WoRMS Mollusca (id 1130): test report

[yroskov]

WoRMS Mollusca, id 1130 on prod https://data.catalogueoflife.org/catalogue/3/dataset/1130

• [x] Sector: phylum Mollusca re-established

Plan A = does not work

1. Delete subtree phylum Mollusca = DOES NOT WORK
2. Delete broken sectors in WoRMS Mollusca
3. Assemble phylum Mollusca, sync
4. Re-assemble orders Ammonoidea & Belemnitida from PalepBioDB.

(WoRMS Mollusca has only one genus Actinoceras bigsbyi from subclass(!) Ammonoidea = Blocked

Plan B

1. Delete all 8 class-sectors and 7 order-sectors in nested class: Aaaah! Process is extremely slow (2021-03-29 ~14.15 CDT). = COMPLETED next day
2. Delete subtree phylum Mollusca = COMPLETED
3. Assemble phylum Mollusca, synced = COMPLETED
4. Re-assemble orders Ammonoidea & Belemnitida from PaleoBioDB. = COMPLETED

• [ ] Metadata: Not updated
• [x] Imports: 98872 spp vs 77955 in ac19

Reminder for PaleoBioDB orders:

[yroskov]

ISSUES (selected only) 2021-03-30

• [x] strange report Missing Genus, 3. Non-sci names for groups at rank of family & section.
• [x] assigned

[yroskov]

TASKS 2021-03-30

Reports might be interesting for WoRMS authors (@bart-v):

• [x] ACC-SYN species (different accepted; same authors), 108 names https://data.catalogueoflife.org/catalogue/3/dataset/1130/duplicates?acceptedDifferent=true&authorshipDifferent=false&category=binomial&limit=500&minSize=2&mode=STRICT&offset=0&status=accepted&status=synonym
• [x] SYN-SYN species (different accepted; same authors), 186 names https://data.catalogueoflife.org/catalogue/3/dataset/1130/duplicates?acceptedDifferent=true&authorshipDifferent=false&category=binomial&limit=500&minSize=2&mode=STRICT&offset=0&status=synonym

Resolved:

[yroskov]

Synced 2021-03-30. Sync need to be repeated after metadata fixes

[yroskov]

Checks at preview (of 2021-04-05)

Spp 98872 - 77955 = +20,917

Subterclass is interpreted as Unranked. All other ranks look good.

[yroskov]

TASKS 2021-07-08

• [x] Broken decisions: 26; re-matched all: 47. Deleted.

Resolved:

[yroskov]

version of 2021-07-01

Example of dis-integrity in the classification: Family Carditidae has a family Condylocardiidae as a child.

[yroskov]

TASKS (ver 2021-07-01) 2021-07-16

• [x] Broken decisions: 11; re-matched = 6. Deleted.

Resolved:

[yroskov]

CoL release 2021-10-18: keep eye on possible overlaps between PaleoBioDB Cephalopoda: Belemnitida & Ammonoidea and WoRMS Mollusca. Classifications might be different.

So far I can find an overlap: family Orthoceratidae - genus Orthoceras with a single sp Orthoceras regularis in WoRMS Mollusca and family Orthoceratidae - genus Orthoceras with 5 spp in PaleobioDB:

[yroskov]

ver 2021-11-01

TASKS - there are changes

• [x] Broken decisions, 35; RematchAll = 73 broken; RematchAll again = 73 broken; deleted all.

• [x] Identical family, genus are marked as acc - prov acc by the dataprovider; no decision needed, except one case.

• [x] Manuscript names, 3. All marked as "bare names" by the software. No decisions.

Resolved 2021-11-04

[yroskov]

Revisiting "decisions" after fixes https://github.com/CatalogueOfLife/testing/issues/184#issuecomment-1055567444

TASKS 2022-03-04

Resolved 2022-03-04:

Synced 2022-03-04

[yroskov]

TASKS as 2022-07-26

Resolved:

Synced 2022-07-26

[yroskov]

ver 2022-08-01

TASKS

Resolved:

Re-synced 2022-08-04

[yroskov]

ver 2023-05-01

TASKS

• Broken decisions, 1060: all deleted

Resolved 2023-05-08:

Re-synced 2023-05-08

[yroskov]

@bart-v, you might be interested: there are two entries for Dermomurex kilikiensis Landau, Harzhauser, İslamoğlu & Silva, 2013 † in MolluscaBase: https://www.marinespecies.org/aphia.php?p=taxdetails&id=1596066 and https://www.marinespecies.org/aphia.php?p=taxdetails&id=1642950

Genus Barroisocaulus Gubanov, Blodgett & Lytochkin, 1995 appears in different families (placement in the family Ptychocaulidaey has no children species)

Genus Euconospira Ulrich, 1897 appears in different families (both placements have per one child species).

