WLoC, World List of Cycads (id 1163): test report

[yroskov]

The export received from Michael Calonje on 2024-07-11 as _World_List_of_Cycads_Export20240711190713.xlsx export file from BRAHMS; plus _Genera_Export20240712110746.xlsx and _Families_Export20240712110714.xlsx with authors for genera and families.

Export files converted by @mdoering. Imported on DEV https://www.dev.checklistbank.org/dataset/1163/imports

[yroskov]

Imported on DEV 2024-07-24, iteration 1 https://www.dev.checklistbank.org/dataset/1163/imports

Metrics:

• [ ] Imported: 394 spp (vs 355 spp of Feb 2019)

• [x] Metadata: alias applied as WLoC (before cycads list had no short name in CoL; version corrected as Jul 2024 / 2024-07-11. Other metadata were copied from previous version.

• [x] Classification: ranks order (1) - family (2) - genus (10) - species (394) - infraspecific names (35)

• [x] Infraspecific names need to be split into ranks subspecies, variety & forma. Fields in the source file: Subspecies |SubspeciesAuthorName | Variety | VarietyAuthorName | Forma | FormaAuthorName = FIXED in Iteration 3

• [x] Families and genera have authorstrings

• [x] Shall we include in the CoL names with TaxStatus Invalid & NomenDubium (other values Accepted & Synonym): yes, if they have parent accepted name; no (bare name), if they have no parent accepted name = need to be confirmed with Michael. In the iteration 2024-07-24, NomenDubium names got a status "prov acc". See also field Invalid with values inv & blank. Sometimes inv in Invalid does not equal to invalid in TaxStatus = FIXED IN ITERATION 3

Note: number in square brackets in CalcFullName in the source file indicates homonyms (e.g. Ceratozamia fuscoviridis [1] & Ceratozamia fuscoviridis [2])

• [x] Binomials are incorrectly placed as synonyms of the genus (e.g. Eriozamia hort ex J.Schust. (nomen invalidum), Eriozamia latifolia Hort. ex J.Schust. (nomen invalidum), Palmifolium Kuntze (nomen legitimum), Zamia amplifrons Hort. ex J.Schust. (nomen invalidum), Zamia brachyphylla Hort. ex J.Schust. (nomen invalidum) etc. are synonyms of Zamia L.) These are mainly names with status nomen invalidum (field TaxStatus with value Invalid) = FIXED in Iterations 2-3 https://www.dev.checklistbank.org/dataset/1163/taxon/41b2a097-b108-4852-9ce1-c39ddfb0b25f Almost all genera have binomials in synonymy.

• [ ] Sector:

• [ ] Extinct flag: n/a

[mdoering]

I have just uploaded a new version which improves handling of nomen dubium, invalid & illegitimate names. I will stop here and leave it as it is during my absence. So you can review

Now all accepted names are placed in the genus, incl infraspecific names. Doubtful and invalid names are treated as bare names, unless they have an explicit synof relationship (which is rare)

[yroskov]

Thanks! I'll continue with a new iteration.

Seems, proper tests and consultations with WLoC will take a time. Have a nice vacations!

[mdoering]

I see infraspecifc names lack a proper rank. I will fix that quickly and upload. 5 minutes...

[mdoering]

searching for tridentata gives you a nice idea of bare names vs synonyms

[yroskov]

Imported on DEV 2024-07-24, iteration 3

Metrics:

• [x] Imported: 376 spp (vs 394 spp of 2024-07-24 iteration 1)

• [x] Classification: ranks order (1) - family (2) - genus (10) - species (376) - subspecies (12) - variety (2) - (no accepted forms in the source file)

• [x] Extinct flag: n/a

• [x] Distribution: OK

• [x] Link to the species page in the original website

[yroskov]

Iteration 3 (imported on DEV 2024-07-24, 4:14 PM ) summary of remaining issues

• [x] All Invalid & NomenDubium names in TaxStatus should have "bare name" status in CoL. I have checked 10 remaining Invalid names (9 spp & 1 var) which have status "synonym" in the Iteration 3 against WLoC website: these names are not included in synonymy; they listed separately as Invalid Name Publication = IT'S WEBSITE INTERPRETATION ONLY

= After discussion with Michael: KEEP THESE 10 in COL AS THEY ARE NOW IN ITERATION 3 (i.e. as synonyms)

Example: Encephalartos caffer (Thunb.) Lehm. in DEV https://www.dev.checklistbank.org/dataset/1163/taxon/8784b87c-e197-4aea-bb62-8b55abae668d

Encephalartos caffer (Thunb.) Lehm. in WLoC http://cycadlist.org/taxon.php?Taxon_ID=280 Encephalartos cycadis Sweet INVALID in WLoC http://cycadlist.org/taxon.php?Taxon_ID=624

Here is a list of 10 names:

Zamia nana [2] Macrozamia pectinata Macrozamia littoralis Encephalartos villosus var. nobilis Encephalartos douglasii Macrozamia hopei [1] Encephalartos pumilus Zamia parasitica Encephalartos latifolius Encephalartos cycadis

