Towards 2023 Annual Checklist

[yroskov]

Delivery date: June 2023

@olafbanki, Ed, @dhobern, you are very welcome to add milestones & targets for 2023 Annual Checklist (i.e. "must-to-do" GSDs (both new & old), changes in the classification, etc.)

[yroskov]

TASKS 2023-05-01

[yroskov]

ACC-ACC sp, same auth, 16 duplicates

scientificName	Authorship	Status	GSD	Results
†Alekhosara reticulata (paleo)	Aristov, 2008	acc sp	SF Orthoptera
†Alekhosara reticulata (paleo)	Aristov, 2008	acc sp	SF Grylloblattodea
Clonia (Clonia) zernyi	Kaltenbach, 1971	acc sp	SF Orthoptera
Clonia (Clonia) zernyi	Kaltenbach, 1971	acc sp	SF Orthoptera	blocked
†Dermomurex kilikiensis	Landau, Harzhauser, İslamoğlu & Silva, 2013	acc sp	WoRMS Mollusca
†Dermomurex kilikiensis	Landau, Harzhauser, İslamoğlu & Silva, 2013	acc sp	WoRMS Mollusca
intermedia		acc sp	WoRMS Ostracoda Beyrichioidea > Beyrichiidae > Beyrichia
intermedia		acc sp	WoRMS Ostracoda Platycopida > Kloedenellidae > Kloedenella
koslowi		acc sp	WoRMS Turbellarians Planariidae > Polycelis > Polycelis
koslowi		acc sp	WoRMS Turbellarians Planariidae > Polycelis > Polycelidia
Lipsothrix jiri	Podenas, 2020	acc sp	Systema Dipterorum
Lipsothrix jiri	Podenas, 2020	acc sp	CCW
†Necrocarcinus rathbunae	Roberts, 1962	acc sp	WoRMS Brachyura	broken import
†Necrocarcinus rathbunae	Roberts, 1962	acc sp	WoRMS Brachyura	broken import
Ovipoculum album	Zhu L. Yang & R. Kirschner	acc sp	Species Fungorum Plus - Oomycota	old SF+; unfixable
Ovipoculum album	Zhu L. Yang & R. Kirschner	acc sp	Species Fungorum Plus - Basidiomycota	current SF+; unfixable
†Palaeomesorthopteron pullus	Aristov, Grauvogel-Stamm & Marchal-Papier, 2011	acc sp	SF Embioptera
†Palaeomesorthopteron pullus	Aristov, Grauvogel-Stamm & Marchal-Papier, 2011	acc sp	SF Grylloblattodea
†Paranecrocarcinus libanoticus	Förster, 1968	acc sp	WoRMS Brachyura	broken import
†Paranecrocarcinus libanoticus	Förster, 1968	acc sp	WoRMS Brachyura	broken import
†Propontocypris dromas	Aiello, Barra & Bonaduce, 2000	acc sp	WoRMS Ostracoda
†Propontocypris dromas	Aiello, Barra & Bonaduce, 2000	acc sp	WoRMS Ostracoda
†Protonecrocarcinus ovalis	(Stenzel, 1945)	acc sp	WoRMS Brachyura	broken import
†Protonecrocarcinus ovalis	(Stenzel, 1945)	acc sp	WoRMS Brachyura	broken import
†Pseudonecrocarcinus gamma	(Roberts, 1962)	acc sp	WoRMS Brachyura	broken import
†Pseudonecrocarcinus gamma	(Roberts, 1962)	acc sp	WoRMS Brachyura	broken import
†Pseudonecrocarcinus quadriscissus	(Noetling, 1881)	acc sp	WoRMS Brachyura	broken import
†Pseudonecrocarcinus quadriscissus	(Noetling, 1881)	acc sp	WoRMS Brachyura	broken import
Shirakiacris yunkweiensis	(Chang, 1937)	acc sp	SF Orthoptera
Shirakiacris yunkweiensis	(Chang, 1937)	acc sp	SF Orthoptera	blocked
Steinernema australe	Edgington, Buddie, Tymo, Hunt, Nguyen, France, Merino & Moore, 2009	acc sp	WoRMS Nematoda
Steinernema australe	Edgington, Buddie, Tymo, Hunt, Nguyen, France, Merino & Moore, 2009	acc sp	WoRMS Nematoda

