CoL of February 2024 - Githubissues

yroskov commented 10 months ago

[x] WoRMS of 2024-02-01; imported 2024-02-02; synced 2024-02-03
[ ] ITIS
[x] Scarabs of 2024-02-05; imported 2024-02-05; synced 2024-02-05
[x] 3i Auchenorrhyncha - Added suborders in Hemiptera; imported 2024-02-06; synced 2024-02-19
[x] Entiminae Feb 2024 / 2024-02-06; imported 2024-02-06; synced 2024-02-14
[x] SF Isoptera imported 2024-02-07; synced 2024-02-20
[x] SF Orthoptera Feb 2024 / 2024-02-07; imported 2024-02-06; synced 2024-02-14
[x] SF Dermaptera imported 2024-02-07; synced 2024-02-20
[x] SF Embioptera imported 2024-02-07; synced 2024-02-20
[x] SF Plecoptera imported 2024-02-07; synced 2024-02-20
[x] SF Psocodea imported 2024-02-07; synced 2024-02-20 (monthly starts from January 2024. I would suggest to do “manual” data export between 5th-10th day of each month)
[x] WCO (Opiliones) imported 2024-02-06; synced 2024-02-21
[x] WOL (Odonata) imported 2024-02-06; synced 2024-02-21
[x] GLI ~~1.1.24.028 / 2024-01-28~~, 1.1.24.040 / 2024-02-09; synced 2024-02-02, re-synced 2024-02-05, re-synced 2024-02-21
[x] Gelechiidae (Lepidoptera) ~~1.1.24.23 (23 Jan 2024) / 2024-01-23~~, 1.1.24.53 (22 Feb 2024) / 2024-02-22; synced 2024-02-02, re-synced 2024-02-22
[ ] Hepialidae (Lepidoptera) = no new import
[ ] Pterophoroidea (Lepidoptera) = no new import
[x] Sesiidae (Lepidoptera) 2024-02-02 / 2024-02-02; synced 2024-02-02, re-synced 2024-02-05
[ ] SF Permopsocida is not yet in CoL; I have submitted its adoption to the CoL Taxon Group. (see email of 2023-11-10, Heidi)
[x] Systema Dipterorum ver. 5 of Jan 2024 received 2024-01-08; imported 2024-02-07; synced 2024-02-12
[ ] RJB Geranium received 2024-01-17
[x] WWW ver 18 Jan 2024 / 2024-01-18; imported 2024-01-19 (see also attempt of January https://github.com/CatalogueOfLife/testing/issues/213#issuecomment-1900944688) attempt of February also failed (https://github.com/CatalogueOfLife/testing/issues/213#issuecomment-1932204793). Synced 2024-02-14, re-synced 2024-02-16
[x] World Plants ver. 18.4, 2024-01-31; received 2024-01-31; imported 2024-02-02; synced 2024-02-06
[x] World Ferns ver. 18.4, 2024-01-31; received 2024-01-31, replacement 2024-02-04; synced 2024-02-07
[x] LWS fleas ver. 2.0 / 2024-02-21; imported 2.0 / 2024-02-20; synced 2024-02-21 @camiplata, 2024-02-20: The Fleas update is ready https://www.checklistbank.org/dataset/54170, there are still some thing that I want to improve but can be left for next month. The current version reflect all major changes.

=============================

Conifers as a part of WFO - Nov?
ScaleNet
UCD in Nov?
WCVP ver 11.0 / 2023-04-20
LPSN
Rotifers
Species Files via TW (in Nov - Dec) - check with Heidi on a new SF Permopsocida (39 paleospp)
FishBase - ?
Paris/DBTNT - ?
Species Fungorum via API (should be confirmed by Paul)
LDL Neuropterida

=============================

Filling gaps:

Suborder Symphyta (Hymenoptera) https://github.com/CatalogueOfLife/data/issues/579 Class/order Diplura https://github.com/CatalogueOfLife/data/issues/577 Order †Permopsocida (Insecta) https://github.com/CatalogueOfLife/data/issues/578 Family Promecheilidae (Tenebrionoidea, Coleoptera) https://github.com/CatalogueOfLife/data/issues/580

yroskov commented 10 months ago

[ ] Add suborders in Hemiptera with DD. https://hoppers.speciesfile.org/otus/318/overview

3 new suborders Auchenorrhyncha, Heteroptera & Sternorrhyncha in addition to existing Coleorrhyncha.

dhobern commented 10 months ago

World Wide Wattle has been updated (as has the Global Lepidoptera Index)

yroskov commented 10 months ago

World Wide Wattle has been updated (as has the Global Lepidoptera Index)

I have tried to process WWW on 2024-01-19 (see https://github.com/CatalogueOfLife/testing/issues/213#issuecomment-1900944688 for identified issues). However, final sync failed (code 400)

OK, it's clear, "Source license OTHER... is not compatible with license CC_BY of project 3". License changed to CC-BY. = FIXED

Synced 2024-02-14.

