Template talk:Virusbox

Including Italic title

Can this template include something like {{Italic title}} for all ranks except virus and virus group? See Negarnaviricota for a title that should be italicized but isn't. --Nessie (talk) 16:58, 7 November 2018 (UTC)

@NessieVL: this should be fixed now (but there remain some problems with Virusbox). Peter coxhead (talk) 02:11, 29 November 2018 (UTC)

@Peter coxhead: It's italicizing virus strains now. see Norovirus GII.4 Sydney.--Nessie (talk) 20:38, 30 November 2018 (UTC)

Yes, I'm working on a proper fix – I'd rather do this than keep patching. Peter coxhead (talk) 20:56, 30 November 2018 (UTC)

@NessieVL: the taxobox rows are now fixed at Norovirus GII.4 Sydney; as noted below, the taxobox name and page title are not. Peter coxhead (talk) 23:35, 30 November 2018 (UTC)

Template for Deletion 2018 November 27

Please see Wikipedia:Templates for discussion/Log/2018 November 27#Template:Virusbox concerning the status of this template. --Nessie (talk) 20:03, 27 November 2018 (UTC)

Problem with the template

There's a problem with the template at present: deep down it doesn't use the new Lua code for traversing taxonomy templates. One effect of this is that it does not correctly handle piped links in taxonomy templates. I found this out when I "fixed" Template:Taxonomy/Rudiviridae, which should have

|link = Rudivirus|Rudiviridae

to ensure that the monotypic family Rudiviridae appears in bold in the taxobox at Rudivirus, but found that my "fix" broke the taxobox. [Note that the taxobox is ok now because of the work-around below.]

The problem can be illustrated by applying Virusbox to Amborella as opposite. All the taxa above Amborella are displayed as the link, not the link text (e.g. the value for Family should be equivalent to the wikitext [[Amborella|Amborellaceae]] but is instead just [[Amborella]]).

This doesn't appear simple to fix; the problem is that when Bob the Wikipedian restored Virusbox, he continued to use the old obsolete template code for traversing taxonomy templates, whereas the template needs to use the new Lua code in Module:Autotaxobox. I will work on it. Peter coxhead (talk) 01:56, 29 November 2018 (UTC)

Work-around There's a temporary work-around, but it should only be used if really necessary, because it may not work when a proper fix is made. To pipe the link in a virus taxonomy template, use {{!}} instead of |, i.e. something like

|link = Rudivirus{{!}}Rudiviridae

Peter coxhead (talk) 02:21, 29 November 2018 (UTC)

Yeah, any modifications that were made after the template was deleted will need checked on the virusbox. I changed as little of the code as possible in restoring it. Bob the WikipediaN ^{(talk • contribs)} 18:37, 30 November 2018 (UTC)

Fixed The template has been updated to use the Lua autotaxobox module, with some modifications to handle the italicization of virus taxon names.

• The work-around noted above should not now be used; in some cases it will cause errors.
• Please report here any problems with the italicization of virus taxon names in a taxobox that uses Virusbox.
• Automatic italicization of the name of the taxobox and the title of the page are not yet correct.
• Virus taxon names are not italicized correctly when viewing taxonomy templates – a task for the future. Done.

Peter coxhead (talk) 11:52, 13 January 2019 (UTC)

Handling species better

{{Virusbox}} has been fixed so that it works like {{Speciesbox}}, i.e. it's not normally necessary to create taxonomy templates for species. Now in {{Virusbox}}:

• |taxon= is used, as in {{Automatic taxobox}}, for ranks of genus and above; it can also be used in exceptional cases for a species where there is a good reason for having a species taxonomy template
• |genus= + |species= is used, as in {{Speciesbox}}, for species; however note that the value of |species= here is the whole species name, not just the specific epithet/name.

See African swine fever virus for an example.

Apologies that I didn't fix this earlier, meaning that editors had to create now unnecessary taxonomy templates for virus species.

