Species Fungorum Plus (id 2073): test report

yroskov commented 3 years ago

Species Fungorum Plus has been exported for the CoL on Feb 2020 / 2020-02-14.

Export to the CoLDP format was produced by Paul Kirk.

The new dataset brings together previously independent GSDs such as Dothideomycetes, Glomeromycota, Phyllachorales, Rhytismatales, Saccharomycetes, Species Fungorum, Trichomycetes, Xylariaceae & Zygomycetes. It also temporarily replaces lichenized fungi previously covered by LIAS.
Species Fungorum Plus also contributes taxonomically unplaced names from Index Fungorum.

thomasstjerne commented 3 years ago

Currently only ranks species and below seem to be included in the export. These are the names in the source whereas these are generated by COL through normalization It would be desirable to have names for higher ranks in the export as well, as this would allow for preserving their source IDs (Index Fungorum Identifiers). Child taxa should be linked to their parent using col:parentID

yroskov commented 2 years ago

See: https://github.com/gbif/backbone-feedback/issues/275

mdoering commented 2 years ago

Is the IF ColDP dataset generated regularly so we can update potentially on a monthly basis? If it is manual work for Paul we could consider to use the IF API to build an archive programmatically, so we can schedule that automatically.

http://www.indexfungorum.org/ixfwebservice/fungus.asmx http://www.indexfungorum.org/ixfwebservice/fungus.asmx/NameByKey?NameKey=827760

yroskov commented 1 year ago

Species Fungorum Plus, received 2023-01-17; imported 2023-01-19

[ ] Imported: 154,569 spp (of them, 146 spp paleo/extinct - check with Paul).
[ ] Metadata: ask Paul to update. Full name change?
[ ] Classification: phyla Fossil Ascomycota, Fossil Basidiomycota, Fossil Blastocladiomycota etc; Fossil Fungi. = AGRRED with GO: (1) populate "Extinct" flag with all children spp, (2) convert Fossil Fungi into kingdom Fungi, Fossil Basidiomycota into phylum Basidiomycota, etc. Incertae sedis nodes = Agreed with GO: eliminate Incertae sedis nodes by converter script

There are no chromistian fungi in this update: Chromista - phyla Cercozoa, Oomycota, Bigyra are missing. Only kingdom Fungi.

[x] Sectors: sectors (phyla) Cercozoa, Oomycota, Bigyra are broken = no data in the update; sector Fungi OK
[ ] Check for ortho variants in the PREVIEW (Phomopsis semiimmersa (acc) - Phomopsis semi-immersa (ortho), name in Taxon table)

yroskov commented 1 year ago

ISSUES assessed 2023-01-27

Unmatched Name Brackets, 6 Authorstring corrected as Kodamaea restingae (Rosa, Lachance, Starmer, Barker, Bowles & Schlag-Edler) C.Y. Chai & F.L. Hui https://mycokeys.pensoft.net/article/81119/

yroskov commented 1 year ago

TASKS

Broken decisions, 1139: all deleted

Resolved 2001-27:

Few questions on taxa split between different branches sent to Paul.

Synced 2023-01-27

yroskov commented 1 year ago

[x] Any uninomial 34 of 40 Few questions on taxa split between different branches sent to Paul 2023-01-27.

PK: And the queries below – those which are incorrect are highlighted in red. YR: I am not sure that Geoff and I will be able to fix all misplacements with our tools. May I just flag “taxa in red” as “provisionally accepted”? PK: Yes, your solution is pragmatic and acceptable. = FIXED 2023-02-06 as:

yroskov commented 1 year ago

Re-synced 2023-02-06

yroskov commented 1 year ago

[x] "there are several taxa that do not exist" in modern fungi classification https://github.com/CatalogueOfLife/testing/issues/220#issuecomment-1436722887

sergbolshakov, 2023-02-20: Hello, everyone.

In the classification of Fungi (https://www.checklistbank.org/dataset/2073/), there are several taxa that do not exist. For a mycologist familiar with the modern classification of fungi, these look like unfortunate typos that have no place on such a reputable source of knowledge. I have not yet written directly to Paul Kirk, perhaps it should be passed on from you so that this can be corrected as soon as possible.

When preparing Index Fungorum data for export to CoL, one would have to include checks to see if the taxon name used in the classification at any rank is present among all existing names in IF db.

According to the results of the check (I do it in R with a snapshot of the full IF database, obtained by the API in 2023-01-22), these names are not exist:

phylum Agaricomycota — should be Basidiomycota
phylum Cladochytriomycota — should be Chytridiomycota
order Allotrechisporales — should be Trechisporales
family Allotrechisporaceae — should be Hydnodontaceae

And two more orthographic variants, for which there are accepted variants:

order Asterotexiales — orthographic variant of Asterotexales
family Nannizziopsiaceae — orthographic variant of Nannizziopsidaceae

They probably arose when the authors of the new taxa filled in the corresponding fields of the classification. It is desirable to ensure validation of the data entered to prevent such cases.