[yroskov]

https://github.com/CatalogueOfLife/data/milestone/4

[yroskov]

• [x] Redundant, accepted higher taxa There are still 215 redundant families and above in the COL checklist (https://github.com/CatalogueOfLife/data/issues/463)

https://www.checklistbank.org/catalogue/3/duplicates?catalogueKey=3&category=uninomial&limit=100&minSize=2&mode=STRICT&offset=0&rank=family&rank=class&rank=order&rank=phylum&rank=suborder&rank=infraorder&rank=superfamily&rank=subfamily&rank=suprageneric%20name&rank=superorder&rank=subclass&rank=superclass&rank=subphylum&rankDifferent=false&status=accepted&withDecision=false

There is no CLB tool to resolve these issues! = Now we have it! (don't forget to sync GSDs, where decisions made).

• Number of remaining unresolved duplicates dropped to 98, 2023-05-12 (mainly, internal duplicates in Systema Dipterorum). CilCat Lagynidae (prov. acc.) vs WoRMS Foraminifera Lagynidae Schultze, 1854 = I am afraid to sync CilCat of ac19, because there is no gurantee that data will not be corrupted.

• Number of remaining unresolved duplicates increased to 152, 2023-06-06 after updates in WoRMS (majority of internal duplicates in Systema Dipterorum, WoRMS Ostracoda (!), Bryozoa (6), Trematoda (1), Turbellarians (1) (also need to sync MilliBase, Holothuroidea = synced all listed here WoRMS 2023-06-06)

• Number of remaining unresolved duplicates dropped to 98, 2023-06-06 after resolved internal duplicates in WoRMS

• Number of remaining unresolved duplicates dropped to 6 (3 pairs), 2023-06-12 after resolved duplicates in Systema Dipterorum 4.2.2.

[dhobern]

@yroskov - do you have any suggestion what such a tool would look like? From a quick scan, I can see that a few relate to different treatment in two datasets, but others (like the Systema Dipterorum ones) seem to be the result of trying to normalise denormalised datasets which may not have used their columns in exactly the way we expect. See the Ceratopogoninae example. It would be valuable to review these and communicate with the dataset holders or with whoever wrote the script to scrape them.

[yroskov]

do you have any suggestion what such a tool would look like?

Yes, I have. CoL@CLB needs two tools (both are similar to TASKS manager with minor improvements; TASKS reports on duplicates across GSDs should include GSD name and full classification (preferably with ranks)): (1) TASKS for the GSD vs whole CoL (i.e. all CoL sectors) (2) TASKS for the project (i.e. reports on duplicates for whole CoL). A mock-up of this tool is already available inside the project menu, but it is not functional - decisions are not applicable, export CSV file does not have indication of source GSD.

[yroskov]

others (like the Systema Dipterorum ones) seem to be the result of trying to normalise denormalised datasets which may not have used their columns in exactly the way we expect. See the Ceratopogoninae example. It would be valuable to review these and communicate with the dataset holders or with whoever wrote the script to scrape

I can see the only way for Systema Dipterorum, it needs better software for data management and an international team of proactive editors, who may take curatorial responsibilities over data. Plus, it would be nice to keep taxonomically unresolved data outside taxonomic checklist released to public.

@gdower, would you please introduce @dhobern to Systema Dipterorum export file and our interactions with SD? (We discussed our vision for SD best opportunities many times and have a consensus).

And general comment: attempts to fix problems with "internal data integrity" on CoL side cannot be much successful if we do regular updates. The problems need to be cleaned up on GSD side.

