CoL of October 2023

[yroskov]

• [x] WoRMS of 2023-10-01 (check auths/eds in WoRMS Mollusca & Nemys); imported 2023-10-02; synced 2023-10-03

• [x] ITIS of 2023-09-26; imported 2023-10-02; synced 2023-10-02

• [ ] Scarabs - no update in Oct

• [x] 3i Auchenorrhyncha (check duplicates in synonymy with uninomials = FIXED); imported 2023-10-04; synced 2023-10-04

• [x] Entiminae; imported 2023-10-04; synced 2023-10-05

• [x] SF Isoptera; imported 2023-10-04, re-imported 2023-10-05; synced 2023-10-05

• [x] WCO (Opiliones); imported 2023-10-04; synced 2023-10-05

• [x] WOL (Odonata); imported 2023-10-04; synced 2023-10-05

• [x] GLI 1.1.23.269 / 2023-09-26; imported 2023-09-26; synced 2023-10-12

• [x] Gelechiidae 1.1.23.244 (01 Sep 2023) / 2023-09-01; imported 2023-09-01; synced 2023-10-13

• [x] Pterophoroidea 1.1.23.284 (11 Oct 2023) / 2023-01-05; imported 2323-10-11; synced 2023-10-13

• [x] World Plants ver 16.4 of 2023-09-20; imported 2023-09-22; synced 2023-09-22

• [x] World Ferns ver 16.4 of 2023-09-20; imported 2023-09-21; synced 2023-09-22

• [x] PaleoBioDB of 2022-03-01 / 2022-03-01; synced 2023-09-21

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

• Hepialidae (Lepidoptera) Oct/Nov

• WCVP ver 11.0 / 2023-04-20

• ScaleNet

• LPSN

• Species Files via TW (in Oct - Nov (Dec))

• FishBase - ?

• Paris/DBTNT - ?

• UCD

• Species Fungorum via API (should be confirmed by Paul)

• LDL Neuropterida

[yroskov]

Release for/before 2023-10-19 (request from @olafbanki of 2023-09-19)

[yroskov]

• [x] Subclass Ammonoidea and order Belemnitida from PaleoBioDB are listed as direct children of Animalia. In August version, they were listed under Mollusca/Cephalopoda: https://github.com/CatalogueOfLife/data/issues/565

All 3 PaleoBioDB sectors are broken now: missing subjects.

2023-09-21: all subjects in 3 sectors updated. Sectors synced. = FIXED in COL23.9, id 268877, 2023-09-22

[yroskov]

• [ ] Data of PaleoBioDB ver 2022-03-01 / 2022-03-01 in CLB are in absolute mess. It's not the version, which was used before in the CoL (Feb 2018 / 2018-02-16).

Plus, dagger symbols are missing with taxa of all ranks.

@mdoering, @gdower, do we have an option to re-store PaleoBioDB checklist of Feb 2018 / 2018-02-16 in the CoL?

[yroskov]

• [x] Empty superclass Aplacophora https://github.com/CatalogueOfLife/testing/issues/70#issuecomment-1730255125 block it? = Empty superclass Aplacophora is blocked 2023-09-22

= FIXED in COL23.9, id 268877, 2023-09-22

[mdoering]

• [ ] Data of PaleoBioDB ver 2022-03-01 / 2022-03-01 in CLB are in absolute mess. It's not the version, which was used before in the CoL (Feb 2018 / 2018-02-16).

Plus, dagger symbols are missing with taxa of all ranks.

@mdoering, @gdower, do we have an option to re-store PaleoBioDB checklist of Feb 2018 / 2018-02-16 in the CoL?

We do have the ACEF 2019 version of PBDB: https://github.com/CatalogueOfLife/data/raw/master/ACEF/174.tar.gz But I am not convinced we should use it. Its old and probably very patchy. But give it a try on dev if it matches your expectations.

PaleoBioDB is known to be a problematic source with an old, custom export script by GBIF that never was great as the source db is difficult to understand. It would be best to contact them for a proper export, maybe using the new IPT?

Another option would be to use the COL AC23 release as the sector(s) to sync from. This way you get all existing data. The source metadata would be entirely wrong, but you would just add a complete patch to it to be PBDB again.

[yroskov]

PREVIEW release started 2023-09-22, 10:06 pm (server time) Finished as COL23.9, id 268877, 2023-09-22 Deployed to the preview website 2023-09-25

Check: (1) Subclass Ammonoidea and order Belemnitida from PaleoBioDB = position in the classification FIXED; (2) classification in Mollusca = FIXED; (3) families Surianaceae & Pentaphragmataceae = present in correct position

[yroskov]

• [x] Check this report https://www.checklistbank.org/dataset/3/names?nameType=placeholder for incertae sedis names after WoRMS update (https://github.com/CatalogueOfLife/data/issues/567) = No changes

[dhobern]

Yes - small changes in Gelechiidae and Pterophoroidea. Also ongoing updates to GLI.

I hope Hepialidae will get approved this week too. (https://www.checklistbank.org/dataset/265709/about)

Thanks.

[yroskov]

PREVIEW release started 2023-10-04, 9:36 pm (server time) Finished as COL23.10, id 270788, 2023-10-04 Deployed to the preview website 2023-10-05

CHECKS

• [ ] incertae sedis names from WoRMS checklists have not been removed in the CoL-project after updates of 2-3 October: https://www.checklistbank.org/dataset/3/names?nameType=placeholder @mdoering, please advise on appropriate steps (for @gdower attention)

[yroskov]

PREVIEW release started 2023-10-06, 12:50 pm (server time) Finished as COL23.10, id 270972, 2023-10-06, 2:25 pm; id 270976, 6:37 pm
Deployed to the preview website 2023-10-06

• [x] Check total species numbers in Eumycetozoa.com after a block of incertae sedis names (2 orders, 3 families) https://www.checklistbank.org/catalogue/3/dataset/1053/workbench?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=incertae%20sedis). Eumycetozoa.com synced 2023-10-05

1296 - 1281 = 15 spp loss (Echinosteliopsis oligospora; Trichioides iridescens; etc)

Block removed. Decision "Ignore" applied to incertae sedis names (2 orders, 3 families). Synced 2023-10-06. id 270976: 15 spp are back

[yroskov]

PREVIEW release started 2023-10-13, 5:53 pm (server time) Finished as COL23.10, id 272442, 2023-10-13, 7:21 pm Deployed to the preview website 2023-10-13

[yroskov]

PREVIEW release started 2023-10-16, 3:05 pm (server time) Finished as COL23.10, id 272972, 2023-10-16, 4:34 pm Deployed to the preview website 2023-10-16

[yroskov]

For attention of @olafbanki, @mdoering: CoL of October (id 272972) is ready for deployment to the portal.

[olafbanki]

@mdoering CoL of October can be published online; blog post written. Thanks @yroskov and @gdower!

[mdoering]

done https://www.catalogueoflife.org/data/metadata