Wikidata talk:WikiProject Taxonomy/Archive/2015/06

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Help:Description#No initial articles (a, an, the)

There are few items related to this project that have initial articles, e.g.

• Q15739916 "a species of plants" instead of "species of plants".
• Q10647199 "a species of fungi" instead of "species of fungi"

They are included in the list currently at http://quarry.wmflabs.org/query/3351 .

I suppose I can go ahead an change them? --- Jura 21:57, 26 April 2015 (UTC)

As far as I am concerned, it would be welcome to replace any "a species of" by "species of", and any "a genus of" by "genus of". Propably also "a family of" by "family of" and "an order of" by "an order of". - Brya (talk) 04:55, 27 April 2015 (UTC)

Thanks for your feedback. In that case, I will go ahead and remove it. --- Jura 11:19, 2 May 2015 (UTC)

 Done --- Jura 12:12, 2 May 2015 (UTC)

Should be "species of plant" and "species of fungus", surely? Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 12:22, 2 May 2015 (UTC)

Currently plural (fungi, plants) seems more frequent, but we could fix that as well. --- Jura 12:25, 2 May 2015 (UTC)

• "species of moth" 17762
• "species of plant" 2400
• "species of plants" 1512
• "Pokémon species" 723
• "species of insect" 697
• "species of beetle" 589
• "species of fish" 584
• "Fish species" 551
• "species of plant in the genus Bulbophyllum" 493
• "species of wasp" 266
• "species of fungus" 235
• "species of bird" 211
• "evolution of a Pokémon species" 171
• "species of moth of the Arctiidae family" 164
• "species of bacteria" 141
• "species of fungi" 131
• "species of plant in the genus Astragalus" 120
• "species of sea snail" 116
• "Beetle species" 97
• "species of insects" 94

Forget what I just wrote, see above. --- Jura 12:40, 2 May 2015 (UTC)

Here are a few changes we could do:

current	new	occur.
"species of plants"	"species of plant"	1512
"Fish species"	"species of fish"	551
"species of fungi"	"species of fungus"	131
"Beetle species"	"species of beetle"	97
"species of insects"	"species of insect"	94
"Butterfly species"	"species of butterfly"	82
"Bird species"	"species of bird"	82
"Plant species"	"species of plant"	68
"Insect species"	"species of insect"	30
"Spider species"	"species of spider"	25
"species of beetles"	"species of beetle"	23
"species of birds"	"species of bird"	19
"Moth species"	"species of moth"	19
"species of fishes"	"species of fish"	18
"species of butterflies"	"species of butterfly"	12
"species of worms"	"species of worm"	8
"species of flies"	"species of fly"	8
"fly species"	"species of fly"	7

What do you think of it? --- Jura 15:40, 2 May 2015 (UTC)

Oh, sure. I am fine with it, although for convenience's sake I am putting all insects in "species of insect". - Brya (talk) 17:43, 4 May 2015 (UTC)

•  Done last week --- Jura 15:36, 1 June 2015 (UTC)

Good. Thank you! - Brya (talk) 16:37, 1 June 2015 (UTC)

"A higher level classification of all living organisms"

This article "A higher level classification of all living organisms" popped up in the french biology project in Wikipedia and seems of major importance in taxonomy. It claims to be a consensus of 3000 taxonomists, so you must already know it exists, but just in case I put this here and I'll read it. TomT0m ^(talk) 16:34, 4 May 2015 (UTC)

Addition To be complete and to continue an ongoing discussion with Succu and Brya, metaclasses offers ways to mark that some taxons are parts of this precise high level classification by marking the taxons as such

⟨ The Taxon ⟩ instance of (P31) ⟨ Rugierro et al. classification's taxon ⟩

, with

⟨ Rugierro et al. classification's taxon ⟩ subclass of (P279) ⟨ taxon ⟩

. TomT0m ^(talk) 16:52, 4 May 2015 (UTC)

It does not claim to be a consensus of 3000 taxonomists; it is a consensus of the nine authors. The 3000 taxonomists have contributed to CoL. As it claims to be not strictly phylogenetic, perhaps you will find your paraphyletic taxa here? It may be a good idea to add this at relevant places as a reference (yet one more taxonomic system). - Brya (talk) 17:24, 4 May 2015 (UTC)

@Brya: Yep, but they are not the rule, they are the exception. If it's incorrect to use subclass of in those cases just don't use it. What I can see right now is that you don't really have a way to find them easily, although everybody seems to acknowledge that as far as it is possible a taxon should be a clade ... Don't you think this is a problem ? Plus find any place where I said they should not be in Wikidata. I provide tools to class them as such, that's all. TomT0m ^(talk) 17:44, 4 May 2015 (UTC)