A task to be completed is adding {{Italic title}} automatically when |species= is used. Done. Peter coxhead (talk) 10:25, 13 January 2019 (UTC)

@Peter coxhead: does |parent= not work? I tried updating Middle East respiratory syndrome coronavirus with |genus=, |species=, and |parent= but it skipped the subgenus, and didn't even ask to create a taxonomy template. There are 60 virus subgenera in the 2018 update, and though some are monotypic many are not.

Test
Scientific classification
Kingdom:	Plantae
Clade:	Tracheophytes
Clade:	Angiosperms
Clade:	Eudicots
Clade:	Asterids
Order:	Ericales
Family:	Ericaceae
Genus:	Rhododendron
Species:	A. negundo
Binomial name
Acer negundo

Not yet. It's being worked on! See below.
(I started by using {{Speciesbox}} as a model, but I've realized that it doesn't work as it really should. It's partly Linnaeus's fault! In a hierarchy for non-viruses, say species – subgenus – genus, the genus appears two or three times, depending on how the subgenus is written. It turns out that in {{Speciesbox}}, you can make these different, as in the taxobox opposite. This needs to be fixed, and the logic for viruses designed from scratch.)

Peter coxhead (talk) 20:05, 13 January 2019 (UTC)

@NessieVL: ok, if you delete |genus= in the taxobox at Middle East respiratory syndrome coronavirus, it works, picking up the automated taxonomy from Template:Taxonomy/Merbecovirus. Treat this as beta/experimental for now, as there's no error checking if an invalid combination of parameters is supplied. Valid combinations are:

• |taxon= – any rank, Template:Taxonomy/taxon must exist

*|genus=+|species= – Template:Taxonomy/genus must exist

• |parent=+|species= – Template:Taxonomy/parent must exist, and should be a rank above species and up to and including genus (I think only genus and subgenus for viruses)

Peter coxhead (talk) 11:29, 14 January 2019 (UTC)

OK, Looks good. I'll wait on updating any other articles in subgenera for now. Fortunately I think subgenus is the only rank of viruses between species and genus. And FYI I put the list of them at Category talk:Virus subgenera. --Nessie (talk) 21:37, 13 January 2019 (UTC)

@NessieVL: actually, I could simplify the parameters by just using |parent= for all ranks above species, including genus. This would make error-checking much easier. So, yes, wait a bit before using these parameters. Peter coxhead (talk) 21:52, 13 January 2019 (UTC)

This is just for species and lower taxa? --Nessie (talk) 01:55, 14 January 2019 (UTC)

@NessieVL: currently it works, including error-checking, as per the documentation, so can be used (let me know if you encounter any errors).

• A species with no taxoboxes for its lower ranked taxa doesn't need a taxonomy template, so use |parent=+|species=, where the parent is either a subgenus or a genus that has a taxonomy template.
• All other cases currently require a taxonomy template, so use |taxon=.

I'm working on changing {{Virusbox}} so that where there is one rank below species, e.g. serotype, strain or just virus, this too could be specified in the taxobox using e.g. |parent=+|species=+|strain=. Then only parent would need a taxonomy template. Peter coxhead (talk) 10:27, 14 January 2019 (UTC)

What about using |genus= and |subgenus= instead of |parent=? If subgenus use it as parent, else if genus use that, else look at taxon. It might be clearer for new users to use genus/subgenus + species rather than parent + species.   Jts1882 | talk  10:52, 14 January 2019 (UTC)