[yroskov]

GSD updates in June:

• [x] WoRMS of 2023-06-01; imported 2023-06-02 (see progress https://github.com/CatalogueOfLife/testing/issues/227)

• [x] ITIS of 2023-05-25 imported 2023-06-01; synced 2023-06-05

• [x] Scarabs of 2023-05-30; imported 2023-05-30; synced 2023-05-31

DH, 2023-05-18 >I've updated Global Lepidoptera Index and Pterophoroidea this month

• [x] GLI 0.32.3 / 2023-05-10; imported 2023-05-10; synced 2023-05-19

• [x] Pterophoroidea 1.1.23.136 (16 May 2023); imported 2023-05-16; synced 2023-05-18; re-synced 2023-05-19; re-synced 2023-05-31; re-synced 2023-06-02

• [x] Gelechiidae 1.1.23.140 (20 May 2023); imported 2023-05-20; synced 2023-05-22; re-synced 2023-06-02

DH, 2023-05-18 > The Sesiidae dataset is now public and approved for use to replace the corresponding part of the Global Lepidoptera Index dataset

• [x] Sesiidae (new) of 2023-03-16; imported 2023-05-17; synced 2023-05-18; re-synced 2023-05-19

Re-synced: 2023-05-19 - Tortricid.net, ver. 4.0 of 2018-12-31

Adriano, 2023-05-24 > In May we made lots of important and numerous changes in our database. ...it would be best if you could produce another version soon enough.

• [x] Opiliones of 2023-05-31; imported 2023-05-31; synced 2023-05-31

• [x] Tortricid.net; imported 2023-05-24; synced 2023-05-31

• [x] Systema Dipterorum ver. 4.2.2, May 2023; imported 2023-05-30; synced 2023-06-12 === No sync before AC23 release!!!: https://github.com/CatalogueOfLife/testing/issues/127#issuecomment-1593467055

• [x] LWS fleas of 2023-06-22; imported 2023-06-22; synced 2023-06-22; re-synced 2023-06-23

[yroskov]

• [x] family Xenoturbellidae is in phylum Not Assigned = FIXED 2023-05-23 https://github.com/CatalogueOfLife/testing/issues/45#issuecomment-1559391135

[yroskov]

• [x] Old abstract in World Ferns. It's a new one in CLB = re-synced 2023-05-31 = Need to be checked in the PREVIEW = OK, correct abstract
• [x] Sector Caryophyllales of World Plants re-synced 2023-05-31 = In the PREVIEW: Bosea yervamora - missing authorstring = decision corrected, re-synced 2023-05-31

[yroskov]

Release Alias Template changed as COL{date,yy} (see https://github.com/CatalogueOfLife/testing/issues/201#issuecomment-1209435378)

PREVIEW release started 2023-05-31, 3:17 pm (server time) Finished as COL23, 2023-05-31, id 9895, 4:40 pm Deployed to the preview website 2023-05-31.

CHECKS:

• [x] There is no "Annual Checklist" in the title:

Release Version Template CHANGED as Annual Checklist 2023

• [x] Tortricid.net: extant spp number dropped from 11327 to 11266 (-61), why? = re-synced 2023-05-05-31 (updated(?) copy with the same version in metadata) = PREVIEW_20230-05-31_2nd: 11306 spp.

[yroskov]

PREVIEW release started 2023-05-31, 5:51 pm (server time) Finished as COL23, Catalogue of Life Checklist, Annual Checklist 2023, id 9896, 7:15 pm Deployed to the preview website 2023-05-31.

[yroskov]

• [ ] 28 sectors are broken 2023-06-01 https://github.com/CatalogueOfLife/data/issues/535#issuecomment-1572513294

• [x] Alucitoidea superfamily: Alucitoidea order: Lepidoptera = REMATCHED 2023-06-01 (done via rematch button)

• [x] Brassicaceae family: Brassicaceae order: Brassicales = REMATCHED 2023-06-01 (done via rematch button) = Shown as broken again 2023-06-02

• [x] Bryonames order: Incertae sedis subkingdom: Bryobiotina = REMATCHED 2023-06-01 (done via rematch button) = Shown as broken again 2023-06-02

• [x] Gelechiidae family: Gelechiidae Gelechioidea = REMATCHED 2023-06-01 (done via rematch button); 2023-06-05 (done via rematch button)

