[Taxacom] LSID versus names

Fri Jun 22 02:53:19 CDT 2012

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_Royal_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._Miller), 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.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>>
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>>>>>>> either of these methods:
>>>>>>>
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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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>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> _________________
>>>>> 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)

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