No, this is careless phrasing again, "everybody seems to acknowledge that as far as it is possible a taxon should be a clade" is not true. I still see no reason to mess about with subclasses (except as a rank). - Brya (talk) 17:49, 4 May 2015 (UTC)

@Brya: Continue to focus on the wording if you don't want to focus on the meaning, very smart. But it is such a non important question that the authors of this article just document and justify every exception, and that it is a major taxonomic school ... TomT0m ^(talk) 18:03, 4 May 2015 (UTC)

Again your wording is careless: „document and justifies every exception”. That's not true, TomT0m. --Succu (talk) 18:08, 4 May 2015 (UTC)

Fair enough, can we continue ? TomT0m ^(talk) 18:17, 4 May 2015 (UTC)

With what? „justify every exception” is not true. --Succu (talk) 18:43, 4 May 2015 (UTC)

TomT0m, do you really want to replace references this way and create classes like

• ⟨ The Taxon ⟩ instance of (P31) ⟨ Linnè's classification's taxon used in Species Plantarum 1st edition ⟩
• ⟨ The Taxon ⟩ instance of (P31) ⟨ Linnè's classification's taxon used in Species Plantarum 2nd edition ⟩
• ⟨ The Taxon ⟩ instance of (P31) ⟨ Linnè's classification's taxon used in Species Plantarum 3rd edition ⟩
• ⟨ The Taxon ⟩ instance of (P31) ⟨ XYZ's classification's taxon used in referenec ABC ⟩
  ?

--Succu (talk) 20:32, 4 May 2015 (UTC)

No, not in every case, but sometime it might be justified (and disambigs would be the to put preferably on the ). Can't a taxon change everything, like be splitted and change parent, or be emptied of most of its supposed organisms by subsequent refinment or revision ? Or is it always renamed in those major changes cases ? (real question). TomT0m ^(talk) 06:14, 5 May 2015 (UTC)

We had a similar discussion about planets on wikidata ml, see this thread. The problems seems kind of close after all. TomT0m ^(talk) 06:18, 5 May 2015 (UTC)

Isn't that the problem, that it all looks the same to you? - Brya (talk) 10:56, 5 May 2015 (UTC)

@Brya: To explain what is different, one must also understand what's similar ... This is a basic taxonomy principle, isn't it ? :p So, please express yourself and tell me what's common and different. One one hand we have groups of planets, on the other groups of organisms ... TomT0m ^(talk) 11:23, 5 May 2015 (UTC)

 Info I created A higher level classification of all living organisms (Q19858624). --Succu (talk) 14:24, 5 May 2015 (UTC)

Ah, on the one hand a very limited and definite numbers of hunks of matter sitting there in predictable orbits, on the other a very great number of organisms that are all over the place, changing constantly. What would be the similarities? - Brya (talk) 16:40, 5 May 2015 (UTC)

@Brya: On one hand, definition of planets change, there is unit of classification of astronomical objects. On the other taxonomists try to find good definitions of taxons, there is units of classification of taxon, taxonomists try to find good definitions of taxons (leading to important definitions like "monophyletic" taxons). Of course taxonomy is more complex, but there is a strong connexion beetween the goals and means in both way. There is subclasses (ontologic sense) of planets (tellurics, ...), subclasses of living organisms. The question is "how do we choose classes". But the use of classes of organisms (Ontology sense) is natural in both cases. Sometime we can use subclass of as defined, sometime we can't to express childhood taxons relationships. But in the case of monophyletic taxons (still, a major taxonomy school), we can, and we should. TomT0m ^(talk) 07:50, 6 May 2015 (UTC)

Of course it is possible to distort one's perspective so that everything looks like something else, but this only says something about the person who is doing the distorting. - Brya (talk) 11:25, 6 May 2015 (UTC)

@Brya: No, the discrepancy is just on the nature of taxons, and on types of taxons. But cladistic is indeed a major taxonomic tool and it has no problem to be modeled by properties who are standards like instance/subclass. But maybe I distort things :) And other sources can concur with that, for example a paper that cite the model with metaclass as the conceptual part of a model, while a subclass hierarchy is the population part. They indeed cite biological taxonomy as an example. TomT0m ^(talk) 11:58, 6 May 2015 (UTC)

Well, if you want to point out that it is possible to model anything in a number of ways, well, that is not news. - Brya (talk) 16:30, 6 May 2015 (UTC)

