[Nhcoll-l] Unique IDs for museum objects versus specimens

Thu Aug 14 09:33:22 EDT 2014

  I took Dean Pentcheff's (excellent) suggestions to not simply be about
how to create identifiers linking specimens to their derivatives, but also
about the semantics needed to represent those relationships.  Simply having
identifiers  that note a "root" material sample and all its derivatives
doesn't seem like the solution that can work outside a single collection,
and I'd prefer to look for generally scalable solutions.  And it certainly
doesn't tell me what the derivatives are simply by having an appended
value.

  The following paper published earlier this year "Semantics in Support of
Biodiversity Knowledge Discovery: An Introduction to the Biological
Collections Ontology and Related Ontologies" in PLOS ONE (
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0089606)
is really all about this very issue of relating samples and derivatives,
and how it could and should work not just within a collection but across
them.

Best, Rob

On Thu, Aug 14, 2014 at 7:19 AM, Callomon,Paul <prc44 at drexel.edu> wrote:

>  One problem with such “cascading” numbers is the high likelihood of
> errors in earlier, non-digital work. We have about 460,000 catalog numbers
> in our mollusk collection, so none is larger than six digits. Over two
> thirds were generated before computers came into use, and over the years
> thousands of duplicate numbers (different records with the same number)
> have been created. Nowadays we are working out of a single database, so
> there are safeguards against this kind of error, but finding and fixing the
> existing duplicates will take years.
>
>
>
> *Paul Callomon*
> *Collection Manager, Malacology, Invertebrate Paleontology and General
> Invertebrates*
>  ------------------------------
>
> *Academy of Natural Sciences of Drexel University, Philadelphia*
>
> 1900 Benjamin Franklin Parkway, Philadelphia PA 19103-1195, USA
> *callomon at ansp.org <callomon at ansp.org> Tel 215-405-5096 <215-405-5096> -
> Fax 215-299-1170 <215-299-1170>*
>
>
>
>
>
>
>
> *From:* nhcoll-l-bounces at mailman.yale.edu [mailto:
> nhcoll-l-bounces at mailman.yale.edu] *On Behalf Of *Lena Hernandez
> *Sent:* Thursday, August 14, 2014 9:05 AM
> *To:* nhcoll-l at mailman.yale.edu
>
> *Subject:* Re: [Nhcoll-l] Unique IDs for museum objects versus specimens
>
>
>
> My Natural Science Collection is relatively small, so I haven’t run into
> this problem there, but in our History Collection we have a similar issue
> with portfolios and the like. The way it is dealt with there is the set as
> a whole gets a number say 2014.13 (transaction number, 13th transaction of
> 2014)then an object number 2014.13.1 (first object of transaction 2014.13)
> and then if it is something like a portfolio is can be broken down further
> 2014.13.1.3 (third photo of portfolio 2014.13.1) or alternatively
> 2014.13.1A-C (first object of 2014.13, three parts).  Perhaps you can use
> something similar, the parent number is always there and you can see how
> far down the line this object came out as well as what it came from more
> recently.
>
>
>
> To use Dean’s example.
>
>
>
> 2014.13- Dredge Material
>
> 2014.13.1-jar o’ crustacea
>
> 2014.13.1.1-single crustacean from the jar o’ crustacean
>
> 2014.13.1.1A-D- four parasitic crustacea from your single crustacean
>
> Or alternatively (Just make sure you are consistent in which way you parse
> it out)
>
> 2014.13.1.1.1- first parasitic crustacea from your single crustacean
>
>
>
>
>
> I hope that make sense, I‘m a bit tired this morning and my brain is not
> yet up to full speed.
>
>
>
> Lena
>
>
>
>
>
> Lena Hernandez
>
> Collections Manager/Registrar
>
>
>
> Museum of Science & History
>
> 1025 Museum Circle
>
> Jacksonville, FL 32207
>
> (904)396-6674 x212
>
> lhernandez at themosh.org
>
>
>
> *From:* nhcoll-l-bounces at mailman.yale.edu [
> mailto:nhcoll-l-bounces at mailman.yale.edu
