[Taxacom] LSID versus names
Paul Kirk
p.kirk at cabi.org
Fri Jun 22 03:19:00 CDT 2012
And ... if we all pull together (in the same direction) to build a fully functional and populated GNUB we will have the potential to cut through much of the mess we all, to a greater or lesser extent, still 'muck about in' ... :-) ... have a good weekend.
Paul
-----Original Message-----
From: Dr.B.J.Tindall [mailto:bti at dsmz.de]
Sent: 22 June 2012 09:12
To: Stephen Thorpe
Cc: Paul Kirk; Jim Croft; TAXACOM
Subject: Re: [Taxacom] LSID versus names
Which is why we have discussion involving users of different Codes as well as the ICB (International Committee on Bionomenclature).
Brian
Quoting Stephen Thorpe <stephen_thorpe at yahoo.co.nz>:
> well, perhaps the botanical/fungal code is less problematic, but the
> ICZN code doesn't really determine a well defined boundary between
> chresonyms/new names, or homonyms/misidentifications for the older
> literature. It doesn't specify exactly what it means to validly
> designate a holotype, and it doesn't regulate new combinations at all
> ... i.e., BIG MESS!
>
>
>
> ________________________________
> From: Paul Kirk <p.kirk at cabi.org>
> To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>; Dr.B.J.Tindall
> <bti at dsmz.de>; Jim Croft <jim.croft at gmail.com>
> Cc: TAXACOM <taxacom at mailman.nhm.ku.edu>
> Sent: Friday, 22 June 2012 8:01 PM
> Subject: RE: [Taxacom] LSID versus names
>
>
>
> the ?Code governed event? where the name (ICNafp) is established is
> what?s on the page (not every name occurence/usage) ? after all the
> taxonomy (in one ?research project?) is done the choice of name
> requires access to protologues to determine which name has priority ?
> and access to types, or type label data, which is not as well advanced
> as the literature linking in IF.
>
> Paul
>
> From:Stephen Thorpe [mailto:stephen_thorpe at yahoo.co.nz]
> Sent: 22 June 2012 08:53
> To: Paul Kirk; Dr.B.J.Tindall; Jim Croft
> Cc: TAXACOM
> Subject: Re: [Taxacom] LSID versus names
>
> perhaps I don't fully understand what you are doing exactly? Linking
> to scanned literature is good, but doesn't in itself solve much. The
> nomenclature needs to be verified, and the literature integrated into
> a coherent and meaningful whole, so you can get good up-to-date
> information on taxa ...
>
> Stephen
>
>
> ________________________________
>
> From:Paul Kirk <p.kirk at cabi.org>
> To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>; Dr.B.J.Tindall
> <bti at dsmz.de>; Jim Croft <jim.croft at gmail.com>
> Cc: TAXACOM <taxacom at mailman.nhm.ku.edu>
> Sent: Friday, 22 June 2012 7:49 PM
> Subject: RE: [Taxacom] LSID versus names
>
>
> From the start (sometime in mid 2004), this has probably taken 4-8
> weeks (160-320 hours spread over 8 years). Others, of course, do the
> scanning, I have just built the links.
>
> Paul
>
> From:Stephen Thorpe [mailto:stephen_thorpe at yahoo.co.nz]
> Sent: 22 June 2012 08:39
> To: Paul Kirk; Dr.B.J.Tindall; Jim Croft
> Cc: TAXACOM
> Subject: Re: [Taxacom] LSID versus names
>
> Yes, I too link to BHL whenever possible, but I prioritise stuff that
> isn't O/A, for obvious reasons ...
>
> It would be interesting to know how long it took to "do" 80,000 fungal
> names (out of 460,000, i.e., approx one fifth)? In zoology, there are
> maybe 2 million names, as a rough order of magnitude ...
>
> Incidentally, I am at the moment indexing some literature with only a
> few articles available O/A on scattered websites:
> http://species.wikimedia.org/wiki/ISSN_0303-6758#Transactions_of_the_R
> oyal_Society_of_New_Zealand.2C_biological_sciences
>
> Stephen
>
>
> ________________________________
>
> From:Paul Kirk <p.kirk at cabi.org>
> To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>; Dr.B.J.Tindall
> <bti at dsmz.de>; Jim Croft <jim.croft at gmail.com>
> Cc: TAXACOM <taxacom at mailman.nhm.ku.edu>
> Sent: Friday, 22 June 2012 7:27 PM
> Subject: RE: [Taxacom] LSID versus names
>
> I agree Stephen ... the mycologist (well, this mycologist) is already
> doing it ... with something less perfect that DOI's but always 'open'
> http://biodiversitylibrary.org/page/483995. IF has nearly 80,000 names
> (out of 460,000) already done.