@Jts1882: that's how I started, but now I'd rather wait and see if these parameters do actually cause confusion or difficulty. One problem with proliferating parameters is that error-checking, setting the name of the taxobox, etc., become more and more complex. Also I think that in the long run, making |parent= (perhaps renamed or aliased as something like – but probably not exactly – "autotaxon") always the entry into the automated taxobox system will be better for editors. Remember that in {{Speciesbox}}, |subgenus= is not an entry into the automated taxobox system, but a 'manual' rank, handled by the taxobox itself, and so not requiring a taxonomy template. Using |subgenus= in {{Virusbox}} for a taxon that must have a taxonomy template would be confusing, I think. (An obvious follow-on question is why not handle virus subgenera outside the automated taxobox system; my answer is that unlike other groups, which use styles like "Genus (Subgenus)" or "Genus subg. Subgenus", virus taxonomy doesn't, so there's no natural connection between these ranks, hence putting the connections into taxonomy templates is better.) Peter coxhead (talk) 11:23, 14 January 2019 (UTC)

I'm currently working through virus entries in Category:Taxonomy templates for species, fixing the articles and marking the taxonomy templates as unnecessary whenever the species template isn't used by a lower level taxon. So far I've got up to and including "L". Assistance welcome! Peter coxhead (talk) 18:00, 14 January 2019 (UTC)

Am I understanding this correctly that {{Taxonomy/Zaire ebolavirus}} is necessary because of Ebola_virus, while {{Taxonomy/Yingvirus}} is unnecessary if Yingvirus uses |parent=Qinviridae and |species=Yingvirus instead of |taxon=Yingvirus (change made). How do you mark a template unnecessary?   Jts1882 | talk  13:10, 14 January 2019 (UTC)

{{Taxonomy/Yellow head virus}} - unnecessary (change Yellow head virus taxobox to to parent+species)

Agreed; put in Category:Unnecessary taxonomy templates. Peter coxhead (talk) 18:16, 14 January 2019 (UTC)

{{Taxonomy/West Nile virus}} - unnecessary (was using {{taxobox}}; now converted to {{virusbox}} with parent+species)

Agreed; put in Category:Unnecessary taxonomy templates. Peter coxhead (talk) 18:16, 14 January 2019 (UTC)

{{Taxonomy/Vibrio virus CTXphi}} - unnecessary (using |parent=Incertae sedis/Inoviridae with species parameter).

Agreed; put in Category:Unnecessary taxonomy templates. Peter coxhead (talk) 18:16, 14 January 2019 (UTC)

{{Taxonomy/Vibrio phage CTX}} - unnecessary? Linked page redirects to Vibrio virus CTXphi. The taxonomy template gives a genus, whereas that for the linked one is incerta sedis.

@NessieVL: the taxonomy in the templates {{Taxonomy/Vibrio phage CTX}} and {{Template:Taxonomy/V. cholera phage/prophage CTXφ}} isn't in the ICTV as far as I can see; both marked as unnecessary

Check the citation in the template It shows species Vibrio phage CTX with strain V. cholera phage/prophage CTXφ. If you "Select to search across all ICTV releases" at ICTV and then click history you can see the species was renamed to Vibrio virus CTXphi, which is often written Vibrio virus CTXφ. I know it was messy but the orthography was not very consistent in the sources, and seaeching with "φ" does not show matches with "phi". I thought I had made those 'sameas' redirects. --Nessie (talk) 18:47, 14 January 2019 (UTC)

{{Taxonomy/Vaccinia virus}} - used by Rabbitpox

{{Taxonomy/Ungulate protoparvovirus 1}} and {{Taxonomy/Porcine parvovirus}} - both unnecessary as target of latter redirects to Ungulate protoparvovirus 1 (virusbox changed to species+parent)

Ah, but at present if an article is created at Porcine parvovirus then the templates would be needed. Peter coxhead (talk) 18:21, 14 January 2019 (UTC)

The templates above marked unnecessary have had changes to the taxobox.   Jts1882 | talk  13:30, 14 January 2019 (UTC)

@Jts1882: see e.g. Template:Taxonomy/Human gammaherpesvirus 4 for how to mark them as unnecessary. If they don't get re-used after a month or so then templates in Category:Unnecessary taxonomy templates can be nominated for deletion. Peter coxhead (talk) 16:29, 14 January 2019 (UTC)

References

Ranks below species

Ranks below species for viruses seem to me somewhat confused. They are not regulated by the ICTV, apparently, and there seems to be no clear ordering. So my current idea is to allow only one infra-specific rank.

