[tdwg-tag] Specimen identifiers [SEC=UNCLASSIFIED]

Sun Feb 26 22:39:55 CET 2012

Yes. And I would qualify what you said as follows:

On Sat, Feb 25, 2012 at 4:55 AM, Roderic Page <r.page at bio.gla.ac.uk> wrote:
> Dear Dean,
>
> In essence, yes, so long as we:
>
> a) avoid collisions due to non-unique acronyms (hence we can't automatically
> generate URIs from specimen codes without some fussing)

It's the function of the centralizing agency to ensure this when they
accept a "listing formula" from an organization. If the URI-generating
formula could result in a collision with an existing listing, the
formula would have to be renegotiated before being accepted for the
registry.

> b) realise that we can't necessarily unpack a URI and use that to locate the
> specimen (often we could, sometimes we won't be able to, in this sense the
> identifiers are "opaque")

Yep. I'm all in favor of opaque, non-information-bearing identifiers.
The moment you accuse the text of the identifier of having intrinsic
meaning, you accept all the ugliness of figuring out how to "update"
the identifier when the underlying data are updated. [Real-life case
in point: some departments in our institution had a system of minting
specimen IDs based on the year of collection plus other digits. With
some frequency we discover that the specimens were actually collected
in some other year. So either: (a) we change the identifier
(unacceptable for all the reasons we know and love); or (b) we know
that we cannot trust the year-part of any identifier (so we used this
formula why?).]

> c) avoid changing the URI if a specimen moves collection/institution or if
> the host institution relabels it. Once minted the identifier doesn't change
> (because that will break any links to it, defeating the point of having the
> URIs).

Yes. It's supposed to be a non-data-bearing opaque identifier. In the
worse (but inevitable) case where specimens get additional
identifiers, or get subsampled into additional identifiable pieces,
there has to be a "synonymy" service that would (perhaps recursively)
return the other relevant identifiers. That would be (cough, cough)
trivial to implement as long as any subsequent identifier assignment
includes a reference to the already-existing identifier.

