Missing CoL name status in synonymy on species details page

[yroskov]

For attention of @mdoering & @thomasstjerne

There is no indication of CoL name statuses in a list of synonyms on Species Details page. Statuses used in the database: synonym, ambiguous synonym, misapplied name.

For example, Trifolium johnstonii sensu Edwards Edwards & Bogdan is fllaged in the database as "misapplied name", but there is no such information on the page: https://www.catalogueoflife.org/data/taxon/58Q6G

Note: these statuses displayed in the Search, but it's not enough.

[mdoering]

I think the UI shows misapplied names and synonyms in different categories. The example you have given shows Misapplied names as the label, so that is a clear case. It will only leave ambiguous synonyms vs regular synonyms. @thomasstjerne do we somehow show that difference? It does not seem to be the case, it is lumped with other synonyms: https://www.catalogueoflife.org/data/taxon/8HDT

How should we best show ambiguous synonyms? If I remember correctly ambiguous means there are different accepted names for this name. Should we in such cases not also show or link to the other instances? In that case we could provide a new category like we do for misapplied names, labelled Ambiguous synonyms and for each of them show also all other accepted names?

Btw, provisionally accepted species are labeled as such in the status field: https://www.catalogueoflife.org/data/taxon/8HB7

[mdoering]

@yroskov @gdower the reference in above's link looks bad. Created a new issue https://github.com/CatalogueOfLife/data/issues/334

[yroskov]

I would prefer to keep misapplied names and ambiguous synonyms in the same block "Synonyms & Combinations" on Species Page, but with appropriate labels "Misapplied name", "Ambiguous synonym", "Orthographic variant".

Perhaps, it might be a good idea to add a link to alternative Species Page(s) with each Ambiguous synonym or Misapplied name.

[mdoering]

Yes, we should discuss how to best display the "synonymy" information. In the portal we only have taxon / accepted name pages that list the synonyms and provide a list of references behind the icon: https://www.catalogueoflife.org/data/taxon/73T8K

We could probably show more information in the long run and then we should consider if we should also have a distinct page for each synonym.

In CLB we do have "names" pages which are unfinished and rather raw, but they exist for each synonyms: https://data.catalogueoflife.org/dataset/3LR/taxon/73T8K https://data.catalogueoflife.org/dataset/3LR/name/1a51cf66-592f-44a2-bd8a-556401dd308e

The data model would allow us to show various references, name relations, type material, taxonomic "treatments" ala plazi & pensoft and crosslinks to other selected datasets, e.g. IPNI/ZooBank, IUCN, etc.

@thomasstjerne @olafbanki @chantalhuijbers @dhobern we should talk this through some time.

[yroskov]

In 2001-2004, the CoL interface had individual page for each synonym - a Name Page (a practice taken from FishBase). It caused a lot of confusion among users. They taken each name as a Species. With new data model and new software, the CoL abandoned Name Pages in 2005, and aggregated all information for the species in a single taxon page. This was supported by all participated GSDs.

Instead of Name Page for each synonym, I would like to see a link from the CoL to appropriate Name Page in nomenclator resources such as IPNI, Index Fungorum, ZooBank. NAMES is their "subject area", TAXONOMIC CONCEPTS is the CoL unique area. If we succeed to build smart links from CoL to global nomenclators and BHL, useful informatic ecosystem will be created. (Well, I forget to mention also links to GBIF maps, to sequences in GeneBank and BOLD, to specimen images in collection databases, to images in iNaturalists, to encyclopedic data in Wikipedia, etc.).

