Wikidata talk:WikiProject Taxonomy/Archive/2023/11

This page is an archive. Please do not modify it. Use the current page, even to continue an old discussion.

Updates to Species File databases

The Species File Databases are being updated to use TaxonWorks. All the Species Files websites were frozen on 14 August 2023, pending the update (e.g. see note on SF Mantodea). Only a few of the new sites are currently available, e.g. SF Mantophasmatodea (the old version is available as an archive), SF Cockroach, SF Zoraptera, SF Isoptera, etc.. The new websites uses different URLs and IDs. I did change the formatterURL at Property:P6052, but then noticed that the IDs have also been changed. It seems to be the same database content ported to a new software system.

They are still in the process of updating the sites, so this is just a heads up. At some point the IDs need to be updated to the new ones or perhaps a new identifier is appropriate, in which case the old ones can link to the archived pages. Jts1882 (talk) 13:54, 24 September 2023 (UTC)

@Jts1882: Thanks for your hint. I had a brief look some days ago, but I need more time to adopt my bot. Please remember me. --Succu (talk) 21:25, 3 November 2023 (UTC)

@Succu: More of the Species Files have been updated but some are still only in development at GitHub. The current situation is:

• Specie Files with existing Wikidata identifier, but with new IDs: Orthoptera SF, Cockroach SF, Blattodea SF.
• Species Files with exisitng Wikidate identifiers, pending update (can be seen at GitHUb): Mantodea SF, Phasmida SF, Coreoidea SF, SF Lygaeoidea
• New Species Files that will need a Wikidata identifier: Zoraptera SF, Plecoptera SF, Dermaptera SF, Grylloblattodea SF, Mantophasmatodea SF, SF Isoptera , Aphid SF, Coleorrhyncha SF.

I have summarised the status of the changes, along with the links to Wikidata items and identifier properties on a user page at English Wikipedia: en:User:Jts1882/Phylogeny_and_taxonomy_resources#Species_Files. Jts1882 (talk) 17:53, 22 November 2023 (UTC)

Property "of" (P642) deprecated but needed for synonyms

@succu, Christian Ferrer, Plantdrew: Hello. Often old taxon names become superseded, especially in the case of fungi, and when this happens it is important to have a convenient link from the non-current taxon item to the current taxon item. According to the tutorial, this can be done by adding a "instance of (P31)" = "synonym (Q1040689)" statement (in addition to the normal "instance of = taxon" value) and adding the qualifier "of (P642)" with a value equal to the preferred taxon item. But P642 is currently being deprecated (see various discussions starting from Property_talk:P642#Essay:_P642_considered_harmful etc.) Linking from the current name to the synonym is no problem, since "taxon synonym (P1420)" allows this, but following the link in reverse is not a solution as it is complicated (necessitating a SPARQL query) and it is subject to caching delays.

Do we need to take action to insure that there is a suitable property to make the link from the old item to the new one? What should be the standard way of adding this information? Strobilomyces (talk) 14:00, 17 October 2023 (UTC)

• @Strobilomyces: see Ophioglypha palliata (Q105400292) and the use of "subject has role". Christian Ferrer (talk) 14:15, 17 October 2023 (UTC)

  @Christian Ferrer: Thanks for answering. So I conclude that your preferred way of giving the link from the non-current item to the current item is with property "subject has role (P2868)" having qualifier "of (P642)" showing the current taxon item. I have also been using that method, but I couldn't find it documented. Do you know if a decision to do it that way is recorded somewhere?

In any case property "of (P642)" is needed, but it may soon become unavailable. Do we need to take some action on this?

