Template talk:Coronaviridae

From Wikipedia the free encyclopedia

WikiProject COVID-19 (Rated Template-class)
WikiProject iconThis template is within the scope of WikiProject COVID-19, a project to coordinate efforts to improve all COVID-19-related articles. If you would like to help, you are invited to join and to participate in project discussions.
 Template  This template does not require a rating on the project's quality scale.
 
WikiProject Viruses (Rated Template-class)
WikiProject iconThis template is within the scope of WikiProject Viruses, a collaborative effort to improve the coverage of viruses on Wikipedia. If you would like to participate, please visit the project page, where you can join the discussion and see a list of open tasks.
 Template  This template does not require a rating on the project's quality scale.
 

Untitled[edit]

Merry Christmas!!!

I have just finished translating this template from Chinese to English.

I like this template, compared with "Human coronaviruses", which I just REDIRECT here, Its a DeAnthropocentrism template.

--Htmlzycq (talk) 16:24, 24 December 2020 (UTC)

Thank you Ypna (talk)
Considering the improvements I have now made, you may like to consider cleaning up the Chinese version. Ypna (talk) 14:41, 27 January 2021 (UTC)
  • @Ypna and Htmlzycq: Hi, Greetings. I am the one who originally wrote this template in Chinese Wikipedia (the version Htmlzycq translated here [1]). The reason we used the nested format, instead of the current concise version in English Wikipedia, is to provide phylogenetic relationships of these viruses. For example, in the Chinese version, it is very clear that among all the 5 beta-CoVs subgenuses, the one phylogenetically closest to Sarbevirus is Hibecovirus, followed by Nobecovirus. In the current English version, however, such hierarchical information is not shown. The 5 subgenuses are listed in parallel; thus, readers couldn't tell their specific phylogenetic relationships from the template.
We only include well-established clades supported by multiple studies in the template. In addition, we only show the phylogenetically relationships that are broadly accepted in the field (ex the ones in Betacoronavirus. For gamma and delta, since their relationships remain elusive, we don't use the nested format). Therefore I would strongly recommend the format used in Chinese Wikipedia ([2]), as it contains more information for readers.
3 side notes:
  1. I personally don't recommend copy the list from ICTV, as it does not include all important viruses (ex, it includes BtKYNL63-9b, but not BtKYNL63-9a and BtKYNL63-9c, which does not make much sense to me). It includes many viruses that probably do not meet the notability criteria of Wikipedia (ex Myotis ricketti alphacoronavirus Sax-2011, Myotis ricketti alphacoronavirus Sax-2011 etc, which are merely viral sequences detected in samples from some large-scale survey studies), but miss many that do qualify an article (However, I guess the inclusion criteria is up to en-wikipedians to decide.) The subgenuses ICTV created are rarely used in practice, and they don't provide much information (as most subgenuses only contain one strain of virus).
  2. a major mistake in the current template: you seemed to misplace gamma and delta coronaviruses. Andecovirus, Buldecovirus and Herdecovirus are deltacoronaviruse, not gammacoronaviruses, as clearly stated in the paper [3]. On the other hand, IBV and whale coronaviruses are gammacoronaviruses. Some of them are also labeled incorrectly in the articles, ex Buldecovirus, the problem of which comes from the taxonomy template Template:Taxonomy/Buldecovirus. I don't know whether these mistakes come from the ICTV website (the taxonomy list on its website is not functioning now).
  3. some articles you recently created, ex NL63-related bat coronavirus strain BtKYNL63-9b, Myodes coronavirus 2JL14 etc, are viral strains instead of separate species. I recommend describe them as "strains of XXcoronaviruses" instead of "species".

