Open yroskov opened 3 years ago
In ac19 we have taken from 3i Auchenorrhyncha (additional paleotaxa are missing) :
Animalia - Arthropoda - Insecta - Hemiptera - superfamily Cicadoidea Animalia - Arthropoda - Insecta - Hemiptera - Membracoidea - families Aetalionidae, Melizoderidae, Myerslopiidae and subfamilies Cicadellinae & Typhlocybinae from Cicadellidae
In CoL 2021-06-10 from 3i Auchenorrhyncha (including paleotaxa):
Animalia > Arthropoda > Insecta > Hemiptera: Myerslopiidae, Pereborioidea, Palaeontinoidea, Prosboloidea, Cicadoidea, Scytinopteroidea, Hylicelloidea, Dysmorphoptiloidea, Blattoprosboloidea, Ligavenoidea Animalia > Arthropoda > Insecta > Hemiptera > Membracoidea: Cicadellidae, Melizoderidae, Aetalionidae
[by a mistake] I have completed assembly of 3i Auchenorrhyncha dev (id 2317) on prod.
Taxa assembled & synced: Blattoprosboloidea, Cicadoidea (+family Membracidae from MOWD), Dysmorphoptiloidea, Hylicelloidea, Ligavenoidea Palaeontinoidea, Pereborioidea, Prosboloidea, Prosbolopseoidea
All sectors synced 2021-07-09.
@gdower, could you please "replace" old version of 3i Auchenorrhyncha (id 1189) with the newly assembled checklist from 3i Auchenorrhyncha dev (id 2317). Please keep old metadata (1189) with a new checklist. (I was not able to modify metadata in 2317 - have no access). = FIXED 2021-07-15: metadata have been updated for 2317. Now, 2317 is a master id for the dataset.
No any ISSUES & TASKS resolved in the checklistbank, because 3i Auchenorrhyncha much bigger then those sectors which we took in the CoL.
Checks through the public interface at PREVIEW https://preview.catalogueoflife.org/?taxonKey=HP 2021-07-12.
Example: Blattoprosbole tomiensis
In ac19: http://www.catalogueoflife.org/annual-checklist/2019/browse/tree/id/8d5dfb968886f536be02b56f350d70f9
In PREVIEW: https://preview.catalogueoflife.org/data/browse?taxonKey=8HDXD
@geoff, could you pls have look on this after your return.
To be translated later:
From: Dmitry Dmitriev Sent: Monday, July 12, 2021 14:45 To: Roskov, Yury yroskov@illinois.edu Subject: Re: 3i Auchenorrhyncha in CoL
Юра, те проблемы которые мне попались:
Не помечены вымершие таксоны
Роды привязанные к подтрибам и сами подтрибы просто выпали. Пример род Hecalus. Находится в подтрибе Hecalina, триба Hecalini. В списке есть только Hecalini - пустая триба, все что привязано к трибе - отсутствует.
Подрод Gargara (Gargara). Все виды привязанные к подроду - попали в группу not assigned.
Типовой подвид выпадает из списка. Gargara pallida lineata есть, a Gargara pallida pallida - Отсутствует.
Если вид был описан в другом роде - пропали год описания и скобки в авторской строке, пример Gargara patruelis. Также выпала первоначальная комбинация. Но это не у всех видов. Например, Erasmoneura vulnerata выглядит нормально.
Из списка синонимов вы выбрасываете последнюю комбинацию с цитатой. Erasmoneura vulnerata (Fitch, 1851). В списке синонимов отсутствует "Erasmoneura vulnerata (Fitch, 1851)" и кто создал эту комбинацию. Я понимаю, что эта комбинация совпадает с современным названием виды, но в Зоологии это важно, у нас автор комбинации не включается в авторскую строку вида.
E. vulnerata имеет синоним. E. gradata. Я так понимаю должна быть значек цитаты с библиографической ссылкой. Но таковой отсутствует.
Виды привязанные к надвидам попали в список unassigned. Пример: род Dilobopyga.
в TW семейство Cicadellidae включает в себя 420 подвидов, 23181 вадидных названий видов. 2790 родов. In TW, Cicadellidae family consists of 2790 genera, 23181 valid species & 420 subspecies. YR: in recent CoL preview version: 2079 genera, 17771 valid spp, & 307 subspecies. https://preview.catalogueoflife.org/data/search?TAXON_ID=8HBPW&facet=rank&facet=issue&facet=status&facet=nomStatus&facet=nameType&facet=field&facet=authorship&facet=extinct&facet=environment&limit=50&offset=0&rank=species&sortBy=taxonomic&status=accepted
@gdower
Metadata updated with @proceps. Re-synced 2021-07-15.
