[Taxacom] From Re: Taxacom Digest, Vol 110, Issue 19 to Globally useful plant nomenclatural databases
Weakley, Alan
weakley at bio.unc.edu
Sat May 23 08:19:08 CDT 2015
Let's be sure we don't muddle up two admittedly interrelated but quite different things:
1. A checklist that presents at a point in time what is believed to be the most accurate possible set of taxa for an area (country, continent, state, world). The accepted taxonomy.
2. A nomenclator that presents information on all the names that have ever been proposed, their authorship, date, nomenclatural validity, nomenclatural 'conservation', citation to publication, etc.
The Plant List was an attempt to do #1 for the World, and I agree with Paul, Neil, Gurchuran, and others about its shortcomings. There are MUCH more useful such compilations for various areas (though not for the world, which was a gigantically ambitious undertaking and as has been pointed out before on this listserv was done too mechanically and with too little involvement of experts --- the Kew World Checklist seems to be advancing on this in a better way). In the US, there is USDA Plants, for North America BONAP's online resource and the NatureServe Explorer website. Many countries have more-or-less official "country lists", that are also "more-or-less" kept up-to-date. It should be pointed out that having a Checklist of this kind is very useful for scientific work, but also is critically necessary for conservation efforts, and for use by other "user groups" of taxonomy: foresters, gardeners, natural resource managers, monitors of global change, etc. Such lists are maintained for birds and other organism groups -- IOC Checklists, AOU checklists. But of course there is a 30-40X scale difference in numbers of species. These more accurate checklists I use every day (I don't ever use the Plant List because there are far superior resources available for the area of my primary interest -- vascular plants of eastern North America).
IPNI and Tropicos are examples of #2, and provide that very different service/value quite well. The user groups for #2 are essentially other plant taxonomists. The great majority of user groups don't need to and don't want to know the nomenclatural arcanery -- they want to know how many oak species there are in eastern North America, what the "right" name to apply to each one is, what its distribution is, and if it is rare rangewide or in one or more subnational jurisdictions. I use IPNI and Tropicos almost every day.
For birds, Avibase (http://avibase.bsc-eoc.org/avibase.jsp?lang=EN&pg=home) rather elegantly manages to do both #1 and #2, at http://avibase.bsc-eoc.org/compare.jsp?source1=ioc&version1=IOC5_01&source2=ioc&version2=IOC5_02&continent=%C2%AE_type=3. Note, too, that when done elegantly, such lists can actually manage to combine (or at least offer both of) standardization based on the authority of experts (you can accept List Y and use it if you choose to) with democracy/chaos/eccentricity (no one is forcing you to use List Y).
-----Original Message-----
From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Mary Barkworth
Sent: Saturday, May 23, 2015 6:15 AM
To: taxacom at mailman.nhm.ku.edu
Subject: [Taxacom] From Re: Taxacom Digest, Vol 110, Issue 19 to Globally useful plant nomenclatural databases
Creating and maintaining a one-stop shopping list for names is, IMO, essentially impossible, probably thankless, and undoubtedly time consuming. I speak as one who has complained to the editors of the Plant List, one of my complaints being use of the word "Accepted" without stating, as Tropicos does, where the name is treated as an accepted name.
But let's be reasonable. Kew has been through enormous budget cuts. I agree it would be good to have on each page a statement that it is no longer being maintained on a regular basis. I suspect that some groups may curate their own portion of it more regularly than others and for them it is probably a useful resource. Even adding such a comment would require time on the part of their greatly reduced IT staff who also have many other projects to work on. So let's be thankful for what is there, consult it as a potential shortcut to what would otherwise take years to do but recognize that it may not be able to assist us and that we may not like its choices even when it is current for a particular group.
A broader topic, and one that all botanists should consider is whether we need to change the funding model for global resources. Perhaps we should ask our national botanical societies to provide some ongoing support to institutions that maintain, or try to maintain, globally useful plant nomenclatural databases. The two that come to my mind are IPNI and TROPICOS and, less frequently, the Taxonomic Names Resolution Service (TNRS; http://tnrs.iplantcollaborative.org/). I would be interested in knowing from other plant taxonomists what global nomenclatural databases they use on a regular basis. If you let me know, personally or via taxacom, I shall compile a list of those mentioned and share the results in about 4 weeks (i.e., around June 23) Mary
-----Original Message-----
From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Paul van Rijckevorsel
Sent: Saturday, May 23, 2015 2:06 AM
To: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Taxacom Digest, Vol 110, Issue 19
Well:
1) there is a distinct want for a one-stop-shopping list
2) The Plant List indicates it is a "work in progress"
Ergo, it is logical to expect regular updates, which will be better and better. These updates do no happen.