Also, in the current classification there are cases when the same taxon appears in different parent taxa:

rank name parent

1 class Agaricomycetes Basidiomycota 2 class Agaricomycetes Agaricomycota 3 class Kickxellomycetes Mucoromycota 4 class Kickxellomycetes Kickxellomycota 5 order Chaetothyriales Eurotiomycetes 6 order Chaetothyriales Chaetothyriomycetes 7 order Cladochytriales Chytridiomycetes 8 order Cladochytriales Cladochytriomycetes 9 order Helotiales Leotiomycetes 10 order Helotiales Dothideomycetes 11 family Apiosporaceae Incertae sedis 12 family Apiosporaceae Xylariales 13 family Clypeosphaeriaceae Amphisphaeriales 14 family Clypeosphaeriaceae Xylariales 15 family Dissoconiaceae Capnodiales 16 family Dissoconiaceae Mycosphaerellales 17 family Kirschsteiniotheliaceae Pleosporales 18 family Kirschsteiniotheliaceae Kirschsteiniotheliales 19 family Septochytriaceae Cladochytriales 20 family Septochytriaceae Chytridiales According to the current accepted classification of Fungi*, the parental taxa should be: Agaricomycetes — Basidiomycota Kickxellomycetes — Kickxellomycota Chaetothyriales — Eurotiomycetes Cladochytriales — Cladochytriomycetes Helotiales — Leotiomycetes Apiosporaceae— Amphisphaeriales Clypeosphaeriaceae — Xylariales Dissoconiaceae — Mycosphaerellales Kirschsteiniotheliaceae — Kirschsteiniotheliales Septochytriaceae — Cladochytriales And still missing all the intraspecific tautonyms of accepted names — see example below. To solve this problem, it is obviously necessary to assign the same acceptedNameID to all taxa with the same basionymID. However, in some cases for infraspecific tautonyms there are different basionymIDs for some reason. sqlite> SELECT ...> name_of_fungus ...> , infraspecific_epithet ...> , basionym_record_number ...> , current_name_record_number ...> FROM if_raw ...> WHERE (name_of_fungus != 'UNPUBLISHED NAME') ...> AND (accessrights IS NULL) ...> AND (name_of_fungus LIKE 'Agaricus bisporus%') ...> ORDER BY ...> basionym_record_number ...> ; name_of_fungus infraspecific_epithet basionym_record_number current_name_record_number -------------------------------------- --------------------- ---------------------- -------------------------- Agaricus bisporus var. perrubescens perrubescens 117700 531546 Agaricus bisporus f. microspora microspora 124277 531546 Agaricus bisporus 267375 531546 Agaricus bisporus 267375 531546 Agaricus bisporus 267375 531546 Agaricus bisporus f. bisporus bisporus 267375 Agaricus bisporus var. bisporus bisporus 267375 Agaricus bisporus var. albidus albidus 348995 531546 Agaricus bisporus var. avellaneus avellaneus 348996 531546 Agaricus bisporus f. conicopodus conicopodus 348997 531546 Agaricus bisporus f. depressus depressus 348998 531546 Agaricus bisporus f. langei langei 353243 531546 Agaricus bisporus var. burnettii burnettii 357921 531546 Agaricus bisporus var. eurotetrasporus eurotetrasporus 466019 531546 **Forwarded to Paul 2023-02-27**. **Spoke to Sergey 2023-02-28.** Cleanings should be done before the import in CLB. However, we can block unwanted taxa, if they have small number of children species. **Completed 2023-03-06:** phylum Agaricomycota = blocked (2 spp) phylum Cladochytriomycota = blocked (2 spp) order Allotrechisporales = blocked (3 spp) order Asterotexiales = blocked (1 sp) family Nannizziopsiaceae = blocked (1 sp) **Re-synced 2023-03-06** **Completed 2023-03-07:** **class Agaricomycetes Basidiomycota** class Agaricomycetes Agaricomycota = blocked (2 spp) class Kickxellomycetes Zygomycota = blocked (2 spp) Fungi > Mucoromycota - Kickxellomycetes = prov acc (many children taxa & spp) = unresolved **class Kickxellomycetes Kickxellomycota** **order Chaetothyriales Eurotiomycetes** order Chaetothyriales Chaetothyriomycetes = blocked (1 sp) order Cladochytriales Chytridiomycetes **order Cladochytriales Cladochytriomycetes** = unresolved, remains in Chytridiomycetes, but once **order Helotiales Leotiomycetes** order Helotiales Dothideomycetes = blocked (1 sp) family Apiosporaceae Incertae sedis, should be in Amphisphaeriales = unresolved family Apiosporaceae Xylariales = blocked (4 spp) family Clypeosphaeriaceae Amphisphaeriales **family Clypeosphaeriaceae Xylariales** = unresolved, remains in Amphisphaeriales, but once (1 sp deleted) family Dissoconiaceae Capnodiales **family Dissoconiaceae Mycosphaerellales** = unresolved, remains in Capnodiales, but once (1 sp deleted) family Kirschsteiniotheliaceae Pleosporales **family Kirschsteiniotheliaceae Kirschsteiniotheliales** = unresolved, remains in Pleosporales, but once (1 sp deleted) **family Septochytriaceae Cladochytriales** = unresolved, remains in Chytridiales, but once family Septochytriaceae Chytridiales

yroskov commented 1 year ago

[ ] https://github.com/CatalogueOfLife/data/issues/518

All these names present in Species Fungorum Plus @ CLB souce, but flagged as "bare names", and didn't pass to the Catalogue of Life.

