factsmission/synospecies

taxonomic names in Synospecies

Opened this issue · 22 comments

myrmoteras commented

The representation of taxonomic names on the left side in the taxon display in Synospecies is unusual and not according taxonomic practice.

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e.g. Nanotyrannus lancensis (Gilmore, 1946) / Gilmore, 1946 / (Gilmore, 1946) Bakker et al., 1988 / (Gilmore, 1946) Bakker, Currie & Williams, 1988

in Zoology, the name should be Nanotyrannus lancensis (Gilmore, 1946), whereby the change of generic name is indictated by a bracket.

in Botany, the change is indicated by the authority that made the change.

currently, the name includes all the nomenclatural changes.

@millerjeremya suggests to display the names according to taxonomic rules.

A solution could be to add a comment explaining the unique display of names?

millerjeremya commented

I don't think it makes any sense to employ a unique authority system on a platform that is intended to resolve issues of taxonomic nomenclature. The authority is a part of the species name, so by introducing something novel, synospecies misses its core purpose of mapping relationships among treatments based on citations. The synospecies authority system is not explained, and is not needed.
See also this related issue:
https://github.com/plazi/names_LOD/issues/154

nleanba commented

I agree that the current solution is unsatisfactory. However, I am not sure on how to fix it.

The issue is that Synospecies is not "displaying all nomenclatural changes", but rather that each authority (separated by "/") is a separate entry in the data, stemming from different treatments.

e.g. there is a treatment which says "Genus species Name A 1234" and one that says "Genus species (Name A 1234)" and Synospecies has no way to decide which one of these is correct/current; so current behavior is to display "Genus species Name A 1234 / (Name A 1234)".

How should Synospecies (or ideally gg2rdf) decide which of the authorities to show? Open to suggestions

millerjeremya commented

I think this situation is not possible in Zoological nomenclature.
"Genus species Name A 1234" and one that says "Genus species (Name A 1234)"
One of these is correct, the other is wrong. That is to say, you can't have the same Genus species strong with the authority alternatively inside or outside parentheses.
But I don't understand where things are going wrong. How do we make progress on this?

nleanba commented

Impossible or not, it occurs in the data:

I admit the latter two examples are bad examples, as for Animalia gg2rdf should ignore the authority if a baseAuthority is given, I will fix this. However, the general problem still exists, and this also happens for non-Animialia taxa, so situations like with the latter two treatments should still be handled properly.

My point is, those four treatments considered in isolation (and assuming non-Animalia) all are apparently correct translations of the XML markup into RDF. No one of the treaments alone contains the information that there is a mismatch and what authority is the correct one.

Addendum: The relevant RDF property here is dwc:scientificNameAuthorship, these entries are what SynoSpecies lists (with "/" in-between) as the authority.

I originally implemented the listing with "/" as I assumed that this is a rare case that there are multiple authorities and this seemed like a simple fix. It seems however that this is a common issue.

millerjeremya commented

Thanks for this example. I think it's a useful approach to work through.
So the thing that jumps out at me has to do with Treatment 03A1879DFFD0FFE95E7FF664FEA6A618
You provide these annotations in the example

<taxonomicName authorityName="Gilmore" authorityYear="1946" ...>Nanotyrannus
→

http://taxon-concept.plazi.org/id/Animalia/Nanotyrannus_lancensis_Gilmore_1946
dwc:authorityName "Gilmore" ;
dwc:authorityYear "1946" ;
dwc:scientificNameAuthorship "Gilmore, 1946" .

This was indeed a tricky one to annotate. It is a genus level treatment (new genus) but of a monotypic genus, so it works kind of like a species level treatment. So I'm changing the authorityName and authorityYear annotations into baseAuthorityName and baseAuthorityYear annotations. How does that effect the result on Synospecies?

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nleanba commented

If it is annotated as base authority, it will receive the parentheses. So this should fix this particular example

millerjeremya commented

Ok, so how do we find sources of conflict in the authority?
For example,
Tyrannosaurus rex (Osborn, 1905) / Osborn, 1905
If I understand correctly, this indicates that in at least one place, Osborn is assigned to the field baseAuthorityName instead of AuthorityName.
But as I scan down the list of treatments, all give the authority as though is is AuthorityName, i.e., no parentheses.

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myrmoteras commented
millerjeremya commented

Making a google calendar invitation - how to invite nleanba?

millerjeremya commented

I don't have an email address for nleanba, so here are the details for an online meeting on Thursday morning.

