yroskov
commented
2 years ago For attention of @mdoering:
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[ ] the problem with a placement of hybrid genera in the classification:
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many (if not all) genera with hybrid symbol are placed in the root of the tree, outside any families. They have no children species:
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there is a bunch for genera with hybrid symbol placed in artificial genus "xx" in Orchidaceae family. These genera have no children species:
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species with hybrid symbol have no children infraspecific taxa; all infraspecific taxa which are children of hybrid species are placed outside their parents (see genus Dactylorhiza): https://data.catalogueoflife.org/dataset/2232/classification?taxonKey=55153-wcs
(Unfortunately, we cannot go ahead with WCVP until this problem will be fixed).
mdoering
WCVP, The World Checklist of Vascular Plants of 2021-02-21 was imported on PROD 2021-12-03 by @mdoering.
(see also report on DEV data: https://github.com/CatalogueOfLife/testing/issues/175)
[x] Imported: 351,046 spp families ? (no data) genera 16,473 subsp 22,299 var 20,166 f 476
[ ] Metadata: no version; alias included in full name; no editor, creator "The Royal Botanic Gardens, KewLondon, GB" - contact Rafael for metadata in CoL.
[ ] Classification: top rank - families; no orders. Many genera are in the root (outside families). They are mainly genera with hybrid symbol - all hybrid genera outside families?. Actually, the same problem is with hybrid taxa of all ranks - they are not placed in their parent taxa (see below)
[ ] It's not clear to me, how to clean up "(!) unwanted" names in final product. All necessary information is in taxon_status field in the source file, but these data are not available in the clearinghouse.
Interpretation of WCVP statuses into CoL statuses.
Total: 1,048,575 names in my Excel spreadsheet (seems, incomplete list imported in the Excel due to its limits)
Field taxon_status: Accepted (308,084) = accepted Synonym (634,237; 901 of them have no parent accepted name, i.e. empty accepted_plant_name_id field ) = synonym (except those 901 names = bare names) Misapplied (947; all with parent accepted name) = misapplied name Othographic (1,574; 3 of them have no parent accepted name) = synonym. Not clear, what to do with those 3 accepted "orthograpic" names: Cassine congonha A.St.-Hil.; Aspidosperma clerceanum Iljin & Krasch.; Croton benzoe L.
Unplaced (47,165; 47,139 of them have no parent accepted name) = (!) all bare names Illegitimate (32,277; 43 of them have no parent accepted name) = synonyms (except those 43 names = (!) bare names) Invalid (22,792; 69 of them have no parent accepted name) = synonyms (except those 69 names = (!) bare names) Local Biotype (100; all with parent accepted name) = synonyms Artificial Hybrid (1,395; 318 of them have rank "genus", 1,072 "species", 2 "variety", 3 blank)