New version was exported from https://sfg.taxonworks.org/downloads/220 and imported to DEV 2021-09-10: https://data.dev.catalogueoflife.org/dataset/1189/classification
Test results: (for attention of @proceps, @gdower, @mjy)
[ ] Extinct taxa are not flagged. YR: still a problem. Example: †Ligavena gracilipes https://data.dev.catalogueoflife.org/dataset/1189/classification?taxonKey=13446
[x] Subtribes and their children genera are missed. See empty tribe Hecalini. YR: fixed. Tribe Hecalini has 2 subtribes, genera and species as children: https://data.dev.catalogueoflife.org/dataset/1189/classification?taxonKey=25580
[x] All children species of subgenus Gargara (Gargara) dropped in NotAssigned node. Type subspecies Gargara pallida pallida is missing. There is only subspecies Gargara pallida lineata YR: fixed. See https://data.dev.catalogueoflife.org/dataset/1189/classification?taxonKey=49650. Gargara pallida pallida is also present.
[x] In some (not all) species, the original combination is missing (see Gargara patruelis). The Year and brackets are missing in the authorstring of subsequent combination YR: all are fine in data from 3i dataset. https://data.dev.catalogueoflife.org/dataset/1189/taxon/49801
[ ] You have thrown away the latest combination with a reference. For example, Erasmoneura vulnerata (Fitch, 1851) is missing in the list of synonyms and no reference top the publication, where this combination was established. I do understand, that this combination is an accepted name, but reference with the combination is important in Zoology. _YR: Hmm. Probably, there is still a problem. Erasmoneura vulnerata (Fitch, 1851) have got 2 original combinations: ≡ Erythroneura vulnerata Fitch, 1851 and ≡ Typhlocyba vulneata Fitch, 1851, whereas Typhlocyba vulneata is misspelling: https://data.dev.catalogueoflife.org/dataset/1189/taxon/44300_ Original view in TW: https://sfg.taxonworks.org/tasks/nomenclature/browse?taxon_name_id=374430
[x] Erasmoneura vulnerata has a synonym Erasmoneura gradata. I am expecting to see a bibliographic reference with the synonym, but it is absent. YR: Seems, still a problem, references with synonyms are missing: https://data.dev.catalogueoflife.org/dataset/1189/taxon/44300 Original view in TW: https://sfg.taxonworks.org/tasks/nomenclature/browse?taxon_name_id=374430
[ ] Species, which are children of superspecies, dropped in NotAssigned node. For example, genus Dilobopyga. YR: superspecies have a CoL status "species aggregate". However, parent-child relationships between superspecies and children species are broken, as result, all species dropped in NotAssigned "species aggregate": https://data.dev.catalogueoflife.org/dataset/1189/classification?taxonKey=9073. Not sure that checklist bank software correctly interpreted portion "supersp", it's shown in italics
Shortcut fix: all 3i names with portion "supersp" were blocked in the workbench 2021-10-18. Synced.
The issues are missing references, and missing fossil status, correct? Names all seem OK?
As for me, yes: refs & fossil status are main unresolved issues.
Good, this makes sense given what we understand.
I feel like we'll make notes optional. IIRC some of the SFs GSDs passed them on.
Yes, Notes are optional in CoL and definded by GSD wish/needs. However, we cannot take them off on our side, in the checklistbank.
It is a stopper for 3i updates.
2021-10-19: NEW EXPORT from https://sfg.taxonworks.org/downloads/238; file 3i_world_auchenorrhyncha_database_coldp_otu_id_319_2021-10-19t133625+0000
@gdower has deleted data in comments field. File 3i_Aurchenorrhyncha_2021-10-19_no_remarks was imported.
[x] Imported: 46740 spp total (vs 46305 spp in ver. of 2021-06-11)
[x] Metadata: dates updated
[x] Classification:
[x] Sector: unchanged Taxonomic coverage in previous CoL, as shown by the portal software (2021-10-18): Animalia > Arthropoda > Insecta > Hemiptera: Blattoprosboloidea, Prosbolopsemorpha, Prosbolomorpha Animalia > Arthropoda > Insecta > Hemiptera > Cicadomorpha: Cicadoidea, Hylicelloidea, Ligavenoidea, Membracoidea
[x] ISSUES assessed
[x] TASKS:
Resolved:
Tasks SYN-SYN sp (diff acc, same auth) and SYN-SYN sp (same acc, same auth) remains unresolved.
