Closed yroskov closed 4 months ago
Tests of data ver. 2022-08-03
data of 2022-08-03
Universal Chalcidoidea Database (UCD) - Hymenoptera, ver 0.34.5 / 2023-10-16; imported 2023-10-16 https://www.checklistbank.org/dataset/124661/imports
Superfamily Chalcidoidea Latreille, 1817 = 27706 spp, (5 subgen), 2274 gen, (1 subtribe), 40 tribes , 81 subfam, 28 fam Superfamily Mymarommatoidea Debauche, 1948 = 36 spp, 6 gen, 2 fam Superfamily Serphitoidea Brues, 1937 = 15 spp, 5 gen, 2 fam
Superfamily Chalcidoidea Latreille, 1817 = 27706 spp (vs 19835 spp in UCD of Sep 2007), (5 subgen), 2274 gen, (1 subtribe), 40 tribes , 81 subfam, 28 fam https://www.checklistbank.org/dataset/124661/taxon/92634
Superfamily Serphitoidea Brues, 1937 = 15 spp (vs 11 spp in UCD of Sep 2007), 5 gen, 2 fam https://www.checklistbank.org/dataset/124661/taxon/93061
Superfamily Mymarommatoidea Debauche, 1948 = 36 spp, 6 gen, 2 fam https://www.checklistbank.org/dataset/124661/taxon/92929 The superfamily name is not present in UCD of Sep 2007. The family Mymarommatidae was the only child in superfamily Serphitoidea:
Classification (continue), superfamily Chalcidoidea
https://www.checklistbank.org/dataset/124661/classification?taxonKey=92634
Classification (continue), superfamily Chalcidoidea https://www.checklistbank.org/dataset/124661/classification?taxonKey=92634
[ ] Few empty subfamilies. Examples: Azotinae Nikol'skaya & Yasnosh, 1966 - as in TW; Eriaphytinae Hayat, 1978; Otitesellinae Joseph, 1964; Chalcimerinae Bouček, 1978 - twice; Podagrionidae Ashmead, 1904 - as in TW
[ ] Few empty tribes. Examples: Heydenini Hedqvist, 1961 - misspelled? need to be blocked - tribe Heydeniini Hedqvist, 1961 has children.
Haltichellini Ashmead, 1904 (attention: it's a type tribe in subfamily Haltichellinae)
Encyrtina Walker, 1837 (attention: it's a type tribe in subfamily Encyrtinae)
Few empty genera. Examples: one Ablerus Howard, 1894 is empty, another Ablerus Howard, 1894 has children; one Systasis Walker, 1834 is empty, another Systasis Walker, 1834 has children; Pegoscapus Cameron, 1906; Ceratosolen Mayr, 1885 (see "duplicated genera" below)
https://www.checklistbank.org/dataset/124661/classification?taxonKey=92774
https://www.checklistbank.org/dataset/124661/classification?taxonKey=92923
ISSUES
@gdower, we need to investigate these reports on duplicates:
[ ] ACC-ACC species (same authors) 0 of 872: 872 identical species - OTUs or something different caused it? - two OTU
[ ] ACC-SYN species (different accepted, same authors) 0 of 79: very strange report - the same name repeted 2-, 3-, 4- times - multiple OTU
[ ] Identical genus 0 of 107 - Strange: identical genera with the same position in the classification, but with different IDs. See above: https://github.com/CatalogueOfLife/testing/issues/205#issuecomment-1769064714 - two OTU
...and also:
[ ] ACC-SYN species (same accepted, same authors) 0 of 1089 - easy resolvable in CLB. Double check: does TW-CLB script translate it correctly? (such report typical for some other GSDs) - GO: looks like a script issue
[ ] SYN-SYN species (different accepted, same authors) 0 of 2473 - not easy resolvable in CLB. Double check: does TW-CLB script translate it correctly? - two OTU with accepted species (guess: resolving identical ACC-ACC with 2 OTU may fix this)
[ ] SYN-SYN species (same accepted, same authors) 0 of 111 - easy resolvable in CLB. Double check: does TW-CLB script translate it correctly? - GO: looks like a script issue
ASSEMBLY OF THE PROOF 1
UCD Draft ver. 0.40.3 / 2024-04-18; imported 2024-04-19
Metrics
ISSUES assessed 2024-04-30
TASKS
