC)
 * TOL or Automated taxobox system probably have more watchers than Microbiology. There are manual taxoboxes I haven't tackled because they use ranks that aren't supported by automatic taxoboxes. Forma and forma specialis are defined by ICNafp. There are several infrasubspecific ranks defined in the ICNP; see pages 91-92 of this PDF; the ranks are given as connecting terms, so Infraspeciesbox would be the appropriate template to add support for further ranks.Plantdrew (talk) 18:41, 17 October 2021 (UTC)
 * Yes, definitely Infraspeciesbox. Rather than keep adding extra named ranks, I was wondering about adding a couple of lowest level ranks for which the name of the rank could be specified, something like RANK_NAME + TAXON_NAME. Just a thought at present. (Italicization or not would be an issue.) Peter coxhead (talk) 18:52, 17 October 2021 (UTC)
 * These ranks keep popping up. I thought I found them all with all the work I did on  and then I discovered biovar and that's how I found El Tor.  In some places it is Vibrio cholrae bv. eltor.  These informal ranks are rather unruly, and I feel a little ego-driven ("This bacteria I discovered is not a mere strain!  It is a biovar.").  I don't know what the other taxonomic codes say on these ranks, but ICTV refuses to even comment on anything below species.  Until they do, I feel we're going to keep getting new ranks under species.  --awkwafaba (📥) 20:54, 17 October 2021 (UTC)
 * Peter, I think parameters that allow free text are probably the best approach (rather than hard coding several ranks that might only be used in a handful of articles across Wikipeda). Italicization can be applied with standard wiki markup when necessary. Basically the same solution as using binomial_text in Automatic taxobox to deal with miscellaneous weird cases. Plantdrew (talk) 22:55, 17 October 2021 (UTC)
 * yes, I agree that some kind of free text approach is the best. Some parts of the code of the taxobox system (automated and manual) are hard to understand and maintain because they deal with unusual and little used 'ranks' or other conventions (like the use of double quotes) which actually more difficult to implement than standard cases. I'll post something at Template talk:Infraspeciesbox, I think, and we can advertise it elsewhere if it develops. Peter coxhead (talk) 07:37, 18 October 2021 (UTC)

please see Template talk:Infraspeciesbox. Is the proposal clear/complete? I'd like to check this before advertising the thread more widely. Peter coxhead (talk) 08:25, 18 October 2021 (UTC)
 * All looks good thanks. Shall monitor! YorkshireExpat (talk) 19:44, 18 October 2021 (UTC)

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Synonyms and taxonbars
Hello Awkwafaba,

Thank you again for fixing the incorrect taxonbar I added to Daviesia brachyphylla.

With respect to adding taxonbar entries for synonyms to plant articles as you have done to the D. brachyphylla article, I have three questions for you to consider -
 * 1. Plants of the World Online lists 78 synonyms for Dendrobium, 70 of which have Wikidata entries (the other 8 could easily be added), 33 for Solanum and 109 for Eclipta prostrata. Do you think taxonbars should be added to these articles for all these synonyms?
 * 2. How does adding taxonbars for synonyms add to the value of the article?
 * 3. In your edit summary, you added "Either way this is consensus". Can you describe where the issue was discussed and consensus reached? (I read the taxonbar template, but can't find a requirement that Wikidata IDs for synonyms must be added to articles.) Gderrin (talk) 22:52, 26 October 2021 (UTC)
 * you can check the archives at Template talk:Taxonbar, but perhaps this discussion would be best had there. As for my quick answers, for 1 it autocollapses.  For 2, it adds the same value as for the accepted name, and if someone is more familiar with a different name they can easily click on more information on the name change.  --awkwafaba (📥) 01:58, 27 October 2021 (UTC)
 * There certainly isn't consensus to add taxonbar entries for EVERY synonym. Daviesia incrassata var. brachyphylla is the only synonym of Daviesia brachyphylla given in POWO, and TPL accepts the taxon as a variety. The names are homotypic; via reference to the type, they encompass the exact same assemblage of living plants growing in the world, but differ in whether this assemblage is best understood as a species or variety. Having two taxonbar entries (one the only synonym) at Daviesia brachyphylla is helpful. While I'm thinking of it, I do want to note that some taxonbar links are much more valuable than others; for Australian plants, Florabase gives quite a bit of content, but APNI has little. Flora of China and Flora of North America taxonbar links are information rich, IPNI not so much. (Not to discount what APNI/IPNI do, but...). Additional taxonbar entries should absolutely be included when another Wikidata item holds the link to an information rich source. But this really should be discussed further in a broader venue. Plantdrew (talk) 03:35, 27 October 2021 (UTC)
 * It's worth noting that most of the taxon name items in Wikidata (not taxon items whatever is claimed over there) have been added by bots, not knowledgeable editors, who would probably have considered whether a synonym had been used sufficiently often to be notable. So I'm definitely against blindly adding a synonym to the taxonbar just because there's a Wikidata item. (As an aside, Wikidata's inability or unwillingness to properly distinguish taxa from taxon names may have encouraged smaller wikis, e.g. viwiki, to create separate articles for synonymous names with Wikidata entries, which is a separate but related issue because clicking on the Wikidata link in the taxonbar entry will show these redundant articles.) Peter coxhead (talk) 09:57, 27 October 2021 (UTC)