Synced 2021-10-19
Examples: Aceratagallia humilis Oman, 1933 is a synonym for Aceratagallia (Aceratagallia) humilis Oman, 1933 and Aceratagallia (Aceratagallia) humilis humilis Oman, 1933 Aceratagallia nanella Oman, 1933 is a synonym for Aceratagallia (Aceratagallia) nanella Oman, 1933 and Aceratagallia (Aceratagallia) nanella nanella Oman, 1933 Alaca wygodzinskyi Linnavuori, 1954 is a synonym for Paratanus wygodzinskyi (Linnavuori, 1954) and Paratanus wygodzinskyi wygodzinskyi (Linnavuori, 1954) Aphelonema convergens Bunn, 1930 is a synonym for Nenema convergens (Bunn, 1930) and Nenema convergens convergens (Bunn, 1930)
(@gdower, @proceps it looks like the issue with synonymy of type subspecies exists in 3i data as well as in SFs not-maintained in TW)
in 3i database: Aceratagallia humilis Oman, 1933 is an original combination for both species and nominotipical susbspecies: Aceratagallia (Aceratagallia) humilis Oman, 1933 and Aceratagallia (Aceratagallia) humilis humilis Oman, 1933 I do not see any contradiction. In TW we have original combination for each protonym. In cases of coordinate names, it should be identical. All other synonymy is automatically moved from species to subspecies, when soft_validation is used.
Species are not assigned to superspecies: See for example Enchenopa supersp. lanceolata
The subsequent combination, which has identicall spelling with the current name of the taxon, is not on the list. That combination has a reference indicating when the current combination is created. Apparantly the name was dropped because it has identical spelling with the current name, but together with the name, the reference was also dropped.
What happens to species distribution. It it migrated?
fossils are not marked as such.
The subsequent combination, which has identicall spelling with the current name of the taxon...
Such names eliminated in the CoL via TASKS in the checklistbank. If you would like to keep reference with a special comment in the Remarks field, we need to find an appropriate solution at the stage of export from TW in CoLDP. @gdower?
What happens to species distribution. It it migrated?
Distribution data are not exported yet for all SFs (https://github.com/CatalogueOfLife/testing/issues/163#issuecomment-938685188). Seems, the same true for all exports from TW.
fossils are not marked as such
I guess, it is 3i data specific issue. SFs species have "extinct" flag. @gdower?
Species are not assigned to superspecies
Unfortunately, it is another known but unresolved yet bug. As a shortcut solution, I have eliminated superspecies/species aggregates as a rank in the CoL.
Aceratagallia humilis Oman, 1933 is an original combination for both species and nominotipical susbspecies: Aceratagallia (Aceratagallia) humilis Oman, 1933 and Aceratagallia (Aceratagallia) humilis humilis Oman, 1933 I do not see any contradiction. In TW we have original combination for each protonym. In cases of coordinate names, it should be identical. All other synonymy is automatically moved from species to subspecies, when soft_validation is used.
Such approach has no sense in the CoL, because synonymy in the taxonomic checklist is forming species as a taxonomic concepts. Aceratagallia humilis humilis, Aceratagallia humilis alvarana and Aceratagallia humilis interior are different subsets of Aceratagallia humilis. We are expecting that synonymy in CoL reflects taxa, but not formal nomenclatural relationships between names.
I mentioned many times, that treating combinations (including original combination) as synonym is incorrect according to ICZN. Also it is incorrect referring to original combination as basionym. It completely distorts the concept.
In the case of the taxonomic checklist, both synonyms and combinations are "semantic synonyms" which reflects a taxonomic concept.
treating combinations (including original combination) as synonym is incorrect according to ICZN. Also it is incorrect referring to original combination as basionym. It completely distorts the concept.
@mdoering, could you please have a look this Dmitry's comment. Does checklistnbank software accommodate what Dmitry stated on behalf of ICZN?
I do not see any "semantic" on the website. What I can see is completerly new terminology poroposed.
As you all know we don't follow ICZN or ICNafp for both nomenclatural and taxonomic status, but instead want a "unified" view across all codes and therefore have settled on new terminology instead of overloading existing one.