@Brya: Nope, I want to point out that this project is not an exception and can be modeled exactly like the rest of Wikidata tends to be modelled, and that such an homogenisation is desirable for everyone as overall, this simplifies things. TomT0m ^(talk) 16:41, 6 May 2015 (UTC)

And that the metaclass concept has a real power to model the complexity of the field inside that golobal things, which enlights that this is both possible and desirable, but also that it is powerful enough to model complex things with those not so hard concepts. Everybody seems to have understood the notion of car model as a metaclass. TomT0m ^(talk) 16:44, 6 May 2015 (UTC)

TomT0m: „...can be modeled exactly like the rest of Wikidata tends to be modelled” - Then work on the rest. Prove your ideas and get acceptance. Thanks. --Succu (talk) 16:47, 6 May 2015 (UTC)

@Succu: Well, we deleted almost every specialized property ... see this diff, which means the idea of using subclass of is well accepted globally, and a lot of opposition in Wikidata:Requests_for_comment/Adopt_Help:Classification_as_an_official_help_page are just on the form of the document, or out of scope. The concept of metaclass has strong support and foundations in literature (just added the reference to the article I linked today here in the Wikipedia article we wrote with Emw), it even gained support of Template:U'Emw who was a strong opponent. I was added into OWL DL with punning because this feature lacked and it was proved it's possible to use it without computational penalty in OWL. TomT0m ^(talk) 16:58, 6 May 2015 (UTC)

TomT0m: Sometimes it is time to say goodbye to talks like this. Sorry, but this WikiProject had tons of real work to do. Chatting with you is no real help. --Succu (talk) 17:39, 6 May 2015 (UTC)

What do you want ? constraints ? TomT0m ^(talk) 18:08, 6 May 2015 (UTC)

We have a lot of constrains to work with, TomT0m. And dubious taxa, missing authors, missing references. All coming from a working model. And a some open questions how to refine this one. --Succu (talk) 18:32, 6 May 2015 (UTC)

I doubt these constraints depends on parent taxon, or they should be easily expressable with instance of taxon instead. As for the refinment of the model, ask yourself if things like subclassing taxon would help :) anyway, as animals are instance of some species and the taxon is also an instance of <taxon>, you already use metaclasses. Then parent taxon is not of much actually. TomT0m ^(talk) 18:41, 6 May 2015 (UTC)

TomT0m, read what I wrote. --Succu (talk) 18:52, 6 May 2015 (UTC)

I reread, seems still relevant. And maybe the refinment of a model would be easier with ... a slighlty different model, who knows ? TomT0m ^(talk) 18:59, 6 May 2015 (UTC)

I meant real work, aka adding/correcting information to this project. That's all. This is one of our open questions. --Succu (talk) 19:51, 6 May 2015 (UTC)

I've made a rough check: We are „missing“ around a quarter of the listed CoL names. --Succu (talk) 19:29, 2 June 2015 (UTC)

I suppose we should count our blessings. - Brya (talk) 04:43, 3 June 2015 (UTC)

Template:Parent taxon tree

Template:Parent taxon tree. Visite fortuitement prolongée (talk) 19:07, 31 May 2015 (UTC)

Visite fortuitement prolongée, the „tree“ of Cactaceae (Q14560) is not correct. Cactaceae (Q14560) has four parent taxa. Only one is shown. --Succu (talk) 20:30, 31 May 2015 (UTC)

Indeed. @Zolo: Can you preview {{Parent taxon tree|Q14560}}? Visite fortuitement prolongée (talk) 20:58, 31 May 2015 (UTC)

You can not use Template:Tree because the is not a single taxonomic tree, but a lot of opinions how taxa are related. --Succu (talk) 21:07, 31 May 2015 (UTC)

Yes he can, as a matter of fact he did :) It's a matter of how we read the output tree. In fact I think our model should be good enough to reconstruct all the trees. For the parents, is it that the chosen edge is of preferred rank ? TomT0m ^(talk) 10:02, 1 June 2015 (UTC)

┌────────────────────────────────────────────────────────────────────────────────────────────────────┘I have changed the template so that graph size can be customized using the "max" parameter and that only parents given by a spcecific source will returned using a 'source" parameter :

{{Parent taxon tree|item=Q14560|source=Q14244038|max=10}}
{{Parent taxon tree|item=Q14560|source=Q14244038|max=2}}

• Cactaceae
  • Caryophyllales
    • Caryophyllidae
      • Magnoliopsida
        • Magnoliophyta ⊸

• Cactaceae
  • Caryophyllales
    • Caryophyllidae ^…

--Zolo (talk) 15:31, 1 June 2015 (UTC)

Thank you. Visite fortuitement prolongée (talk) 20:18, 1 June 2015 (UTC)

