Allow virus species names to include numbers

[jameskdouch]

The nomenclature used in the taxonomy of viruses is somewhat different to that of cellular organisms. The International Committee on Taxonomy of Viruses (ICTV; the authority on virus taxonomy and nomenclature; comparable to the ICN and ICZN in botany and zoology, respectively) states that virus species names are allowed to contain numbers. This is stated in section 3.12 of the ICTV Code. However, iNaturalist does not allow species names to include numbers (which is appropriate for cellular nomenclature), but this has forced curators to deviate from correct virus names and spell numbers out. For example:

• Alphapapillomavirus seven – Actual name: Alphapapillomavirus 7
• Alphapapillomavirus ten – Actual name: Alphapapillomavirus 10
• Deltapapillomavirus two – Actual name: Deltapapillomavirus 2
• Deltapapillomavirus seven – Actual name: Deltapapillomavirus 7
• Etapapillomavirus one – Actual name: Etapapillomavirus 1
• Chelonid alphaherpesvirus five – Actual name: Chelonid alphaherpesvirus 5
• Human alphaherpesvirus one – Actual name: Human alphaherpesvirus 1
• Human alphaherpesvirus three – Actual name: Human alphaherpesvirus 3

I believe presenting all nomenclature consistent with the accepted form is a goal to which iNaturalist should strive. This helps to reduce confusion with names and contributes towards iNaturalist’s reputation as a serious and reliable resource.

[cthawley]

Don’t forget to vote for your own request! (which I think is reasonable)

[bobmcd]

Your request just makes sense.

Currently the iNat system for viruses has an English spoken version of the numeral*(number) in the name instead of the Arabic numerals following the Latin genus. This means that non English knowledge users need to translate the numeral they are looking for into the spoken English version. It would seem that if they are filtering through species of a genus, the order has the potential to be in English spelling of the number rather than in numerical order - am I correct? Granted every language does not use Arabic numerals but I would think in scientific literature they do.

from Wikipedia " A numeral is a figure, symbol, or group of figures or symbols denoting a number."

[cmcheatle]

Just as background, numbers used to be allowed in species names and was removed.

They were removed as an additional block on people entering undescribed species, which is not supposed to happen under site guidelines, but some folks persisted in doing it regardless.

[bobmcd]

Is that block still needed?

[cmcheatle]

If curators were either unaware of the guidelines, or even worse were aware of them and felt ignoring them was appropriate then, I dont think there is any reason to believe that will have changed.

[bobmcd]

Interesting that at least in the common names, bacteria can have symbols used. For instance Proteobacteria:
Α-Proteobacteria Class Alphaproteobacteria

Β-Proteobacteria Class Betaproteobacteria

Δ-Proteobacteria Class Deltaproteobacteria

Ε-Proteobacteria Class Epsilonproteobacteria

Γ-Proteobacteria Class Gammaproteobacteria

[jameskdouch]

I’m glad you agree. Arabic numeral is the term I should have used in the title of this post.

I didn’t think of this before, but you’re right that by me establishing the taxon Deltapapillomavirus one instead of Deltapapillomavirus 1, I’ve arbitrarily asserted my pro-English bias. An Italian curator would have been equally justified to have established the taxon Deltapapillomavirus uno. I think the fact that Deltapapillomavirus 1 is the correct form is reason enough to make this feature request, but you’ve identified an additional problem.

The species names in question do sort alphabetically rather than numerically (example).

[jameskdouch]

Yes, there are two virus species names in use on iNaturalist that are written correctly, I’m told as relicts of a time before the block:

• Invertebrate iridescent virus 31
• Kappapapillomavirus 2

[pisum]

if this is to be done, it probably should be done in conjunction with the other virus name feature request (Italicise all viral taxa - Feature Requests - iNaturalist Community Forum). there’s a note in the Github issue referenced over there which indicates that the change will not be trivial and will require some up front tasks (some of which you may be able to provide input on). if there are other things related to virus names, it might be efficient to describe them all together, rather than as separate requests, so that they can all be done at the same time.

[jameskdouch]

I made that feature request as well. I made these two requests separately under the presumption that that’s what the administrators would prefer.

To my knowledge there are no further virus-name-related feature requests to be made. I do have an additional potential feature request on my mind, but I assume it’ll be more difficult to implement and so I haven’t mentioned it until now. It is: move Viruses from Kingdom rank to an unranked taxon at the very top, and establish the rank of Realm. This would allow the higher taxonomy of viruses to be properly represented (Viruses [unranked] > Realm > Kingdom > Phylum > Class > Order > Family > Genus > Species).

[trh_blue]

Each request should be separate, but it is helpful to include links to related requests. Otherwise we can just use the search bar… haha

[jameskdouch]

To avoid this issue in the meantime, what do people think about using Roman numerals rather than English words?

[bobmcd]

@jameskdouch

Roman numerals rather than English words

Is this in standard usage any where?

[jameskdouch]

No, but as long as we’re using something other than Arabic numerals as in the correct version of the name, everything is non-standard. At least with Roman numerals it’s comprehensible across (I assume most) languages and sorts alphabetically from one to eight.

[kiwifergus]

is there any significant advantage to being able to sort alphabetically within the species? and especially given that only the first eight would be sorted…? Surely a partial solution like that takes the pressure off a more “correct” and workable solution being implemented, so I would rather see the effort be towards bringing the taxonomy into conformance, as it were.

[kiwifergus]

Clearly iNat taxonomy is capable of handling the arabic numerals, so perhaps lists could be submitted to staff such that they can implement the numeralled taxon names manually from the back end, rather than opening up all taxonomy into allowing it. How big of a list would it be?

[edit] I’m thinking that going forward, ie after the bulk of the already entered names are fixed, the english (or french or whatever) spelling could be used initially, and then a flag raised for staff to implement the numeralled version to replace it. Or perhaps staff can somehow grant permissions for a suitable curator to handle that… (it’s not me, btw… I’m amateur as…)

[jameskdouch]

I think there’s only one small advantage to species sorting alphabetically/numerically, and that is being able to locate the desired species quickly in a list. But I agree this isn’t of critical importance. What is important in my mind is that the names are written correctly.