Taxonomic status values are based on existing COL values that existed for a long time and mostly also correspond to recommended DwC values: http://api.catalogueoflife.org/vocab/taxonomicstatus The only exception there is "ambiguous synonym" which I sometimes doubt is very useful and might just be collapsed with plain "synonym".
Nomenclatural status values are here, with translations to zoology and botany as the main codes: http://api.catalogueoflife.org/vocab/nomstatus
We should show these code specific values on the portal pages I suppose. @thomasstjerne do we actually do on the portal and CLB this in case the code is given?
As for the terminology of "synonyms" we have discussed this many times in different places. I think "Synonyms and combinations" as we have it now makes sense and should be agreeable?
Basionym there was an endless discussion whether this should be "original name" like in DwC. It is known to most zoologists and I don't see much ambiguity or overloading here really, thats why we opted to keep basionym.
Providing labels similar to those defined in the codes but having completely different meaning would be a constant source of confusion.
What case would that be? It is exactly what we try to avoid. With the exception of "synonym" which I still think is common to also taxonomists in zoology as it never showed up as a problem in 20 years of GBIF, TDWG TCS, ontologies & Darwin Core. ITIS and WoRMS as a foundation for COL have it, but WoRMS calls them Synonymised names now: http://www.marinespecies.org/aphia.php?p=taxdetails&id=248562
Revisiting "decisions" after fixes https://github.com/CatalogueOfLife/testing/issues/184#issuecomment-1055567444
TASKS 2022-03-04
2022-03-04, Comment after talk to Dmitry: original combination should be linked as CoL synonym to the type subspecies (not to the parent species). Example: Synonym | Accepted |
---|---|
Batracomorphus (Batracomorphus) dirke Linnavuori & Quartau, 1975 | |
Batracomorphus dirke Linnavuori & Quartau, 1975 | Batracomorphus (Batracomorphus) dirke dirke Linnavuori & Quartau, 1975 |
Whereas in botany, it's different: in the same case, original combination should be linked as CoL synonym to the species (not to the type subspecies child).
2022-08-29: NEW EXPORT by GO with updated TW exporter (resolved "looped synonymy in type subspecies"; distribution added) Imported on PROD: https://www.checklistbank.org/dataset/2317/classification
[x] Imported: 46901 spp total
[x] Metadata: dates updated. @proceps, could you pls check other metadata: https://www.checklistbank.org/dataset/2317/about. Let us know, if you like to make changes.
[ ] Classification:
20 subspecies are in a root of the Tree https://www.checklistbank.org/dataset/2317/classification
It looks like, parent species are flagged as "bare names" by the CLB @gdower?
@gdower & @proceps, all these names are in Parent Id Invalid report https://www.checklistbank.org/catalogue/3/dataset/2317/workbench?facet=rank&facet=issue&facet=status&facet=nomStatus&facet=nameType&facet=field&facet=authorship&facet=authorshipYear&facet=extinct&facet=environment&facet=origin&issue=parent%20id%20invalid&limit=100&offset=0 and in Parent Species Missing report https://www.checklistbank.org/catalogue/3/dataset/2317/workbench?facet=rank&facet=issue&facet=status&facet=nomStatus&facet=nameType&facet=field&facet=authorship&facet=authorshipYear&facet=extinct&facet=environment&facet=origin&issue=parent%20species%20missing&limit=100&offset=0
= infraoder Blattoprosbolomorpha established as a sector 2022-09-02
[x] ISSUES assessed 2022-09-02
[x] TASKS:
Broken decisions: 1857; deleted all
ACC-ACC sp, same auth Four identical pairs of names with identical IDs (!). Even names were blocked.