At present there are taxonomy templates at {{Taxonomy/Feline coronavirus}} (rank = virus) and at its parent species, {{Taxonomy/Alphacoronavirus 1}}, and grandparent subgenus, {{Taxonomy/Tegacovirus}}. So with the current version of Virusbox, it's possible to create the taxobox in one of three ways:

Wikitext	Result
Use {{Taxonomy/Feline coronavirus}}: {{Virusbox | taxon = Feline coronavirus | display_parents = 4 }}	{{Virusbox | taxon = Feline coronavirus | display_parents = 4 }}
Use {{Taxonomy/Alphacoronavirus 1}}: (Species should NOT be in bold) {{Virusbox | parent = Alphacoronavirus 1 | virus = Feline coronavirus | display_parents = 4 }}	{{Virusbox | parent = Alphacoronavirus 1 | virus = Feline coronavirus | display_parents = 4 }}
Use {{Taxonomy/Tegacovirus}}: {{Virusbox | parent = Tegacovirus | species = Alphacoronavirus 1 | virus = Feline coronavirus | display_parents = 4 }}	{{Virusbox | parent = Tegacovirus | species = Alphacoronavirus 1 | virus = Feline coronavirus | display_parents = 4 }}

If you specify more than one infra-specific rank, only one is used (currently in the order serotype-strain-virus, but error-checking remains to be added), so:

Wikitext	Result
Add a strain parameter – virus parameter is ignored: {{Virusbox | parent = Tegacovirus | species = Alphacoronavirus 1 | virus = Feline coronavirus | strain = Feline coronavirus C1Je | display_parents = 4 }}	Virus classification (unranked): Virus Realm: Riboviria Kingdom: Orthornavirae Phylum: Pisuviricota Class: Pisoniviricetes Order: Nidovirales Family: Coronaviridae Subfamily: Orthocoronavirinae Genus: Alphacoronavirus Subgenus: Tegacovirus Species: Alphacoronavirus 1 Strain: Feline coronavirus C1Je

Questions

Before I do any more work, I'd like to gather some opinions:

1. Is it acceptable to display only one infra-specific rank for viruses?
2. If not, in what order should the infra-specific ranks be displayed in taxoboxes?
3. Are taxon authorities used with virus names? The ICTV list doesn't give them, and I haven't yet found any taxoboxes that use the authority parameters.

Peter coxhead (talk) 15:29, 16 January 2019 (UTC)

• Off the top of my head are Pandemic H1N1/09 virus and Goose Guandong virus which use both serotype and strain below species. I feel like there was one that had virus and strain too. Check the ones in Category:Infraspecific virus taxa. I agree the terms are vague, poorly defined, and often used interchangeably, but occasionally they do explicitly state an order for a virus/strain/isolate. When I have been adding virusboxes I tried to use the terms mentioned at ICTV, but these again were inconsistent. Should we email them for clarification? --Nessie (talk) 12:41, 15 January 2019 (UTC)

@NessieVL: I had a very quick look at the references at Pandemic H1N1/09 virus and Goose Guandong virus and couldn't see anything that explained the classifications. It's logical that Influenza A virus subtype H1N1 has Pandemic H1N1/09 virus as a subordinate rank, given the "H1N1" and "H1N1/09", but is this ordering applied consistently? If we could get some clarification from the ICTV or elsewhere this would be good. Peter coxhead (talk) 13:53, 15 January 2019 (UTC)

I forgot to post that ICTV got back to me and basically were agnostic on infraspecific ranks. They suggested that i could contact each of the working groups to see how they handle it in their taxa, but I imagine that won't bring much consistency. --Nessie (talk) 21:14, 1 February 2019 (UTC)