>
>
> Regards
>
> Rod
>
>
> On 24 Feb 2012, at 17:29, Dean Pentcheff wrote:
>
> This is directly in response to Rod's response to Paul. I think the two of
> you may have just articulated nearly the same idea, though you seem not to
> think you did.
>
> Paul envisions institutions each declaring their own URI-creating formula
> (to resolve down to a specimen at that institution), promulgated at a
> "forum" location.
>
> Rod envisions URI formulation as happening at a GBIFesque centralized site.
>
> If Paul's forum were GBIF (or similar), with an added function that GBIF (or
> similar) renegotiates any institutional declaration that collides with a
> pre-existing declaration, does that map to the same thing for both of you?
>
> -Dean
> --
> Dean Pentcheff
> pentcheff at gmail.com
> dpentche at nhm.org
>
> On Fri, Feb 24, 2012 at 12:23 AM, Roderic Page <r.page at bio.gla.ac.uk> wrote:
>>
>> Dear Paul,
>>
>> A few quick comments.
>>
>> Constructing URLs from specimen codes is a nice ideal, but in practise
>> breaks down because museum acronyms are not globally unique, and specimen
>> codes are not always unique within institutions (this is a big issue for
>> vertebrate collections where the same code may be a used for a fish, a herp,
>> a mammal, and a bird). So we need ways to disambiguate these. The Darwin
>> Core triplet I've been complaining about on my blog is one attempt to do
>> this by using collectionCodes as part of the specimen code. But these are
>> not terribly stable (a lot of the duplication in GBIF is due to museums
>> mucking about with collection codes).
>>
>> I personally don't hold out much hope for museums being able to develop
>> and maintain rules for converting specimen codes into URIs. Let's be
>> realistic, most museums have no idea about the web beyond creating pretty
>> public interfaces. There are DiGiR servers at major museums running on
>> machines with no domain name, just an IP address.
>>
>> I suspect it's going to be easier to delegate resolving specimens this to
>> something like GBIF. As a data consumer, I'd much prefer going to one place
>> and getting the codes resolved, rather than have to first figure out where
>> to go to find out the rule.  If I want metadata for a scientific article I
>> go to CrossRef, not the individual publisher. Distributed begats
>> centralised.
>>
>> I think not insisting on resolvable identifiers is a big mistake. It's
>> like saying it's OK to publish source code that you haven't actually
>> bothered to check whether it compiles. If they don't have to resolve I can
>> publish any identifier I want (witness the number of "fake" LSIDs in the
>> wild) and I've made zero commitment that it means anything. And you've taken
>> away the ability of the user to test whether your identifier is meaningful,
>> and thus build any degree of trust. The acid test of whether you are serious
>> is whether your identifiers are "live." The minute we say it's OK for them
>> to be unresolvable we are buggered.
>>
>> Regards
>>
>> Rod
>>
>>
>>
>>
>> On 24 Feb 2012, at 06:14, Paul Murray wrote:
>>
>>
>> On 23/02/2012, at 9:37 PM, Roderic Page wrote:
>>
>> I've recently written an number of posts on the implications of the lack
>> of specimen-level identifiers, which makes it very hard to link different
>> sources of data together, such as GBIF and Genbank
>> http://iphylo.blogspot.com/2012/02/linking-gbif-and-genbank.html , and are
>> also a factor in creating duplicate records in GBIF
>> http://iphylo.blogspot.com/2012/02/how-many-specimens-does-gbif-really.html
>>
>>
>> This is definitely an issue. In AFD (which is not a specimen database), we
>> hold a "museum code" and an "accession number" for types specimens. Ideally,
>> I would like to be able to get from these two fields to a URI.
>>
>> For instance, given the data
>> nameT typeTypeT museumT museumDesc accessonNo materialElement latLong
>> locality comments
>> Holothuria bivittata Mitsukuri, 1912 Syntype TIU Tokyo Imperial
>> University, Tokyo, Japan 1217 Okinawa, Riu Kiu and Yayeyana Ils, Japan
>> Holothuria bivittata Mitsukuri, 1912 Syntype TIU Tokyo Imperial
>> University, Tokyo, Japan 1218
>>
>> I would like the AFD type specimen records (which are anonymous nodes in
>> our profile data) to point to
>> "http://collections.tiu.edu.jp/colleciton-X/1217" (or whatever), which could
>> be generated from the data we already have. The key is the individual
>> institutions holding collections.
>>
>> The only way I can imagine this happening is for each institution with
>> collections to state "you construct URIs from our accession numbers like
>> so". With that declaration, stores exposing data (such as the boa silos) can
>> perform the mapping when the news reaches them. Once this is in place,
>> anyone handling (for instance) TIU accession numbers can publish correct
>> URIs in their RDF. Most particularly, other institutions accepting specimens
>> from TUI could publish that their new URI for the item is "owl:sameAs" the
>> TUI one. And the whole thing begins to knit together.
>>
>> Importantly: it is not necessary to actually make these URIs resolvable.
>> Hopefully, one day there *would* be something at that URL which would issue
>> a 303 redirect, but the existence of the identifier as an identifier doesn't
>> rely on it. All that is needed is that commitment to the namespace on the
>> part of the issuer.
>>
>> My point is first, that this can be done in stages, and doesn't depend on
>> everybody implementing a big and expensive solution right away or in
>> synchrony; and second, that we don't need a top-down assignment of
>> identifiers. A bottom-up solution can work. Perhaps the main thing missing
>> is a forum on which an institution can announce its creation and assignment
>> of a URI namespace for persistent identifiers.
>>
>> Having said all that, Rod's point is about identification of individuals.
>> An accession number is put on a "token", of course, a given individual may
>> have many "tokens". A case in point is this record in AFD:
>>
>> nameT typeTypeT museumT museumDesc accessonNo materialElement latLong
>> locality comments
>> Bregmaceros pseudolanceolatus Torii, Javonillo & Ozawa, 2004 Paratype URM
>> University of the Ryukyus, Nishihara, Okinawa, Japan P. 12156, 27508–27511,
>> 29172, 29620, 33056
>>
>> The type specimen has 8 URM accession numbers, and there's really no way
>> around that.
>>
>> Even then, however, the question of identifying the individuals comes down
>> to the same solution: if it's to happen, then it will have to be done by the
>> curators of the collections - it's only the curators who actually know what
>> items are from the same individual. A third party generating UUIDs for all
>> these things just isn't going to work out - they won't get it right. What is
>> needed is for the curator to announce, for instance, "individuals shall be
>> identified by http://specimens.mymuseum.edu/<collection id>/<collector's
>> field number for the individual>". It really doesn't matter how the URIs are
>> done, as long as it's consistent, persistent, and public.
>>
>>
>>
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>>
>> ---------------------------------------------------------
>> Roderic Page
>> Professor of Taxonomy
>> Institute of Biodiversity, Animal Health and Comparative Medicine
>> College of Medical, Veterinary and Life Sciences
>> Graham Kerr Building
>> University of Glasgow
>> Glasgow G12 8QQ, UK
>>
>> Email: r.page at bio.gla.ac.uk
>> Tel: +44 141 330 4778
>> Fax: +44 141 330 2792
>> AIM: rodpage1962 at aim.com
>> Facebook: http://www.facebook.com/profile.php?id=1112517192
>> Twitter: http://twitter.com/rdmpage
>> Blog: http://iphylo.blogspot.com
>> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
>>
>>
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>
>
> ---------------------------------------------------------
> Roderic Page
> Professor of Taxonomy
> Institute of Biodiversity, Animal Health and Comparative Medicine
> College of Medical, Veterinary and Life Sciences
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QQ, UK
>
> Email: r.page at bio.gla.ac.uk
> Tel: +44 141 330 4778
> Fax: +44 141 330 2792
> AIM: rodpage1962 at aim.com
> Facebook: http://www.facebook.com/profile.php?id=1112517192
> Twitter: http://twitter.com/rdmpage
> Blog: http://iphylo.blogspot.com
> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
>