[yroskov]

Iteration 3 (imported on DEV 2024-07-24, 4:14 PM ) summary of remaining issues

• [x] References: missing Author(s) and Year. For plants, we usually create CoL bibliographic reference from the "nomenclatural citation" (fields SpeciesAuthorName (in the case of combination, we take only author(s) after right bracket only (i.e. (Salisb.) Miq.) ) + PublishYear + ProtologueCitation). Usually, I also ask to add preposition with colon In: in the Source/Title. For example, Bowenia serrulata (W.Bull) Chamb. - Ref Chamb. In: Bot. Gaz. 54: 419. (1912). https://www.catalogueoflife.org/data/taxon/5WQC2 = FIXED in prod version of 2024-08-14

[yroskov]

Iteration 3 (imported on DEV 2024-07-24, 4:14 PM ) summary of remaining issues

ISSUES

[yroskov]

Iteration 3 (imported on DEV 2024-07-24, 4:14 PM ) summary of remaining issues

ISSUES

• [x] Parent Species Missing & Accepted Name Missing, 14: subspecies which are not assigned to the parent species. Links between subspecies and parent species are missing = FIXED in prod version of 2024-08-14 https://www.dev.checklistbank.org/dataset/1163/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&issue=parent%20species%20missing&limit=50&offset=0

In the Tree, they appear in the parent genus, i.e. outside existing species. For example: https://www.dev.checklistbank.org/dataset/1163/classification?taxonKey=210f828b-069f-456b-9afc-d82421a62ae4

[mdoering]

I have fixed the missing species issue for infraspecies, but there are still synonyms missing an accepted name. The original data is lacking some information, e.g. Cycas longipetiolula claims to have the accepted name Cycas bifida x c. multipinnata with id e781d518-6d82-4dfb-be67-893e1d026cff, both which do not exist in the spreadsheet. Not much I can do here.

The original website does have that info: http://cycadlist.org/taxon.php?Taxon_ID=151

Another example of a missing species referenced from synonyms is

5eafe3fa-bee5-4fa3-be3f-480cb7c08ff1 Phoenix dactylifera

[mdoering]

For the references I am uncertain if adding the nomenclatural author is improving the data. It is not a botanical practice you find on the source site, IPNI, WFO or others.

Does it hurt to leave it as it is?

[mdoering]

I have uploaded the latest version with no reference change to prod - where I only updated the version/issued date metadata

[yroskov]

It is CoL standard for building bibliographic reference from nomenclatural citation in the botanical scientific name. If you need help on how to do it, please talk to @gdower. He completed this for many botanical GSDs.

[yroskov]

I have uploaded the latest version

Thank you, Markus!

[mdoering]

ok, I have tried my best to also change the references. It's on prod already.

[mdoering]

Damn, there are some problems with the references. Going to fix that ... https://www.checklistbank.org/dataset/1163/references?limit=50&offset=0

[mdoering]

Now they look good to me: https://www.checklistbank.org/dataset/1163/references?limit=50&offset=0 I stop here

[yroskov]

Wow! Perfect. Many thanks!

[yroskov]

IPNI, WFO or others

Yeah, it would be nice if all these resources send us properly prepared bibliographic references (and with page/publicaion URLs). Unfortunately, most of them are far behind their users expectations. That's why we at CoL do our best to improve their data slightly and temporarily.

[yroskov]

WLoC: World List of Cycads of 2024-07-11; imported 2024-08-14 (converted by Markus)

• [x] Imported: 376 spp (vs 355 spp of Feb 2019)
• [x] Metadata: Alias added as WLoC (see email exchange with Michael Calonje); version applied as Jul 2024 / 2024-07-11. Other metadata were saved from previous version.
• [x] Classification: OK.
• [x] Sector: broken (previous sector was Class Cycadopsida). Order Cycadales re-established as a sector 2024-08-14 via editing Target & Subject in Sector https://www.checklistbank.org/catalogue/3/sector?limit=100&offset=0&subjectDatasetKey=1163
• [x] flag "extinct": n/a
• [ ] DOI:

Metrics

ISSUES assessed 2024-08-15

TASKS

Resolved 2024-08-15:

Synced 2024-08-15

See colon in Target - will this affect results of sync?

[yroskov]

So far, deletion of the sector failed: "with status code 503. The SyncManager is currently not available"

[mdoering]

yes, see slack. I had to do some urgent changes in the db and stop all write operations for the next 1-2 hours probably. Wasn't expected, sorry

[yroskov]

• [x] Sector: See colon in Target - will this affect results of sync? = Yes, order Cycadales is placed in the top of the tree:

Resolved:

Step 1. Delete sector in full. Node disappeared in the Tree, but software says Request failed with status code 404. Sector 3:98 does not exist. HTTP method: GET. https://api.checklistbank.org/dataset/3/sector/98 Step 2. Establish class Cycadopsida Brongn. (it was vanished) Step 3. Establish order Cycadales inside Cycadopsida as a sector

Re-synced 2024-08-15