dhobern commented 10 months ago

@yroskov - can you please offer an update on the shift to the pruned higher classification for vertebrates? This was shared a couple of months ago - is something holding up its adoption?

https://www.checklistbank.org/dataset/279229/classification?taxonKey=21

dhobern commented 10 months ago

The Gelechiidae dataset has been updated following the move of a genus from Gelechiidae to Depressariidae. GLI has also been updated to include the genus.

yroskov commented 10 months ago

@yroskov - can you please offer an update on the shift to the pruned higher classification for vertebrates? This was shared a couple of months ago - is something holding up its adoption?

https://www.checklistbank.org/dataset/279229/classification?taxonKey=21

@dhobern, there were no actions after I sent you this email:

-----Original Message----- From: Roskov, Yury Sent: Tuesday, November 28, 2023 15:32 To: 'Markus Döring'; Donald Hobern Cc: Camila Plata; Diana Hernandez; Olaf Banki Subject: RE: Chordate classification

Dear Donald,

I had a look through the dataset id279229 in CLB: https://www.checklistbank.org/dataset/279229/classification. (Could you please confirm that you were referring to this dataset in your email below? I picked up the link from Markus' email).

Here is my assessment of your classification vs Nicolas version implemented in the CoL: https://github.com/CatalogueOfLife/testing/issues/186#issuecomment-1828674947. As I can see, there are only few changes which need to be made in the CoL via CLB Tree editor. That is easy task*.

The main problem, your version (as well as Nicolas version) does not match classification used by ReptileDB: http://www.reptile-database.org/db-info/taxa.html#Sau. If we implement your version, we'll have the same (i.e. identical) names for reptile classes and orders in the CoL, or we will lose order as a rank in all reptile data (like now). Do you have any solution for this?

*) Changes might be made in December edition, if I'll get green light to do the work and have a clear order on what to do with orders.

Yours, Yury

dhobern commented 10 months ago

Sorry @yroskov - this is incorrect. The version of the COL Chordata list that was uploaded on 27 November has the four reptile orders at the same rank as ReptileDB:

https://www.checklistbank.org/dataset/279229/classification?taxonKey=21

This isssue was fixed, so I believe the new Chordata classification should be ready to use.

dhobern commented 10 months ago

Maybe you understood this already and were just concerned that we have no named classes for the reptile orders. For the time being, I think we should just do as shown - treat these orders as siblings for the other classes in the megaclass. We will have a conversation with ReptileDB about whether they expect to add classes.

yroskov commented 10 months ago

Complete CoL of Feb before 22-23 February

yroskov commented 10 months ago

[x] Duplicated family Progonocimicidae https://github.com/CatalogueOfLife/data/issues/617 = FIXED 2024-02-01

yroskov commented 10 months ago

PREVIEW release started 2024-02-01, 7:40 pm (server time) Fixed Progonocimicidae duplication = FIXED Finished as COL24.2, id 287018, 2024-02-01 Deployed to the preview website 2024-02-02

dhobern commented 10 months ago

Sesiidae have been updated with 10 more species

yroskov commented 10 months ago

[x] Changes in Vertebrata classification: https://github.com/CatalogueOfLife/testing/issues/186#issuecomment-1828674947 = COMPLETED

(1) Subphylum Vertebrata - infraphylum Gnathostomata - parvphylum Osteichthyes = EXCLUDE gigaclass Actinopterygii & create class Actinopterygii with FishBase orders as they are in CoL; EXCLUDE gigaclass Sarcopterygii = DONE 2024-02-05 (2) Subphylum Vertebrata - infraphylum Gnathostomata - parvphylum Osteichthyes - gigaclass Sarcopterygii - megaclass Tetrapoda = EXCLUDE superclass Amniota = DONE 2024-02-05 (3) Synonym "Reptilia" with 4 orders Rhynchocephalia, Squamata, Crocodylia & Testudines. Implemented 2024-02-05: these four orders established as new sectors from the resource id 279229, synced; ReptileDB children taxa re-established as sectors under orders of resource id 279229. = NEED TO BE CHECKED IN THE PREVIEW

AS A RESULT of implementing the classification from the resource id 279229 "COL Checklist Chordata Higher Classification, ver 1.0 / 2023-11-27", rank Class is missing now for all reptiles.

yroskov commented 10 months ago

[ ] Cleaning up outdated decisions in whole CoL, 4,711: https://www.checklistbank.org/catalogue/3/tasks

= Option "delete all" in World Plants ver. 18.4, Jan 2024 / 2024-01-31 (3195 names) = DOES NOT WORK. They should be deleted one-by-one - 1959 left - 1403 left - 801 left - 400 left - 0 = DELETED 2024-02-05

2024-02-07: 1,351 left; mainly in ReptileDB. The same subspecies is accepted name and synonym to its parent species

yroskov commented 10 months ago

PREVIEW release started 2024-02-05, 9:39 pm (server time) Changes in Vertebrata classification. Reptilia as a synonym. = CHECKED 2024-02-06 Finished as COL24.2, id 287332, 2024-02-05 Deployed to the preview website 2024-02-06