ID | Decision | Status | scientificName | Authorship | Accepted | Rank | Classification | |
---|---|---|---|---|---|---|---|---|
752802 | accepted | Bubalopa iguaque | Flórez-Valencia & Evangelista de Souza, 2021 | species | Darninae>Hyphinoini>Bubalopa | |||
752802 | accepted | Bubalopa iguaque | Flórez-Valencia & Evangelista de Souza, 2021 | species | Darninae>Hyphinoini>Bubalopa | |||
757475 | accepted | Eurhadina (Singhardina) amacularis | Zhang & Huang, 2022 | species | Typhlocybini>Eurhadina>Eurhadina (Singhardina) | |||
757475 | accepted | Eurhadina (Singhardina) amacularis | Zhang & Huang, 2022 | species | Typhlocybini>Eurhadina>Eurhadina (Singhardina) | |||
753244 | accepted | Eurhadina (Singhardina) dissimilis | Zhang & Huang, 2021 | species | Typhlocybini>Eurhadina>Eurhadina (Singhardina) | |||
753244 | accepted | Eurhadina (Singhardina) dissimilis | Zhang & Huang, 2021 | species | Typhlocybini>Eurhadina>Eurhadina (Singhardina) | |||
757473 | accepted | Eurhadina (Singhardina) scamba | Zhang & Huang, 2022 | species | Typhlocybini>Eurhadina>Eurhadina (Singhardina) | |||
757473 | accepted | Eurhadina (Singhardina) scamba | Zhang & Huang, 2022 | species | Typhlocybini>Eurhadina>Eurhadina (Singhardina) |
Resolve 2022-09-02:
Synced 2022-09-02
Metadata are ok. Distribution seems to be exported correctly.
of the fossil sectors, you can take Blattoprosbolomorpha; Prosbolomorpha; Prosbolopsemorpha
Thanks!
So, @gdower, remaining issue is/are only(!) 20 subspecies in the tree root. It's not clear why it was happened. Dmitry confirmed that all look fine in TW with these subspecies. At least, they have OTUs.
@mdoering There are two cases of strange synonymy reported in GBIF Global Checklist:
Both are common European species. I got a request from people working in European collection asking why are those incorrectly treated by GBIF. In both cases the species get link to some other species as a homotypic synonym, but if you look, in both cases the name has different author string. Something have to be done on the data migration, so that the data coming form CoL get higher weight and not get replaced with some obscure datasets. I tried to trace for a source of confusion. And I could not.
This is odd indeed and not immediately obvious why that is.
N. guttulatus was also accepted in the November 21 version of COL that was used to build the GBIF backbone: https://www.checklistbank.org/dataset/2351/taxon/6S79V
TAXREF is cited as the primary source for the name in the backbone, not COL which is weird, but that also claims the name is accepted: https://www.gbif.org/species/161540641
The backbone species page has a warning Conflicting basionym combination
, I suspect this is the source for the problem. Just both 3i and TAXREF do not list any "basionym".
From the build logs I can see it was indeed forced (wrongly) to be a synonym because of "homotypic grouping":
Consolidating basionym group with HOMOTYPIC_SYNONYM primary usage Jassus guttulata (Stål, 1862): Jassus guttulata (Stål, 1862); Neoaliturus guttulatus (Kirschbaum, 1868)
Convert SPECIES Neoaliturus guttulatus (Kirschbaum, 1868) [5299693] into a HOMOTYPIC_SYNONYM of SPECIES Paracarinolidia guttulata (Stål, 1862) [2038349]
Also convert descendant SPECIES Neoaliturus guttulatus (Kirschbaum, 1868) [5299693] into a synonym of SPECIES Paracarinolidia guttulata (Stål, 1862) [2038349]
Because of Jassus guttulata it now becomes a synonym of Paracarinolidia guttulata (Stål, 1862).
The source for this seems to be FaunaEuropaea which indeed lists Jassus guttulatus Kirschbaum, 1868 as the basionym of Neoaliturus guttulatus (Kirschbaum, 1868): https://www.gbif.org/species/123296966
For the next build I will prevend that specific grouping.
Cicadula frontalis is listed as many ambiguous synonyms in COL at the time we build the backbone: https://www.checklistbank.org/dataset/2351/names?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=Cicadula%20frontalis%20&sortBy=taxonomic
https://www.gbif.org/species/184030962
That must have been the cause in that case.
@mdoering The key factor in all those case is the author string. In zoology, the authorship does not change when a new combination is created. There is also a factor of homonymy. I would estimate, that up to 5% of the names will have a homonym, listed as synonym of another name. This is in my upderstanding the problem with with interpritations in both cases. For zoological names you can more or less safly synonymize the name which have the same author and year strings. So guttulata (Stål, 1862) and guttulatus (Kirschbaum, 1868) could never be treated as homotypic synonyms. In plants situation is somewhat different, the author string changes when the species is moved from one genus to another.
Yes, thats clear. It is an implementation problem when integrating the sources (aka backbone build) coupled with an issue of false data (see FaEu above).
