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Species Fungorum Plus - lichen species possibly missing #428

Open ManonGros opened 2 years ago

ManonGros commented 2 years ago

Describe the problem: Issues originally logged in the GBIF Feedback portal: https://github.com/gbif/backbone-feedback/issues/284 by @rukayaj

Would it be possible to review whether to add the following species to Species Fungorum Plus/CoL?

Link to effected CoL webpages: https://www.catalogueoflife.org/data/taxon/63SB9 https://www.catalogueoflife.org/data/taxon/3JH2 https://www.catalogueoflife.org/data/taxon/7BN4 https://www.catalogueoflife.org/data/taxon/66H3

Literature references:

yroskov commented 2 years ago

Forwarded to Species Fungorum author

thomasstjerne commented 2 years ago

The name is indeed in the Species Fungorum for Col+ dataset, but as a bare name: https://www.checklistbank.org/dataset/2073/names?facet=rank&facet=issue&facet=status&facet=nomStatus&facet=nameType&facet=field&facet=authorship&facet=authorshipYear&facet=extinct&facet=environment&facet=origin&limit=50&offset=0&q=Rinodina%20abolescens&sortBy=taxonomic

I am currently testing an API crawler for Index Fungorum, this seem to include the requested names:

https://www.dev.checklistbank.org/dataset/53548/taxon/370081 https://www.dev.checklistbank.org/dataset/53548/taxon/444758 https://www.dev.checklistbank.org/dataset/53548/taxon/414128 https://www.dev.checklistbank.org/dataset/53548/taxon/413628

JonKleps commented 2 years ago

I was suggested to leave a note here regarding more issues and flags related to "Taxon match fuzzy" and "Taxon match higgerrank" encountered when publishing another dataset at GBIF. The dataset in question is "Norwegian specimen stored in private herbarium", the publisher is Biorehab Klepsland. This is my original message to helpdesk GBIF Norge: 1) 27 records are flagged as "Taxon match fuzzy". I looked at these and almost all are due to a wrong interpretation of my original Taxon names in the spreadsheet. For some reasons the names have changed somewhat when published and don't match the correct nomenclature. Why has this happened? Anyway to avoid this? (ex. Parmeliella triptophylla converted wrongly to P. thriptophylla). A few false interpretations are quite strongly wrong and might be due to lack of the species in the GBIF backbone (ex: Porina collina is wrongly converted to Porina conica). Miriquidica porphyrospora might have a fuzzy match because it is a synonym to Myochroidea porphyrospora. Spongipellis spumeus is the same as Sarcodontia spumea. Polyporus melanopus is now Picipes melanopus. 2) As many as 71 records are flagged as "Taxon match higherrank". I wonder if most of these are due to the poor update of the current nomenclature on fungi. GBIF really should use Index Fungorum as backbone for fungi. All (or at least nearly all) taxa flagged as "Taxon match higherrank" in my dataset are rather new names (new synonyms or newly described species), but they are all found in Index Fungorum.

thomasstjerne commented 2 years ago

We should discuss using a dynamic API link for Index Fungorum. The API crawler can now produce a COLDP archive, with References, TypeMaterial and NameRelations (for Basionyms)

The advantages of using this would be:

  1. Higher taxa will get proper IDs, Synonyms, References, Typification details etc
  2. Monthly or even weekly updates possible - making it possible to correct errors faster
  3. Richer data: TypeSpecimens and NameRelations

Disadvantages might be

  1. It is Nomenclatural data - there might unwanted "dirty" data coming through. But this should again be possible to fix rather quickly by either doing decisions in CLB or modifying the crawler

Some further data examples for comparison:

  1. The genus Agaricus Current version - New version
  2. Species Exophiala castellanii Current version - New version with Type material
  3. Species Graphis lutea Current version - New version with name relation
  4. Further examples of Lichens missing in the current version : Parmelia wildeae C.W. Dodge, Porina collina Orange, Palice & Klepsland
mdoering commented 2 years ago

We should discuss this with Paul Kirk primarily. @dhobern , but maybe the Taxonomy Group is interested as well?

dhobern commented 2 years ago

I think the Taxonomy Group would be interested, but perhaps we could start by making sure we understand what is necessary and how it would work and then we can communicate effectively with the TG.