[bart-v]

All fixed in WoRMS.

[yroskov]

ver. 2023-06-01

TASKS

• Broken decisions, 1199: all deleted

Resolved 2023-06-05:

Re-synced 2023-06-05

[yroskov]

• [x] Superclass Aplacophora Ihering, 1876 is empty in the WoRMS Mollusca@CLB classification:

It looks like, the superclass has no children on the WoRMS website: https://www.marinespecies.org/aphia.php?p=taxdetails&id=411

As I can see, potential children of Aplacophora (i.e. classes Caudofoveata Solenogastres) are regarded as direct children of phylum Mollusca: https://www.marinespecies.org/aphia.php?p=taxdetails&id=151365 https://www.marinespecies.org/aphia.php?p=taxdetails&id=2094

@bart-v, may we block the superclass Aplacophora in CoL? (if Mollusca editors have no plans to attach children classes in Aplacophora)

[bart-v]

There is a note attached to this taxon: https://www.marinespecies.org/aphia.php?p=taxdetails&id=411#notes

Includes Classes Solenogastres and Caudofoveata, now considered a clade (see Kocot et al. 2019) but at some time dismissed as a paraphyletic group

So for now, maybe OK to ignore.

[yroskov]

Thank you, @bart-v! I have blocked empty superclass Aplacophora in CoL, in a preparation for October update.

[yroskov]

• [ ] Missing WoRMS Mollusca data in CoL of 2024-03-25 (There are only 792 name usages from WoRMS Mollusca in CoL March 2024 edition ?!?! https://github.com/CatalogueOfLife/data/issues/634)

Syncs of 2024-03-03 & 2024-03-03 were cancelled.

Statistics wrongly shows full set of taxa (!):

[yroskov]

@bart-v, you might be interested to fix the authorstrings with strange year "18997". There are 12 names in MolluscBase with authorstring K. J. Bush, 18997. (I guess, it should be K. J. Bush, 1897). Full list is here:

https://www.checklistbank.org/dataset/1130/names?facet=rank&facet=issue&facet=status&facet=nomStatus&facet=nomCode&facet=nameType&facet=field&facet=authorship&facet=authorshipYear&facet=extinct&facet=environment&facet=origin&facet=sectorMode&issue=unparsable%20authorship&limit=50&offset=0&q=18997

Example on the master website: https://www.molluscabase.org/aphia.php?p=taxdetails&id=138502

...and 11 names with authorstring K. J. Bush, 18993 (should be K. J. Bush, 1893 ?):

https://www.checklistbank.org/dataset/1130/names?facet=rank&facet=issue&facet=status&facet=nomStatus&facet=nomCode&facet=nameType&facet=field&facet=authorship&facet=authorshipYear&facet=extinct&facet=environment&facet=origin&facet=sectorMode&issue=unparsable%20authorship&limit=50&offset=0&q=18993

Example on the master website: https://www.molluscabase.org/aphia.php?p=taxdetails&id=509651

...and 4 names with authorstring K. J. Bush, 18999 (should be K. J. Bush, 1899 ?):

https://www.checklistbank.org/dataset/1130/names?facet=rank&facet=issue&facet=status&facet=nomStatus&facet=nomCode&facet=nameType&facet=field&facet=authorship&facet=authorshipYear&facet=extinct&facet=environment&facet=origin&facet=sectorMode&issue=unparsable%20authorship&limit=50&offset=0&q=18999

Example on the master website: https://www.molluscabase.org/aphia.php?p=taxdetails&id=588607

[bart-v]

Thanks, all fixed

[gdower]

@bart-v, it seems that the extinct and referenceID column headers are reversed, so all referenceIDs are invalid:

https://www.checklistbank.org/dataset/1130/issues

Provisional also looks incorrect:

[gdower]

It seems that maybe there is a tab in the scrutinizer field which frameshifted everything?

[gdower]

Nevermind, there is no frameshift error. All the bad referenceIDs are on distribution records in which the references probably were not exported.

[yroskov]

ver 2024-05-01

TASKS

Resolved 2024-05-07:

Re-synced 2024-05-07

[yroskov]

ver 2024-06-01

TASKS

• Broken decisions, 2547 = all deleted
• Outdated decisions, 2 = no actions (ref: the problem of decisions between GSDs)

Resolved 2024-06-03:

Synced 2024-06-03