AntCat (id 54937): test report

[yroskov]

AntCat in CLB: https://www.checklistbank.org/dataset/54937/classification

See also https://github.com/CatalogueOfLife/data/issues/517

Adoption by the Taxonomy Group is needed.

[yroskov]

AntCat of 2024-08-04 / 2024-08-04 imported 2024-08-08

• [ ] Imported: 21,314 spp in family Formicidae (vs 10,213 spp Formicidae in ITIS@CoL of 2024-07-18) = 11K+ = TOO MANY. Is the nomenclatural status translated correctly? Names with nomenclatural status unavailable / not established cannot be flagged as CoL accepted names. (When I excluded not established species names in the filter https://www.checklistbank.org/dataset/54937/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&facet=secondarySourceGroup&facet=sectorDatasetKey&facet=group&limit=50&nomStatus=established&offset=0&rank=species&reverse=false&sortBy=name&status=accepted&status=provisionally%20accepted, I have got 15,080 accepted species. It looks more realistic.

Metrics: See: Created by importer

[yroskov]

• [ ] Metadata: need to be filled; no logo

Full Name: An Online Catalog of the Ants of the World Alias: AntCat Version / Issued: 2024-08-04 / 2024-08-04 DOI: no Description: AntCat is a catalog and bibliography of the taxonomy of the world's ants. Is it enough to describe AntCat? Contact: Fisher, Brian Publisher: No information Creator: Bolton, BarryUS; Fisher, BrianUS Editor: No information Contributor: No information Taxonomic scope: Formicidae Need an English name of the group. Ants? Geographic scope: global Temporal scope: No information Keywords: No information Origin: external Type: taxonomic License: cc by Checklist Confidence: No information Origin: external Completeness: No information Url (website): https://antcat.org/ Citation: Bolton, B., & Fisher, B. (2024). An Online Catalog of the Ants of the World (Version 2024-08-04). https://antcat.org/ Released from Source No information Notes No information Last successful import attempt 23 Created March 17th 2023, 4:11:20 pm by markus Modified August 8th 2024, 2:02:27 pm by importer

[yroskov]

• [x] Classification: ranks Family Formicidae Latreille, 1802> Subfamily (115) > Tribe (67) > Genus (673) > Subgenus (463) > Species (21314) > Subspecies (5431)

• [ ] There are many subfamilies with the name "Incertae sedis"; some of them are empty (no children) = (1) REMOVE value "Incertae sedis", (2) EXCLUDE EMPTY "Incertae sedis" subfamilies It looks like, names inside all "Incertae sedis" subfamilies were misinterpreted as accepted taxa (see, for example genus Atopogyne in CoL https://www.checklistbank.org/dataset/54937/classification?taxonKey=451318 and on AntCat website https://antcat.org/catalog/451318

• [ ] There are empty tribes (with unavailable Nomenclatural Status) = BARE NAMES For example: Armaniini Dlussky, 1983 https://www.checklistbank.org/dataset/54937/taxon/430176 It's parent subfamily Armaniinae Dlussky, 1983 has only one empty tribe = EXCLUDE

8 empty tribes in Dorylinae subfamily with unavailable status (Acanthostichini Emery, 1901; Aenictini Emery, 1901; Aenictogitonini Ashmead, 1905; etc.): = BARE NAMES

• [ ] There are empty genera (flagged as accepted but with unavailable Nomenclatural Status = BARE NAMES For example: Lithomyrmex Carpenter, 1930 https://www.checklistbank.org/dataset/54937/taxon/430018 Protamblyopone Dlussky, 1981 https://www.checklistbank.org/dataset/54937/taxon/430036 etc. Especially, there are many empty genera in "Incertae sedis" subfamilies . Some genera are split there, for example, genus Baikuris split between 5 "Incertae sedis" subfamilies: and view in the Tree:

• [ ] Broken hierarchy (see tribe Dorylini with tribe Dorylii inside) - empty!
  

• [ ] All genera in the subfamily Dorylinae Leach, 1815 are outside empty tribes the same for subfamily Haidomyrmecinae Bolton, 2003 (tribe Haidomyrmecini is empty) = parent-child relationships in subfamily Dorylinae need to be fixed

• [ ] Some genera have no authorstrings = it looks like these names are synonyms of other genera; there are authorstrings in AntCat website For example: Hypoclinea https://www.checklistbank.org/dataset/54937/taxon/xHC - synonym of Dolichoderus, see https://antcat.org/catalog/429080 Conomyrma https://www.checklistbank.org/dataset/54937/taxon/xH7 - synonym of Dorymyrmex https://antcat.org/catalog/429097 Phyracaces https://www.checklistbank.org/dataset/54937/taxon/xG6 Typhlatta https://www.checklistbank.org/dataset/54937/taxon/xH3 Woitkowskia https://www.checklistbank.org/dataset/54937/taxon/xDN etc.

• [ ] Misinterpreted species synonyms. It looks like combination (= CoL synonym) is placed as a subspecies in the hierarchy and labelled as a species inside species.
  

• [ ] Misinterpreted subspecies synonyms. (1) Subspecies is located outside parent species; (2) subspecies combination (= CoL synonym) and accepted subspecies is interpreted as child & parent:
  This and previous bugs might be caused by broken parent-child relationships between species and subspecies See also ISSUE Parent Species Missing, 2378

• [ ] Missing combinations in synonymy compare with AntCat (AntCat also have incomplete set of combinations - they are "hidden" in the field "Combination in [Acropyga (Rhizomyrma)]") For example: Acc sp Acropyga goeldii Forel, 1893 https://www.checklistbank.org/dataset/54937/taxon/430416 vs AntCat https://antcat.org/catalog/430416 missing Acropyga (Rhizomyrma) goeldii Forel, 1893

[yroskov]

• [ ] Extinct flag is missing with paleo taxa
• [x] Distribution: NO; no on AntCat website
• [x] Environment: NO; no on AntCat website
• [x] Common names: NO; no on AntCat website
• [x] References: OK (not all refs from AntCat website included)
• [x] Completeness of CoL synonymy: incomplete set of subsequent combinations (as on AntCat website)
• [x] Link to the sp page in the source website: OK

[yroskov]

ISSUES assessed 2024-08-09

Needs fixes:

• [ ] Parent Species Missing, 2374

• [ ] Classification Rank Order Invalid, 6327

• [ ] Parent Name Mismatch, 6694

• [ ] Taxonomic Status Invalid, 10402

[mdoering]

Taxonomic scope: ~Formicidae~ Need an English name of the group. Ants?

taxonomicScope is supposed to be a list of latin names. taxonomicScopeInEnglish is for the english name of the group(s)

See https://github.com/CatalogueOfLife/coldp/blob/master/metadata.yaml#L163

[mdoering]

Various fixes applied on dev, incl extinct flag, better synonym treatment, no incertaesedis subfamilies and a few more things. These are all status values for names in AntCat and how they are currently mapped to COL/CLB. @yroskov any changes?

  case "valid" -> TaxonomicStatus.ACCEPTED;
  case "synonym", "obsolete combination", "unavailable misspelling", "unavailable", "homonym" -> TaxonomicStatus.SYNONYM;
  case "unidentifiable" -> TaxonomicStatus.PROVISIONALLY_ACCEPTED;
  case "excluded from formicidae" -> TaxonomicStatus.BARE_NAME;
  default -> TaxonomicStatus.PROVISIONALLY_ACCEPTED;

[mdoering]

I have uploaded the latest version to prod. @yroskov please take a look, it should be a lot better now.

I've also written Brian Fisher with a few questions, e.g. on how to obtain type species information.