@mdoering Each species comming from 3i has a basionym associated with the name. Please see the examples I provided (https://www.catalogueoflife.org/data/taxon/6S79V). May be those get lost when converted to GBIF backbone? But the real problem is homonymy that is involved. Jassus guttulatus Kirschbaum is a basionym of of Neoaliturus guttulatus. There is also Jassus guttulata (Stål, 1862) which is one of the subsequent combinations of Paracarinolidia guttulata (Stål, 1862), completely unrelated species. I can see, if the script does not take the author and year into accout, both Jassus guttulatus Kirschbaum and Jassus guttulata Stal could be mixed, and this will bring unexpected synonymy.
3i Auchenorrhyncha 2022-10-19 (imported by GO)
ISSUES
TASKS
Broken decisions: 205; deleted all
ACC-ACC sp, same auth: 3 pairs of identical species names with identical IDs = NO ACTION, reported as a software bug https://github.com/CatalogueOfLife/checklistbank/issues/1117 https://www.checklistbank.org/catalogue/3/dataset/2317/duplicates?authorshipDifferent=false&catalogueKey=3&category=binomial&limit=500&minSize=2&mode=STRICT&offset=0&status=accepted&withDecision=false
@mdoering & @gdower, this is a consistent now [frontend or backend?] problem which appeared in CLB after September release. I have reported it with few Species Files. Geoff mentioned that there are no duplicated entries in the database. But we have them in the CLB report.
@mdoering & @gdower, even more curious case: identical synonyms names with identical IDs linked to the same accepted species listed in this report. Something seriously wrong with reports on duplicates in CLB.
Resolved 2022-10-19:
Synced 2022-10-20
3i Auchenorrhyncha 2022-10-19; re-imported 2022-11-16 with fixed 24 subspecies
TASKS
Resolved 2022-11-16:
Synced 2022-11-16
3i Auchenorrhyncha of 0.28.1 / 2022-11-22; imported 2022-11-22 with fixed extinct flag (GO: plus, with a draft of types and species interactions)
TASKS
@gdower, do you think, this report works correctly?
= NO ACTION until report will be confirmed or resolved
Example:
SYN-SYN infraspecies (different accepted, same authors) 11 of 27: similar to above case https://www.checklistbank.org/catalogue/3/dataset/2317/duplicates?acceptedDifferent=true&authorshipDifferent=false&catalogueKey=3&category=trinomial&limit=500&minSize=2&mode=STRICT&offset=0&status=synonym&withDecision=false = NO ACTION
Identical genus, 1 of 5: three pairs of absolutely identical accepted genera in identical position in the classification with different IDs. @gdower, could you pls have a look on this and below reports https://www.checklistbank.org/catalogue/3/dataset/2317/duplicates?catalogueKey=3&category=uninomial&limit=500&minSize=2&mode=STRICT&rank=genus&status=accepted&withDecision=false = NO ACTION
Idenical tribe, 0 of 7: the same as above https://www.checklistbank.org/catalogue/3/dataset/2317/duplicates?catalogueKey=3&category=uninomial&limit=500&minSize=2&mode=STRICT&offset=0&rank=tribe&status=accepted&withDecision=false
SYN-SYN species (same accepted, different authors) 5 of 361 = I was not able to open this report: https://github.com/CatalogueOfLife/backend/issues/1182 = FIXED
Resolved 2022-11-22:
Resolved 2022-12-02:
Synced 2022-12-02
3i Auchenorrhyncha of 0.28.1 / 2023-01-03; imported 2023-01-04 from Geoff's laptop
TASKS
Broken decisions, 264: deleted all
Any [duplicated] uninomial, 13 https://www.checklistbank.org/catalogue/3/dataset/2317/duplicates?catalogueKey=3&category=uninomial&limit=500&minSize=2&mode=STRICT&offset=0&status=accepted @gdower, there are duplicated accepted genera and subfamilies in this report with identical position in the classification, but one record in the pair is empty (i.e. has no children), second has full set of children. Should the export script be modified and eliminate "empty" taxa?
