This template is within the scope of WikiProject Microbiology, a collaborative effort to improve the coverage of
Microbiology 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.MicrobiologyWikipedia:WikiProject MicrobiologyTemplate:WikiProject MicrobiologyMicrobiology articles
This template is within the scope of WikiProject Tree of Life, a collaborative effort to improve the coverage of
taxonomy and the
phylogenetictree of life 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.Tree of LifeWikipedia:WikiProject Tree of LifeTemplate:WikiProject Tree of Lifetaxonomic articles
This 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.VirusesWikipedia:WikiProject VirusesTemplate:WikiProject Virusesvirus articles
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]]).
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
{{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.
@
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.
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.)
@
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)
@
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)reply
@
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)reply
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 |
talk10:52, 14 January 2019 (UTC)reply
@
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)reply
{{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.
^"Inoviridae". International Committee on Taxonomy of Viruses (ICTV). Retrieved 18 December 2018.
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:
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:
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)reply
@
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)reply
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)reply
@
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)reply
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)reply
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)reply
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)reply
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)reply
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)reply
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)reply
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)reply
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)reply
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)reply
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)reply
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)reply
"
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)reply
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)reply