Also I see that some taxa use the "instance of" = "synonym" method, also with "of (P642)". Should we try to agree a single solution and then convert all to the same solution? Strobilomyces (talk) 14:44, 17 October 2023 (UTC)

I did not remember where, and even if, there was a formal decision... But I am ready support the creation of a property "is synonym of" with an inverse constraint with taxon synonym (P1420). A dedicated property is the best way to have "a single solution and then convert all to the same solution". Christian Ferrer (talk) 15:21, 17 October 2023 (UTC)

Note that there is potentially the same kind of issue if we want inverse properties for original combination (P1403) and basionym (P566). Christian Ferrer (talk) 15:28, 17 October 2023 (UTC) FWIT for those two properties I mysefl would have done only one property called "original combination/basionym".... and the single needed inverse property would have be "is original combination/basionym of" .... and to push the reasoning further a single property in a broader sense "original name" (with its inverse "is the original name of" would allow to be used for botany, zoology and even in the cases where e.g. a variety or a subspecies is raised at specific rank which is not less relevant than a recombination. Christian Ferrer (talk) 15:37, 17 October 2023 (UTC)

@Christian Ferrer: Yes, it is a very good point that we want to use "of (P642)" also for basionyms, protonyms etc. In fact at Wikidata:WikiProject_Taxonomy#Related_items, there is a long list of roles which might be used in this way - and that is currently allowed. So I think we need a single property to replace P642, rather than creating new properties "is protonym of", "is synonym of", "is basionym of", etc. Could we just change over to using "relative to (P2210)" instead of P642? Would that solve the main problem relatively easily? Strobilomyces (talk) 19:43, 18 October 2023 (UTC)

Yes this seems like a good idea. Christian Ferrer (talk) 06:22, 19 October 2023 (UTC)

At the P642 talk page, User:Wostr has suggested that we should have the replacing item at the higher level and add the type of replacement to that as a qualifier. For instance, the synonym item could have "replaced by (P1366)" set to the current item and have a qualifier such as "replacement type" = "synonym (Q1040689)". I think that would indeed be better, but it would be more difficult to bring about the change in WD, so I will not pursue that possibility.

@Christian Ferrer, Succu, Peter coxhead, Daniel Mietchen, Plantdrew, Tom.Reding: Should I create a WikiData request for comment, proposing that for taxonomy items, the use of "of (P642)" should be replaced by "relative to (P2210)"? Strobilomyces (talk) 09:47, 19 October 2023 (UTC)

I don't know... if really deprecated I'm a little curious about how/when they will replace "of" within the surely very impressive number of items where it is used. Christian Ferrer (talk) 18:16, 19 October 2023 (UTC)

I can't see that "relative to" is a good substitute to "of". In principle, I would prefer there to be two properties in every case (e.g. "basionym" + "basionym of", "replaced synonym" + "replacement name"), but unless this is agreed and implemented consistently, "of" is better. Peter coxhead (talk) 08:33, 22 October 2023 (UTC)

Thank you for your answer. The main reason that "of" is to be deprecated is that it does not translate well - possession is shown differently in different languages. I suppose that if we agree that "relative to" should be used in this way, it would work. Strobilomyces (talk) 10:32, 26 October 2023 (UTC)

basionym (P566), replaced synonym (for nom. nov.) (P694) and original combination (P1403) have a property inverse label item (P7087). You'll find the inverse statements under the section "Derived statements" in the UI. --Succu (talk) 16:55, 23 October 2023 (UTC)

@Succu: Hello. I am sorry, but I do not understand this. Please could you explicitly specify a page with the "Derived statements" section to which you refer? The value of the property inverse label item (P7087) is an item, not a property, but I think what we need is a property pointing in the inverse direction. Actually there is a property inverse property (P1696) and it would be fine if we could use that, but the inverse properties do not exist. I do not understand how you would propose to set up the inverse pointer - please could you give an example of that? I don't think that a solution is satisfactory if it requires the execution of a SPARQL query to follow the reverse pointer. Strobilomyces (talk) 18:48, 28 October 2023 (UTC)

@Strobilomyces: Did you read Wikidata usage instructions (P2559) of inverse property (P1696)? "Derived statements" is the section where inverse properties are listed., All you have to do is to add inverse label item (P7087) to a property. Neolloydia warnockii (Q14947661) is the basionym of three new combinations. Simply scroll down to "Derived statements"! --Succu (talk) 16:30, 30 October 2023 (UTC)

@Succu: Hello and thank you for this suggestion. I hadn't read the data usage instructions which you mention, but I have now. After some effort, I think I understand the solution which you are describing. You are saying that instead of having a statement of the synonym item pointing at the current item, we can use the "relateditems" gadget to show the inverse properties of a given item.