Resolved 2023-01-05:
Synced 2023-01-05
For the names with the same rank and authorships in that report, it's because there is more than 1 OTU:
ID | decision | status | rank | label | scientificName | authorship | genus | specificEpithet | infraspecificEpithet | accepted | classification |
---|---|---|---|---|---|---|---|---|---|---|---|
13557 | ACCEPTED | SUBFAMILY | Biturritiinae Metcalf, 1951 | Biturritiinae | Metcalf, 1951 | Auchenorrhyncha > Cicadomorpha > Membracoidea > Aetalionidae | |||||
13556 | BLOCK | ACCEPTED | SUBFAMILY | Biturritiinae Metcalf, 1951 | Biturritiinae | Metcalf, 1951 | Auchenorrhyncha > Cicadomorpha > Membracoidea > Aetalionidae | ||||
48813 | BLOCK | ACCEPTED | SUBFAMILY | Centronodinae Deitz, 1975 | Centronodinae | Deitz, 1975 | Auchenorrhyncha > Cicadomorpha > Membracoidea > Membracidae | ||||
48814 | ACCEPTED | SUBFAMILY | Centronodinae Deitz, 1975 | Centronodinae | Deitz, 1975 | Auchenorrhyncha > Cicadomorpha > Membracoidea > Membracidae | |||||
320 | ACCEPTED | INFRAORDER | Cicadomorpha Evans, 1946 | Cicadomorpha | Evans, 1946 | Auchenorrhyncha | |||||
55442 | ACCEPTED | GENUS | Cicadomorpha Martynov, 1927 | Cicadomorpha | Martynov, 1927 | Auchenorrhyncha > Prosbolomorpha > Palaeontinoidea > Palaeontinidae > Palaeontininae | |||||
51803 | BLOCK | ACCEPTED | SUBFAMILY | Endoiastinae Deitz & Dietrich, 1993 | Endoiastinae | Deitz & Dietrich, 1993 | Auchenorrhyncha > Cicadomorpha > Membracoidea > Membracidae | ||||
51802 | ACCEPTED | SUBFAMILY | Endoiastinae Deitz & Dietrich, 1993 | Endoiastinae | Deitz & Dietrich, 1993 | Auchenorrhyncha > Cicadomorpha > Membracoidea > Membracidae | |||||
70998 | ACCEPTED | GENUS | Flatina Melichar, 1902 | Flatina | Melichar, 1902 | Auchenorrhyncha > Fulgoromorpha > Fulgoroidea > Flatidae | |||||
615990 | ACCEPTED | SUBTRIBE | Flatina Spinola, 1839 | Flatina | Spinola, 1839 | Auchenorrhyncha > Fulgoromorpha > Fulgoroidea > Flatidae > Flatinae > Flatini | |||||
21330 | BLOCK | ACCEPTED | GENUS | Hardya Edwards, 1922 | Hardya | Edwards, 1922 | Auchenorrhyncha > Cicadomorpha > Membracoidea > Cicadellidae > Deltocephalinae > Cicadulini | ||||
21339 | ACCEPTED | GENUS | Hardya Edwards, 1922 | Hardya | Edwards, 1922 | Auchenorrhyncha > Cicadomorpha > Membracoidea > Cicadellidae > Deltocephalinae > Cicadulini | |||||
55117 | BLOCK | ACCEPTED | GENUS | Lycoderes Germar, 1835 | Lycoderes | Germar, 1835 | Auchenorrhyncha > Cicadomorpha > Membracoidea > Membracidae > Stegaspidinae > Stegaspidini | ||||
55118 | ACCEPTED | GENUS | Lycoderes Germar, 1835 | Lycoderes | Germar, 1835 | Auchenorrhyncha > Cicadomorpha > Membracoidea > Membracidae > Stegaspidinae > Stegaspidini | |||||
26580 | ACCEPTED | GENUS | Macrosteles Fieber, 1866 | Macrosteles | Fieber, 1866 | Auchenorrhyncha > Cicadomorpha > Membracoidea > Cicadellidae > Deltocephalinae > Macrostelini | |||||
26571 | BLOCK | ACCEPTED | GENUS | Macrosteles Fieber, 1866 | Macrosteles | Fieber, 1866 | Auchenorrhyncha > Cicadomorpha > Membracoidea > Cicadellidae > Deltocephalinae > Macrostelini | ||||
55335 | BLOCK | ACCEPTED | SUBFAMILY | Myerslopiinae Evans, 1957 | Myerslopiinae | Evans, 1957 | Auchenorrhyncha > Cicadomorpha > Membracoidea > Myerslopiidae | ||||
55343 | ACCEPTED | SUBFAMILY | Myerslopiinae Evans, 1957 | Myerslopiinae | Evans, 1957 | Auchenorrhyncha > Cicadomorpha > Membracoidea > Myerslopiidae | |||||