>
> Paul
>
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Stephen
> Thorpe
> Sent: 22 June 2012 08:19
> To: Dr.B.J.Tindall; Jim Croft
> Cc: TAXACOM
> Subject: Re: [Taxacom] LSID versus names
>
> I doubt that (m)any botanists, nevermind bacteriologists, fully grasp
> the gigantic mess that is zoological nomenclature/taxonomy.
> LSIDs, ZooBank, etc. do little or nothing to improve that mess.
> There are far more important things to be done first, like just
> sorting out and linking together names and literature, something along
> these lines
> (http://species.wikimedia.org/wiki/Category:Publications_of_M.C._Mille
> r), but for *all groups/authors*. This is a task so huge that it may
> never be completed, and yet it must take priority over LSIDs, etc....
>
> Stephen
>
>
>
> ________________________________
> From: Dr.B.J.Tindall <bti at dsmz.de>
> To: Jim Croft <jim.croft at gmail.com>
> Cc: TAXACOM <taxacom at mailman.nhm.ku.edu>
> Sent: Friday, 22 June 2012 7:03 PM
> Subject: Re: [Taxacom] LSID versus names
>
> Jim,
> I know a lot of the background and from where I stand there is a big
> difference between the discussions I have heard and what has actually
> been implmented elsewhere. You summarised the benefits
> nicely:
>
> "Back to the purpose of a/the list? To make our collective lives
> easier, to make taxonomy more efficient and productive, but most
> importantly, it is a shit tedious but essential job and we do not want
> to have people do it more than once and be freed up to do more
> taxonomy....."
>
> Which is why ZooBank and MycoBank are following the lead made under
> the Bacteriological Code. No its not perfect, but it is a start and it
> can be improved upon.
>
> LSIDs - an interesting statement. I haven't heard anyone questioning
> who issues IP addresses or DOIs for publications.
>
> Brian
>
> Quoting Jim Croft <jim.croft at gmail.com>:
>
>> The last time a centralized system was seriously proposed for plants,
>> the botanical community freaked and started torching the code and
>> burning effigies in the streets. The suggestion is still there, but I
>> am not sure we are ready for it yet. A lot will depend on the
>> implementation mechanisms.
>>
>> As with LSIDS, the idea is one thing, but who gets to implement it
>> and call the shots is another thing entirely.
>>
>> jim
>>
>> On Fri, Jun 22, 2012 at 4:35 PM, Dr.B.J.Tindall <bti at dsmz.de> wrote:
>>> Jim,
>>> Actually you seem to have covered a lot of the relevant points in
>>> your reply. Perhaps the only major difference is the fact that since
>>> I work with prokaryotes I have become used to dealing with a
>>> centralised system, which is anchored in the Bacteriological Code.
>>> The system operates with all the potential problems you list, but
>>> this is not the fault of the system, rather whether the correct
>>> information is supplied in the first place. It depends on the rigour
>>> of those who maintain the system along with the willingness of those
>>> who should comply to do so.
>>>
>>> Brian
>>>
>>> Quoting Jim Croft <jim.croft at gmail.com>:
>>>
>>>> Sorry Brian - I am having difficulty in keeping up... :)
>>>>
>>>> At the moment a 'list' is, in botany at least, an index, a tool to
>>>> stop you having to scour through the literature for tke killer fact
>>>> that will make or break a decision. Someone, bless their souls, has
>>>> already done that work for us.
>>>>
>>>> With registration, the game changes. A list will or could become
>>>> the list. What hapens to the point of truth? Is it the type? The
>>>> publication? the list? Or a murky combination? What if the
>>>> publication contains different information to the type (shock!)? Or
>>>> the the list contains different information to both (horror!). Or
>>>> all three are different (oh the humanity!). Which ones can or
>>>> should get 'corrected'? Of course, things like this will never happen...
>>>>
>>>> Our 'list', APNI, aims to record and document everything that was
>>>> ever said, by anyone, about the nomenclature and taxononomy of an
>>>> Australian plant, even ambiguity and errors - the good the bad and
>>>> the downright ugly (you want ugly Rich, we'll give you ugly!).
>>>> Essentially your a) through d). But it is still, when you break it
>>>> down, as rigourous, perfect and useful as we like to imagine it
>>>> could be, just a list of names and list of assertions about those
>>>> names, with no legal standing under The Code at all.
>>>>
>>>> Obviously this task will never be completed in my life time, or at
>>>> all when you think about it. But the journey of a thousand miles,
>>>> etc...
>>>>
>>>> Back to the purpose of a/the list? To make our collective lives
>>>> easier, to make taxonomy more efficient and productive, but most
>>>> importantly, it is a shit tedious but essential job and we do not
>>>> want to have people do it more than once and be freed up to do more
>>>> taxonomy... which creates more names and more assertions which...