@Christian Ferrer, Peter coxhead: I will restate the solution as follows.

1. The user has to to enable the "relateditems" gadget by selecting it in the Wikidata user preferences. I have done that now.
2. Then when the user displays a synonym item, such as Neolloydia warnockii (Q14947661), there will be a box labelled "show derived statements" after the "Identifiers" section. The user should click on this box.
3. The gadget will then execute a SPARQL query to find all statements in Wikidata having the synonym item as object where also the property of the statement has a inverse label item (P7087) statement. Since Pediocactus warnockii (Q94384978) has property basionym (P566) with value Q14947661, and since P566 has property inverse label item (P7087) (actually set to basionym of (Q117187914)), the gadget will find and display this "basionym of" related item. Also it finds two others.

This system actually works at present, is quite fast (due to the cache), and can easily be extended to other types of replaced names.

I think this system has three problems.

• Firstly, when the interactive user looks at a taxon item, there is no indication whether the name has been replaced and is now only a synonym. The user has to actively run the gadget to find this out.
• Secondly, since the system relies on SPARQL, after a change is made, there will be a caching delay before the gadget will show the change. I know from experience that this delay may be many hours and can be inconvenient.
• Thirdly the "Wikidata usage instructions" which Succu mentions warn against using this feature often.

The second and third problems may not be critical, but I think the first problem is very bad, and not really acceptable. Please could you comment on whether this solution is feasible? If not, what should we do? Should I propose an inverse property to taxon synonym (P1420), with the intention later of proposing one for basionym (P566) etc. if that succeeds? Strobilomyces (talk) 20:25, 30 October 2023 (UTC)

I'm not aware a gadget is involved. But try (if not done) to make it a mandantorty one. --Succu (talk) 21:38, 30 October 2023 (UTC)

The gadjet Strobilomyces is talking about is MediaWiki:Gadget-relateditems.js, this is usefull indeed, e.g. with Neolloydia warnockii (Q14947661) it gives you the list of 3 items having basionym (P566) → Neolloydia warnockii (Q14947661) regardless of the fact we use "subject has role" or not. What worries Strobilomyces is that the users who don't have the gadget enabled, or have it enabled but don't use it (i.e. don't click on "show derived statements"), then they may miss those important informations. I guess it is possible to write a very similar gadjet that 1/ is enabled for every one by default 2/ works only for taxa 3/the infos are displayed automatically, in the purpose that if someone comes in a taxon item then he automatically know thoses infos. However I'm not able to do such a tool. Christian Ferrer (talk) 10:24, 1 November 2023 (UTC)

Requiring a gadget to achieve the required effect is a thoroughly bad idea, regardless of whether it is made mandatory. Much better is to have the inverse properties, then run some code to ensure consistency between the main and inverse properties automatically. This keeps the actual static database complete. Peter coxhead (talk) 07:52, 2 November 2023 (UTC)

I think that really the main requirement that we have for an inverse relationship such as "synonym of" is that a naive user will be alerted and think "Ah! There is another taxon name which apparently should replace this one." But the "relateditems" gadget does not meet this requirement.

@Christian Ferrer, Peter coxhead, Succu:My perception is that for those who have left comments, the most acceptable solution would be to have new inverse properties such as "synonym of", "basionym of", "protonym of" etc., pointing to the replacing item in each case. I suppose that such properties would be translatable to other natural languages. I suggest that we should propose the new property "synonym of" as inverse of of (P642), and I am willing to do this if nobody else wants to. If that property is approved, we should also be able to have properties "basionym of", "protonym of" etc. created. Please say if you agree with this. Strobilomyces (talk) 14:59, 2 November 2023 (UTC)

• I agree. Peter coxhead (talk) 16:06, 2 November 2023 (UTC)
• I can live with our current situation but I will support such property(ies) proposal(s). Christian Ferrer (talk) 17:43, 2 November 2023 (UTC)

1. Would the new proposed property "taxon synonym of" supersede this item with that label Q117188224?

2. I think that it would be better to have "taxon synonym" be its own inverse property for heterotypic synonyms, as taxonomists may legitimately disagree on which synonym to accept, and the respective synonyms may each be nomenclaturally valid. At the moment I think the property "taxon synonym" is used to designate both homotypic and heterotypic synonyms.

3. I support proposing inverse properties for "basionym", "original combination", and "protonym" Kbseah (talk) 10:07, 3 November 2023 (UTC)

@Kbseah: Hello. Thank you for your answer. In your first point, I think you are asking whether, according to the proposal, the item given as the object of "taxon synonym of" should supersede the item having the "taxon synonym of" property. I think the answer is "yes, that is the intention".

For your second point, indeed, "taxon synonym" is used for both homotypic and heterotypic synonyms, and these are distinctly different cases from the taxonomist's point of view. But I think that the same data structure can be used for both and in Species Fungorum they are mixed together. Taxonomists can disagree about homotypic synonyms just as well as about heterotypic synonyms - that is not a difference! For instance, mycologists are constantly inventing new genera of fungi and moving some species into them, so the old combinations are homotypic synonyms of the new combinations. Sometimes the new genus "catches on" and sometimes not. The solution to that is that property taxon synonym (P1420) and its inverses should always have a reference to indicate the authority; one name item may have multiple synonym properties with different references and another name item may have multiple "taxon synonym of" links with different references.

To each real-world taxon there corresponds a whole set of names which can have corresponding Wikidata taxon items. I think that a good way of using the word "synonym" would be to call all the names which have been applied to a taxon "synonyms", whether they are the current name, a valid synonym, or an invalid synonym. I think that that is in line with your suggestion that property "taxon synonym" should be its own inverse property for heterotypic synonyms. I think it would be good idea if the Wikidata data structure were arranged like that; all the equivalent names would be linked together through the synonym property and then some of them could be marked as invalid or "current name" (according to a particular reference). But (unfortunately in my view) the taxonomy project page and the taxonomy tutorial page use the word synonym in a sense where the current name is not included as a synonym. In order to specify an equivalent name at all, you have to choose what the current name is, since only that item can have the property P1420 (for a given reference). I would agree to using P1420 in both directions if in addition there were some way of marking the (purported) current name. But anyway I think that such a change in meaning would be too big for us to carry out now, it is not practical. Strobilomyces (talk) 14:47, 3 November 2023 (UTC)

Thanks for your detailed response! I think I understand the issue better now. Even if we don't take a position on which is the "current" name, it would still be useful to indicate which is the current name from the point of view of the cited reference. Encoding this information in the property is more straightforward than adding qualifiers to the statement, so I support the proposal for an inverse property "taxon synonym of".

In the talk page for P1420 I see now that "taxon synonym" was explicitly intended to be asymmetrical. However this isn't obvious from the item description. Would it be helpful to revise the description to something like "non-current name listed as a synonym of a current (accepted) taxon name"? Kbseah (talk) 15:06, 3 November 2023 (UTC)

Yes, I agree that the description of P1420 should be updated like that to make it clear that the current name is not a synonym. Also the Documentation part of the talk page should say that a reference should always be provided and that this property should only be used on a current name item ("current" according to the reference). Strobilomyces (talk) 17:39, 3 November 2023 (UTC)

@Christian Ferrer, Peter coxhead, Succu, Kbseah: Please can I ask another question? Instead of giving the name "taxon synonym of" to the proposed inverse property to taxon synonym (P1420), would it be a good idea to name it "current name" or "accepted name"? Strobilomyces (talk) 17:51, 3 November 2023 (UTC)