ACC-ACC species (same authors) 879 of 879. I guess, these are different OTUs with identical valid name. Comment for @gdower: if exporter will choose only one OTU from 2 or more, would it be possible to check distribution and keep a record with distribution data? = ~so far, left unresolved because CLB interface is very slow (today?)~~ See also the same issue of non-merged OTU https://github.com/CatalogueOfLife/testing/issues/135#issuecomment-2075678406 = RESOLVED for now in CLB 2024-04-30
SYN-SYN species (different accepted, different authors) 245 of 245. @gdower, there are cases in this report like this. What may caused them (different OTU with parent accepted name?)? Is there a way to resolve them in the exporter? = RESOLVED for now in CLB 2024-04-30
SYN-SYN species (different accepted, same authors) 129 of 2477. There are many cases with identical parent names. Perhaps it relates to different OTUs in ACC-ACC species (same authors) 0 of 879 = Untouched now. Come back after ACC-ACC species (same authors). Indeed, all(?) cases in pairs are resolved after sync. Duplicates remain in clusters with 4-6 names (see, Callimome abbreviatus, Cirrospilus quadristriata, etc.). Clusters of 4&6 resolved case-by-case. Clusters of 3 remain, just few with duplicates in the preview (e.g. Homoporus templarius). = RESOLVED for now in CLB 2024-04-30
Resolved 2024-04-30:
Synced & re-synced 2024-04-30
Question to Jim Woolley: is this expected?
PROOF 2
UCD Draft ver. 0.41.0 / 2024-05-06; imported 2024-05-06
Metrics
TASKS = seems no new decisions needed
Synced 2024-05-06
2nd proof of 2024-05-07:
John: this is the family checklist, including insertae sedis taxa, from UCD (https://ucd.chalcid.org).
Agaonidae Aphelinidae Asaphesinae Aspidopleura Austrosystasinae Azotidae Boucekiidae Calesidae Callimomoinae Ceidae Cerocephalidae Chalcedectidae Chalcididae Chrysolampidae Cleonymidae Coelocybidae Cynipencyrtidae Diparidae Ditropinotellinae Diversinitidae Elachertoidea Encyrtidae Enoggerinae Eopelma Epichrysomallidae Eubeckerella Eucharitidae Eulophidae Eunotidae Eupelmidae Eurytomidae Eutrichosomatidae Glyphotoma Herbertiidae Hetreulophidae Heydenidae Heydeniidae Idioporidae Jambiya Keryinae Leptoomidae Leucospidae Lithobelyta Lyciscidae Macromesidae Megastigmidae Melanosomellidae Metapelmatidae Micradelinae Moranilidae Mymaridae Neanastatidae Neapterolelapinae Neodiparidae Ooderidae Ormyridae Parasaphodinae Pelecinellidae Perilampidae Pirenidae Promerisus Protoitidae Pteromalidae Pyramidophoriella Rivasia Rotoitidae Selimnus Sennia Signiphoridae Spalangiidae Storeyinae Sympotomus Systasidae Tanaostigmatidae Tetracampidae Torymidae Trichogrammatidae Tripteromalus
John on 2nd proof:
Sorry but there are still many errors in how the ‘unassigned’ subfamilies and tribes are being pulled (and many of the incertae sedis taxa I pointed out before. John
Some of these are not pulling correctly - the following are all valid families: Azotidae Ceidae Cerocephalidae Chalcedectidae Chrysolampidae (Chrysolampinae, Philomidinae) Coelocybidae Diparidae Eurytomidae (Eurytominae, Heimbrinae, Rileyinae) Herbertiidae Macromesidae Metapelmatidae Micradelidae Neanastatidae Neodiparidae Not assigned subfamilies
the following are all valid families: Hetreulophidae Heydeniidae (why listed twice?) Idioporidae Lycisidae Mellanosomellidae Moranilidae Ooderidae Not assigned tribes
YR: Azotidae, Ceidae, Cerocephalidae, etc. are flagged as “bare names” in CLB, and are not included in CoL. Why, if they supposed to be valid families? These families rejected by the CLB produce “not assigned” subfamilies & tribes.