• [ ] IRMNG class: Bolidophyceae phylum: Ochrophyta

• [ ] IRMNG class: Chrysomerophyceae phylum: Ochrophyta

• [ ] IRMNG class: Chrysophyceae phylum: Ochrophyta

• [ ] IRMNG class: Dictyochophyceae phylum: Ochrophyta

• [ ] IRMNG class: Eustigmatophyceae phylum: Ochrophyta

• [ ] IRMNG class: Phaeophyceae phylum: Ochrophyta

• [ ] IRMNG class: Phaeothamniophyceae phylum: Ochrophyta

• [ ] IRMNG class: Picophagophyceae phylum: Ochrophyta

• [ ] IRMNG class: Pinguiophyceae phylum: Ochrophyta

• [ ] IRMNG class: Raphidophyceae phylum: Ochrophyta

• [ ] IRMNG class: Schizocladiophyceae phylum: Ochrophyta

• [ ] IRMNG class: Xanthophyceae phylum: Ochrophyta

• [ ] IRMNG order: Againococcidiida phylum: Miozoa

• [x] Nepticuloidea superfamily: Nepticuloidea order: Lepidoptera = REMATCHED 2023-06-01 (done via rematch button); 2023-06-05 (done via rematch button)

• [ ] PaleoBioDB class: Trilobita phylum: Arthropoda

• [ ] PaleoBioDB order: Ammonoidea class: Cephalopoda

• [ ] PaleoBioDB order: Belemnitida class: Cephalopoda

• [ ] Species Fungorum Plus phylum: Bigyra kingdom: Chromista

• [ ] Species Fungorum Plus phylum: Cercozoa kingdom: Chromista

• [ ] Species Fungorum Plus phylum: Oomycota kingdom: Chromista

• [x] Trichomycetes class: Ichthyosporea phylum: Choanozoa = REMATCHED 2023-06-01 (done via rematch button) = Shown as broken again 2023-06-02

• [x] Trichomycetes genus: Amoebosporus phylum: Choanozoa = REMATCHED 2023-06-01 (done via rematch button) = Shown as broken again 2023-06-02

• [x] WoRMS brachyura section: Eubrachyura infraorder: Brachyura = FIXED as a single sector by somebody 2023-06-02

• [x] WoRMS brachyura section: Podotremata infraorder: Brachyura = FIXED as a single sector by somebody 2023-06-02

IRMNG = CoL uses version Mar 2018 / 2018-03-20, but not a version 2023-05-19 / 2023-05-19 as it is in CLB now PaleoBioDB = CoL uses version Feb 2018 / 2018-02-16, but not a version 2022-03-01 / 2022-03-01 as it is in CLB now Species Fungorum Plus = CoL uses version Jan 2023 / 2023-01-17, where taxa Bigyra, Cercozoa & Oomycota are not present (they were preserved from version Feb 2020 / 2020-02-14)

[yroskov]

• [x] 2023-06-02, there are 23 broken sectors in WoRMS today (https://www.checklistbank.org/catalogue/3/sector?broken=true&limit=100&offset=0).

@gdower, taken in account what @mdoering says about sectors management in CLB here , how WoRMS pipelines dealing with broken sectors?

Did we have so many broken sectors in the imports of previous months? (My recollection, no).

2023-06-06, there are 2 broken sectors in WoRMS today: WoRMS Tantulocarida & WoRMS Brachypoda (https://github.com/CatalogueOfLife/testing/issues/227#issuecomment-1577372794)

= FIXED 2023-06-06 (WoRMS Tantulocarida synced 2023-06-06)

[yroskov]

• [x] Final review of TASKS in top 30 WoRMS checklists: https://github.com/CatalogueOfLife/testing/issues/227#issuecomment-1538676753 = FIXED

A new problem (2023-06-05): incorrect behaviour of decision maker buttons in ACC-ACC species (https://github.com/CatalogueOfLife/checklistbank/issues/1243).

