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CoL of November 2023 #239

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16 of 17 tasks
yroskov opened this issue Oct 18, 2023 · 21 comments
Closed
16 of 17 tasks

CoL of November 2023 #239

yroskov opened this issue Oct 18, 2023 · 21 comments

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@yroskov
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yroskov commented Oct 18, 2023 •
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  • WoRMS of 2023-11-01 (check auths/eds in WoRMS Mollusca & Nemys); all syncs of 2023-11-03 failed (Syncs failing with BindingException backend#1269); synced 2023-11-07

  • ITIS of 2023-10-31 (incl. a new global checklist for the mite superfamily Anystoidea); imported 2023-11-02; synced 2023-11-03 - CHECK ITIS SYNC! = all 122 failed; synced 2023-11-07

  • Scarabs of 2023-11-06; imported 2023-11-06; synced 2023-11-07

  • 3i Auchenorrhyncha of Nov 2023; imported 2023-11-08; synced 2023-11-10

  • Entiminae of Nov 2023; imported 2023-11-09; synced 2023-11-09

  • SF Isoptera of 2023-11-08; imported 2023-11-09; synced 2023-11-09

  • WCO (Opiliones) of 2023-11-08; imported 2023-11-09; synced 2023-11-09

  • WOL (Odonata) of 2023-11-08; imported 2023-11-09; synced 2023-11-10

  • GLI synced 2023-11-07, re-synced 2023-11-13

  • Gelechiidae ver 1.1.23.315 (11 Nov 2023) / 2023-11-11; imported 2023-11-11; synced 2023-11-13

  • Pterophoroidea = There is no update since CoL of Oct 2023. No need to re-sync.

  • Hepialidae (Lepidoptera), new; ver 1.0 of ?; imported 2023-10-01; synced 2023-10-27

  • PaleoBioDB replaced with previous version of Feb 2018 / 2018-02-16 (id 268676); synced 2023-11-06 = Need to be re-imported when 'extinct' flag appear in Options for import. This will resolve issue of non-extinct genera in PaleoBioDB sectors.

  • World Plants ver 18.1 of 2023-11-08; imported 2023-11-15; synced 2023-11-15

  • World Ferns ver 18.1 of 2023-11-08; imported 2023-11-14; synced 2023-11-15

  • WCVP-Fabaceae ver. 2023v.4 / 2023-08-02; synced 2023-11-13

  • SF Orthoptera ver. 0.35.2 / 2023-11-09; imported 2023-11-14; synced 2023-11-15

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

  • Conifers as a part of WFO - Nov?

  • UCD in Nov?

  • WCVP ver 11.0 / 2023-04-20

  • ScaleNet

  • LPSN

  • 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) CatalogueOfLife/data#579
Class/order Diplura CatalogueOfLife/data#577
Order †Permopsocida (Insecta) CatalogueOfLife/data#578
Family Promecheilidae (Tenebrionoidea, Coleoptera) CatalogueOfLife/data#580
@dhobern
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dhobern commented Oct 19, 2023

The COL TG has approved the replacement of the family Hepialidae (Lepidoptera) with this new dataset:

https://www.checklistbank.org/dataset/265709/about

@yroskov
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yroskov commented Oct 20, 2023 •
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@yroskov
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yroskov commented Oct 25, 2023 •
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  • PaleoBioDB update of Oct: missing "extinct" flag with 4615 spp (data absent in CLB source). Consider reverting to a previous cleaned version.

See also CatalogueOfLife/data#581

Replaced with previous version of Feb 2018 / 2018-02-16 (id 268676)

@sergbolshakov
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sergbolshakov commented Oct 26, 2023 •
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Hello!
In the latest version for names from Bryonames in the status of synonyms there are no links.
But online in the link field there are links to the name page in Tropicos.
E. g. https://www.checklistbank.org/dataset/272972/name/4a2f4d14-e255-4c55-a8a4-b5df5608bf6c vs grep Takakiophyta NameUsage.tsv
Is this a bug or a feature?

@yroskov
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yroskov commented Oct 30, 2023 •
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The list of GSDs awaiting re-sync: CatalogueOfLife/backend#1277

key modified count alias date of re-sync
2317 2023-10-04 68033 3i Auchenorrhyncha 2023-11-10
55434 2023-10-12 1341 GLI 2023-11-07
2144 2023-10-02 315280 ITIS 2023-11-03 2023-11-07
XXXX 2023-10-03 4260 all WoRMS 2023-11-07
1141 2023-09-28 8708 World Plants 2023-11-07
1021 2023-05-12 70 SF Orthoptera 2023-11-07
1101 2023-06-14 48 Systema Dipterorum 2023-11-07

@yroskov
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yroskov commented Nov 1, 2023 •
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Donald, 2023-10-29: ... I needed to confirm to you that the Taxonomy Group supports the two decisions here:
https://docs.google.com/document/d/1YLcC7dHrMA40UKViZ5ww39Yc99IcgGCo/edit?usp=sharing&ouid=113140186902620905250&rtpof=true&sd=true
https://docs.google.com/document/d/1HUkQxthfXSb6Sr8BNv2837T7bUGas95-3XE73GS_X-w/edit
Please do anything else that needs to happen to replace these sections in COL.

  • Hepialidae (ghost moths)
  • WFO conifers = Not in November; see email from Olaf, 2023-11-07:
    -Before the conifer database from WFO can be included into the COL Checklist, several issues need to be resolved.
    -However, we have no current model to allocate the proper metadata to the conifer database. A thought could be to assign metadata to a sector. It needs to be worked out more what the implications would be, and what needs to be implemented.
    -Given that discussion and implementation may take some time, it is probably best if we find a pragmatic solution for now so that the inclusion of the conifer database from WFO into the COL Checklist does not have to wait too long.

@gdower
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gdower commented Nov 3, 2023

@sergbolshakov, that's likely an exporter bug. Please open a ticket here.

@yroskov
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yroskov commented Nov 7, 2023 •
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PREVIEW release started 2023-11-07, 11:06 pm (server time)
Finished as COL23.11, id 276829, 2023-11-07
Deployed to the preview website 2023-10-08

@yroskov
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yroskov commented Nov 8, 2023 •
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@yroskov
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yroskov commented Nov 10, 2023 •
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PREVIEW release started 2023-11-10, 10:08 pm (server time)
Finished as COL23.11, id 276888, 2023-11-10
Deployed to the preview website 2023-11-13

  • All GSDs with "unstable UUID identifiers" have been re-synced in this preview release. Does it resolve the issue?
    checked names:

Panthera leo (Linnaeus, 1758) https://preview.catalogueoflife.org/data/taxon/C7FRR
No match with https://www.catalogueoflife.org/data/taxon/4CGXP (CatalogueOfLife/backend#1277)

Apis mellifera Linnaeus, 1758 https://preview.catalogueoflife.org/data/taxon/BXX37
No match with https://www.catalogueoflife.org/data/taxon/FN46 (CatalogueOfLife/backend#1277)

Not sure that issue with incorrect UUIDs is resolved now.

@yroskov
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yroskov commented Nov 13, 2023 •
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@yroskov
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yroskov commented Nov 13, 2023 •
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  • Missing Nomenclatural Code setting. Undefined codes data#583
    Gymnodinium, Microsporidia and WCVP-Fabaceae, Tortricid.net re-synced 2023-11-13

Are there any other GSDs with missing Codes?

Does this report http://api.checklistbank.org/dataset/3/nameusage/search?nomCode=_NULL&facet=rank&facet=SECTOR_DATASET_KEY have an answer to the question, which GSDs in CoL still have no Code assignment?

How to assign Code to the nodes in the management classification (there are no sectors there)?

@yroskov
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yroskov commented Nov 13, 2023 •
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PREVIEW release started 2023-11-13, 9:27 pm (server time)
Finished as COL23.11, id 277214, 2023-11-13
Deployed to the preview website 2023-11-16

  • No GSD logos (list of Souce Datasets, GSD page, Species page)
  • WCO (Opiliones) & other TW exports: check authorstrings with extinct taxa ("1") = FIXED

@yroskov
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yroskov commented Nov 16, 2023 •
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PREVIEW release started 2023-11-16, 1:50 pm (server time)
Finished as COL23.11, id 277685, 2023-11-16, 3:34 pm
Deployed to the preview website 2023-11-16

  • "supersp" = species aggregate in SF Orthoptera were blocked; check for children spp = CORRECTLY FIXED
  • Missing home URL for SF Orthoptera. Also, added SF Isoptera URL
  • UUIDs: different in this release

Panthera leo (Linnaeus, 1758)
https://www.catalogueoflife.org/data/taxon/4CGXP
(History: First issued in release COL20.12. Last used in release COL23.9)
PREVIEW 2023-11-10:
https://preview.catalogueoflife.org/data/taxon/C7FRR
PREVIEW 2023-11-16:
https://preview.catalogueoflife.org/data/taxon/C7M6H

Apis mellifera Linnaeus, 1758
https://www.catalogueoflife.org/data/taxon/FN46
(History: First issued in release COL20.12. Last used in release COL23.9)
PREVIEW 2023-11-10:
https://preview.catalogueoflife.org/data/taxon/BXX37
PREVIEW 2023-11-16:
https://preview.catalogueoflife.org/data/taxon/BXZ4J