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Untagged articles
I've been working through the taxobox articles without WikiProject banners. Everything that's left now has some issue(s) I want to resolve before tagging. For the most part, it's monotypy, where I want to add taxonbar from parameters, and make sure redirects exist and are categorized. There are a few that are also at the wrong title. There are a handful of other issues; the ones that come to mind immediately are: Robertdollfusidae and Robertdollfusiidae need to be merged, and Rhamphina needs to be disambiguated and new taxonomy template needs to be created. I'll get to them all in the next few days.

There may be some newly created articles showing up in the search for untagged articles; everything I'm wanting to work on further starts with the letters C, P or R, and none of them are binomials.

I'm not planning on tagging drafts at the moment, if you want to work on those. Plantdrew (talk) 18:46, 29 October 2021 (UTC)
 * i noticed you were making quick progress and realized i should be helping more. But i’ll hold back on the ones in CPR mainspace now.  Just lmk when you want me back in the china shop :) --awkwafaba (📥) 00:58, 30 October 2021 (UTC)
 * All done. Plantdrew (talk) 03:06, 30 October 2021 (UTC)

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Transposable element
Hello Awkwafaba. I strongly apologise to bother you, but if you do not mind, I would like to ask a question regarding the article Transposable element. I believe it should include some information on the so-called Class III TEs. The 'draft' I created: Some scientists also distinguish a third category of transposable elements. Class III TEs have been described as "a grab-bag consisting of transposons that don't clearly fit into the other two categories". Examples include Foldback (FB) elements, TU elements, and Miniature Inverted-repeat Transposable Elements. References: Capy P (1998). Dynamics and evolution of transposable elements. New York: Chapman & Hall. ISBN 978-3-540-61190-5 (definition of Class III elements + examples); Boutanaev AM, Osbourn AE (July 2018). "Multigenome analysis implicates miniature inverted-repeat transposable elements (MITEs) in metabolic diversification in eudicots". Proceedings of the National Academy of Sciences of the United States of America. 115 (28): E6650–E6658. doi:10.1073/pnas.1721318115. PMC 6048515. PMID 29941591 (MITEs as Class III TEs); Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, Frise E, Wheeler DA, Lewis SE, Rubin GM, Ashburner M, Celniker SE (2002). "The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective". Genome Biology. 3 (12): RESEARCH0084. doi:10.1186/gb-2002-3-12-research0084. PMC 151186. PMID 12537573 ("Foldback (FB) elements, which are characterized by their property of reannealing after denaturation with zero-order kinetics, are quite distinct from prototypical class I or II elements…"); Baez J (2005). "Subcellular Life Forms" (PDF) (review of P. Capy's scientific book + examples). Could you add it to the Wikipedia article re. transposable elements (TEs), please? However, I am not sure where exactly, and perhaps the text needs some copy edits and other minor fixes. If necessary, please feel free to make further changes, additions and adjustments. Thanks a lot! :-) Kind regards, --Pinoczet (talk) 22:00, 28 November 2021 (UTC)
 * I’m afraid I’m not very current on the topic, but that source seems like it would be reliable. Perhaps you should join the conversation at Talk:Transposable element? --awkwafaba (📥) 02:19, 29 November 2021 (UTC)

Opuntia setispina Engelmann
Hello, Awkwafaba,

When you move an article to Draft space, could you tag the original page for speedy deletion, CSD R2? It just makes things a bit easier for admins patrolling speedy deletion categories. Thank you! Liz Read! Talk! 01:21, 4 December 2021 (UTC)
 * i tried to move Opuntia setispina Engelmann to Opuntia setispina, but that existed already. I did not realize it was a redirect, so I assumed it a duplicate and moved it to Draft.  I cannot delete pages, so at that point I could move it no further.  --awkwafaba (📥) 03:17, 4 December 2021 (UTC)

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Happy First Edit Day!
 Happy First Edit Day! Have a very happy first edit anniversary!

From the Birthday Committee, CAPTAIN RAJU (T) 18:31, 5 January 2022 (UTC)
 * Aww, thanks and the Birthday Committee!  --awkwafaba (📥) 02:28, 6 January 2022 (UTC)

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"Canis wikilupus" listed at Redirects for discussion
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Liking your user name choice
A mixture of a rapper/actress and a most curious chickpea byproduct. Awesome! Honestly, wish I thought of it first! Steel1943 (talk) 20:41, 1 February 2022 (UTC)
 * thanks. It took me a while to think it up.  I keep misspelling aquafaba now, though.--awkwafaba (📥) 02:54, 2 February 2022 (UTC)

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