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Consistancy across Wikipedia nomenclatural platforms[edit]

For instance: Wikipedia: Roccellaceae includes genus Opegrapha & — The preceding unsigned comment was added by 96.54.23.37 (talkcontribs) 19:03, 2 March 2018‎.

IRMNG as a potential resource for Wikispecies[edit]

Hi all, I am not currently a Wikispecies contributor (because there are only so many hours a day and my energies are mainly directed elsewhere, see below) but do lurk occasionally at the WS Village Pump to catch what is going on. However I thought it might be worthwhile to introduce my taxonomic names-collecting project to you, IRMNG, the Interim Register of Marine and Nonmarine Genera, in case there are aspects of it that might help Wikispecies - for example for gap analysis or as a source of names you might otherwise not find so easily. IRMNG contains as many genus names as I have been able to locate over the lifetime of the project (2006 onwards), currently over 485,000, with more added on an intermittent basis, all arranged in a coherent taxonomic hierarchy (although not all are allocated to family at this time). In addition to a simple name search and a browsable taxon tree, one of the things that distinguishes IRMNG from some other compilations (apart from its scope which, like Wikispecies, is "all life", both extant and fossil) is the facility to fine tune searches to one's particular needs e.g. filter by taxonomic group and by cited year - this facility being available via the IRMNG "advanced search" page at http://www.irmng.org/aphia.php?p=search&adv=1. For example, a search for genus names published in 2010 in Coleoptera yields 248 names and is set up as follows:

  • Authority [contains] 2010
  • Rank [is] Genus
  • Belongs to: Coleoptera (selected from picklist once "Coleoptera" is entered)

The resulting list looks like this (start):

IRMNG Taxon list

Search returned 248 matching records, showing records 1-100.

Click on one of the taxon names listed below to check the details.

List of names

(etc.)

Of course you can do similar things with any other taxonomic group or with all names, or search for a particular author name, etc. etc. The entire IRMNG dataset (down to genus) can also be downloaded without restriction, see http://www.irmng.org/download.php, and the download file is updated from the master (web) version a couple of times a year at this time.

Just mentioning this in case it is of value. I spend quite a lot of time trawling various resources out there (although always more work to be done!) and integrating the results so may be able to save downstream users such as yourselves a bit of time, perhaps. Of course in an ideal world this stuff would only require to be entered once into a single location and then flow seamlessly to other projects but that state of nirvana is still a little way off :) Best regards - Tony Rees Tony 1212 (talk) 00:28, 7 April 2018 (UTC)