@yroskov
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yroskov commented Nov 16, 2023 •
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PREVIEW release started 2023-11-16, 1:50 pm (server time)
Finished as COL23.11, id 277686, 2023-11-16, 3:34 pm
Deployed to the preview website 2023-11-16

@yroskov
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yroskov commented Nov 16, 2023

@olafbanki, @mdoering, CoL of November (id 277686) is completed now and ready for deployment to the portal

@mdoering
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The IDs are wrong, so this cannot go live

@yroskov
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yroskov commented Nov 17, 2023

Hopefully the release will only be needed after you fix the problem. Please follow your schedule, and finally do a release & deployment. (Also please do all re-syncs if & where they will be needed).

@mdoering
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As far as I can see we should only need to do another release. That means you gotta stop working towards the December release in the project. If we are lucky I have found a way to bypass the problem already.

@mdoering
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mdoering commented Nov 24, 2023 •
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It took a while, but I fixed various smaller bugs related to name matches, updated the matched content of previous releases and . The preview release from today looks good to me to go now: https://www.checklistbank.org/dataset/3:188/

There are only 91 names left in this release with temporary identifiers - all of which are expected as they are not proper names found in the names index:

                  id                  |    rank    |              scientific_name               |              authorship              
--------------------------------------+------------+--------------------------------------------+--------------------------------------
 5V8By6INFvNu8_0b6z1Wj2               | TRIBE      | *TPorricondylinae                          | 
 KbK6J-xP-OuB4tqupz_Rn0               | SPECIES    | [Dexia] parvicornis                        | Wulp, 1867
 NCrEer0DO2v59hdy0tEEv2               | GENUS      | [Nepalia]                                  | 
 NSBBIFVNQcfe4CG17VksY0               | SPECIES    | [Dexia] suavis                             | Wulp, 1867
 TO75R9RJKuv27ONhm71Cm1               | SPECIES    | [non-Uristidae] albinus                    | (K.H. Barnard, 1932)
 TS4pLEaQLFtY8hoT-RFyY2               | SPECIES    | [Degeeria] albomarginata                   | Wulp, 1890
 Wxt6H0mL3mc14OThEma8S2               | SPECIES    | [Dexia] triquetra                          | Macquart, 1844
 _991TVUzYENX5067eJeMK                | GENUS      | [Drapetis]                                 | 
 aHB53udeRkexA8GttL1Rk0               | TRIBE      | *TLestremiinae                             | 
 aVCwmB9u-7st3d99ioZMG                | SPECIES    | “Montereina” purcina                       | (Ev. Marcus & Er. Marcus, 1967)
 c2y7Z7G2XnvU40IsR8pZO1               | GENUS      | [Cylindromyia]                             | 
 eDWzqBexTRNJ-hF5tWBho0               | SPECIES    | “Montereina” mortenseni                    | (Ev. Marcus & Er. Marcus, 1963)
 mQ6NFkWDxiAs7CKrZkmaQ2               | TRIBE      | *TTachininae                               | 
 oaWKt1qQ5c9Y5pk8UjWPT0               | GENUS      | [Dexiosoma]                                | 
 vHTK1vefBjv9Dxuws3R062               | TRIBE      | *FSteganinae                               | 
 9702b1a2-c387-420a-8599-7068de247eb7 | SPECIES    | × jezoensoides                             | 
 AwinGc_VmDPG-GC28f56O2               | SPECIES    | [Dexia] genuina                            | Wulp, 1867
 GlcctmdWZXdz5WGpSrpG70               | SPECIES    | [Degeeria] longipes                        | Wulp, 1890
 O3FEgXNx7ytE0OGFg5G2-0               | SPECIES    | “Montereina” branneri                      | (MacFarland, 1909)
 RAXSo2G9eK7F2OZQFTbk_                | SPECIES    | [Degeeria] cruralis                        | Giglio-Tos, 1893