Visite fortuitement prolongée, Zolo: Are there any use cases for this specialized template? --Succu (talk) 21:24, 1 June 2015 (UTC)

@Zolo, Visite fortuitemnt prolongée: I want to do something like this presented in colums with instance of (P31) and subclass of (P279) since forever but nether finished. The ida is to extract the algorith that builds the tree structure and instead of displaying like this display in two columns :

Cactaceae	family
Caryophyllales	…
Caryophyllidae	…
Magnoliopsida	…
Magnoliophyta	…

if for example Cactaceae is an instance of family. This would be enough to generate a generic infobox. TomT0m ^(talk) 20:45, 2 June 2015 (UTC)

You saw our Module:Taxobox?  — Felix Reimann (talk) 08:42, 3 June 2015 (UTC)

Tropicos

On an off, I have been looking at the mess on The Plant List when it comes to names from Tropicos. Part of the problem lies in names that are unresolved in Tropicos, and these are fairly hopeless, there just is no real information. But for quite a few there is actually good information in Tropicos, and The Plant List just read it wrong. Isn't there a way to read information directly out of Tropicos, with a bot? - Brya (talk) 18:19, 8 June 2015 (UTC)

Yes and no. There is a Tropicos Web Services which states „Since screen scraping in not encouraged, this is the preferred interface.” But Tropicos provides only limited information using this API. Actually they block a screen scraping application after a while. So it would be helpful if you could refine your request. --Succu (talk) 21:21, 8 June 2015 (UTC)

Refining is not easy. It is clear enough that the place where there is a lot of useful information (not included in The Plant List) is in the mosses, so it concerns a limited number of families only. What would be valuable to have a bot importing information on is 1) illegitimate generic names, marked by a *, and then have the bot eliminate all the species names with these generic name as a "taxon name" and 2) synonymy at species level (and below): there is actually a lot of information on moss species, with accepted species marked by a ! and with lists of references, for both preferred names and synonyms. Given that we now have four or five names for a moss species, without any indication of what would be preferable, this would be quite valuable. There are also the non-existing generic names (marked by **), but there seem only a few of them. But I don't see at all how this can be done with the provided API. - Brya (talk) 05:07, 9 June 2015 (UTC)

Myxogastria

Please could people comment at Wikidata:Project chat#Myxogastria (Q46309) and Myxomycota (Q10334205) and help to sort out these species of fungi? Thanks MSGJ (talk) 08:07, 11 June 2015 (UTC)

You don't need a botanist, but a protistologist, but I will see what I can do. - Brya (talk) 16:30, 11 June 2015 (UTC)

Ежевика / blackberry / Brombeere

Merge. Do you also think that we need an item for subgenus (or group of species?) and an item for fruit? --Infovarius (talk) 21:46, 14 June 2015 (UTC)

This is a pretty big mess. In Vargenau's defence, he is consistent: he is not so much merging these items, but is denying that a taxon is involved. Still, this would be more convincing if he had gone to all the Wikipedia's and had removed all the taxoboxes. Another complication is that those taxoboxes are not in close agreement as to which taxon is involved (one of those iw-links even goes to a species). I am in favour of a simple rule-of-thumb: if it has a taxobox it is about a taxon. - Brya (talk) 04:57, 15 June 2015 (UTC)

Vargenau, any explanation for removing these properties? --Succu (talk) 06:27, 15 June 2015 (UTC)

Hello,

For me Q13180 is about a fruit, not a taxon. The taxons are Q13541716 (Rubus fruticosus) and Q15699806 (Rubus plicatus).

Regards,

Vargenau (talk) 09:57, 15 June 2015 (UTC)

Vargenau, you can not simply change the underlying concept of an item. Several items are unsing the taxon Rubus subg. Rubus (Q13180) (Rubus subg. Rubus) as parent taxon e.g. Rubus plicatus (Q15699806). The item for the fruit was blackberry (Q19842373), which you merged in. Maybe not all links were correctly placed. BTW, Brya: At least de:Brombeeren is about the taxon and not the fruit. --Succu (talk) 14:57, 15 June 2015 (UTC)

Hi,

If you really want two items, one for the fruit and one for Rubus subg. Rubus then yes the links before the merge were mostly inconsistent. blackberry (Q19842373) had only 4 interwiki links, which is clearly not enough. Feel free to recreate two items, but with correct interwiki links.

