Wikidata talk:WikiProject Taxonomy/Tutorial

I used the example Nanger dama (Pallas, 1766), selected at random. It is not immediately obvious how in such cases author(s) names should be entered in Wikidata. The obvious idea would be to enter these with the original name Gazella dama and use the basionym property? - Brya (talk) 05:38, 6 December 2013 (UTC)

Option 2

You once said, basionym (P566) (basionym) is only for plants, as "basionym" is not defined for animals. Now you present it in the tutorial?  — Felix Reimann (talk) 12:26, 12 December 2013 (UTC)

Indeed, basionym exists only in the ICNafp, although the prokaryote Code uses the same concept.

        I am still trying to find something that works. The simple thing would be to allow strings for author citations; anything else is likely to be confusing to many users. It appears that for algae, fungi and plants we are moving to the model where the current name has the author(s) and ex author(s) of the current name, while the author(s) and ex author(s) of the basionym is included with the item of the basionym. This can work, although it requires the Taxobox module maker to design a fairly complex algorithm. It incidentally also requires every name to have its own item.

        I still don't see what is being adopted for animals, but I don't really see an alternative to the above. If a string is not allowed, the easiest way seems to be to use the same structure. Of course, in the zoological Code there is no such thing as a basionym, but it has "an original combination" which is roughly the same concept (but pretty close if basionym is limited to species and subspecies). We could have a new property "original combination" or we could have a new property like "parentheses", but this seems the least hassle? - Brya (talk) 17:59, 12 December 2013 (UTC)

The only difference in the approach is that the basionym/orig. combination is not an extra item. Thus, we just have one more P225 for the name of the basionym (which has a qualifier "instance of basionym/orig. combination"). The rest is the same. Advantage: We do not need to move interwiki links back and forth. Your 3 options you need to cope with interwikis and which all are not "perfect" from the users point of view (as either are mapped to an item which properties do not fit to the article) or cannot be linked as Wikipedias are used to.  — Felix Reimann (talk) 18:24, 12 December 2013 (UTC)

I see. And how can parent taxon be made a qualifier of "taxon name"?

        Perfect mapping is not going to be possible, not as long as taxa themselves are variable. Rather, it is a matter of finding the least imperfect solution. - Brya (talk) 04:15, 13 December 2013 (UTC)

Types

@Succu: I'm not aware of other kind of types that type specimen, can you provide a link ? What is their name ?  – The preceding unsigned comment was added by TomT0m (talk • contribs).

type (Q3707858). --Succu (talk) 10:35, 13 August 2015 (UTC)

@TomT0m, you have listened too much to the wrong kind of propaganda (perhaps by cladists?). - Brya (talk) 10:43, 13 August 2015 (UTC)

Would "nomenclatural type" go as a title ? It's the label used in several languages for the item. author  TomT0m / talk page 10:48, 13 August 2015 (UTC)

Well, "nomenclatural type" is the term used in the ICNafp, but not in the zoological Code. - Brya (talk) 11:06, 13 August 2015 (UTC)

Personally outside of taxonomy I read type of a name as given name or family name, so I'm not sure it totally solves the ambiguity issue I wanted to solve initially. author  TomT0m / talk page 11:34, 13 August 2015 (UTC) The current discussion is so much a plead for Flow in discussions /o\

User page

As this is full of personal opinions, some even rejected by the community and only edited by very few users and therefore have no consensus I propose a swift move to a user page or a deletion. --Averater (talk) 05:25, 6 June 2016 (UTC)

This page you vandalized is full of knowledge you intent to ignore. Maybe some parts are a litte biased, but you gave no hints what should be adapted. --Succu (talk) 21:03, 9 June 2016 (UTC)

To remove personal opinions and mumbo jumbo is not to vandalize. I did give edit comments. If a page is only allowed to be edited by a few users (without discussion) and others are reverted the best solution is to delete it as no consensus could ever be achieved. --Averater (talk) 07:10, 10 June 2016 (UTC)

"instance of recombination"

Hi,
concerning In Wikidata, the presence of parentheses can be indicated by adding "instance of recombination" as a qualifier. - I think in this case the use of recombination (Q14594740) is meant, right? -- Achim Raschka (talk) 08:59, 15 June 2016 (UTC)

Yes. I added instance of (P31)=recombination (Q14594740) to make it more clear. --Succu (talk) 10:34, 15 June 2016 (UTC)

Summary of rules for Plant and Fungal Author information

Hello. Relating to the way that the author information is entered in WikiData in the case of plant species and fungal species (see also "Option 2" above), I think this is correctly given in the "Authorship" section of the Project Taxonomy tutorial, but I would like to re-state the rules here as it is very easy to misunderstand something.

We have to follow the following rules for a given species taxon, say item T.

1. Each author of the "taxon name" combination of T must have an item in WD, with botanist author abbreviation (P428) property. Also if there are "ex" taxon author(s) of taxon T, they must each be present as items in WD, with botanist author abbreviation (P428) property.
2. If T had an earlier accepted name (basionym) other than T, a WD item, say B, must exist for the basionym and T must include the basionym (P566) property pointing at B. B should only represent the old name, not the actual plant or fungus. If there is no such earlier name, I suppose that T can still have the (basionym (P566)) property pointing at itself.
3. IThe basionym item B must also define its list of authors and its "ex" list of authors if appropriate, and all those authors must be present as items in WD, with botanist author abbreviation (P428) property.

The following algorithm can be used to generate the actual author string for a taxon which is in WD item T. I hope the notation is clear.

Procedure generate_full_author_string(item T) {
  If T has basionym (P566) property with value B and B is different from T {
    Output "(".
    Apply generate_author_list to B.
    Output ") ".
  }
  Apply generate_author_list to T.
} 
Sub-procedure generate_author_list(item X) {
  Find the number of ex taxon author (P697) qualifiers, n, of the taxon name (P225) statement of X.
  If n > 0 {
    For each ex taxon author (P697) of the taxon name (P225) statement of X {
      Output the author abbreviation, which will be found in botanist author abbreviation (P428).
      If this is not the last or last-but-one author {
        Output ", ".
      }
      If this is the last-but-one author {
        Output " & ".
      }
    }
    Output " ex ".
  }
  Find number of taxon author (P405) qualifiers of the taxon name (P225) statement of X (that will be useful to show if a given author is the last or last-but-one).
  For each taxon author (P405) of the taxon name (P225) statement of X {
    Output the author abbreviation, which will be found in botanist author abbreviation (P428).
    If this is not the last or last-but-one author {
      Output ", ".
    }
    If this is the last-but-one author {
      Output " & ".
    }
  }
}

One thing which worries me is that I think that the order of multiple authors in a list is important, but this order does not seem to be defined in WD.

Please could someone tell me if I have made any mistakes in the above summary, or whether it is correct? I am sorry to bother you if think this is all obvious, but it seems to me that it is quite complicated and it should be worthwhile to write it down explicitly. Strobilomyces (talk) 17:03, 27 March 2017 (UTC)

It is moderately complicated (I once compiled a formula with all the permutations), but above all the rules are very precise.

        It is possible to rank the authors by using "series ordinal" (series ordinal (P1545)), although adding this has been started recently. Adding an author can only be done if indeed there is an item. Such an item should include the "standard form" in "also known as" (so that this standard form can be entered in the taxon name field).

        It would be nice if basionyms existed for all names, but we are missing a shocking number of them. Basionyms can be correct names (happens a lot), although not at the same time. A name can not be a basionym of itself. There can be earlier names that are not basionyms (we probably need a property for "is homotypic with"). - Brya (talk) 18:08, 27 March 2017 (UTC)

Hello Brya. Sorry, I don't understand how to use series ordinal (P1545) to specify the order of the authors. For instance Gymnopus putillus (Q10543295) has three taxon authors, Antonín, Haling and Noordeloos, in that order. Please could you add the series ordinal (P1545) information to Gymnopus putillus (Q10543295) so that the order is defined correctly in Wikidata? Strobilomyces (talk) 16:24, 28 March 2017 (UTC)

It's not possible to use series ordinal (P1545) for this purpose, because we use ex taxon author (P697) etc. as qualifiers. --Succu (talk) 17:25, 28 March 2017 (UTC)

OK, sorry about that. For authors of publications series ordinal (P1545) is being added, but it is indeed not possible here. Would be an argument to use taxon author as a property statement. However, so far, qualifiers stay in the order they are entered (which is not always true for property statements). - Brya (talk) 17:39, 28 March 2017 (UTC)

Origin of this page

Is this based on some community consensus (Request for comment etc.)? I am especially interested in the Homotypic names section. This is used as a heavy argument in some cases, where pages are intentionally left in half-baken state and unconnected instead of merging or redirecting. This practice is confusing and offen leads to unnecessary conflicts, especially when the behaviour of the project maintainer User:Succu is often suboptimal. People are editing in good faith and when they are brushed off with "I am the superior authority" answers, they are repelled from further editing of Wikidata. --Vachovec1 (talk) 17:36, 20 July 2017 (UTC)

I'm not aware that I'm having any conflict with you, Vachovec1. So please do not voice such things. --Succu (talk) 17:48, 20 July 2017 (UTC) PS: cs:Diskuse_s_wikipedistou:Vachovec1#Wikidata --Succu (talk) 19:34, 20 July 2017 (UTC)

Did I mention any conflict with me? Our only conflict (because I am not a frequent Wikdata contributor) was at Talk:Q486672 about nine months back (the situation there is still unresolved btw.). This time I was asked for advice by User:OJJ about the edits at Q541492. This is really not helpful. If your main argument should be Homotypic names section of this tutorial (because the IUCN entry is otherwise crystal clear), I want to know the base for this argumentation, because that section as a whole looks dubious to me. --Vachovec1 (talk) 19:54, 20 July 2017 (UTC)

Comments like „especially when the behaviour of the project maintainer User:Succu is often suboptimal“ or „with "I am the superior authority" answers“ are not helpfull. And no, this has nothing to do with objective synonyms. For an answer about Hypotaenidia wakensis (Q28065127), Wake Island Rail (Q541492) (and Rallus wakensis (Q33125380)) see my talk page. --Succu (talk) 20:03, 20 July 2017 (UTC)

Databases

"Quality of databases can vary strongly. Some databases are known to have significant amounts of outright nonsense, like ZipcodeZoo (Q15078690), Catalogue of Life (Q38840) (CoL), The Plant List (Q625817) (for the material wrongly copied from Tropicos). Such sites as Global Biodiversity Information Facility (Q1531570) (GBIF) and Encyclopedia of Life (Q82486) (EoL) copy all the content of Catalogue of Life, and are therefore not reliable as such. The Integrated Taxonomic Information System (Q82575) (ITIS) is better, but is mostly behind the times."

I'd like to see some evidence for the claim that The Plant List (Q625817) contains significant amounts of outright nonsense. Thanks. --Drgirasol (talk) 13:55, 8 December 2018 (UTC)

What kind of evidence? Given how widely the nonsensical items range, it would seem to require effort to miss them. However, this does short-change GBIF, which did copy all the content of Catalogue of Life, but have made a great effort to clear up the junk. Succesfully, as far as I can see. - Brya (talk) 16:21, 8 December 2018 (UTC)

For starters, how about some examples of "nonsensical" items from The Plant List? --Drgirasol (talk) 19:12, 8 December 2018 (UTC)

You are not a "starter", but the wording „outright nonsense” is inappropriate here. --Succu (talk) 22:21, 8 December 2018 (UTC)

"for starters" --Drgirasol (talk) 12:46, 9 December 2018 (UTC)

A few cases

• Tropicos has Acroscyphus N. Kitag. (1984), clearly marked as illegitimate (that is, there never was a taxon by that name, and never will be), with four species-level names (that also never were correct names of taxa, and never will be). The Plant List miss-copies that and presents it as an (otherwise non-existent) genus Acroscyphus with three accepted (but otherwise non-existent) species. Outright nonsense, to put it politely.
• Tropicos has Astrophyllum Neck. ex Lindb. (1878), clearly marked as illegitimate. The Plant List miss-copies that and presents it as an (otherwise non-existent) genus Astrophyllum with some accepted twenty (but otherwise non-existent) species.
• Tropicos has Brachypodium arbuscula (Gay ex St.-Yves) Gay ex St.-Yves (1934) clearly marked as not validly published (that is, there is not only not a species by that name, but there is no such formal name). The Plant List miss-copies that and presents it as an accepted (but otherwise non-existent) species.
• Tropicos has Brachypodium Brid. (1826), clearly marked as illegitimate, with three species-level names (that also never were correct names of taxa, and never will be. Actually, one of these three species-level names is misplaced there, but it does not matter as it was not validly published, anyway). The Plant List miss-copies two of those species-level names and present these as (otherwise non-existent) species Brachypodium crispatum and Brachypodium parasiticum.

- Brya (talk) 04:52, 9 December 2018 (UTC)

Thanks. Are there any non Bryophyte examples you could provide? And can you supply a concrete number of how many records have been identified to be incorrectly copied? --Drgirasol (talk) 12:46, 9 December 2018 (UTC)

Yes, there are non-Bryophyte examples (there is one included above). There does exist a marked difference: Bryophytes are a disaster area, for non-Bryophytes the database is merely unreliable. And as far as I know, nobody counted them (there is no point), or even seriously tried to track them. But lots and lots of them. - Brya (talk) 14:54, 9 December 2018 (UTC)

Ok, so far we established that according to your judgment there are errors in the bryophyte data set. But no quantification exists. Additionally you say that all other parts of the plant list are unreliable. I assume there is also no quantitative data available to support this claim? If not, the paragraph I quoted above contains mostly unfounded generalizations. If all items imported from tropicos were flawed then roughly a third of the plant list is affected. However, i doubt that all major groups would be affected in the same way (e.g. 99% of Bryophyt names come from tropicos vs. 14% of angiosperm names). So my suggestion to make the paragraph more helpful would be to only use statements that are objectively true. That will be easier if you including rather more than less details. Instead of trying to provide a general measure of quality for those databases (without providing a definition of quality that can by applied to all the databases!), stick with providing whats actually wrong with them. As someone using the plant list as primary reference for flowering plant names, I am always interested in information that has the potential to increase quality in this major group. --Drgirasol (talk) 14:58, 13 December 2018 (UTC)

It would help if you phrased more carefully. It is hard to follow the thread of your argument with all this meandering.

        However, it is very good that you indicate that you write as someone with a vested interest in defending the image of The Plant List. Unfortunately it is not possible "to increase quality in this major group [of The Plant List]", as The Plant List is dead and will not be updated. It is pointless to spend time and energy trying to determine how bad it is exactly. Doubly so, as any user has the option of just using Tropicos instead, and will then have better information.

        I have no vested interest, beyond trying to encourage that Wikidata provides as much factual information as possible. What is needed is a general warning against putting too much reliance on The Plant List (pointing out that it is not a reliable source), and a special warning against basing Wikipedia pages on The Plant List. In general, it is not a good idea to base a Wikipedia page on any database entry, as database entries have limited information and even the best database will have really bad errors. However, it proves that it being unwise has not stopped some users. - Brya (talk) 04:56, 14 December 2018 (UTC)

I am not sure how to make it more clear than this: There is a claim, and there is missing evidence. --Drgirasol (talk) 09:22, 20 December 2018 (UTC)

There is lots of evidence, it is just not tabulated in a way that convinces you. - Brya (talk) 17:46, 20 December 2018 (UTC)

Really? Did I ask for any data that is tabulated in a specific way? You haven't shown me any examples regarding angiosperms and also none that are not related to tropicos. --Drgirasol (talk) 17:36, 27 December 2018 (UTC)