>>>> you get the picture... :)
>>>>
>>>> jim
>>>>
>>>> On Thu, Jun 21, 2012 at 9:52 PM, Dr.B.J.Tindall <bti at dsmz.de> wrote:
>>>>>
>>>>> Jim,
>>>>> which begs the question what is the purpose of the list? As far as
>>>>> I am concerened the list (which is not necessarily simply limited
>>>>> to "names") does not replace the main information concerning the
>>>>> properties of the taxon in question etc. It summarises critical
>>>>> information, which in the case of the Bacteriological Code would
>>>>> be:
>>>>> a) the name and where it was published (in our case in a Code
>>>>> compliant fashion).
>>>>> b) where one finds the description
>>>>> c) where the types are located
>>>>> d) given the relevance of specialist databases for data such as
>>>>> gene/protein sequences the links to the relevant sequence
>>>>> accession numbers.
>>>>> e) documenting assertions of synonym (without determining whether
>>>>> such assertions are to be followed), or rulings affecting the use
>>>>> of names made by appropriate authorities that deal with such
>>>>> matters.
>>>>>
>>>>> That is a good start. Both ZooBank and MycoBank look like that
>>>>> they would like to head for being far more than being just lists of names.
>>>>>
>>>>> Brian
>>>>>
>>>>>
>>>>> Quoting Jim Croft <jim.croft at gmail.com>:
>>>>>
>>>>>> Absolutely... which is why as a community we invest in things
>>>>>> like IPNI, APNI, etc.
>>>>>>
>>>>>> But I think there is a risk, if not a problem, in assigning the
>>>>>> point of authority to an abstracted list rather the publication.
>>>>>>
>>>>>> Having said that, the crystal ball and bat entrails are insisting
>>>>>> that time and technology will inevitably take us to a place where
>>>>>> 'the list is the thing'. They don't tell me when or how it is
>>>>>> going to work, but they are pretty sure it is going to happen.
>>>>>>
>>>>>> jim
>>>>>>
>>>>>> On Wed, Jun 20, 2012 at 10:57 PM, Dr.B.J.Tindall <bti at dsmz.de> wrote:
>>>>>>>
>>>>>>>
>>>>>>> Jim,
>>>>>>> Well, if anything is going to be "authoritative" it would have
>>>>>>> to be the fact that certain nomenclatural and taxonomic
>>>>>>> events/acts have taken place.
>>>>>>> There is no better way of doing this than to make sure that
>>>>>>> these acts/events are properly documented. In bacteriology and
>>>>>>> virology this is via a centralised system. To my knowledge the
>>>>>>> virologists maintain an authoritative list of names on the ICTV
>>>>>>> website and there were suggestions that bacteriologists should
>>>>>>> do the same - the only issue being who pays the bills.
>>>>>>>
>>>>>>> The only issue that is problematic is when there is an "authoritative"
>>>>>>> list
>>>>>>> (which in bacteriology would document new names and new
>>>>>>> combinations) and other lists surface which are
>>>>>>> misleading/erroneous and undermine the work of those who try to
>>>>>>> make sure that the "authoritative lists" are accurate.
>>>>>>>
>>>>>>> Brian
>>>>>>>
>>>>>>> Quoting Jim Croft <jim.croft at gmail.com>:
>>>>>>>
>>>>>>>> This kind of thinking is a big problem and one of the reasons
>>>>>>>> we get into messes like this. NONE of these databases is
>>>>>>>> authoritative. They are not mentioned in the Code, they have
>>>>>>>> not legislated priority and have no official standing in
>>>>>>>> nomenclature or taxonomy at all. They are at best useful and
>>>>>>>> reliable indices to the literature (with the type and cited
>>>>>>>> specimens, the real authority), at worst, incomplete
>>>>>>>> perpetuators of falsehoods.
>>>>>>>>
>>>>>>>> There is no point looking for a single point of truth when
>>>>>>>> there isn't one. Well ok, it might be core business for
>>>>>>>> religion and politics. But it is not going to work for
>>>>>>>> nomenclature and taxonomy, unless we change the Code radically
>>>>>>>> and create one (ducks quickly, to avoid the ugly reg* word).
