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Outdated checklist in the Backbone #504

Open gbif-portal opened 1 week ago

gbif-portal commented 1 week ago

Outdated checklist in the Backbone

We recently received this message on helpdesk.

In Gbif, Begonia holostyla is corresponding to two different taxa. The second one is "doubtful".

The only accepted species according to IPNI is actually the first one (https://www.ipni.org/?q=Begonia%20holostyla) : Begonia holostyla Y.M.Shui & W.H.Chen

The second one is now a synonym of Begonia grandis subsp. holostyla Irmsch. as stated in Padme (https://padme.rbge.org.uk/Begonia/Data/nomenclature?padme_species_epithet_s=holostyla)

It looks like this name comes from a dataset that hasn't been updated in a long time: https://www.gbif.org/dataset/d9a4eedb-e985-4456-ad46-3df8472e00e8. On the website of the Plant List, they refer to a different website for which this particular issue has been corrected: https://wfoplantlist.org/taxon/wfo-0001360513-2024-06?matched_id=wfo-0001266721&page=1

Github user: @ManonGros User: See in registry - Send email System: Safari 17.5.0 / Mac OS X 10.15.7 Referer: https://www.gbif.org/species/8251320 Window size: width 1728 - height 926 API log&_a=(columns:!(_source),filters:!(),index:'3390a910-fcda-11ea-a9ab-4375f2a9d11c',interval:auto,query:(language:kuery,query:''),sort:!())) Site log&_a=(columns:!(_source),filters:!(),index:'5c73f360-fce3-11ea-a9ab-4375f2a9d11c',interval:auto,query:(language:kuery,query:''),sort:!())) System health at time of feedback: INFO

ManonGros commented 1 week ago

I am not sure if the Plant List with literature can be updated since the source should now be the WFO plantlist. @rdmpage, you originally shared the dataset on GBIF. Could this dataset be updated?

If this isn't possible, perhaps should the Plant List shouldn't integrated in the xrelease. What do you think @DianRHR @camiplata?

camiplata commented 1 week ago

Hi @ManonGros we could exclude the name or even the entire source, nevertheless the problem goes deeper than that as TPL is not the only source were Begonia holostyla appears as an accepted species. Furthermore, the entire Begoniaceae family is missing in COL. We probably need to first adress this issue at the base COL.

rdmpage commented 1 week ago

@camiplata Wow, how did COL lose the Begoniaceae? It was present in earlier releases, for example https://www.checklistbank.org/dataset/292011/taxon/7NG4T (= COL.24.3) I note that it was absent in COL.24.4, and also the current COL24 release.

rdmpage commented 1 week ago

@ManonGros The Plant List with Literature is pretty much frozen as it was based on old export of the Plant List to which I added literature links (e.g., DOIs). Today I'm adding those to a version of the IPNI database. Removing The Plant List with Literature might simply some taxonomic issues, but will lose links to the primary taxonomic literature. I hope one day COL tackles the problem of links to literature, but so far they seem reluctant to do so.

camiplata commented 1 week ago

@rdmpage We are testing how to merge The Plant List with Literature to COL to gain more links to literature. We have yet to overcome how to handle outdated names or how to keep only the literature information and not the taxonomic one.

rdmpage commented 1 week ago

@camiplata I struggle with the notion of names being "outdated", names themselves persist indefinitely, however which names we regard as being the ones to use for a given taxon change. I think COL would benefit from cleanly separating names and associated literature from taxonomy. It attempts to do this with "name usages" but it's still messy.

Personally I would — in the case of plants — separate out IPNI (as a list of names and literature), add additional literature to those names (i.e., https://www.checklistbank.org/dataset/164203), then make every plant taxonomy used by COL include IPNI identifiers for names. That way you separate names from taxonomy, and taxonomy becomes simple a view on the status of each name. This keeps names and taxa separate, and enables you to easily provide multiple alternative classifications, and/or replace one classification by another. This could be done right now for WFO and POWO has each uses (mostly) IPNI identifiers for names.

Then do the same for fungi and animals.