[yroskov]

• [x] Empty creator, editor, contributor fields in WoRMS metadata https://github.com/CatalogueOfLife/testing/issues/227#issuecomment-1574363577

[yroskov]

PREVIEW release started 2023-06-07, 5:26 pm (server time) Finished as COL23, Catalogue of Life Checklist, Annual Checklist 2023, id 9898 Deployed to the preview website 2023-06-08

CHECKS

• [x] WoRMS Rhombozoa: 1 extant spp vs 122 in May = FIXED 2023-06-08

Problem with sectors:

Sectors report:

[yroskov]

PREVIEW release started 2023-06-08, 7:11 pm (server time) Finished as COL23, Catalogue of Life Checklist, Annual Checklist 2023, id 9899 Deployed to the preview website 2023-06-08

[yroskov]

• [x] search for possible overlaps in the classification in whole CoL:

• accepted species with identical authorstrings, 0: https://www.checklistbank.org/catalogue/3/duplicates?authorshipDifferent=false&catalogueKey=3&category=binomial&limit=500&rankDifferent=false&status=accepted

• accepted species with different authorstrings, 281: https://www.checklistbank.org/catalogue/3/duplicates?authorshipDifferent=true&catalogueKey=3&category=binomial&limit=500&rankDifferent=false&status=accepted.

• [x] There is a set of internal duplicates in WoRMS Foraminifera = FIXED https://github.com/CatalogueOfLife/testing/issues/61#issuecomment-1584715819, WoRMS Ostracoda = FIXED https://github.com/CatalogueOfLife/testing/issues/103#issuecomment-1584851125

[yroskov]

PREVIEW release started 2023-06-12, 8:26 pm (server time) Finished as COL23, Catalogue of Life Checklist, Annual Checklist 2023, id 9900, 9:51 pm

[yroskov]

• [x] Species entry Status unresolved in Brassicaceae = FIXED 2023-06-12 (deleted in CoL-Draft assembly) https://www.catalogueoflife.org/data/search?facet=rank&facet=issue&facet=status&facet=nomStatus&facet=nameType&facet=field&facet=authorship&facet=extinct&facet=environment&limit=50&offset=0&q=Status%20unresolved&sortBy=taxonomic

See also https://github.com/CatalogueOfLife/data/issues/527

[yroskov]

PREVIEW release started 2023-06-12, 10:54 pm (server time) Finished as COL23, Catalogue of Life Checklist, Annual Checklist 2023, id 9901, 2023-06-13 12:13 am Deployed to the preview website 2023-06-13

[yroskov]

• [x] Species Fungorum Plus, ver Jan 2023 / 2023-01-17 (imported 2023-01-19) re-synced 2023-06-13.
• [x] Sector Ranunculales of World Plants re-synced 2023-06-13.

[yroskov]

• [x] Replacement of Mites GSD Ologamasidae & Mites GSD Rhodacaridae with ITIS families Ologamasidae & Rhodacaridae = completed 2023-06-13, two new sectors synced

https://github.com/CatalogueOfLife/testing/issues/8#issuecomment-1587804117

[yroskov]

PREVIEW release started 2023-06-13, 8:16 pm (server time) Finished as COL23, Catalogue of Life Checklist, Annual Checklist 2023, id 9902, 2023-06-13 9.36 pm Deployed to the preview website 2023-06-13

[yroskov]

PREVIEW release started 2023-06-14, 7:36 pm (server time) Finished as COL23, Catalogue of Life Checklist, Annual Checklist 2023, id 9903, 2023-06-14 8:56 pm Deployed to the preview website 2023-06-14

[yroskov]

PREVIEW release started 2023-06-15, 2:47 pm (server time) Finished as COL23, Catalogue of Life Checklist, Annual Checklist 2023, id 9904, 2023-06-15 4:07 pm Deployed to the preview website 2023-06-15

[yroskov]

• [x] Requested update of 3i Auchenorrhyncha abstract. Completed 2023-06-17

PREVIEW release started 2023-06-17, 11:03 pm (server time) Finished as COL23, Catalogue of Life Checklist, Annual Checklist 2023, id 9905, 2023-06-18 Deployed to the preview website 2023-06-22

[yroskov]

@olafbanki, do you have a final decision on replacement of Siphonaptera and continuation with all SFs checklists in AC23? Have you updated AC23 metadata as you wish?

We have two days on this week to finalize remaining issues.

If all are fine from your point of view, the checklist with id 9905 of June 18th at https://www.checklistbank.org/dataset/9905 is ready as 2023 Annual Checklist.