 UIX5gtQL1eNBAdgjyCEnR                | SUBTRIBE   | *FTephritini                               | 
 _p_P1A4kkyNkA4a5GIPP3                | SPECIES    | [Drapetis] marginata                       | Meigen, 1838
 _r45Wpma9OsT3p9xGzUY50               | SPECIES    | [Ctenophorocera] polleniina                | Bezzi, 1908
 jv7jifn3RWdW6h_BqZsRs0               | SPECIES    | [Dexia] convexa                            | Walker, 1849
 udlVyL_A3ftq9GW8CfXku2               | SPECIES    | “Montereina” flindersi                     | (Burn, 1962)
 2UfB6IIWU_7fB8Afskckq2               | SPECIES    | [Degeeria] mexicana                        | Giglio-Tos, 1893
 2b74879d-a3a1-4977-abda-20cdd0ca235d | SPECIES    | [GENUS NOT SPECIFIED] duchaillui           | Rehn, 1960
 3IgDbhvIyHABBdx7P8rmp0               | TRIBE      | *TLomatiinae                               | 
 AAAVGG0GqKv32Ses62x1d                | SPECIES    | CHironomus flaviventris                    | Johannsen, 1907
 JspKrX83T4td8OtxuqA2x1               | SPECIES    | [Dexia] triangularis                       | Wulp, 1867
 N3_v1har24OG6hM340f_7                | GENUS      | [Dexia]                                    | 
 NAOtE-EVuBPw-ps5A-koj0               | SPECIES    | “Montereina” lippa                         | (Á. Valdés, 2001)
 ToVhTo0okFcq3xFgsQCyr1               | SPECIES    | [non-Uristidae] dawsoni                    | Hurley, 1963
 TwXnah5pUCuAE_KgQtPKd                | SPECIES    | “Montereina” aurila                        | (Marcus & Marcus, 1967)
 U1k-k5vKFTPT-SDRqdVZl1               | GENUS      | [non-Uristidae]                            | 
 XN5rz8dAMeQz7pSOTE8nU2               | SPECIES    | [Nepalia] filipes                          | Kieffer, 1911
 oNw6xnICbMt13O-U8zHg_1               | SPECIES    | [non-Uristidae] georgianus                 | (Schellenberg, 1931)
 p9QltgYJq3eR4dofyB_Fq1               | SPECIES    | “Montereina” coerulescens                  | (Bergh, 1888)
 3db5f536-9a79-42c5-a77c-584439ad023d | SPECIES    | × columbiana                               | 
 FLfM6MMqhac470HcPnIMy                | TRIBE      | *FTephritinae                              | 
 IpzF50saHScGA0pBK5lZX0               | TRIBE      | *FDrosophilinae                            | 
 PIa_2SG_EzA1AtCWpbtE1                | SPECIES    | [Dexia] effulgens                          | Wood, 1874
 PIu996n8jN8J1_PwKoDCb                | SPECIES    | [Dexia] brunnicornis                       | Macquart, 1844
 SVLUyRp2UyA86CSHpHkEu                | SPECIES    | [non-Uristidae] natalensis                 | K.H. Barnard, 1916
 c14_chhPCttDCWwt1dCBj1               | SPECIES    | “Montereina” aurea                         | (Eliot, 1903)
 cnu-OEvOR2s69pywlVy6X                | SPECIES    | [Degeeria] leucocyla                       | Wulp, 1890
 e8dd62ff-85ed-4215-a4be-18a105027d1a | SPECIES    | Psyllaphorura unnamed                      | Shveenkova, YB & Babenko, AB, 2021
 hzzTuWIAJh809h5Qjg3-M                | SPECIES    | [Dexia] cremides                           | Walker, 1849
 l4GcO0R_s-dV-4lfWTYe1                | SPECIES    | [Degeeria] insecta                         | Giglio-Tos, 1893
 mjaijsHZ02tk9KqonG29k0               | TRIBE      | *FEristalinae                              | 
 n91g9J22QbA36K9TBYL8Z                | SPECIES    | [Dexia] dejeanii                           | Robineau-Desvoidy, 1830
 suSFcNI-jD9T5SAUckGON                | TRIBE      | *FChironominae                             | 
 wV1Ta8kIQ99i8SvfyaZnz0               | SPECIES    | [Cylindromyia] lobata                      | Sabrosky, 1967
 3bf368f7-754c-4ac1-a1fc-a24be6162bea | FAMILY     | Not assigned                               | 
 3ce10f7f-08e1-4392-9c3f-afb4d48909ba | SPECIES    | × medusae-populina                         | 
 4WXY-4w3qqtb0K8zid9VA0               | SPECIES    | “Montereina” phoca                         | (Ev. Marcus & Er. Marcus, 1967)
 PkMiuN7vt2sw7lBD9GbTw                | SPECIES    | “Montereina” rubra                         | (Bergh, 1905)
 TEQWQ9aSLJeW9dD3ouiI-2               | SPECIES    | “Montereina” greeleyi                      | (MacFarland, 1909)
