[Nhcoll-l] global unique identifiers and naturalhistory collections
Robert Guralnick
Robert.Guralnick at colorado.edu
Mon Oct 15 12:26:06 EDT 2012
Hi all --- Appreciate the great conversation swirling around this
important topic! One of the things that we have talked a lot about
is this issue of unique identifiers versus things like an Institution
Code+Collection Code+Collection number. Enough has been said here,
but I do want to strongly re-affirm that, at least in my view, both
are important.
One epiphany we have had (or at least I think and hope it is an
epiphany) is the difference between true tracking of records, and what
we might call "rediscovery". Here is an example of the difference.
Lets say people put globally unique identifiers on a set of specimens
collected in the field, and one specimen ends up being sent to one
herbarium (say the NYBG) and the other specimen is sent to another
herbarium (say the Missouri Botanic Gardens). With guids and good
metadata, we can directly track that those came from the same
collecting event. In most cases, guids aren't assigned either during
the collection of specimens, or when put into individual collections,
so typically we have lost that provenance trail. We have to instead
"rediscover" those relationships after the fact when they are
published to an aggregator such as GBIF or Virtual Herbarium or
iDigBio. We can do that by putting unique identifiers on metadata
records and matching collector+date+location fields (e.g. "globally
identified specimen X is inferred to be from the same collecting even
as globally identified specimen Y").
The big thing is to remember that all of what we are talking about is
really enhancing tracking and discovery outside of local institutions,
where locally unique identifiers are great and needed, and in the
realm of globally available data, where you need globally unique
identidiers -- a name and address --- to find those records.
Finally, I keep thinking about how much we scan barcodes all the time
and don't care at all about the numbers in those barcodes that get us
onto airplanes, or that get us groceries. Between sticking guids in
QR codes or cutting and pasting them and resolving their contents to a
record, does anyone _ever_ really transcribe an identifier number for
number? Maybe its me, but I just can't see this issue about error
correction being relevant. What am I missing?
Best, Rob
On Mon, Oct 15, 2012 at 9:09 AM, Chuck Miller <Chuck.Miller at mobot.org> wrote:
> I believe this is the best reason I've seen so far against totally opague IDs. Error correction. Totally opague unique IDs rely upon the IDs being perfectly recorded every time they are used. Inclusion of some intelligible portion in the ID enhances error correction down the line as William Poly describes. But, there are many use cases in the biodiversity informatics universe and this ID error correction issue may only apply to some of them.
>
> Chuck
>
> -----Original Message-----
> From: nhcoll-l-bounces at mailman.yale.edu [mailto:nhcoll-l-bounces at mailman.yale.edu] On Behalf Of Poly, William
> Sent: Monday, October 15, 2012 8:34 AM
> To: NH-COLL listserv
> Subject: Re: [Nhcoll-l] global unique identifiers and naturalhistory collections
>
> All,
>
> Expanding on what Mark just wrote, standardization of institutional codes for museums has been going on for decades:
>
> 1) http://www.biodiversitycollectionindex.org/static/index.html
>
> 2) Leviton, A.E., R.H. Gibbs, Jr., E. Heal, and C.E. Dawson. 1985. Standards in herpetology and ichthyology: Part I. Standard symbolic codes for institutional resource collections in herpetology and ichthyology. Copeia 1985(3): 802-832.
>
> 3) Leviton, A.E. and R.H. Gibbs, Jr. 1988. Standards in herpetology and ichthyology. Standard symbolic codes for institution resource collections in herpetology and ichthyology. Supplement No. 1: additions and corrections. Copeia 1988(1): 280-282.
>
> 4) http://www.asih.org/codons.pdf
>
> These acronyms and associated catalog numbers are used widely in the literature. What is the need for a new system that is "global?" Museum acronyms convey useful information that is easy to interpret, whereas a long numeric code alone or an alphanumeric string such as "A3P578930ZBW" does not. When typos occur in long strings how does one even begin to discern the intended object? A typo in CAS 20050 as CAS 20059 can be tracked much more easily. Similarly, when a typo occurs in GPS coordinates without an associated locality description, it's difficult or impossible to resolve.