[yroskov]

@olafbanki, 2023-06-22:

On SF, it is clear that at least for now SF Cockroach cannot be used by COL because of a license that is not supported. It needs to be removed from the COL Checklist, but can live in ChecklistBank for now.

• [x] SF Cockroach removed (i.e. sectors deleted) 2023-06-22 https://github.com/CatalogueOfLife/testing/issues/161#issuecomment-1603050638

PREVIEW release started 2023-06-22, 5:20 pm (server time) Finished as COL23, Catalogue of Life Checklist, Annual Checklist 2023, id 9905, 2023-06-22, 6:41 pm

[yroskov]

@olafbanki, 2023-06-22:

I am still waiting for Matt's guidance on SF Coreoidea and SF Mantodea. Phoronida, Emig, might request a license that is more restrictive than what seems to be common scientific practice. Discussion is still ongoing, but possibly it has to be removed. For next months we might consider a replacement from WoRMS.

It looks like we are heading to publication of AC 2023 on either next Tuesday or Wednesday. [2023-06-27 -28]

[yroskov]

• [x] LWS fleas: Lewis Flea (Siphonaptera) World Species List replaced Parhost World Database of Fleas 2023-06-22

PREVIEW release started 2023-06-22, 7:38 pm (server time) Finished as COL23, Catalogue of Life Checklist, Annual Checklist 2023, id 9907, 2023-06-22, 8:58 pm Deployed to the preview website 2023-06-23

[yroskov]

PREVIEW release started 2023-06-23, 5:49 pm (server time) Finished as COL23, Catalogue of Life Checklist, Annual Checklist 2023, id 9908, 2023-06-23

[yroskov]

PREVIEW release started 2023-06-26, 9:45 pm (server time) = 23.45 Leiden Finished as COL23, Catalogue of Life Checklist, Annual Checklist 2023, id 9909, 2023-06-26, 11:04 pm Deployed to the preview website 2023-06-27

[yroskov]

• [x] 2023-06-27, full title of id 54170 is changed back as Robert E. Lewis World Species Flea (Siphonaptera) List
• [x] @olafbanki, 2023-06-27: I have finalised the changes to the licenses and the metadata. Please run another and final release of the Annual COL Checklist 2023.

PREVIEW release started 2023-06-27, 8:38 pm (server time) = 22.38 Leiden

[olafbanki]

Licenses changed to CC-BY from the following GSDs:

Cilcat https://www.checklistbank.org/dataset/1113/about, Fada Rotifera https://www.checklistbank.org/dataset/1047/about, Globis https://www.checklistbank.org/dataset/1046/about, Mites GSD Phytoseiidae https://www.checklistbank.org/dataset/1070/about Mites GSD Tenuipalpidae https://www.checklistbank.org/dataset/1078/about PBI Plant Bug https://www.checklistbank.org/dataset/1171/about Phoronida https://www.checklistbank.org/dataset/1104/about Taxapad https://www.checklistbank.org/dataset/1068/about Tineidae https://www.checklistbank.org/dataset/1031/about Zoological-Botanical Database (Vespoidea) https://www.checklistbank.org/dataset/1037/about

Licenses changed in the UI of CLB, and metadata locked

[olafbanki]

CC-BY license added to the COL Checklist

[olafbanki]

Metadata of creators of the COL Checklist changed to also include: Diana Hernández, Camila Plata, Thomas Jeppesen, and Ari Örn; Dave Remsen removed.

COL Checklist 2023 dedicated to the memory of David Remsen

[yroskov]

PREVIEW release started 2023-06-27, 8:38 pm (server time) = 22.38 Leiden Finished as COL23, Catalogue of Life Checklist, Annual Checklist 2023, id 9910, 2023-06-27, 9:58 pm Deployed to the preview website 2023-06-27

@olafbanki, I have checked results of this release at https://preview.catalogueoflife.org. The checklist content is fine and consistent with few previous drafts. Adjustments to AC23 metadata are in place. AC23 is ready to be published on the portal.

[olafbanki]

@yroskov I have made an accompanying blog post and that also looks good in preview. I will now proceed with the publication of AC 2023.

[olafbanki]

The AC2023 is published.