> <nhcoll-l-bounces at mailman.yale.edu>] *On Behalf Of *Dean Pentcheff
> *Sent:* Wednesday, August 13, 2014 9:12 PM
> *To:* Colin Favret
> *Cc:* nhcoll-l at mailman.yale.edu
> *Subject:* Re: [Nhcoll-l] Unique IDs for museum objects versus specimens
>
>
>
> This is an issue that I've raised in the past with the Specify team (and
> plan to raise again in the near future — fair warning, guys :)
>
>
>
> The precipitating example for us comes from marine specimens. Often an
> unsorted jar of material will arrive (e.g. from a dredge sample) to be
> cataloged in the collection — this unsorted lot should get a unique ID — it
> may be around for years before it's touched. Then we may pull out (for
> example) all the crustacea into another jar. This partly-sorted lot also
> needs a unique ID (it may go to a different room under different staff, so
> just keeping it with the original jar is not an option). Then we may pull
> out a single individual, identify it, and use that in a publication, so
> that, too, needs an ID. A visiting researcher then examines that individual
> and pulls off parasitic crustacea, identifying each and putting them into
> individual vials, each of which needs an ID. Etc.
>
>
>
> What we have is a clear hierarchical branching parent-child relationship
> from the initial unsorted lot down to the individual parasites (and their
> parasites, and their molecular derivatives, etc.). Logically, the way to
> accommodate this is to have any "thing" in the collection identified with a
> unique ID. Any derived or subsorted "thing" gets another unique ID and (and
> this is critical) is linked to its parent so that all the information from
> the parent (and on up the chain to the top) is immediately available via
> any "child" ID.
>
>
>
> Every "thing" gets a first-class ID (no sub-IDs or a limited list of
> "preps" from an initial object). Key to the concept is retaining the
> parent-child-grandchild-... chain. At any moment, one should be able to
> retrieve any ID's entire chain of parents (and their associated data), or
> any ID's entire chain of derived children (and their associated data).
>
>
>
> It is a mystery to me why this scheme is not the standard model for
>  specimen databases where there is a habit of creating chains of
> derivatives over time. There certainly are implementation details that need
> careful consideration (for example with propagation of data down the chain,
> how "locked" that propagation is, and how to handle things that get
> completely subdivided so they no longer exist as such, but whose data must
> persist), but it seems like a very clean, very flexible base model.
>
>
>  -Dean
> --
> Dean Pentcheff
> pentcheff at gmail.com
> dpentche at nhm.org
>
>
>
> On Wed, Aug 13, 2014 at 4:01 PM, Colin Favret <ColinFavret at aphidnet.org>
> wrote:
>
> Has anyone dealt with the distinction between issuing unique IDs (for
> labels and database records) for museum objects versus specimens? A case in
> point might be a microscope slide with 100 specimens on it (or a jar,
> envelope, etc.). These specimens can be of multiple taxa, different sexes,
> life stages, etc. I believe most collections label the museum object
> (slide, jar, envelope, etc.) with a unique identifier and then treat the
> specimens as a lot, but this doesn't fully parse out the data associated
> with the various specimens in a specimen database.
>
>
>
> I've developed my own solution (unique ID label for the object, decimal
> numbers but no label for the individual specimens or specimen lots - e.g.
> INST123456 for the slide, INST123456.001 for the first specimen lot,
> INST123456.002 for the second, etc.).
>
>
>
> But I'm wondering what others have done or if there is anything out there
> approaching an industry standard.
>
>
>
> Thanks for your input!
>
>
>
> Colin
>
>
>
> Colin Favret
>
> Université de Montréal
>
> Favret.AphidNet.org <http://favret.aphidnet.org/>
>
>
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