--Wikimycotatalk) 21:15, 27 January 2021 (UTC)

Hi @靖天子:. Thanks for writing the Chinese version and taking the time to write your message here. I didn't realise before, but I can now appreciate the level of thought you have put into the Chinese version. My suggestion above that the Chinese version should be modelled after the English version must have seemed arrogant! But actually I'm happy to collaborate with you to find a good solution.
Regarding the nested format: I appreciate that you have an interest in displaying the phylogenetic relationships with a high level of detail. I too am interested in this. However, despite my fondness for phylogenetic trees and my familiarity with navbox templates, when I saw the Chinese version, not only did it look quite cluttered but I actually assumed I was looking at the result of poor, redundant formatting rather than the deliberate representation of the phylogenetics. This is probably because many of the boxes / clades have no name written. If I didn't understand, I wonder whether the average person would understand. Furthermore, it is written somewhere (at least on the English side) that the purpose of navboxes is to provide a simple list of links, not to cram so much information in at the expense of clarity. To apply this principle to the current situation, I would suggest leaving detailed phylogenetic information to the articles. In the end this is a matter of style and there's no objectively correct answer. But maybe you'll be able to convince me your way is better.
Regarding side note 1 – inclusion / exclusion criteria: To my understanding, the job of an encyclopaedia is to present the information published by relevant authorities. In our context, the ICTV if of course the ultimate authority. The way I see it is that it's not our responsibility to decide what is "important" or not, which is prone to subjectivity. On the English wikipedia all species (and especially higher taxa) are considered notable enough to warrant an article. The way I see it is that all species accepted by the ICTV deserve an article, and all species not (yet) accepted by the ICTV do not (yet) deserve an article. It's a dogmatic approach but (unless I'm mistaken?) it's also the (English) Wikipedia's standard style.
Regarding side note 2 – errors: You're absolutely right. Thanks for pointing these mistakes out. The ICTV's taxonomy list is functioning for me; I just checked it and it turns out the list is written correctly and it's me that got confused. I'll fix these errors soon.
Regarding side note 3 – strains?: For some reason the ICTV lists NL63-related bat coronavirus strain BtKYNL63-9b and Myodes coronavirus 2JL14 as species. The former species even has the word "strain" in the name. Is it possible that there's a species with the word "strain" in it or is the ICTV taxonomy list wrong? Ypna (talk) 14:18, 28 January 2021 (UTC)

@Ypna:Thank you very much for your reply. No worries. I also appreciate your passion for writing coronaviruses articles. And thank you for fixing the errors.

Nesting format: While I personally feel the format is clear to read, I could totally understand that you and some readers may find it confusing. I guess it's up to the community (WP:VIRUS?) to decide which way is better.
side note 1: I believe Wikipedia:Notability determines whether an article should be included in Wikipedia. All species deserve an article because one can always find at least one reliable source with significant coverage of the subject -- that is -- the peer-reviewed scientific paper or book from which the species was originally described and published (For many insignificant species that no one cares about, like several fungi I wrote in Chinese Wikipedia, this is often their only reference). Similarly if a virus meets the notability standard, it should qualify an article, whether it is included by ICTV or not. However if we see ICTV as an authority (I don't agree it's the "ultimate" authority though), I suppose we could also allow articles for viruses included as species by ICTV, but not meeting the notability criteria otherwise. For example, Myotis ricketti alphacoronavirus Sax-2011 is regarded as a species by ICTV; however it is just one of the hundreds of viral sequences found by a big-scale survey study [4], which does not contain "significant coverage of the subject" (in fact it's only mentioned once in the text). Again this is up to en-Wikipedians to discuss. My point is ICTV misses many viruses that qualify Wikipedia's inclusion criteria.
side note 3: As you may know, species delimitation of viruses is always arbitrary because their differences is a continuum (it's like the difference between a language and a dialect). In the field of coronavirus, a 440nt conserved sequence in the ORF1ab RdRP is often used to determine whether 2 viruses are cospecific (>90% similarity making them the same species). However I don't think ICTV consider much about this (as they simply make them all species). Since there really isn't a fundamental difference, I guess it's not wrong to call it either a strain or a species. --Wikimycotatalk) 23:46, 28 January 2021 (UTC)