Taken as a whole, The Plant List has so many errors that it cannot be expressed meaningfully, it is off the scale. But the occurrence of errors is not random, but to a pattern.
Looking at the component databases, it is clear that a major factor is how it deals with Tropicos. It would be a vast improvement if, in harvesting material from Tropicos, it would mark names as "unresolved" if they do not have at least two (or three) references that do accept the name. Also, exclude all names that are marked as illegitimate, and combinations with illegitimate generic names.
The result would not yet be an accurate list, but it would then be possible to see where the problems are. At that stage an editor could be put to work straightening out the worst problems.
If there is no progress, its value would be limited to acting as a front for the Kew World Checklist, and it might indeed be better to "pull the plug".
Paul
----- Original Message -----
From: "Neil Snow" <nwiltonsnow at gmail.com>
To: <taxacom at mailman.nhm.ku.edu>
Sent: Friday, May 22, 2015 7:25 PM
Subject: Re: [Taxacom] Taxacom Digest, Vol 110, Issue 19
> Dear Dr. Signh,
>
> My understanding is that The Plant List is a static database.
>
> It was developed to meet a targeted and cooperative goal to assist in
> global plant conservation.
>
> Many (myself included) were confused and distraught at how inaccurate
> the information was and still is.
>
> While we all can applaud conservation efforts, it begs the question of
> whether keeping a static and admittedly outdated database online is
> causing more confusion than it is worth.
>
> Non-taxonomists also seek nomenclatural guidance. I speak from having
> willingly helped a few colleagues in Hawaii for 3-1/2 years to
> interpret nomenclatural challenges associated with non-native species.
>
> I invite others to share their opinions. But if it were up to me, I'd
> pull the plug.
>
> NS
>
>
>
>
> On Fri, May 22, 2015 at 7:00 PM, <taxacom-request at mailman.nhm.ku.edu> wrote:
>
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>> ____________________________________
>>
>>
>> Today's Topics:
>>
>> 1. Re: Database collection software (Nico Franz)
>> 2. Now Acacia and Vachellia confusion (Gurcharan Singh)
>> 3. Re: Database collection software (Eric Gouda)
>> 4. Re: Now Acacia and Vachellia confusion (Gurcharan Singh)
>>
>>
>> ---------------------------------------------------------------------
>> -
>>
>> Message: 1
>> Date: Thu, 21 May 2015 14:30:06 -0400
>> From: Nico Franz <nico.franz at asu.edu>
>> To: TAXACOM <taxacom at mailman.nhm.ku.edu>
>> Subject: Re: [Taxacom] Database collection software
>> Message-ID:
>> <
>> CALZMekmnbqDLpoJHk3X7NvcmAY14NGWMTf6BzjAJctt8Tbz5MA at mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Hi Chris:
>>
>> Here are two more items of interest; but no claim as to lack of
>> bias. In North America, iDigBio is a wonderful resource to learn more
>> about this subject area.
>>
>> https://www.idigbio.org/content/biological-collections-databases
>> http://bdj.pensoft.net/articles.php?id=1114
>>
>> Cheers, Nico
>>
>>
>>
>> >
>> > -------------------------------------------------------------------
>> > ---
>> >
>> > Message: 1
>> > Date: Wed, 20 May 2015 22:18:44 +0300
>> > From: Χρήστος Γεωργιάδης <cgeorgia at biol.uoa.gr>
>> > To: "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>
>> > Subject: [Taxacom] Database collection software
>> > Message-ID: <D6FDAEE5-9DCB-44B2-AB93-256B0C1A6C43 at biol.uoa.gr>
>> > Content-Type: text/plain; charset=us-ascii
>> >
>> > Dear Colleagues,
>> >
>> > After several hours dwelling into the technical jargon of database
>> > software for collection management I'm still at a loss...
>> >
>> > We are in need of making a decision of which database should we use
>> > in order to register specimens in our Museum. We are thinking of
>> > splitting
>> the
>> > collection in different databases on specimen data information but
>> > having the possibility of using the same tables for collection
>> > events and localities.
>> >
>> > Without putting any names forward so as not to bias anyone, do you
>> > have any comments, suggestions, or even hints and tips?
>> >
>> > Thanks in advance to all who wish to help out in untangling this
>> > conundrum...
>> >
>> > Chris Georgiadis
>> >
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Fri, 22 May 2015 11:04:48 +0530
>> From: Gurcharan Singh <singhg45 at gmail.com>
>> To: "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>
>> Subject: [Taxacom] Now Acacia and Vachellia confusion
>> Message-ID:
>> <CAHiXKpVx-XKJGipieUkWsz-Y2YE36kB8Px=
>> hQ-CGqftcMhfdcw at mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> The Plant list was designed out to help botanists pick out the
>> accepted names and synonym as the opening line on home page indicates
>> '1,064,035 scientific plant names of species rank. Of these 350,699 are accepted'
>> Every time I visit the database to know the accepted name, I find
>> the database more and more confused, and I have communicated most to
>> the authorities in 20 plus communication.
>> This time trying to find accepted name for our common species
>> here in Delhi, I find *Acacia* *nilotica* subsp. *indica* (Benth.)
>> Brenan is an accepted name
>>
>> *Acacia* *nilotica* (L.) Delile is an accepted name but unfortunately
>> although all other subspecies are listed, but not subsp. nilotica And
>> now look under Vachellia,
>> *Acacia* *nilotica* (L.) Delile is an accepted name
>>
>> Not only basionym *Mimosa* *nilotica* L. is missing from the synonyms
>> but there is no mention of eight subspecies recognised under under
>> Acacia nilotica.
>>
>> Where is The Plant List leading
>>
>>
>>
>> Dr. Gurcharan Singh
>> Retired Associate Professor
>> SGTB Khalsa College, University of Delhi, Delhi-110007
>> Res: 932 Anand Kunj, Vikas Puri, New Delhi-110018.
>> Phone: 011-25518297 Mob: 9810359089
>> http://www.gurcharanfamily.com/
>> http://people.du.ac.in/~singhg45/
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Fri, 22 May 2015 09:41:01 +0200
>> From: Eric Gouda <E.J.Gouda at uu.nl>
>> To: <taxacom at mailman.nhm.ku.edu>
>> Subject: Re: [Taxacom] Database collection software
>> Message-ID: <555EDD8D.7040309 at uu.nl>
>> Content-Type: text/plain; charset="utf-8"; format=flowed
>>
>> MySQL is great and yes it is owned by Oracle, but if the open source
>> community will be in conflict with Oracle, there will be a new
>> development like we have seen with OpenOffice and LibereOffice. I
>> think continuity is guaranteed.
>>
>> I'm not sure what Plant record applications are available for this
>> platform, we are using our own developed Taxasoft database interface,
>> that is available for others and it is very flexible for all kind of
>> additional functionality.
>>
>> Eric (BG Utrecht)
>>
>> taxacom-request at mailman.nhm.ku.edu schreef op 21-5-2015 om 19:00:
>> > Date: Wed, 20 May 2015 22:23:18 +0200 From: "Erik Rijkers"
>> > <er at xs4all.nl> To: "Derek Sikes" <dssikes at alaska.edu> Cc:
>> > =?iso-8859-1?Q?=22=D7=F1=DE=F3=F4=EF=F2_=C3=E5=F9=F1=E3=E9=DC=E4=E7=F2?="
>> > <cgeorgia at biol.uoa.gr>, "taxacom at mailman.nhm.ku.edu,
>> > <taxacom at mailman.nhm.ku.edu> Subject: Re: [Taxacom] Database
>> > collection software - Open Source Message-ID:
>> > <1598ff63abc905de30c9e5f5c57e4d96.squirrel at webmail.xs4all.nl>
>> > Content-Type: text/plain;charset=iso-8859-1 On Wed, May 20, 2015
>> > 22:07, Derek Sikes wrote:
>> >> >Here is a FAQs with information about Arctos,
>> >> >
>> >> >http://arctosdb.org/faq/
>> >> >
>> > Oracle?
>> >
>> > It seems dubious in this day and age to dump any money in the
>> > direction
>> of Oracle for this sort of solution. Yes, I know
>> > it's a great database but far too expensive. (btw, Mysql is also
>> > owned
>> by Oracle.)