@gdower, where the problems may occur, in TW data (related to OTU or not?), the exporter, or in CLB?
Matt: check if these protonyms have verbatim name populated.
PROOF 3
UCD Draft ver. 0.41.0 / 2024-05-08; imported 2024-05-08 (OTUs applied by Geoff to resolve "bare names" and not-assigned subfamilies & tribes. This step added some "empty" genera which repeated with "full" genera = perhaps, resolved through TASK reports in CoL view. Examples of duplicated genera: Ceratosolen, Tetrapus, Aphelinus, Aphytis, Centrodora, Marietta, etc.)
@gdower, it looks like 10 (vs 22 in proof 2) subfamilies remain outside families (& one empty tribe Louriciini): https://www.checklistbank.org/dataset/124661/classification?taxonKey=92634
Metrics
TASKS
Resolved 2024-05-08:
Synced 2024-05-08
Missing families in UCD@CoL = FIXED in 3rd proof
UCD master (web) - Chalcidoidea - https://ucd.chalcid.org/#/taxonomicTree?rootTaxonID=455458&rootTaxonName=Chalcidoidea | 2nd proof 2024-05-07 | 3rd proof 2024-05-08 |
---|---|---|
Agaonidae | Agaonidae Walker, 1846 | Agaonidae Walker, 1846 |
Aphelinidae | Aphelinidae Thomson, 1876 | Aphelinidae Thomson, 1876 |
Azotidae | Azotidae Nikol'skaya & Yasnosh, 1966 | |
Boucekiidae | Boucekiidae Gibson, 2003 | Boucekiidae Gibson, 2003 |
Calesidae | Calesidae Mercet, 1929 | Calesidae Mercet, 1929 |
Ceidae | Ceidae Bouček, 1961 | |
Cerocephalidae | Cerocephalidae Gahan, 1946 | |
Chalcedectidae | Chalcedectidae Ashmead, 1904 | |
Chalcididae | Chalcididae Latreille, 1817 | Chalcididae Latreille, 1817 |
Chrysolampidae | Chrysolampidae Dalla Torre, 1898 | |
Cleonymidae | Cleonymidae Walker, 1837 | Cleonymidae Walker, 1837 |
Coelocybidae | Coelocybidae Bouček, 1988 | |
Cynipencyrtidae | Cynipencyrtidae Trjapitzin, 1973 | |
Diparidae | Diparidae Thomson, 1876 | |
Diversinitidae | †Diversinitidae Haas, Burks & Krogmann, 2018 | †Diversinitidae Haas, Burks & Krogmann, 2018 |
Encyrtidae | Encyrtidae Walker, 1837 | Encyrtidae Walker, 1837 |
Epichrysomallidae | Epichrysomallidae Hill & Riek, 1967 | Epichrysomallidae Hill & Riek, 1967 |
Eucharitidae | Eucharitidae Walker, 1846 | Eucharitidae Walker, 1846 |
Eulophidae | Eulophidae Westwood, 1829 | Eulophidae Westwood, 1829 |
Eunotidae | Eunotidae Ashmead, 1904 | Eunotidae Ashmead, 1904 |
Eupelmidae | Eupelmidae Walker, 1833 | Eupelmidae Walker, 1833 |
Eurytomidae | Eurytomidae Walker, 1832 | |
Eutrichosomatidae | Eutrichosomatidae Peck, 1951 | Eutrichosomatidae Peck, 1951 |
Herbertiidae | Herbertiidae Bouček, 1988 | |
Hetreulophidae | Hetreulophidae Girault, 1915 | |
Heydeniidae | Heydeniidae Hedqvist, 1961 & Heydenidae Hedqvist, 1961 | |
Idioporidae | Idioporidae LaSalle, Polaszek & Noyes, 1997 | |
