Wikidata talk:WikiProject Taxonomy

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On this page, old discussions are archived. An overview of all archives can be found at this page's archive index. The current archive is located at 2024/06.

Q374302 and Q25170208[edit]

copied from Help talk:Merge by author  TomT0m / talk page 09:24, 21 March 2024 (UTC)[reply]


house finch (Q374302) is older, but House Finch (Q25170208) is more detailed and has sitelinks. Special:MergeItems complains that the short names don't match up in every language; one of these uses the Latin name in every language, the other the common name. I'm not sure what to do here. Grendelkhan (talk) 22:25, 20 March 2024 (UTC)[reply]

@Grendelkhan Yeah, unfortunately, because the first item is based on the scientific name "Carpodacus mexicanus" and the second on the scientific name "Haemorhous mexicanus", they have to remain separate items per WikiProject Taxonomy's introduction text (some text was bolded in the original, some bolded by me):
As a result, there is not a single, universally accepted classification of the living world. For users of taxonomic information, perhaps the most frustrating consequence of this is that there can be multiple names for the same species. Most taxonomic databases will tell you which species name they prefer (i.e., which name they "accept"), and what is the "correct" classification for that species. But Wikidata includes information from multiple sources, and these sources may disagree on the accepted name for a species, hence to remain neutral Wikidata may have items for each alternative name for a species.
Monster Iestyn (talk) 00:49, 28 March 2024 (UTC)[reply]
@Monster Iestyn It could be possible to have several names on one item, however. author  TomT0m / talk page 08:51, 11 April 2024 (UTC)[reply]
Hi, similar to the separate pages for, eg, Global Biodiversity Information Facility (Q1531570) Felis leo & Panthera leo, there is one scientific name here per item, though the different items can be linked via taxon synonym (P1420), original combination (P1403), etc, Maculosae tegmine lyncis (talk) 09:00, 11 April 2024 (UTC)[reply]
I understand that, I just wanted to stress that I think in the Wikidata case the model is flexible enough to allow to do things differently and put several names in a single item. author  TomT0m / talk page 09:31, 11 April 2024 (UTC)[reply]

New property proposal: Featherbase ID[edit]

As per Wikidata:Property proposal/Featherbase ID. Daniel Mietchen (talk) 21:40, 23 March 2024 (UTC)[reply]

Handling of ambiguities with P9157[edit]

Hi everyone,

Recently, I have been importing a lot of Open Tree of Life ID (P9157), linked to Open Tree of Life reference taxonomy version 3.6 (Q124708476), following the modelling used by @Succu for the previous editions.

As preliminary word, I took the latest (v3.6) Open Tree Taxonomy (https://files.opentreeoflife.org/ott/ott3.6/ott3.6.tgz) and joined all OTT IDs to the mappings OTT has internally (so GBIF, NCBI, IRMNG, WORMS). For all taxa, if one (or multiple) of those were present, I added the corresponding OTT ID.

@Succu already made me aware of some entries which cause constraint violations: https://www.wikidata.org/wiki/Wikidata:Database_reports/Constraint_violations/P9157.

This is because:

- If there are a GBIF ID and an NCBI ID linking to different OTT IDs on the same item, then it will end up having two OTT IDs

- If there are two different GBIF (or else) IDs on two different items linking to the same OTT ID, then this OTT ID will be present on both.

This is expected as the current modelling is about taxon names, so I guess this is OK.

More recently @VladXe also complained (https://www.wikidata.org/w/index.php?title=Topic:Y2gnduj9izdog3pl&topic_showPostId=y2gnduj9j3bqo7nt#flow-post-y2gnduj9j3bqo7nt) I consider these cases as expected and not faulty. I still stopped the upload before clarification.