>>>>>>>>
>>>>>>>> jim
>>>>>>>>
>>>>>>>> On Wed, Jun 20, 2012 at 5:42 PM, Roderic Page
>>>>>>>> <r.page at bio.gla.ac.uk>
>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Plant people are
>>>>>>>>> somewhat better off with IPNI, although one could argue
>>>>>>>>> whether we should regard IPNI, Tropics, or the Plant List as
>>>>>>>>> the definitive authority.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>>
>>>>>>>> Taxacom Mailing List
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>>>>>>>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>>>>>>>>
>>>>>>>> The Taxacom archive going back to 1992 may be searched with
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>>>>>>>>
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>>>>>>>>
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>>>>>>>> here
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Dr.B.J.Tindall
>>>>>>> Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und
>>>>>>> Zellkulturen GmbH Inhoffenstraße 7B
>>>>>>> 38124 Braunschweig
>>>>>>> Germany
>>>>>>> Tel. ++49 531-2616-224
>>>>>>> Fax ++49 531-2616-418
>>>>>>> http://www.dsmz.de
>>>>>>> Director: Prof. Dr. J. Overmann
>>>>>>> Local court: Braunschweig HRB 2570 Chairman of the management
>>>>>>> board: MR Dr. Axel Kollatschny
>>>>>>>
>>>>>>> DSMZ - A member of the Leibniz Association (WGL)
>>>>>>>
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>>>>>>> This message was sent using IMP, the Internet Messaging Program.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> _________________
>>>>>> Jim Croft ~ jim.croft at gmail.com ~ +61-2-62509499 ~
>>>>>> http://about.me/jrc 'Whenever you find yourself on the side of
>>>>>> the majority, it's time to pause and reflect.'
>>>>>> - Mark Twain
>>>>>> 'A civilized society is one which tolerates eccentricity to the
>>>>>> point of doubtful sanity.'
>>>>>> - Robert Frost
>>>>>>
>>>>>> Please send URLs, not attachments:
>>>>>> http://www.gnu.org/philosophy/no-word-attachments.html
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Dr.B.J.Tindall
>>>>> Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und
>>>>> Zellkulturen GmbH Inhoffenstraße 7B
>>>>> 38124 Braunschweig
>>>>> Germany
>>>>> Tel. ++49 531-2616-224
>>>>> Fax ++49 531-2616-418
>>>>> http://www.dsmz.de
>>>>> Director: Prof. Dr. J. Overmann
>>>>> Local court: Braunschweig HRB 2570 Chairman of the management
>>>>> board: MR Dr. Axel Kollatschny
>>>>>
>>>>> DSMZ - A member of the Leibniz Association (WGL)
>>>>>
>>>>> ----------------------------------------------------------------
>>>>> This message was sent using IMP, the Internet Messaging Program.
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> _________________
>>>> Jim Croft ~ jim.croft at gmail.com ~ +61-2-62509499 ~
>>>> http://about.me/jrc 'Without the freedom to criticize, there is no
>>>> true praise.
>>>> - Pierre Beaumarchais
>>>> 'Whenever you find yourself on the side of the majority, it's time
>>>> to pause and reflect.'
>>>> - Mark Twain
>>>> 'A civilized society is one which tolerates eccentricity to the
>>>> point of doubtful sanity.'
>>>> - Robert Frost
>>>>
>>>
>>>
>>>
>>> Dr.B.J.Tindall
>>> Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und
>>> Zellkulturen GmbH Inhoffenstraße 7B
>>> 38124 Braunschweig
>>> Germany
>>> Tel. ++49 531-2616-224
>>> Fax ++49 531-2616-418
>>> http://www.dsmz.de
>>> Director: Prof. Dr. J. Overmann
>>> Local court: Braunschweig HRB 2570
>>> Chairman of the management board: MR Dr. Axel Kollatschny
>>>
>>> DSMZ - A member of the Leibniz Association (WGL)
>>>
>>> ----------------------------------------------------------------
>>> This message was sent using IMP, the Internet Messaging Program.
>>
>>
>>
>> --
>> _________________
>> Jim Croft ~ jim.croft at gmail.com ~ +61-2-62509499 ~
>> http://about.me/jrc 'Without the freedom to criticize, there is no true praise.
>> - Pierre Beaumarchais
>> 'Whenever you find yourself on the side of the majority, it's time to
>> pause and reflect.'
>> - Mark Twain
>> 'A civilized society is one which tolerates eccentricity to the point
>> of doubtful sanity.'
>> - Robert Frost
>>
>
>
>
> Dr.B.J.Tindall
> Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und
> Zellkulturen GmbH Inhoffenstraße 7B
> 38124 Braunschweig
> Germany
> Tel. ++49 531-2616-224
> Fax ++49 531-2616-418
> http://www.dsmz.de
> Director: Prof. Dr. J. Overmann
> Local court: Braunschweig HRB 2570
> Chairman of the management board: MR Dr. Axel Kollatschny
>
> DSMZ - A member of the Leibniz Association (WGL)
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
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Dr.B.J.Tindall
Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH Inhoffenstraße 7B
38124 Braunschweig
Germany
Tel. ++49 531-2616-224
Fax ++49 531-2616-418
http://www.dsmz.de
Director: Prof. Dr. J. Overmann
Local court: Braunschweig HRB 2570
Chairman of the management board: MR Dr. Axel Kollatschny
DSMZ - A member of the Leibniz Association (WGL)
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