53251 | ACCEPTED | SUBFAMILY | Nicomiinae Haupt, 1929 | Nicomiinae | Haupt, 1929 | Auchenorrhyncha > Cicadomorpha > Membracoidea > Membracidae | |||||
53250 | BLOCK | ACCEPTED | SUBFAMILY | Nicomiinae Haupt, 1929 | Nicomiinae | Haupt, 1929 | Auchenorrhyncha > Cicadomorpha > Membracoidea > Membracidae | ||||
55405 | ACCEPTED | GENUS | Prosbolomorpha Riek, 1974 | Prosbolomorpha | Riek, 1974 | Auchenorrhyncha > Prosbolomorpha > Palaeontinoidea > Dunstaniidae | |||||
615627 | ACCEPTED | INFRAORDER | Prosbolomorpha Popov, 1980 | Prosbolomorpha | Popov, 1980 | Auchenorrhyncha | |||||
646797 | BLOCK | ACCEPTED | GENUS | Scaphytopius Ball, 1931 | Scaphytopius | Ball, 1931 | Auchenorrhyncha > Cicadomorpha > Membracoidea > Cicadellidae > Deltocephalinae > Scaphytopiini | ||||
31179 | ACCEPTED | GENUS | Scaphytopius Ball, 1931 | Scaphytopius | Ball, 1931 | Auchenorrhyncha > Cicadomorpha > Membracoidea > Cicadellidae > Deltocephalinae > Scaphytopiini | |||||
3892 | ACCEPTED | GENUS | Synavea Lallemand, 1955 | Synavea | Lallemand, 1955 | Auchenorrhyncha > Cicadomorpha > Cercopoidea > Cercopidae > Cercopinae > Rhinaulacini > Liternina | |||||
65623 | UPDATE | ACCEPTED | GENUS | Synavea Emeljanov, 1995 | Synavea | Emeljanov, 1995 | Auchenorrhyncha > Fulgoromorpha > Fulgoroidea > Derbidae > Otiocerinae > Aquaeliciini |
@proceps, are the extra OTUs intentional?
Some intentional. Some exists just because we do not have a mechanism to delete duplicate OTU names. I always told, that CoL migration should be based on nomenclature, not OTUs, there would be no need to resolve duplicate OTUs and and missing TaxonNames, which do not have OTUs
We will ultimately need to start planning to resolve this properly on TW side, by building explicit sets of OTUs to send to the CoL, rather than using TaxonName proxy. It will take some time to work out, but it then we will truly reflect the core mission of the CoL, "these are the species".
Re-synced 2023-01-06 (extinct flag & version fixed)
3i Auchenorrhyncha of 0.28.1 / 2023-02-02; imported 2023-02-02 from Geoff's laptop
TASKS
Resolved 2023-02-03:
Synced 2023-02-03
3i Auchenorrhyncha of 0.30.3 / 2023-03-06; imported 2023-03-06 from Geoff's laptop
ISSUES assessed 2023-03-08
TASKS
@proceps & @gdower, curious case, I did find Changeondelphax velitchkovskyi (Melichar, 1913) twice in CLB: https://www.checklistbank.org/dataset/2317/classification?taxonKey=61207. Differences between records are: one has distribution data, another has no them; slightly different list of references.
One more species with double appearance: Rosenus pantherinus (Kusnezov, 1929)
(These cases appear in the report SYN-SYN species (different accepted(?!), same authors)
Resolved 2023-03-08:
Synced 2023-03-08
3i Auchenorrhyncha of 0.32.2 / 2023-04-12; imported 2023-04-12 from Geoff's laptop
ISSUES assessed 2023-04-14
TASKS
After deletion of broken decisions:
Resolved 2023-04-17:
Synced 2023-04-17
Geoff pointed to two OTUs:
@proceps, do you have a special reason to establist two OTUs with these 23 species?
3i Auchenorrhyncha dev
https://data.catalogueoflife.org/dataset/2317/classification
[x] Imported: 46305 spp (vs 10,455 spp in ac19). See below: https://github.com/CatalogueOfLife/testing/issues/135#issuecomment-877365142 Now CoL takes 21503 spp in agreed groups.
[x] Classification: many taxa (genera, subgenera, species) are outside suborder Auchenorrhyncha: