[Taxacom] Ebbe Nielsen Challenge submission

Janzen, Daniel H djanzen at sas.upenn.edu
Fri Sep 7 07:02:44 CDT 2018


7 Sep 2018
UPenn

Rod, much thanks for even noticing my question from the corridors of the confernce room.   I am dealing with 10s of thousands of IDs at once, then subsequently specimen by specimen mixed with other IDs of other sorts (and methods) and these numbers steadily climb into hundreds of thousands of IDs at once.  WHICH machine process, when there are multiple machine processes and human subjectivity tossed into the mix at various non-identifiable points along the way?  Scientific Names become nice and very useful collateral for a specimen or event, which they certainly are, especially out of the ivory tower and on the street for the real owners of biodiversity.  But also barcodes and BINs and similar things become other sorts of “names” that work much better than Scientific Names applied by instinct and vision by humans over the past 200+ years, and argued over incessantly as though nature starts in the museum drawer with whatever bits and drabs happen to be still attached to it, also collected by we fragile Pooh Bears and some machines in their singularities.

My question was not meant to stir up any controversy, so much as to suggest from the back of the room that it be on the blackboard along with other questions.  We are setting out with a cast of thousands to DNA barcode an entire county with millions of species of Eucaryotes, and our cottage industry that I have lived for 60 years now is only partly adequate.

Smile. WIll be back in January to all of Taxacom on this topic if not before.

Dan and Winnie and the Catocala on the wall at that building in the University of Guelph and Harry the scorpion who happily (?) hitchhiked on my jacket or hat for four days from CR to Pennsiylvania.

Sure wish we still had Ebbe and John LaSalle.


On Sep 7, 2018, at 4:32 AM, Roderic Page <Roderic.Page at glasgow.ac.uk<mailto:Roderic.Page at glasgow.ac.uk>> wrote:

Dan, David will no doubt have something to say about this, but I think there are frameworks to handle this, such as nanopubs http://nanopub.org/wordpress/ . Put simply, one way to handle machine ids is to have a DOI for, say, a barcode dataset, and use that DOI as the GUID for the identifier. Then we can attribute all these identifications to the machine/process that did the ids. If specimen gets new identification in subsequent analysis, Darwin Core can already handle that (it’s possible to have multiple ids).

Regards,

Rod

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On Fri, Sep 7, 2018 at 4:53 AM +0200, "Janzen, Daniel H" <djanzen at sas.upenn.edu<mailto:djanzen at sas.upenn.edu>> wrote:


what is the plan for when the ID is done by a DNA barcode, a machine, and then equally, later on upgraded or otherwise modified by machine (and collected in the beginning by machine, such as a Malaise trap and never seen by a taxonomist other than a machine).  Or when the ID is done by unknown persons sorting the specimens into unit trays in a museum (whenever).

??

Dan Janzen


> On Sep 6, 2018, at 8:00 PM, Shorthouse, David  wrote:
>
> Thanks! Am pleased it's sparked interest. It means we're on the right track
> with our thoughts about an extension to Darwin Core.
>
> -D
>
> On Thu, Sep 6, 2018 at 3:54 PM Eduardo Dalcin  wrote:
>
>> Well done! Amazing tool.
>>
>> Eduardo
>> --------------------------------
>> [image: photo]
>> *Eduardo Dalcin*
>> Inst. Pesq. Jardim Botânico do Rio de Janeiro
>> +55 21 3204 2116 <+55+21+3204+2116> | +55 21 98393 3344
>> <+55+21+98393+3344> | edalcin at jbrj.org<mailto:edalcin at jbrj.org> | Skype: eduardo.dalcin
>>
>>  | WhatsApp: 55 21 983933344
>> Rua Pacheco Leão 915 - Sl 203 - Rio de Janeiro - RJ - Brazil
>>
>>
>> Portal de Dados: http://dados.jbrj.gov.br
>> Blog: http://eduardo.dalc.in
>> Agende uma reunião: https://doodle.com/edalcin
>> "To organize Brazil's biodiversity information and make it universally
>> accessible and useful."
>>
>>
>> Em qui, 6 de set de 2018 às 11:26, Shorthouse, David <
>> davidpshorthouse at gmail.com<mailto:davidpshorthouse at gmail.com>> escreveu:
>>
>>> All -
>>>
>>> I threw my hat in the ring for GBIF's Ebbe Nielsen Challenge and
>>> welcome you to take a gander at https://bloodhound.shorthouse.net/. If
>>> you also have an ORCID account, try your hand at declaring the
>>> specimens you identified or collected - assuming they're shown to you!
>>> (*ducks and cowers*) And, if you're up for it, make your profile
>>> public.
>>>
>>> I'm using this as fodder to help develop a 1:many extension to Darwin
>>> Core with the joint RDA/TDWG Interest Group who are interested in how
>>> to best attribute occurrence data to people. The extension has yet to
>>> be named but will attempt to express from the source, a better
>>> mechanism to share granular information about the actions people take
>>> when collecting, identifying, and curating occurrence data & will
>>> include identifiers for people. The logical identifier in today's
>>> academic environment is ORCID - thus we can have a collective think
>>> about academic credit systems for people who work at and contribute to
>>> natural history collections -, but we'd expect the extension to be
>>> supportive of other such identifiers. It's early days but here's its
>>> workspace: https://github.com/tdwg/attribution. Others involved in
>>> this possible extension to Darwin Core are cc'd here.
>>>
>>> Cheers,
>>>
>>> David P. Shorthouse
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>>
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