As to tabulated, you were getting there. As to angiosperms, that has not changed since the last time you commented on that: the example is still there. - Brya (talk) 06:32, 2 January 2019 (UTC)

As to where I was getting to, see below (TPL = unreliable). As to angiosperms, thanks, but since we already established that there is a problem with entries derived from tropicos, I was hoping (acting on the assumption TPL = unreliable, see below) to get examples of some non-tropicos cases. If you retract/invalidate that claim, we can stop here. --Drgirasol (talk) 09:22, 6 January 2019 (UTC)

What claim? - Brya (talk) 10:12, 6 January 2019 (UTC)

Data of the plant list is not dead and therefore can be improved. --Drgirasol (talk) 09:22, 20 December 2018 (UTC)

Unless this means that you intend to fund an update (half a million would probably do it), this sounds like empty dogma. - Brya (talk) 17:46, 20 December 2018 (UTC)

You are not helping! If I had the necessary evidence I could invest some time fixing database entries. --Drgirasol (talk) 17:36, 27 December 2018 (UTC)

You now claim that are working for The Plant List? - Brya (talk) 06:32, 2 January 2019 (UTC)

Why are you jumping to conclusions? If you stick to the facts (I said I could fix database entries) than the only thing I am "claiming" is, that I have access to a database containing TPL data which I could fix. I collected the data for a project a while back and used the CSV data provided by TPL (e.g. search?q=Dracocephalum&csv=true). I am not affiliated with the plant list. --Drgirasol (talk) 09:22, 6 January 2019 (UTC)

Why would your own private database be of interest to building up Wikidata? Especially since it is based on avoidable mistakes ... - Brya (talk) 10:12, 6 January 2019 (UTC)

Again, it is not very helpful to make a generalization without having tested that generalization. It's like if I find errors in some of the things you wrote and immediately jump to the conclusion that everything coming from you is unreliable. I'd say this is unwise. --Drgirasol (talk) 09:22, 20 December 2018 (UTC)

There is an observed pattern, that has proven to be consistent ("has been tested" if you like). - Brya (talk) 17:46, 20 December 2018 (UTC)

You keep saying that... I will ask one last time: Please present the observed pattern that shows that the plant list (as a whole) is not reliable. --Drgirasol (talk) 17:36, 27 December 2018 (UTC)

I did not say that. - Brya (talk) 06:32, 2 January 2019 (UTC)

No? I quote:

"Bryophytes are a disaster area, for non-Bryophytes the database is merely unreliable." - Brya 14:54, 9 December 2018 (UTC)

"What is needed is a general warning against putting too much reliance on The Plant List (pointing out that it is not a reliable source)" - Brya 04:56, 14 December 2018 (UTC)

Thanks for the pointer to the tropicos issue... but I think I am done here. --Drgirasol (talk) 09:22, 6 January 2019 (UTC)

Good. - Brya (talk) 10:12, 6 January 2019 (UTC)

Sanctioning author for plants and fungi

If a particular name was sanctioned by the nomenclatural authories, it is normal to include this information in the author string, the sanctioning author following the actual authors separated by a colon. For instance the mushroom Amanita porphyria is referred to as "Amanita porphyria Alb. & Schwein. : Fr." in Funga Nordica, signifying that the name was sanctioned by Fries and cannot be superseded. But in Wikidata I think we have no way of signifying this relationship. I suppose we just ignore it, but this seems strange to me. Also the English WP page on Author citation (botany) does not cover this usage. Shouldn't we have a property for this and a write-up in the tutorial? Strobilomyces (talk) 19:34, 6 April 2020 (UTC)

Label scientific or common name

In this tutorial is stated that the label usually is the scientific name of the taxon. Elsewhere on Wikidata the rule seems to be that the label should be the common name (unless there is none). So there is confusion and inconsistency. How should we deal with this? K.vliet (talk) 16:11, 8 July 2020 (UTC)