Am I missing something here? AdrianoRutz (talk) 12:18, 8 April 2024 (UTC)[reply]

Online translation: Pseudomonadota ≠ Proteobacteria and the bot should take this into account. VladXe (talk) 15:53, 8 April 2024 (UTC)[reply]
I believe this is not reflecting the actual way taxa are modeled on Wikidata, as the items correspond more to taxon names than taxa.
The bot is adding external identifiers corresponding to these taxon names. And based on the external sources, what it does is correct. If you have a rationale to suggest to limit errors coming from them (such as not adding external IDs to items having a replaced synonym (for nom. nov.) (P694) statement as in your example, I will be happy to follow it but could not find any guidance about it so it should also be properly documented. AdrianoRutz (talk) 16:27, 8 April 2024 (UTC)[reply]

New Property Proposal: PlantZAfrica Plants of the Week ID[edit]

I've made a property proposal for PlantZAfrica Plants of the Week ID, which is open for discussion at https://www.wikidata.org/wiki/Wikidata:Property_proposal/PlantZAfrica_Plants_of_the_Week_ID. AdamSeattle (talk) 23:52, 11 April 2024 (UTC)[reply]

Update to discussion of synonyms[edit]

@succu, Christian Ferrer, Plantdrew, Strobilomyces, Peter coxhead, Daniel Mietchen: The previous discussion seemed to conclude with a call to create inverses of original combination (P1403) and basionym (P566). I have folded these into the tables of use cases of P642 ("of"), since the planned deprecation of P642 was the main reason for the discussion. Please review use cases i21, i22, and i23, making sure that I've 1) understood the consensus correctly and 2) captured all the affected statements in my queries, and if not, feel free to edit. And if/when one of you creates proposals for these properties, please update the table. Thanks! Swpb (talk) 14:51, 8 May 2024 (UTC)[reply]

  • For i21, taxon synonym (P1420) is, in my understanding, intended to be assymmetric, so personaly I would remove P31 = "synonym" only to replace it with main statement "synonym of", as for the two others. Why it is assymmetric? that's simple: almost all (if not all) external sources about taxonomy give it assymmetric, there is one "valid, accepted,.." name (according to one specific source) and possibly a list of synonyms for that name. Christian Ferrer (talk) 16:09, 8 May 2024 (UTC)[reply]
    • Ok, so changed. Obviously that asymmetry doesn't square with the lay meaning of "synonym", but I defer to you on its technical use in taxonomy. Swpb (talk) 18:30, 8 May 2024 (UTC)[reply]
My understanding is that, on wikidata, it is symmetric? Maculosae tegmine lyncis (talk) 18:59, 8 May 2024 (UTC)[reply]
  1. I think that the opinion of user:succu is very important since that person makes a lot of changes to these items.
  2. Our tutorial says that taxon synonym (P1420) is asymmetrical and so if P642 is going to disappear, we definitely need the "synonym of" property. That is what the table of use cases says, so that is fine. Personally I think that the data structure would be better if P1420 were symmetrical, but then we would need a "current name" flag to show which synonym was the real current one. I don't suppose that we can agree that change, so let's carry on with the new inverse synonym property.
  3. Our current synonym property, P1420, is named "taxon synonym" and therefore I think the name of the new inverse property needs to be "taxon synonym of" and not "synonym of". In my view, that is quite important in order to make clear that this property "belongs" to the taxonomy context. Unfortunately I myself proposed "synonym of" in the original discussion, but I think that that was a mistake.
  4. Subject to the change that i21 inverse property should be named "taxon synonym of", I agree with the three use cases as they now stand. Strobilomyces (talk) 19:55, 8 May 2024 (UTC)[reply]
Changed to "taxon synonym of" in the table. Of course, labels aren't set in stone even after a property is created. Swpb (talk) 19:27, 9 May 2024 (UTC)[reply]
Wikidata needs to be neutral with respect to taxonomy. So if one reliable source accepts X as the name of a taxon with Y as a synonym, and another reliable source accepts Y as the name of the taxon with X as a synonym, Wikidata must handle both views. So, yes, "taxon synonym" should be assymmetric in relation to a reliable source. The problem in reality is that the reference to the source is often missing. Peter coxhead (talk) 15:46, 9 May 2024 (UTC)[reply]
A citation-needed constraint (Q54554025), with a constraint clarification (P6607) if needed, can be added to taxon synonym (P1420) and "taxon synonym of", and can even be specified in the latter's proposal, when someone creates it. Swpb (talk) 19:34, 9 May 2024 (UTC)[reply]
What are you telling us? --Succu (talk) 21:38, 10 May 2024 (UTC)[reply]
Peter coxhead was saying taxon synonym (P1420) and "taxon synonym of" statements should have references for which name is primary. I was just saying that's easy to enforce. Swpb (talk) 02:06, 11 May 2024 (UTC)[reply]
@succu, Christian Ferrer, Plantdrew, Strobilomyces, Peter coxhead, Daniel Mietchen: In addition to the three inverse properties ("taxon synonym of", "protonym of", and "basionym of") in the tables of use cases of P642 ("of"), we also need a similar inverse of replaced synonym (for nom. nov.) (P694). I suggest that this should be named "replaced synonym of". Please can we add a corresponding row to the use case table?
Added table entry. Swpb (talk) 16:00, 13 May 2024 (UTC)[reply]
@succu: Hello user:succu. Do you see any objection to me proposing the 4 new inverse properties ("taxon synonym of", "protonym of", "basionym of" and "replaced synonym of")? The existence of a reference could be enforced. If no objection, I intend to propose them. Strobilomyces (talk) 15:49, 13 May 2024 (UTC)[reply]
I support these 4 new inverse properties; much better than "subject has role ... of". Peter coxhead (talk) 16:40, 13 May 2024 (UTC)[reply]
+1 Christian Ferrer (talk) 04:58, 14 May 2024 (UTC)[reply]
@succu, Christian Ferrer, Plantdrew, Strobilomyces, Peter coxhead, Kbseah: Hello. I have made a proposal for property "taxon synonym of" here. Please could you add your comments to the discussion section? Strobilomyces (talk) 18:20, 19 May 2024 (UTC)[reply]
We should add a "citation needed" constraint to the property, but I don't know how to specify this. Can anyone tell me? Strobilomyces (talk) 18:25, 19 May 2024 (UTC)[reply]
I would like to ping the whole taxonomy project about this proposal, but the "ping project" template does not work as there are over 50 members. What should I do about this? Strobilomyces (talk) 18:43, 19 May 2024 (UTC)[reply]
@Strobilomyces: In such case I think the practice is to put a new message on the talk page of the project, I just did it [1]. Christian Ferrer (talk) 18:11, 20 May 2024 (UTC)[reply]