>> >
>> > One would expect opensource solutions for this so central problem;
>> > isn't
>> there such a opensource solution? (as a backend,
>> > PostgreSQL comes to mind)
>> >
>> >
>> > Erik Rijkers
>>
>>
>> --
>> University Botanic Gardens
>> att. E.J. Gouda
>> Budapestlaan 17
>> 3584 CD Utrecht
>> Netherlands
>>
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Fri, 22 May 2015 18:12:06 +0530
>> From: Gurcharan Singh <singhg45 at gmail.com>
>> To: "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>
>> Subject: Re: [Taxacom] Now Acacia and Vachellia confusion
>> Message-ID:
>> <CAHiXKpWzTM5Sk02-UZS8TLuGkKt9pAbySGvcmG66Akj4=
>> x_Kpw at mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> I am forwarding it again as Acacia nilotica was repeated by me
>> Vachellia nilotica The Plant list was designed out to help botanists
>> pick out the accepted names and synonym as the opening line on home
>> page indicates '1,064,035 scientific plant names of species rank. Of
>> these 350,699 are accepted'
>> Every time I visit the database to know the accepted name, I find
>> the database more and more confused, and I have communicated most to
>> the authorities in 20 plus communications.
>> This time trying to find accepted name for our common species
>> here in Delhi, I find*Acacia* *nilotica* subsp. *indica* (Benth.)
>> Brenan is an accepted name
>>
>> *Acacia* *nilotica* (L.) Delile is an accepted name but unfortunately
>> although all other subspecies are listed, but not subsp. nilotica And
>> now look under Vachellia,
>> *Vachellia* *nilotica* (L.) P.J.H. Hurter & Mabb.is an accepted name
>>
>> Not only basionym *Mimosa* *nilotica* L. is missing from the synonyms
>> but there is no mention of eight subspecies recognised under under
>> Acacia nilotica.
>>
>> Where is The Plant List leading
>>
>> Dr. Gurcharan Singh
>> Retired Associate Professor
>> SGTB Khalsa College, University of Delhi, Delhi-110007
>> Res: 932 Anand Kunj, Vikas Puri, New Delhi-110018.
>> Phone: 011-25518297 Mob: 9810359089
>> http://www.gurcharanfamily.com/
>> http://people.du.ac.in/~singhg45/
>>
>> On Fri, May 22, 2015 at 11:04 AM, Gurcharan Singh
>> <singhg45 at gmail.com>
>> wrote:
>>
>> > The Plant list was designed out to help botanists pick out the
>> > accepted names and synonym as the opening line on home page
>> > indicates '1,064,035 scientific plant names of species rank. Of these 350,699 are accepted'
>> > Every time I visit the database to know the accepted name, I
>> > find the database more and more confused, and I have communicated
>> > most to the authorities in 20 plus communication.
>> > This time trying to find accepted name for our common species
>> > here
>> in
>> > Delhi, I find *Acacia* *nilotica* subsp. *indica* (Benth.) Brenan
>> > is an accepted name
>> >
>> > *Acacia* *nilotica* (L.) Delile is an accepted name but
>> > unfortunately although all other subspecies are listed, but not
>> > subsp. nilotica And now look under Vachellia,
>> > *Acacia* *nilotica* (L.) Delile is an accepted name
>> >
>> > Not only basionym *Mimosa* *nilotica* L. is missing from the
>> > synonyms but there is no mention of eight subspecies recognised
>> > under under Acacia nilotica.
>> >
>> > Where is The Plant List leading
>> >
>> >
>> >
>> > Dr. Gurcharan Singh
>> > Retired Associate Professor
>> > SGTB Khalsa College, University of Delhi, Delhi-110007
>> > Res: 932 Anand Kunj, Vikas Puri, New Delhi-110018.
>> > Phone: 011-25518297 Mob: 9810359089
>> > http://www.gurcharanfamily.com/ http://people.du.ac.in/~singhg45/
>> >
>>
>>
>> ------------------------------
>>
>> Subject: Digest Footer
>>
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>> Celebrating 28 years of Taxacom in 2015.
>>
>>
>> ------------------------------
>>
>> End of Taxacom Digest, Vol 110, Issue 19
>> ****************************************
>>
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