The usage of taxon synonym (P1420) is not restricted to the item with the "currently accepted name". BTW this property has no inverse property. --Succu (talk) 18:21, 3 November 2023 (UTC)

@Succu: In the "Taxon synonym" section of the tutorial, it states "Synonyms are non-current names (that is, non-current from the referenced point of view)". Also it indicates that the property is not symmetric as follows: 'The reverse relationship ("this name is a synonym of") can be indicated by "instance of: synonym", with a qualifier "of (P642)" pointing at the current name item - but perhaps a new property would be a good idea'.

Also in the Glossary of the tutorial it gives: " taxon synonym / synonym = a scientific name that also applies (in some way) to this taxon, but is not the correct name. "

The answer to Frequently Asked Question "I see that the latest taxonomic paper has changed the name of a species, what do I do?" stipulates the same asymmetric solution: ' "taxon synonym" = "name out of fashion" should be added to the item with the name in fashion, referenced with the relevant paper. In the item with the name out of fashion "instance of" "synonym [scientific name])", with the qualifier "of" "name in fashion" can be added, again referenced with the paper (we may make a separate property "is a synonym of" later, but we do not have one yet). '

The answer to the FAQ ' I sometimes see that "A" is marked as being a synonym of "B", while at the same time "B" is marked as being a synonym of "A". What about that? ' only makes sense with the asymmetric definition of synonym - it explains the both-ways link as due to different taxonomic viewpoints.

Also in various talk page comments I have always had the understanding that this asymmetrical meaning is how the taxon synonym (P1420) property is supposed to be used. To me this implies that P1420 should only be used in the item of the current name - in any case, you are not allowed to mention the current name as a synonym. If a current name changes (in a reference such as Species Fungorum), one should delete the old P1420 statement and create a new one in the item of the new name. Also the inverse properties should be updated accordingly. Strobilomyces (talk) 12:21, 4 November 2023 (UTC)

@Strobilomyces: Some history of the "tutorial" Brya 2015 and Strobilomyces 2017. --Succu (talk) 21:14, 4 November 2023 (UTC)

For me, the lesson of those two links is that a new inverse property would be a good idea. But I'm not sure what your point is. Strobilomyces (talk) 17:33, 5 November 2023 (UTC)

"If a current name changes (in a reference such as Species Fungorum), one should delete the old P1420 statement and create a new one in the item of the new name." Have you ever practised this? Moving sitelinks around for birds for something called "current name" is not a funny task, but mostly well grounded. Prepeared to do this for fungi? --Succu (talk) 22:03, 4 November 2023 (UTC)

I believe that (perhaps unfortunately) there are not an enormous number of P1420 statements on Wikidata fungus items and I would be prepared to have a go at updating them (with inverse statements) based on Species Fungorum synonym information, if the requirement and the data model solution were clearly agreed. Another bigger project would be finding all the WD items which actually should have synonym statements (according to Species Fungorum) and adding them to Wikidata, and I don't know about that. Perhaps I'd try to do that if requested, initially only for some sections. Note that I am sure that only a small fraction of the names in Species Fungorum are notable enough to appropriately have items in Wikidata, and there are even many more non-notable names which come into the Index Fungorum part but not the Species Fungorum part. Strobilomyces (talk) 17:33, 5 November 2023 (UTC)

I'd be open to calling the inverse property "current name" or similar, because that makes the intended asymmetrical meaning clearer. A reference should be required, too.

How would you suggest representing pro parte synonyms? Kbseah (talk) 18:35, 4 November 2023 (UTC)

@Kbseah: Could you please explaine/define your understandig of the term "pro parte synonym". BTW: "current name" is a bad label for a property. --Succu (talk) 21:32, 4 November 2023 (UTC)

pro parte: What one author recognizes as one taxon is considered by another author to consist of more than one taxon, so the synonymy only applies to part of the former.