Different or Same?[edit]

Kindly requesting help with disambiguation please.

Are the below two items the same or different? And should they be merged?

They have different fossil works ID, one has an extra letter 'o' in its spelling, and have different parent taxon (P171), but the same taxon rank (P105) within the same branch. Wallacegromit1 (talk) 05:53, 12 May 2024 (UTC)[reply]

The Fossilworks website seems to be down, so it's hard to say where "Hyperdapedontinae" comes from, but the four hits I found for that name in Google Scholar all appear to be typos for "Hyperodapedontinae". According to https://doi.org/10.1111/1475-4983.00143, "Hyperodapedontinae" is a nomen translatum from the family name Hyperodapedontidae Lydekker, 1885, but I could not find the publication by Chatterjee 1969 online. Kbseah (talk) 09:41, 21 May 2024 (UTC)[reply]
Fossilworks looks like it's gone for good. There are records at the Paleobiology database with the same identifiers: 159208 (for "Hyperdapedontinae" ), 159209 and 92222 (both for "Hyperodapedontinae"; not sure why there are two entries). The record for "Hyperdapedontinae" is incomplete (no parent, sister or child taxa) and only contains information on collections. The genus is Hyperodapedon so "hypero-" must be the correct spelling. Jts1882 (talk) 12:52, 21 May 2024 (UTC)[reply]

Proposals for new Species Files identifiers[edit]

The Species Files databases on insect orders have been updated to use Taxonworks. I have made identifier proposals for nine of these new or updated databases at Wikidata:Property proposal/Identifiers for Species Files databases.