[mdoering]

See also user feedback at https://github.com/CatalogueOfLife/data/issues/406

[mdoering]

The nomenclatural status is also oddly represented in the synonymy: https://www.checklistbank.org/dataset/3LR/taxon/8LVYQ

[mdoering]

We should use the nomenclatural code of the synonym or if missing from the taxon to determine the correct terminology by the code for the nomstatus: http://api.checklistbank.org/vocab/nomstatus

We could also show the abbreviation. Showing our own code agnostic value is probably not ideal for the UI

[mdoering]

We definitely need a dedicated synonyms page that exposes all information about a synonym. It should be very visible that this is not a taxon page, but the following information is shared across all name usages, regardless if accepted or not:

• ID & origin (only show origin if other than source)
• status
• name
• names index link
• external link
• remarks
• accordingTo with link to reference page via accordingToID
• name relations
• type material

[thomasstjerne]

The nomenclatural status is also oddly represented in the synonymy: https://www.checklistbank.org/dataset/3LR/taxon/8LVYQ

It looks like the nomenclatural status is in the labelHtml here: https://api.checklistbank.org/dataset/3LR/taxon/8LVYQ/info The UI translates the code agnostic nomStatus into a code specific one from https://api.catalogueoflife.org/vocab/nomstatus (defaulting to zoological)

If the nomStatus is in the labelHtml, this gives a "double" representation in the UI

[mdoering]

Indeed. I can easily remove it from the label, but I fear it is important in other places like the workbench or duplicate UI. It also seems the UI does not translate the status:

Abax marginalis Letzner, 1852 unavailable name comes from the labelHtml, (not established) is appended by the UI

Here is an IRMNG synonym with the nomstatus given, but not included in the authorship or label: https://api.checklistbank.org/dataset/2007/nameusage/urn%3Alsid%3Airmng.org%3Ataxname%3A1275869

The UI then appends the generic status (not the zoological one) in brackets: https://www.checklistbank.org/dataset/2007/taxon/urn%3Alsid%3Airmng.org%3Ataxname%3A1034966 https://www.checklistbank.org/dataset/2007/name/urn%3Alsid%3Airmng.org%3Ataxname%3A1275869

Here is a World Plants manuscript example Aeonium millennium (O. Arango) comb. ined.: https://www.checklistbank.org/dataset/1141/taxon/Saxifragales-Crassulaceae-Sempervivoideae-Aeonium-millennium-(O.%20Arango)

The comb.ined. part is produced by the API and added to the label, the UI does not add anything: https://api.checklistbank.org/dataset/1141/taxon/Saxifragales-Crassulaceae-Sempervivoideae-Aeonium-millennium-(O.%20Arango)

The problem comes with the nom status given explicitly, as part of the authorship or even the publication:

ID  rank    scientificName  authorship  namePublishedIn nameStatus
1   species Abies alba  (Aiton) Michx., Fl. Bor.-Amer. (Michaux) 2: 207 (1803), nom. illeg.     
2   species Abies alba  (Aiton) Michx.  Fl. Bor.-Amer. (Michaux) 2: 207 (1803)  nom. illeg.
3   species Abies alba  (Aiton) Michx., nom. illeg. Fl. Bor.-Amer. (Michaux) 2: 207 (1803)  
4   species Abies alba  (Aiton) Michx., nom. illeg. Fl. Bor.-Amer. (Michaux) 2: 207 (1803)  nom. illeg.

The importer should interpret that ideally as the same. But when we have a nom.illeg. status extracted should it still be present in the authorship and publication? I have tried to code for removing it, as it would otherwise duplicate things and create inconsistent names/labels.

[mdoering]

The above examples currently ends up as: https://www.dev.checklistbank.org/dataset/117890/names

1. no status, exact authorship retained
2. unacceptable status, authorship retained. nom. illeg. lost - should go into nomenclaturalNote field!
3. unacceptable status, authorship retained incl. nom. illeg. and nom. illeg. also in nomenclaturalNote - should be removed from authorship???
4. unacceptable status, authorship retained incl. nom. illeg. and nom. illeg. also in nomenclaturalNote - should be removed from authorship???

labelHTML:

1. <i>Abies alba</i> (Aiton) Michx., Fl. Bor.-Amer. (Michaux) 2: 207 (1803) , nom. illeg.
2. <i>Abies alba</i> (Aiton) Michx.
3. <i>Abies alba</i> (Aiton) Michx., nom. illeg.
4. <i>Abies alba</i> (Aiton) Michx., nom. illeg.

[mdoering]

I tend to think the label should not include the nom status

[mdoering]

Moved creating synonym pages to its own issue: https://github.com/CatalogueOfLife/checklistbank/issues/1034