BTW I should point out that IRMNG is fairly complete up to around 2012 or so (later for some groups) but less so for the most recently published names - a situation that may be rectified at some point ... Tony 1212 (talk) 00:38, 7 April 2018 (UTC)
Also note the method above works for plant groups as well, since (in contrast to "classic" botanical tradition) I like to keep the publication year as well as the author names for botanical genera, as well as zoological ones. Of course, use of the year in the query filter is optional, if you do not use it you will simply get all names for any desired group (up to a limit of 10,000 per query via the web). Tony 1212 (talk) 05:33, 7 April 2018 (UTC)
The best solution would be to propose a Wikidata property for your identifiers (e.g. "1469897" for Acanthocolum), then load them all into Wikidata's Mix'n'Match tool, and match them to existing Wikidata items, or create new items where necessary. Then, we can run a query on Wikidata, "list all items with an IRMNG ID that has no Wikispecies page". Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 12:51, 7 April 2018 (UTC)
My Wikidata-Bot is able to read the Darwin Core Archive and can match the ID to the correct Wikidata item. --Succu (talk) 14:45, 7 April 2018 (UTC)
Tony 1212, Do you distinguish or are you being able to distinguish between valid genera and genera names in synonymy, genera-names-class such as subgenera, and rank-transferred names. for example: (1) A search for "Empleurus" yields "Empleurus Hope, 1838 accepted as Helophorus Fabricius, 1775" but doesn't indicate that Empleurus is a subgenus of Helophorus. (2) A search for "Tachyusota" yields "Status unaccepted" which is correct, but wrongly states "Accepted Name: Ischnopoda Stephens, 1835" (the correct one is Tachyusa Erichson, 1837). (3) Calischnopoda is listed as "accepted" yet it's a synonymy of Ischnopoda. Mariusm (talk) 15:22, 7 April 2018 (UTC)
Hello Mariusm, thanks for checking out my compilation and for your questions which I will try to answer. For your question (1), as you realise, the taxonomicStatus field (mostly "accepted" or "unaccepted") refers to the presently stored status at generic rather than subgeneric level; IRMNG at present does not attempt to store subgenera as separate entities (a legacy from its original design and rapid assembly nature) although in future it could do so (with a lot of additional work). There is a "notes" field in the master file which, in the cited case of Empleurus Hope, 1838, reads : "Taxonomic remark: As Helophorus (Empleurus) in Hallan, 2000-. Currently valid as subgenus (Hallan, 2000-)." (refer http://www.irmng.org/aphia.php?p=taxdetails&id=1397331); unfortunately these notes are only readable on the web version at present, not in the DwCA archive download (I could maybe ask VLIZ, the present database custodians, to think about preparing the notes fields as a separate table for download). (2) and (3) require me to do some further checking; if there are stated synonymies given in IRMNG they will have come from somewhere (again, sources are viewable via the web version) but they may be outdated compared with more recent sources - hopefully any such errors are for historic reasons rather than actual mistakes.
There is a fourth issue which you have not yet spotted but may become apparent: when I created IRMNG I had a status equivalent to "unassessed" for names of which the taxonomic status had not been further researched (i.e., their valid name or synonym status was not known), however in the current, VLIZ-hosted version that status does not exist and all such names (around 20% of animal genera) are treated as "accepted", although (once again via the web version) their is a note on validity "Not yet assessed" (or some such wording). Again for power users, I could get VLIZ to generate a list of the relevant IRMNG IDs/names if this is important for you. Cheers - Tony Tony 1212 (talk) 23:50, 7 April 2018 (UTC)
OK, I checked the cases you mentioned in points (3) and (4). Tachyusota Casey, 1906 is listed in IRMNG as a synonym of Ischnopoda based on Hallan's Biology Catalog from which I uploaded relevant information in 2012, in which it is given as a subgenus of Ischnopoda. I note, however, that in Löbl & Löbl's 2015 catalogue, Tachyusota is given in the synonymy of Tachyusa Erichson; I can update this in the master IRMNG version, from which it will propagate to the next web download in due course (but not for some months). Calischnopoda is a different case in that it is one of the "unassessed" names in IRMNG (sourced from Nomenclator Zoologicus but not encountered in other taxonomic lists yet used for IRMNG population or markup) but coming through as "accepted" for now via the VLIZ hosting procedure (although it will be on any separately generated list of IRMNG unassessed names). I see that Löbl & Löbl list this as a synonym of Ischnopoda as you point out, so I can update this record also, although there will still be perhaps 100,000 names not yet assessed in the IRMNG master file (along with 300,000+ that have been, at least from one cited source) which is just a fact of the current IRMNG data set that has to be borne in mind (with my apologies).
Perhaps the take-home message is that IRMNG will alert you to names that have been published in a particular group, but you cannot always rely on it for the latest taxonomic status of all the names held which should therefore ideally be verified independently. Over time, the treatment of particular groups is upgraded but because taxonomy is a moving target IRMNG cannot unfortunately be as up-to-date in all respects as other, more specialist compilations; however IRMNG does provide an integrated view across all groups (useful, e.g. for the detection of homonyms in particular) that its equivalents elsewhere typically do not, as well as open access to the data in an easily reusable form. By the way, more details on IRMNG data sources used plus some of its benefits and/or limitations are contained in this 2017 publication: IRMNG 2006–2016: 10 Years of a Global Taxonomic Database Tony 1212 (talk) 03:25, 8 April 2018 (UTC)
@Tony 1212: many thanks for your detailed answer. The IRMNG can indeed be of value when searching for genus-name basic attributes but the details must be double-checked for accuracy. Mariusm (talk) 09:59, 8 April 2018 (UTC)
@Mariusm:Correct! I named it "Interim" for this reason (also because when something better comes along, it can be superseded or retired...) Tony 1212 (talk) 21:09, 8 April 2018 (UTC)
I have now posted a proposal for a Wikidata property, at d:Wikidata:Property proposal/IRMNG taxon ID. Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 13:16, 9 April 2018 (UTC)
Hi @Pigsonthewing:, just letting you know that IRMNG has many duplicated names (homonyms sensu stricto plus sensu lato i.e. between kingdoms, nomina nuda, and published misspellings which collide with other, correctly spelled names of different taxa) that have to be borne in mind for any mapping exercise - see lists at http://www.irmng.org/homonyms.php. When I last looked here were over 70,000 such cases at genus level (perhaps 30,000 discrete names) of which the worst is Wagneria with 14(?) instances... Plus there are also unrecognised cases, e.g. within the last 10 minutes I came across a genus Platydiscus in a botanical paper; the only Platydiscus in the present IRMNG download file is an animal, but this one is indeed a (fossil) plant genus name published in 2001 and not present in the major nomenclators. Incorrect mappings could have some (ahem) 'interesting' consequences. Regards Tony Tony 1212 (talk) 20:12, 9 April 2018 (UTC)

Hi Tony, looks like the IRMNG REST webservice is not working. I'm getting only 404 errors. --Succu (talk) 15:19, 10 April 2018 (UTC)

Hi @Succu:, thanks for notifying us of that. There was a small error in the implementation which is now fixed. As an example, http://www.irmng.org/rest/AphiaRecordByIRMNG_ID/1323486 is now working, with other options described at http://www.irmng.org/rest/ . Cheers - Tony Tony 1212 (talk) 20:15, 11 April 2018 (UTC)
Great, Tony! I will check this tomorrow. --Succu (talk) 20:19, 11 April 2018 (UTC)

Wikidata property now created, as P5055. Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 10:46, 2 May 2018 (UTC)

Translation[edit]

Could somebody create some articles on namespace "MediaWiki" as below:

Thanks. --Garam (talk) 18:24, 11 April 2018 (UTC)

 Done. Thanks! —Justin (koavf)TCM 06:13, 1 May 2018 (UTC)

Translation markup at Welcome templates[edit]

Could you please mark up those templates for the part as follows?

Specifically, two sentences needs to be marked up. "If you have named a taxon, then it is likely that there is (or will be) a Wikispecies page about you, and other pages about your published papers. Please see our [[Special:MyLanguage/Wikispecies:Autobiography|advice and guidance for taxon authors]]"

Thank you! ----Omotecho (talk) 06:27, 2 May 2018 (UTC)

Patronyms[edit]

Category:Patronyms seems under-populated; should it be more widely used?

Also, should it not be "Category:Eponyms"? (And didn't we discuss that, recently?). Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 10:45, 2 May 2018 (UTC)

A patronym is just a subset of an eponym. It is not part of a taxonomy or classification, but if editors want to populate the category(s) it can be seen as harmless fun in the same way as a vernacular name or image. IMO anyway. Andyboorman (talk) 11:01, 2 May 2018 (UTC)

List of virus species[edit]

Can someone confirm if the bot is performing correctly? It looks like it's trying to update links but ended up shifting the links to a different entry. OhanaUnitedTalk page 03:55, 11 May 2018 (UTC)

Temminck's: Nouveau recueil de planches coloriées d’oiseaux[edit]

[ Moved from Wikispecies talk:Village Pump ]

Somebody can help me on how the order works on these references for Temminck. I can find the planche number reference in Zoonomen, but in the 5 volumes of Nouveau recueil de planches coloriées d’oiseaux accessed through BHL the planches are not in a logical order...and it would take a lot of time to find it manually searching the five volumes...Example: plate 2 is followed by plate 407 ???--Hector Bottai (talk) 17:01, 12 May 2018 (UTC)

Hi @Hector Bottai:! Dickinson (2001) may help. Burmeister (talk) 17:18, 12 May 2018 (UTC)

Circular redirect(s)[edit]