@NessieVL: thanks for this information. So it does seem that the 'ranks' below subspecies aren't actually 'ranks', i.e. an ordered sequence, but are used inconsistently. Hence there's really no alternative to the present set-up, where only one such rank can be added manually to a Virusbox, since there's no way of knowing the order of two or more. So we need to try to document better how to set up taxonomy templates and automated taxoboxes for viruses at the level of species and below, since it's not obvious, and is different from how it's done for other groups. Peter coxhead (talk) 09:49, 2 February 2019 (UTC)

Authority parameters not implemented

As no-one has answered (3) above, and I can't find any virus taxoboxes that use them, in converting this template to use Lua, I have left the authority parameters unimplemented. They can be activated if it can be shown that they are needed. Peter coxhead (talk) 15:17, 19 January 2019 (UTC)

Baltimore classification

I noticed that any information about Baltimore classification disappeared. What was the reason for this? Ruslik_Zero 17:57, 17 January 2019 (UTC)

ICTV does not follow Baltimore anymore, and some taxa include members of more than one classification. I think the consensus was to put the information in the text and not the {{Virusbox}}. --Nessie (talk) 19:52, 17 January 2019 (UTC)

The Baltimore groups should be mentioned in the text, but they aren't used in classification now because they aren't monophyletic; hence they don't sppear in updated taxoboxes. The consensus is to follow ICTV 2018. Peter coxhead (talk) 21:04, 17 January 2019 (UTC)

Name parameter no longer ignored

I noticed that there was a bug: |name= was being ignored. This is now fixed. Peter coxhead (talk) 19:50, 1 February 2019 (UTC)

Actually the automatic italicization of the taxobox name when |name= is omitted wasn't quite right in all cases; I think it's fixed now. Peter coxhead (talk) 21:05, 1 February 2019 (UTC)

Viruses gone extinct?

So Variola virus has been eradicated. I updated the Smallpox article to a virusbox, but it does not accept |extinct=yes nor |status=EW. I realize this is a special case of one at the moment, but Polio eradication is approaching and there are a few other viruses in Category:Infectious diseases with eradication efforts, So hopefully this will not be a special case for long. I know of no efforts to give viruses any sort of conservation status, fwiw. --Nessie (talk) 17:42, 12 March 2019 (UTC)

Well, as I understand it, it's not actually extinct. It's thought to be "extinct in the wild" in as much as a virus can be extinct (given that it was never alive), but two labs publicly (and it's suspected other labs secretly) do have some. It's also believed to be present and potentially able to be activated in well-preserved corpses. See also The spectre of smallpox lingers. Peter coxhead (talk) 17:58, 12 March 2019 (UTC)

The whole article is in the past tense, which makes me think consensus is for EW atleast. The article also mentions that de-extinction is perhaps not difficult enough. If I were to pick one, it's pick |status=EW. The only other way to gerry rig this (other than updating {{virusbox}}) Is to create {{Taxonomy/Variola virus}} and add |extinct=yes. But again, that would add the † but not give the 'in the wild' part. --Nessie (talk) 19:49, 12 March 2019 (UTC)

I'm not enthusiastic about adding support for parameters that are hardly ever going to be used (that stems from my efforts to keep TemplateData error reports "clean"). Between corpses in the permafrost and viruses not being alive, I have a hard time thinking of it as being "extinct". Plantdrew (talk) 20:33, 12 March 2019 (UTC)