For example, there's a ciliate class Spirotrichea Q117735, and an infraphylum Spirotrichia Q23069908. The author of the publication Q54018828 accepts Spirotrichea Bütschli, 1889 and calls Spirotrichia a synonym pro parte.

The prokaryote taxonomists apparently do not recognize partial synonyms: https://lpsn.dsmz.de/text/glossary (under "Synonyms"). Kbseah (talk) 22:24, 4 November 2023 (UTC)

Species Fungorum treats pro parte synonyms just like general synonyms, for instance genus Telamonia is proposed for a small part of genus Cortinarius, but it is given as just a synonym. By the way, this is part of a very big change which is coming soon for mushroom enthusiasts and the Wikimedia projects, but Species Fungorum and Mycobank have not taken it on yet. Strobilomyces (talk) 17:33, 5 November 2023 (UTC)

@Christian Ferrer, Peter coxhead, Succu, Kbseah: Hello. To summarize, I think that only one proposal has reasonable support from those who responded - to have new inverse properties such as "synonym of", "basionym of", "protonym of" etc., pointing to the replacing item in each case. My plan is to request such properties if "of (P642)" becomes actually illegal. Strobilomyces (talk) 16:28, 20 November 2023 (UTC)

Fine, for me. Christian Ferrer (talk) 20:12, 20 November 2023 (UTC)

Agreed, too. Peter coxhead (talk) 11:19, 23 November 2023 (UTC)

Fine for me too. I don't think we necessarily have to wait until P642 gets withdrawn, though. Kbseah (talk) 14:55, 30 November 2023 (UTC)

Need for reference

For me, part of the problem with the current situation is the regular absence of references for taxon synonym (P1420). Given that the property is intended to be assymmetric, since a name can be the accepted name for one source but a synonym for another, without a reference it's not clear that the property is being used correctly. It might be better to have a qualifier like "according to" rather than relying on a reference. Peter coxhead (talk) 10:03, 29 November 2023 (UTC)

Is this property intended to be (and, if so, should it be) asymmetric? I understood it to be like the Synonymy heading/section here: Wikispecies:Caretta caretta, i.e., Testudo caretta, Testudo marina, and Caretta caretta are all in synonymy with each other, Maculosae tegmine lyncis (talk) 12:07, 29 November 2023 (UTC)

From the discussion above (before this subheading), it looks like different users have interpreted this property differently, so there is some inconsistency in the usage on Wikidata. Adding references would help, but of course it depends on how the sources themselves define synonymy.... Kbseah (talk) 14:58, 30 November 2023 (UTC)

Help needed with merge request

Can someone take a look at Help_talk:Merge#Merge_request_for_Q4666317_and_Q72725? Mbch331 (talk) 14:18, 15 November 2023 (UTC)

Guidance needed for Tamil Wikipedia

Hello!

I am from Tamil Wikipedia. I want to implement this wikidata based taxobox for botanical Tamil articles. I added Tamil translations to all related items to the following Template. Even though i change the language code in the template as 'ta' here, i can't view the Tamil translations in this page. How can i see? if some one set the wikidata based infobox in this Tamil article w:ta:அகத்திய மல்லி, i will populate the wikidata template to all Tamil botanical articles. And also it will help to get our community consensus for this usage.

Jasminum agastyamalayanum
Systematics
Clade	Angiospermae
Clade	Mesangiosperms
Clade	Eudicots
Clade	Core eudicots
Clade	Asterids
Clade	Lamiids
Order	Lamiales
Family	Oleaceae
Genus	Jasminum
Species	J. agastyamalayanum
Scientific name of species
Jasminum agastyamalayanum
Sabeena, Asmitha, Mulani, E.S.S.Kumar & Sibin (2007)

{{#invoke: Taxobox | taxobox | qid=Q51077658| count= |lang=ta}} Info-farmer (talk) 05:34, 24 November 2023 (UTC)

References