There is also the issue of what to do about five of databases that had identifiers, as the new databases use different taxon IDs so an update of the Formatter URL is not possible. See above link for more information. Jts1882 (talk) 16:59, 18 May 2024 (UTC)[reply]

New property proposal[edit]

Wikidata:Property proposal/taxon synonym of Christian Ferrer (talk) 18:07, 20 May 2024 (UTC)[reply]

Thanks to User:Christian Ferrer for adding this section. Please add your comments to the proposal page. Strobilomyces (talk) 15:38, 21 May 2024 (UTC)[reply]
Now I have added proposals for the related properties Wikidata:Property proposal/protonym of, Wikidata:Property proposal/basionym of and Wikidata:Property proposal/replaced synonym of. Please add comments on these pages too. Also if anybody could include more examples, that would be welcome. Strobilomyces (talk) 17:04, 21 May 2024 (UTC)[reply]
I also put a note in the Village Pump of Wikispecies. Christian Ferrer (talk) 05:27, 22 May 2024 (UTC)[reply]
@succu, Christian Ferrer, Plantdrew, Peter coxhead, Kbseah: Hello. If you are in favour of the four proposed properties, please could you add more examples to them? And any further comments? Strobilomyces (talk) 12:08, 28 May 2024 (UTC)[reply]
✓ Done each proposals has at least 3 exemples. Christian Ferrer (talk) 12:50, 28 May 2024 (UTC)[reply]
user:ZI Jony has now kindly added the properties taxon synonym of (P12763), replaced synonym of (P12764), protonym of (P12765) and basionym of (P12766). I added a citation-needed constraint to "taxon synonym of", "replaced synonym of" and replaced synonym (for nom. nov.) (P694), so these properties give a warning if there is no reference. taxon synonym (P1420) already has this constraint. I am not sure about the requirement for the other properties and I have not added the citation-needed constraint to them. Strobilomyces (talk) 16:20, 29 May 2024 (UTC)[reply]
I updated the project tutorial for the new properties, and I would be interested in any comments. You can find my changes by using a diff. Also I added some of the properties to the table on the project page and deleted the P642 entry. I hope that is OK. Strobilomyces (talk) 20:36, 29 May 2024 (UTC)[reply]
Fine, I added a note about "protonym of" and an other note to use "object has role" instead of "instance of (shouldn't be a qualifier) [2], furthermore "object has role" works well with the infobox, as the relevent module have already be modified that way. Christian Ferrer (talk) 16:46, 30 May 2024 (UTC)[reply]
@Christian Ferrer: I do use Taxoboxes, but I also provide much the same information on the Commons category pages and gallery pages. I am not sure whether for fungi we should change to a system which only uses the Taxoboxes and relies on Wikidata. If you can easily maintain the Taxobox system, that may be a good idea. You only show the new inverse properties, don't you, not the old properties like taxon synonym (P1420)? I did not have much time to spend on it now and I am travelling for about a week from now. Please could you give an example where we can see the new taxobox in action? Strobilomyces (talk) 16:19, 2 June 2024 (UTC)[reply]

Hello, do we also need a proposal for Junior homonym of (eg. Leptodon Gaudry, 1860 (Q126280423) junior homonym of Leptodon (Q545108))? Thank you, Maculosae tegmine lyncis (talk) 19:37, 1 June 2024 (UTC)[reply]

Also, how do we best handle reranking/suffix alterations, eg, Ornithoryncina BHL → Ornithorhynchidae (Q21811), Ornithorhynchoidea (Q126163427), or subgenus to genus, Antilope (Tragoceros) BHL → Tragocerus (Q16707169)? original rank/suffix of? Thank you, Maculosae tegmine lyncis (talk) 19:54, 1 June 2024 (UTC)[reply]
I have also often asked myself the question regarding the change of ranks, especially for changes towards specific and subspecific ranks. I would support a kind of property "original name", broad enough to be applied for all codes (botany, zoology, ect..) and all ranks. Regarding homonymy we also can have a property "homonym" where we add a qualifier "object has role" later homonym (Q17276484) or earlier homonym (Q21651662), but also hemihomonym (Q36033662), that way no need for opposite property. Christian Ferrer (talk) 21:46, 1 June 2024 (UTC)[reply]

Encyclopedia of Life sync?[edit]

How is the quality of EOL data these days? We have just over 1M EOL IDs, and I don't see any other properties from them. Are there any bots that sync updates from a list of substantive entries as they're edited on EOL? Sj (talk) 14:18, 23 May 2024 (UTC)[reply]

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