Thinking on it a little further, |extinct= should probably be deprecated altogether in the taxobox display templates. With taxonomy templates able to be marked as extinct, there's no point for the parameter in {{Automatic taxobox}}. {{Subspeciesbox}} supports |species_extinct= as at Lord Howe starling to mark an extinct species in an extant genus. {{Speciesbox}} and maybe {{Virusbox}} should add support for |species_extinct=. Right now, |extinct= is doing two different things in {{Speciesbox}} and {{Taxobox}}; it's either displaying a dagger with a "yes" value, or a date with any other value. |species_extinct= could drive the dagger, and I'm not sure it's really necessary to display any dates in the taxobox rather than in text. Dates span a range of uncertainty, from death of last EW zoo specimen, to date "declared extinct" with no zoo specimens, to date of last reported human wild kill, to decadal estimate of recent extinction, to ~century radiocarbon date of some island endemic extinct before western scientists observed it. Get extinct dates out of taxoboxes and into text, use |species_extinct= for daggers (when the parent taxonomy template isn't already providing them), and get rid of |extinct=. Plantdrew (talk) 03:01, 13 March 2019 (UTC)

I tend to agree. The use of |extinct= with either a date or a yes/no/true/false value is problematic in the coding – dates should be checked for correct formatting, but this is tedious and hasn't been done, so basically any value other than blank/no/false means "extinct" in a taxobox, but not in a taxonomy template. If we really want the dates in taxoboxes, then there should be an explicit parameter, e.g. |extinction_date=. However, this needs a much wider discussion, because the present system has been in place for a long time. Peter coxhead (talk) 09:43, 13 March 2019 (UTC)

Found another extinct virus, Rinderpest. --Nessie (talk) 03:06, 17 March 2019 (UTC)

But Rinderpest is not extinct either as it is still held in laboratories. It might be "extinct in the wild", but could still be dormant somewhere though. Loopy30 (talk) 11:01, 17 March 2019 (UTC)

Could be, but still officially eradicated. And there is no support for |status=EW. --Nessie (talk) 13:19, 17 March 2019 (UTC)

If there were a standard source supporting a classification like "EW", as per the Red Lists for non-viruses, support would be justified. But if we were to add "EW" to a taxobox, it would be WP:OR or WP:SYNTH. Viruses are not assessed, at least at present. Peter coxhead (talk) 13:24, 17 March 2019 (UTC)

Type species abolished

For your information, the designation of type species was abolished in the ICTV 2020 taxonomy release. Therefore, this parameter should be removed from the Virusbox once we have finished removing entires for this parameter from articles. Ypna (talk) 02:53, 20 May 2021 (UTC)

@Ypna: ok, if you post again here when the removal is finished, I'll do it (if no-one else has). Peter coxhead (talk) 19:09, 20 May 2021 (UTC)

@Peter coxhead:, I think I've removed the last instances of |type_species=. Plantdrew (talk) 01:42, 4 June 2021 (UTC)

 Done

The template still implements |type_genus= and |type_strain=. What is the status of these? The 1 June report shows no uses of |type_genus= and two uses of |type_strain= at Latino mammarenavirus and Mobala mammarenavirus. Peter coxhead (talk) 06:04, 4 June 2021 (UTC)

Turning off italic title

"Tulip breaking virus" should not be in italics. Unfortunately the infobox at that article is in italics and so is the article title, because this template provides no way to turn the italics off. Please add something like |italics=no to allow the user to force the italics to turn off. Hairy Dude (talk) 02:42, 19 May 2022 (UTC)

@Hairy Dude:  Done. I don't work with infoboxes often, so do tell me if this may not be exactly what you intended. The option is |italics=no. Aidan9382 _(talk) 10:51, 19 May 2022 (UTC)

I see you decided to not change it anyways (Talk:Tulip breaking virus#Italics). I'll leave the change implemented either way, since it isnt a major issue. Aidan9382 _(talk) 10:53, 19 May 2022 (UTC)

The name of the parameter should be italic_title to match the same parameter in Template:Automatic taxobox. I fixed it accordingly. Animal lover |666| (talk) 10:58, 19 May 2022 (UTC)

Thanks. In this particular case I changed my mind (although it's five viruses rather than one the literature does support use of italics for this name), but it could still help in other cases. Hairy Dude (talk) 13:47, 19 May 2022 (UTC)