Eupatorium trapezoideum , Where was this supposed to go? ShakespeareFan00 (talk) 09:33, 15 May 2018 (UTC)

Also -

ShakespeareFan00 (talk) 09:34, 15 May 2018 (UTC)

Done Andyboorman (talk) 10:27, 15 May 2018 (UTC)

ON Wikisource...[edit]

This is probably rather old, s:Index:Icones muscorum.djvu but I wonder if it's of interest. ShakespeareFan00 (talk) 19:32, 15 May 2018 (UTC)

Lima (genus)[edit]

Would anyone like to rescue Lima (genus)? Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 15:48, 19 May 2018 (UTC)

Yes. Very important bivalve genus. I need to find pertinent data, then shall do it. Neferkheperre (talk) 21:46, 19 May 2018 (UTC)
WoRMS treatment here, in case this helps: http://www.marinespecies.org/aphia.php?p=taxdetails&id=138125 Regards - Tony Tony 1212 (talk) 23:15, 19 May 2018 (UTC)
I got it rescued as bivalve. WoRMS entry was tremendous help there. There also appears to be some sort of plant involved, maybe one of our botanists can help with it. I edited Lima disambiguation page to include Lima (genus). There is still much more work, as Cretaceous-Tertiary Gulf Coast species are still missing. Neferkheperre (talk) 12:40, 20 May 2018 (UTC)
No Lima in Plantae according to my "exhaustive" genera database (a small number names of names still missing), http://www.irmng.org . Nearest I have is a Limia Vandelli, 1788 (Plantae-Lamiales) (synonym of Vitex L.) which could conceivably appear as a typo "Lima" somewhere, I don't know.
You may also find this GNA (Global Names Index) search useful (or depressing...): http://gni.globalnames.org/name_strings?search_term=gen%3ALima Regards - Tony Tony 1212 (talk) 22:30, 21 May 2018 (UTC)

Category:Accepted species name[edit]

Category:Accepted species name has over 33K members, but is not used comprehensively. What is its purpose, and do we need it? Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 10:39, 25 May 2018 (UTC)

In botany, unless stated otherwise, for example by using {{disputed}}, all taxon pages are "accepted" by a consensus, which ideally is featured in the Reference section. Therefore, this category is superfluous and can be deleted on mass, IMHO. Cheers Andyboorman (talk) 13:26, 25 May 2018 (UTC)
agreed, this is useless information and honestly a given on the basis that the name appears at all. Delete all. Cheers Scott Thomson (Faendalimas) talk 16:14, 25 May 2018 (UTC)
Also agree--names are accepted until we know otherwise. —Justin (koavf)TCM 17:27, 25 May 2018 (UTC)
Perhaps all Category:Accepted names have the same problem and deserve to be deleted altogether. Burmeister (talk) 17:39, 25 May 2018 (UTC)
Totally agree, I am sure they all are unused. Clutter or vanity project, me thinks. Andyboorman (talk) 20:15, 25 May 2018 (UTC)

┌─────────────────────────────────┘
Indeed. Category:Accepted names and all of its subcategories are more or less pointless, and should be deleted. –Tommy Kronkvist (talk), 21:03, 25 May 2018 (UTC).

I feel confident that this is consensus among many long-time users of the site and this is one of many pet projects of User:Stho002. I feel good about deletion. —Justin (koavf)TCM 21:09, 25 May 2018 (UTC)
I would be happy to remove these myself but note that we don't have floodflag on this wiki. How do we want to proceed? —Justin (koavf)TCM 21:11, 25 May 2018 (UTC)
I think they may be mass deleted with Huggle. Dan Koehl (talk) 00:43, 26 May 2018 (UTC)
EDIT: Sorry, I was wrong there of course, this is not a question of mass delete, but category removal. removing that category from files should be easy with AutoWikiBrowser? Dan Koehl (talk) 00:47, 26 May 2018 (UTC)
Oh sure, I'd be happy to do it. I'm just saying that it will clog up special:RecentChanges. If everyone is cool with that, I'll go for it. —Justin (koavf)TCM 01:04, 26 May 2018 (UTC)
Fine by me Andyboorman (talk) 07:28, 26 May 2018 (UTC)
What is the alternative? This is used if species etc. are valid. PeterR (talk) 09:08, 26 May 2018 (UTC)