 b8911045-62e8-421f-8d3b-0f0aee52095a | SUBSPECIES | [GENUS NOT SPECIFIED] lunatum inconjunctum | Pic, 1920
 e-epdnq3p9838lyeRDfIC1               | SPECIES    | DIzygomyza barnesi                         | Hendel, 1933
 eqwilEkCt_fx0lZ3BhASd1               | SPECIES    | “Montereina” achroma                       | (Á. Valdés, 2001)
 f85Z-6Mf84fAEW8cT6okT2               | SPECIES    | [Degeeria] nigrocostalis                   | Wulp, 1890
 o6mI1lfB7pOx-GgfaiS7E1               | SPECIES    | DIzygomyza cambii                          | Hendel, 1931
 vnmSZ7K_hcPc94JDrtmbW0               | SPECIES    | [Dexia] basalis                            | Walker, 1849
 xC6dbIj2pEP278xJknih-2               | SPECIES    | [Drapetis] luteipes                        | Le Peletier & Audinet-Serville, 1828
 3ad0e30f-8260-4cb4-a710-a3d0182be96a | SUBSPECIES | [GENUS NOT SPECIFIED] lunatum rufithorax   | Pic, 1920
 63607f12-54b8-4e99-ab24-89a404086d45 | SUBSPECIES | Cyphoderus undescribed species             | Bellini, BC & Zeppelini, D, 2004
 6u5GCGl9VnQ8AhZPzGXnk1               | SPECIES    | [Dexia] fuscanipennis                      | Macquart, 1844
 DZb8gEcewgOm9lQW-d2gi0               | GENUS      | [Degeeria]                                 | 
 UmTHbxW6FDOq0dv-OCYbN0               | SPECIES    | [Dexiosoma] partita                        | Bigot, 1889
 Uu7Cx337P4ck34-oTV3FQ1               | GENUS      | [Ctenophorocera]                           | 
 V45QAYHdGFfk-0HHVRQvx0               | SPECIES    | “Montereina” erubescens                    | (Bergh, 1884)
 YXXr3mBfngOf4d4b1PC8F1               | SPECIES    | “Montereina” lancei                        | (Millen & Bertsch, 2000)
 YYPOVp2EvUQq0CrqB8jYc1               | SPECIES    | [Degeeria] dicax                           | Giglio-Tos, 1893
 akTFCpE-1QOC2SyGSeyDz                | SPECIES    | [Degeeria] basalis                         | Wulp, 1890
 fNXoRltkU77MExCDFw7UG                | SPECIES    | [Dexia] melanocera                         | Robineau-Desvoidy, 1830
 nQKX2cFQ9d7xDK2tRZmI31               | SPECIES    | [Dexia] tenuicornis                        | Wulp, 1867
 qXZWnNrUXGck-46G4dCkd                | SPECIES    | [Dexia] ogoa                               | Walker, 1849
 xFmu4fXrsFAx5tuCZxXyC0               | SPECIES    | [Degeeria] nervosa                         | Wulp, 1890
 yu5gw_t8zJsSDlQ9a_ECs                | SPECIES    | [Dexia] abzoe                              | Walker, 1849
 Acs99raPvKtl8C_j_2UIn0               | TRIBE      | *FTachininae                               | 
 ObC5Q_jv9_Oh0_iw4aPre2               | SPECIES    | [Dexia] analis                             | Say, 1829
 OgzH9Wv_Blvy9hsKfnSAJ0               | TRIBE      | *FChloropinae                              | 
 ftQN0s0BC1uYBSfJjOlS90               | SPECIES    | “Montereina” lentiginosa                   | (Millen, 1982)
 kg8XK9Wvihcx1pwmDf0ca1               | SPECIES    | “Montereina” punctifera                    | (Abraham, 1877)
 mUZKRYirioNH8StXdh5JK2               | TRIBE      | *FTrypetinae                               | 
 pJKMRqxoUKAH8xQ_JLPGB1               | SPECIES    | [Dexia] nivifera                           | Walker, 1849
 q5ymOW_aPiv984EYR_YlY1               | SPECIES    | “Montereina” labifera                      | (Abraham, 1877)
 q6CIODPIc5NE0xOximbP92               | SPECIES    | [Dexia] gortys                             | Walker, 1849
 vXoqVXchnoQAEKCTox_g82               | SPECIES    | [Degeeria] nigriventris                    | Williston, 1896
 z1G_gqwpbn9mAd9sfqLvY0               | SPECIES    | [Dexia] plana                              | Walker, 1849
(91 rows)

The id reports are also better than the recent ones before:
https://download.checklistbank.org/releases/3/188/

@mdoering
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published: https://www.catalogueoflife.org/2023/11/24/release

@yroskov yroskov closed this as completed May 9, 2024
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@mdoering @gdower @dhobern @yroskov @sergbolshakov