Leptoomidae | †Leptoomidae Gibson, 2023 | †Leptoomidae Gibson, 2023 |
Leucospidae | Leucospidae Walker, 1834 | Leucospidae Walker, 1834 |
Lyciscidae | Lyciscidae Bouček, 1958 | |
Macromesidae | Macromesidae Graham, 1959 | |
Megastigmidae | Megastigmidae Thomson, 1876 | Megastigmidae Thomson, 1876 |
Melanosomellidae | Melanosomellidae Girault, 1913 | |
Metapelmatidae | Metapelmatidae Bouček, 1988 | |
Moranilidae | Moranilidae Bouček, 1988 | |
Mymaridae | Mymaridae Haliday, 1833 | Mymaridae Haliday, 1833 |
Neanastatidae | Neanastatidae Kalina, 1984 | |
Neodiparidae | Neodiparidae Bouček, 1961 | |
Ooderidae | Ooderidae Bouček, 1958 | |
Ormyridae | Ormyridae Förster, 1856 | Ormyridae Förster, 1856 |
Pelecinellidae | Pelecinellidae Ashmead, 1899 | Pelecinellidae Ashmead, 1899 |
Perilampidae | Perilampidae Förster, 1856 | Perilampidae Förster, 1856 |
Pirenidae | Pirenidae Haliday, 1844 | Pirenidae Haliday, 1844 |
Protoitidae | Protoitidae Ulmer & Krogmann, 2023 | Protoitidae Ulmer & Krogmann, 2023 |
Pteromalidae | Pteromalidae Dalman, 1820 | Pteromalidae Dalman, 1820 |
Rotoitidae | Rotoitidae Bouček & Noyes, 1987 | Rotoitidae Bouček & Noyes, 1987 |
Signiphoridae | Signiphoridae Howard, 1894 | Signiphoridae Howard, 1894 |
Spalangiidae | Spalangiidae Haliday, 1833 | Spalangiidae Haliday, 1833 |
Systasidae | Systasidae Bouček, 1988 | |
Tanaostigmatidae | Tanaostigmatidae Ashmead, 1904 | Tanaostigmatidae Ashmead, 1904 |
Tetracampidae | Tetracampidae Förster, 1856 | Tetracampidae Förster, 1856 |
Torymidae | Torymidae Walker, 1833 | Torymidae Walker, 1833 |
Trichogrammatidae | Trichogrammatidae Haliday, 1851 | Trichogrammatidae Haliday, 1851 |
22 families missing | 0 families missing |
Checks of 3rd proof (2024-05-08) with applied OTUs
0 families are missing in Chalcidoidea (see above)
10 subfamilies outside families:
Asaphesinae Burks & Heraty, 2020 Austrosystasinae Bouček, 1988 Callimomoinae Girault, 1926 Ditropinotellinae Bouček, 1988 Enoggerinae Burks, 2022 Keryinae Bouček, 1988 Micradelinae Wall, 1972 Neapterolelapinae Rasplus, Burks & Mitroiu, 2022 Parasaphodinae Bouček, 1988 Storeyinae Bouček, 1988
Logo?
Empty branch Heydenidae: = BLOCKED in Assembly 2024-05-09
2024-05-10:
Looks fantastic!!! Thanks for working with us. As for a logo… I will work on this with Jim next week :-) I am okay for a go. All the best, John
I think it is ready to go. Cheers, Jim
Family Aphelinidae exported from TW in CoLDP and uploaded on DEV 2022-08-03: https://www.dev.checklistbank.org/dataset/212838 - does not work at the moment, alternative copy on prod: https://www.checklistbank.org/dataset/124661/classification
Family Aphelinidae of approx. 1,100 spp & 43 (est!) accepted genera