Names should be assumed to be valid unless we know otherwise. A disputed or invalid name would be noteworthy but correct, standard information is the norm. Why does this need to be categorized? —Justin (koavf)TCM 17:14, 26 May 2018 (UTC)

@Koavf, Andyboorman: I don't see why the rush to delete the Category: Accepted species name before giving it the time for a proper discussion. I also can't understand why botanists should deem it unnecessary when clearly it is a zoology-category and is irrelevant for botany. I think this category is useful because it stands as a counterpart for Category: Invalid species name. I consider this deletion improper and unproductive for WS. Mariusm (talk) 09:17, 26 May 2018 (UTC)

@Mariusm, Koavf: I also never understood the need for Category: Invalid species name, please enlighten me, thanks. Andyboorman (talk) 09:23, 26 May 2018 (UTC)
What instantly looked like a clear case of a consensus, may actually not be so, and further discussions during at least a week may have foregone this action. I'm sure the category changes can be reverted, should there arise a large support of keeping this category. In either case, seems this case should be brought to the community's attention on a broader scale, so everyone can make their opinion heard? Dan Koehl (talk) 09:28, 26 May 2018 (UTC)
@Andyboorman: Category: Invalid species name is VERY important because MANY invalid names have their own page and not merely a redirect. It is VERY important to indicate that these names are invalid. See for example Liogluta nigrobusta. Mariusm (talk) 09:36, 26 May 2018 (UTC)
@Mariusm: That does not really answer my question. To rephrase, what is it about Liogluta nigrobusta that qualifies it for its own taxon page? Why is it different from the synonyms under Cotula? In other words do we need a category to deal with taxon pages that do not belong on WS? Cheers. Andyboorman (talk) 10:02, 26 May 2018 (UTC)
@Andyboorman: What makes you say Liogluta nigrobusta doesn't belong to WS? Of course it does. Many synonyms have a lot of relevant information which can't fit in the valid-species relevant page, and if it does it wont be represented clearly enough. Some species have such a convoluted history that it's necessary to give their synonyms their due place. We never agreed that synonyms can't have their own pages which isn't a redirect. Many databases are giving the synonyms their specific pages where all their relevant data is represented, and I consider it a good practice. Mariusm (talk) 14:30, 26 May 2018 (UTC)
@Mariusm: I think we will have to agree to disagree, as I think that the data can be accommodated on the accepted taxon page. Regards Andyboorman (talk) 16:13, 26 May 2018 (UTC)
Well as a zoologist I see no value for the cat either. To me it is not about botany vs zoology and the slight differences between the codes. Yes the definitions of invalid and unavailable are different, however, accepted is not actually a zoological term either. Names in zoology are either unavailable or available (based on requirements) and if available they may be valid or invalid, based on whether they are the currently used synonymym or ajunior of some type. I see no value myself in junior synonyms having entire pages, redirects to the senior synonym sure, but I see no reason for making pages for taxa that are invalid. All the type data of the synonym and its refs can be included on the main page, why can this not happen. These categories are a waste of time and space. Cheers Scott Thomson (Faendalimas) talk 18:49, 26 May 2018 (UTC)

┌─────────────────────────────────┘
in regards to Category: Invalid species name I am also in favor of deleting this, however, accept that may need more discussion. I ask this, what does it achieve creating a page for an invalid species, only to have it sit in this category plus have a link to its senior synonym and a template showing its invalid. What purpose does this serve for the nomenclature of the living world? Why can this information not be placed on the senior synonyms page. Cheers Scott Thomson (Faendalimas) talk 19:04, 26 May 2018 (UTC)

Wouldn't it make more sense to include all taxon pages using the {{invalid}} template automatically in a Category:Invalid taxon name instead of adding them manually to such a cat? - And yes, I think, invalid taxon pages are useful for documentation purposes. Just in case, a user should want to search for such a name. --Murma174 (talk) 19:23, 26 May 2018 (UTC)