Acarospora jenisejensis H. Magn., Svensk bot. Tidskr. 30: 248 (1936) = BARE NAME Caloplaca subpyracea (Nyl.) Zahlbr., Cat. Lich. Univers. 7: 185 (1931) = BARE NAME Cladonia terrae-novae f. cinerascens Ahti, Ann. bot. Soc. Zool.-Bot. fenn. Vanamo 32(no. 1): 82 (1961) = BARE NAME Fissurina leuconephela Nyl., Flora, Regensburg 52: 73 (1869) = BARE NAME Flavopunctelia darrowii (J.W. Thomson) Hale [as 'darrowi'], Mycotaxon 20(2): 682 (1984) = BARE NAME Graphis virginalis Tuck., in Eckfeldt, Bull. Torrey bot. Club 17: 256 (1890) = BARE NAME Heterodermia linearis Moberg & T.H. Nash [as 'lineare'], Bryologist 102(1): 7 (1999) = BARE NAME Paulia Fée, Linnaea 10: 471 (1836) = Paulia [no author] present https://preview.catalogueoflife.org/?taxonKey=6JN5 Pertusaria moreliensis B. de Lesd., Lich. Mexique: 18 (1914) = BARE NAME Pyrenula herrei Fink ex J. Hedrick, Mycologia 25(4): 309 (1933) = BARE NAME Usnea pallida Motyka, Usnea 2(1): 435 (1937) = BARE NAME

yroskov commented 1 year ago

[x] phylum Kickxellomycota with only 1 species blocked

Species Fungorum Plus, ver Jan 2023 / 2023-01-17 (imported 2023-01-19) re-synced 2023-06-13.

yroskov commented 6 months ago

Species Fungorum Plus, received 2024-04-28; imported 2024-04-29

[x] Imported: 156,035 spp (vs 154,569 spp in 2023).
[x] Metadata: OK
[x] Classification: 15 entries for phyla: Ascomycota, Basidiomycota, Blastocladiomycota, Chytridiomycota, Cladochytriomycota (7 spp), Entomophthoromycota, Entorrhizomycota (13 spp), Glomeromycota, Glomeromycotina = block (1 sp), Mucoromycota, Neocallimastigomycota, Peronosporea = ignore, all children Extinct (1 sp), Sanchytriomycota, Zoopagomycota, Zygomycota

Suspicious classes: = RESOLVED Ascomycota: Lecanomycetes, 4 spp (vs Lecanoromycetes); Lecanoromycetesx000d\nSordariomycetidae, 1 sp; Sordariomycetesx000d\nSordariomycetidae, 42 spp (vs Sordariomycetes). Class Blastocladiomycetes is present in Chytridiomycota (1 sp) and in Blastocladiomycota (213 spp) Class Cladochytriomycetes is present in Chytridiomycota (1 sp) and in Cladochytriomycota (7 spp) Class Entorrhizomycetes is present in Entorrhizomycota (13 spp) and in Basidiomycota (7 spp) Class Glomeromycetes is present in Glomeromycotina (1 sp) and in Glomeromycota (360 spp)
Class Kickxellomycetes is present in Zygomycota (1 sp) and in Mucoromycota (324 spp) https://www.checklistbank.org/dataset/2073/duplicates?limit=50&rank=class

14 cases of split orders: = RESOLVED https://www.checklistbank.org/dataset/2073/duplicates?limit=50&rank=order

Split families: = RESOLVED https://www.checklistbank.org/dataset/2073/duplicates?limit=50&rank=family

Split genera: = RESOLVED https://www.checklistbank.org/dataset/2073/duplicates?limit=50&rank=genus

There are no chromistian fungi in this update: Chromista - phyla Cercozoa, Oomycota, Bigyra are notncluded. Only kingdom Fungi.

[x] Sectors: sectors (phyla) Cercozoa, Oomycota, Bigyra are broken = no data in the update. KEEP AS IT IS; sector Fungi OK
[x] Extinct flag: OK, 155 spp: species rank only; there are no flags with taxa above. Set of genera & family Palaeoclavariaceae in the Tree root are all paleo taxa - not flagged yet (their spp flagged) = Flag applied (39 genera. 1 family)

Metrics

ISSUES assessed 2024-05-03

TASKS

Broken decisions, 1060 = deleted
Outdated decisions, 29 = deleted
Any uninomial 61 of 62: one unresolved case: Claviradulomyces as genus and as family = Family IGNORED

Resolved 2024-05-06:

Synced 2024-05-06

CatalogueOfLife / testing

Species Fungorum Plus (id 2073): test report #153