>
> Bill
>
>
> ________________________________________
> From: nhcoll-l-bounces at mailman.yale.edu [nhcoll-l-bounces at mailman.yale.edu] On Behalf Of Dirk Neumann [Dirk.Neumann at zsm.mwn.de]
> Sent: Monday, October 15, 2012 3:35 AM
> To: CSTURMJR at pitt.edu
> Cc: NH-COLL listserv; John Deck; Nico Cellinese; tomc at cs.uoregon.edu; Robert Guralnick
> Subject: Re: [Nhcoll-l] global unique identifiers and natural history collections
>
> Hi all,
>
> at least for some collections unique (and published) identifiers are available (e.g. provided via the Eschmeyer Catolg of fishes @
> http://research.calacademy.org/redirect?url=http://researcharchive.calacademy.org/research/Ichthyology/catalog/fishcatmain.asp)
>
> It might be essential to have unique identifiers for scientific material in near future - mainly depending on how the Access Benefit Sharing will implement regulations to track down single samples to allow equitable sharing of these (genetic) resources. For botany specimens something similar is already in place called IPEN:
> http://www.bgci.org/resources/ipen/
>
> However, it is crucial that the registration numbers are tied to collections and specimens in the collection, therefore I would rather favour to have the museum acronyms & specimen numbers included in such a code (what would be easily feasible if using a combined alpha numeric & alphabetical coding system). Problem here surely lies with the entomological collections, which can't be individualised in near future, but in the light of ongoing barcoding campaigns one should have in mind that many modern samples (which do have e.g. individual barcodes generated by BOLD) do have unique identifiers as soon as they are processed (this applies also for historic specimens picked form the pin)
> - even if the analyses fails.
>
> Definitely YES! and will be needed in near future, I fear (not because I would wish to have a unique numbering system / numbers)
>
> All the best
> Dirk
>
>
> Am 15.10.2012 00:09, schrieb CSTURMJR at pitt.edu:
>> Curtis,
>>
>> One problem that comes to mind is CMNH as an identifier.
>> I have seen this used for:
>> Carnegie Museum of Natural History ( my preference!) Cleveland Museum
>> of Natural History Cincinnati Museum of Natural History
>>
>> It could also be used for:
>> Colorado (University) Museum of Natural History Canadian Museum of
>> Natural History.
>>
>> Thus, one would have to standardize museum acronyms.
>>
>>> <font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif"
>>> size="2"><div>Forgive my ignorance, as I'm new to the collections
>>> world, but could someone please provide more detail about what you
>>> are talking about exactly? What is wrong with the use of museum
>>> acronyms followed by numbers? Or...am I missing something? Aren't
>>> these "global unique identifiers"? What are the drawbacks to using
>>> these in the traditional manner? Also, how feasible would it be for
>>> all the collections to essentially renumber their entire collections
>>> to participate in this new system? Please help me understand what
>>> this discussion is
>>> about.</div><div><br></div><div>Thanks!</div><div><br></div><div>Curt
>>> is<br><br>______________________________<br><br>Curtis
>>> J. Schmidt<br>Zoological Collections Manager<br>Sternberg Museum of
>>> Natural History<br>Fort Hays State University <br>3000 Sternberg
>>> Drive<br>Hays, KS 67601<br>(785) 628-5504 (collections)<br>(785)
>>> 650-2447 (cell)<br>______________________________</div><br><br><font
>>> color="#990099"><span><a class="smarterwiki-linkify"
>>> href="mailto:-----nhcoll-l-bounces at mailman.yale.edu">-----nhcoll-l-bo
>>> unces at mailman.yale.edu</a>
>>> wrote: -----</span></font><div style="padding-left:5px;"><div
>>> style="padding-right:0px;padding-left:5px;border-left:solid black
>>> 2px;"><span>To: "Bentley, Andrew Charles" <<a
>>> class="smarterwiki-linkify"
>>> href="mailto:abentley at ku.edu">abentley at ku.edu</a>></span><br>From:
>>> Robert Guralnick <robert.guralnick at colorado.edu><br><span>Sent by: <a
>>> class="smarterwiki-linkify"
>>> href="mailto:nhcoll-l-bounces at mailman.yale.edu">nhcoll-l-bounces at mailman.yale.edu</a></span><br>Date:
>>> 10/14/2012 01:33PM<br><span>Cc: <a class="smarterwiki-linkify"
>>> href="mailto:tomc at cs.uoregon.edu,">tomc at cs.uoregon.edu,</a> "NH-COLL
>>> listserv <a class="smarterwiki-linkify"
>>> href="mailto:\(nhcoll-l at mailman.yale.edu\)">\(nhcoll-l at mailman.yale.edu\)</a>"
>>> <<a class="smarterwiki-linkify"
>>> href="mailto:nhcoll-l at mailman.yale.edu">nhcoll-l at mailman.yale.edu</a>
>>> >, John Deck <<a class="smarterwiki-linkify"
>>> href="mailto:jdeck at berkeley.edu">jdeck at berkeley.edu</a>>, Nico
>>> Cellinese <<a class="smarterwiki-linkify"
>>> href="mailto:ncellinese at flmnh.ufl.edu">ncellinese at flmnh.ufl.edu</a>></span><br>Subject:
>>> Re: %5
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> Dirk Neumann
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