Synospecies Authorities
Thursday, September 19 · 2:00 – 3:00pm
Time zone: Europe/Brussels
Google Meet joining info
Video call link: https://meet.google.com/iej-fivz-vha
Or dial: ‪(NL) +31 20 257 3161‬ PIN: ‪132 002 200‬#
More phone numbers: https://tel.meet/iej-fivz-vha?pin=6882431554651

millerjeremya commented

Sorry, Thursday at 14h is no longer available for me. nleanba, can you propose another time when you are available?

myrmoteras commented

Formica herculeana Linne

moved to a new genus by Fabricius, in animalia

Camponotus herculeanus (Linne)

myrmoteras commented

should missing base authorities be corrected in the annotation or in Synospecies?

myrmoteras commented

Nanotyrannus lancensis (Gilmore, 1946) / Gilmore, 1946 shows that there is an inconsistence in the data, that is due to inconsistency in the annotation, i.e. presence or absence of a baseAuthority

A solution is to find the treatments that are missing in the () case the base authority and fix it

nleanba commented

For a given name, we can find all different authorities given by treatments with

PREFIX dwc: <http://rs.tdwg.org/dwc/terms/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX treat: <http://plazi.org/vocab/treatment#>
SELECT ?name ?authority (GROUP_CONCAT(?treatment) AS ?treatments) WHERE {

  # Replace name-uris here as relevant
  VALUES ?name {
    <http://taxon-name.plazi.org/id/Animalia/Nanotyrannus_lancensis>
    <http://taxon-name.plazi.org/id/Animalia/etcetera>
  }

  # For a single name also possible to use this instead:
  # BIND(<http://taxon-name.plazi.org/id/Animalia/Nanotyrannus_lancensis> AS ?name)


  ?tc treat:hasTaxonName ?name .
  GRAPH ?treatment {
    ?tc dwc:scientificNameAuthorship ?authority .
  }
}
GROUP BY ?name ?authority

For Nanotyrannus lancecnis we get these two outliers:

I will make a list for the other names

nleanba commented

Tyrannosaurus synonyms with disagreements over authorities:

myrmoteras commented

Hi @nleanba thanks for this- have all of these couples an error - didn't we calculate 6 or 7 couples max?

Just to be clear, all the new combinations, eg the ones with () need to have a aseAuthorityName="XXX" for example in https://treatment.plazi.org/id/D32F092B552A904C4689FD6C127AF072

nleanba commented

In most cases, the treatments without "()" are missing the baseAuthorityName /-Year or have it wrongly as authorityName /-Year.

This is not always the case, for the two Tyrannosaurus Rex (Osborn 1905) treatments it probably should be authority instead of base authority (to bring it in agreement with the many other treatments which list Osborn as authority, and not as base-authority

nleanba commented

and
Animalia/Nanotyrannus_lancensis — (Bakker, Williams, & Currie, 1988) —
https://treatment.plazi.org/id/A56387B0FF8B704CB2BBFC9392CCFB4A

should have Bakker... as authority, and Gilmore as base-authority as far as I can tell; based on the fact that Bakker et al themselves gave Gilmore as base-authority

nleanba commented

To decide which is the correct base-authority/authority we must compare with the other treatments

nleanba commented

For example, I think that for Laelaps incrassatus, correct is

  • Authority: Cope, 1876
  • base-authority: None

Screenshot_20240925_221056_Firefox.png

nleanba commented

I wonder why this annotation change has not been pushed to the treatments-xml repo though, it would have been correct as far as I can tell

Thanks for this example. I think it's a useful approach to work through.
So the thing that jumps out at me has to do with Treatment 03A1879DFFD0FFE95E7FF664FEA6A618
You provide these annotations in the example

<taxonomicName authorityName="Gilmore" authorityYear="1946" ...>Nanotyrannus
→

http://taxon-concept.plazi.org/id/Animalia/Nanotyrannus_lancensis_Gilmore_1946
dwc:authorityName "Gilmore" ;
dwc:authorityYear "1946" ;
dwc:scientificNameAuthorship "Gilmore, 1946" .

This was indeed a tricky one to annotate. It is a genus level treatment (new genus) but of a monotypic genus, so it works kind of like a species level treatment. So I'm changing the authorityName and authorityYear annotations into baseAuthorityName and baseAuthorityYear annotations. How does that effect the result on Synospecies?

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