Regards,

Vargenau (talk) 16:17, 15 June 2015 (UTC)

Vargenau, I restored the old status. Feel free to move sitelinks from Rubus subg. Rubus (Q13180) (Rubus subg. Rubus) to blackberry (Q19842373) (fruit). --Succu (talk) 16:28, 15 June 2015 (UTC)

The "For me" is not necessarily a reproducible criterium, and a lot of pages don't agree (the German page starts "sind eine Sektion aus der umfangreichen und weltweit verbreiteten Pflanzengattung Rubus"). The English page doesn't agree with the two species mentioned. But yes, the four iw-links were not enough. As I said, this is a mess. - Brya (talk) 16:35, 15 June 2015 (UTC)

@Vargenau: In Wikidata, two concepts = two items. This is necessary to avoid ambiguities. TomT0m ^(talk) 17:05, 15 June 2015 (UTC)

I hope to have it sorted now, five items being involved (with a potential for two more?). - Brya (talk) 05:55, 16 June 2015 (UTC)

Thank you for your work. I updated the French description and aliases for both elements. Description for other languages should probably be updated too.

What are exactly the 5 or 7 elements involved?

Best regards,

Vargenau (talk) 08:37, 16 June 2015 (UTC)

I also moved tr: and br: Not sure about where nl: belongs

Best regards,

Vargenau (talk) 08:52, 16 June 2015 (UTC)

The following concepts are involved:

• blackberry (the fruit)
• Rubus subg. Rubus
• Rubus (the genus)
• Rubus fruticosus
• Rubus caesius
• Ribes (the genus)

(OK, makes six) Potential concepts (not used) :

• Rubus sect. Rubus
• Rubus fruticosus agg. (species complex)

OK as concerns br; nl belongs with blackberry. Not OK as concerns tr. This is mixed up: it has a taxobox, which says that it is about Rubus (the genus), but there already is a separate entry for that, so the taxobox is to be discounted. Leaving aside the taxobox the page is (appears to be) about the blackberry. - Brya (talk) 10:53, 16 June 2015 (UTC)

Thank you.

For nl:, I was wondering if it should not be put alone. It seems to be about culture of blackberries, not blackberries per se.

Regards,

Vargenau (talk) 14:31, 16 June 2015 (UTC)

It looks to me to be about cultivated blackberries, but it is not a 100% match with the others which mostly appear to assume that blackberries come out of a factory. But there is a match. - Brya (talk) 16:24, 16 June 2015 (UTC)

WD:XLINK

Hi, Created WD:XLINK to help us handle the interwikis in those kind of cases, and added the example of fruit/producer in the list. Hope it will enventually help and don't hesitate to add other examples. TomT0m ^(talk) 16:30, 16 June 2015 (UTC)

Synonyms

One similar question about the synonyms. I'm very confused because I saw a lot of different ways to add some synonym to an taxon item. So, what is the correct way to do this, in the Also known as, or in taxon name, or have to create a new item for each one synonym with instance of synonym, or with redirects to the item, or... --Termininja (talk) 12:38, 24 June 2015 (UTC)

Yes, confusion is the name of the game. There is no good way to handle this. In no case put them in taxon name. Otherwise, you are on your own. - Brya (talk) 17:28, 24 June 2015 (UTC)

Yes, there are different ways... It depends on what you try to express. We are far away from a clean support for tons of synonyms yet, sorry --Succu (talk) 17:49, 24 June 2015 (UTC)

• For Posterula sarsii (Q4169967) in taxon name we have the name and the synonym, which is ok, but check the WoRMS-ID for taxa (P850) and GBIF taxon ID (P846). It is not clear which Id for which name is. What you think for this? Is it need to delete synonyms ids or it is need some quialifier here? --Termininja (talk) 12:59, 30 June 2015 (UTC)

In similar cases I'm adding taxon name (P225) to the reference (example). --Succu (talk) 13:19, 30 June 2015 (UTC)

I do my best to eliminate such cases of misspellings. It is best to find the original publication (does not seem to be online in this case), but as there seems to be agreement, it is best to cut the knot. - Brya (talk) 16:51, 30 June 2015 (UTC)

Yes I know and thank you very much for that. In cases of a wrong sprelling and multiple identifiers the identifier pointing to the wrong name should simply removed. Otherwise adding taxon name (P225) to the reference helps to identify the name in a database. --Succu (talk) 17:36, 30 June 2015 (UTC)

There are all kinds of misspellings. Often enough, it is just a typo in a Wikipedia. But beyond that, it may be peculiar to a single database, or be fairly widespread in the literature, etc. - Brya (talk) 18:13, 30 June 2015 (UTC)

Yes. In the Red List you will find a lot of differing spellings. But to keep track of changes of IUCN conservation status (P141) we have to keep them somehow. --Succu (talk) 18:22, 30 June 2015 (UTC)