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

Mon Aug 18 17:53:06 EDT 2014

Colin et al.

I also think simple (dumb) numbers are best for the reasons stated. We use
2D barcodes on specimens and vials (e.g. UAM100057034).

For lots we create a record in Arctos for each identification. Thus a vial
with three species, 12 specimens, becomes 3 Arctos records - each with a
part lot count, for example 1, 1, and 10. All share the container 'vial'
which has a barcode. Each record gets a GUID like:

UAM:Ento:247065

Thus the GUIDs denote records (identifications), the barcodes are for the
containers the parts are in (or in the case of pins, on).

Therefore, 10,000 of our vials might represent 30,000 records if there is
an average of 3 taxa identified per vial. (This is common for projects with
lots of specimens, we only mount on pins or otherwise isolate a
representative series of each taxon).

Preparations / parts (eg a leg in a cryovial) are listed under the single
GUID with each container getting its own barcode. In many cases we have
just one part 'whole organism'. A single specimen (one GUID) could have 3
parts (3 barcodes): body, cryovial leg, and genitalia slide.

So a single container (barcode) can have multiple taxa (GUIDs) and a single
specimen can have multiple barcoded containers.

I like this way of managing bulk samples. For example, a trap sample can be
entered simply as one record 'Arthropoda' or, if inspected, a separate
record for each identification in the sample (Coleoptera, Hemiptera,
Hymenoptera, etc) can be made. This allows this sample to be found if
someone is searching for any of these taxa.

If all the Coleoptera are then removed from the sample and pinned, the
Coleoptera record from the bulk trap sample can be turned into a pinned
specimen record and cloned to make all the remaining pinned specimen
records.

We are just now loaning out a long series of pinned flies that have
phoretic or parasitic mites on them. Each pinned fly has two records in
Arctos - one for the fly and one for the mites. Both share the container
'pin' with a shared barcode. If the mites get moved to a vial or slide,
their barcodes will change. Relationships between the fly and mite will
link these records together, for example a beetle related to a vial of
mites http://arctos.database.museum/guid/UAM:Ento:104251

It can become difficult to isolate a single specimen of a single taxon that
has multiple specimens in a container (eg 10 of the same spider species).

For spiders in vials (eg 10 specimens of 1 species) that we DNA barcode,
rather than make a new vial (which would require a new database record, new
label, etc). We put the spider from which a leg was removed inside a
genitalia vial inside the larger vial and a new small label that indicates
the spider in the genitalia vial is a DNA barcode voucher. If the spider is
too large for this we do transfer it to a new vial. We have plans to move
all our specimens that were successfully DNA barcoded to cryovials into our
-70 freezers to better preserve their remaining genomic material.

-Derek

+++++++++++++++++++++++++++++++++++
Derek S. Sikes, Curator of Insects
Associate Professor of Entomology
University of Alaska Museum
907 Yukon Drive
Fairbanks, AK   99775-6960

dssikes at alaska.edu

phone: 907-474-6278
FAX: 907-474-5469

University of Alaska Museum  -
http://www.uaf.edu/museum/collections/ento/
+++++++++++++++++++++++++++++++++++

Interested in Alaskan Entomology? Join the Alaska Entomological
Society and / or sign up for the email listserv "Alaska Entomological
Network" at
http://www.akentsoc.org/contact.php

On Mon, Aug 18, 2014 at 6:28 AM, Chuck Miller <Chuck.Miller at mobot.org>
wrote:

> Dirk,
>
> There's a start on a unique museum identifier repository at the Global
> Registry of Biological Repositories (GRBio) at www.grbio.org.  But it is
> currently focused on biological/biodiversity collections.
>
>
>
> Chuck
>
>
>
> *Chuck Miller | VP-IT & CIO | Missouri Botanical Garden*
>
> *4344 Shaw Boulevard | Saint Louis, MO 63110 | Phone 314-577-9419
> <314-577-9419>*
>
>
>
> *From:* nhcoll-l-bounces at mailman.yale.edu [mailto:
> nhcoll-l-bounces at mailman.yale.edu] *On Behalf Of *Dirk Neumann
> *Sent:* Monday, August 18, 2014 4:03 AM
> *To:* nhcoll-l at mailman.yale.edu
>
> *Subject:* Re: [Nhcoll-l] Unique IDs for museum objects versus specimens
>
>
>
> Hi all,
>
>
> don't want to add lengthy comments, so just briefly:
>
> The entering into force of the Nagoya Protocol stipulates specific
> reporting requirements, for those *collections based in countries that
> ratified the NP*. Among other, *unique identifiers* allowing tracing and
> origin of genetic resources *should be applied soon.* Application of
> unique identifiers will be part of and further detailed in the reporting
> obligations of respective countries.
>
> To confirm previous comments: yes, we do need a flexible system that
> allows application of *unique identifiers*  to identify batch samples,
> unsorted materials, etc. and *unique* should not be confused with
> identifiers for individual specimens (as some political decision makers did
> during discussions towards the European ABS-legislation).
>
> Unique identifiers should be unique - many molecular barcoding /
> digitalisation projects apply various kinds of barcodes, without testing if
> these are really unique (a high probability rate that barcodes would surely
> be not duplicated is not sufficient in this context).
>
> Any barcode or decimal numbering is *not unique*, because "123456.077"
> might appear as number in various collections or museums, may perfectly
> translates into other types of numberings (e.g. telephone / insurance /
> account numbers), and even adding an abbreviation for the institute , e.g.
> INST-123456.077 might
> a) not result in a be unique ID inside this museum, e.g. if various
> collections / sections inside this museum use a similar numbering system,
> e.g. compinations of accession dates & specimen numbers, as John suggested
> (2014.11.3)
> b) not be unique globally for natural history specimens, unless we do have
> a obligatory list of Museum abbreviations that excludes any duplications
>
> Similar applies e.g. for GenBank numbers; GenBank numbering might be
> unique inside GenBank, but the encoding does not allow to decipher in which
> collection the corresponding specimen is deposited.
>
> This adds an second field that should be considered in this discussion,
> how can we link *unique identifiers *with *unique museum references.* We
> need a kind of master ID, especially for the tissue and DNA collections and
> publication of samples stored in these collections.
>
> Sadly, this receives limited attention at the moment, even though many
> barcoding & digitisation projects outbid each other to gather & publish
> specimen data. I would appreciate if we could enter a active discussion how
> to deal with this.
>
> All the best
> Dirk
>
>
>
>
> Am 14.08.2014 22:55, schrieb Colin Favret:
>
> Thank you to everyone participating in this interesting discussion. I'm at
> least relieved to know that there is no community standard, yet, and so I'm
> not off kilter having developed my own solution. As I understand it,
> palaeontologists assign separate unique identifiers to the different fossil
> specimens in/on a single object (?). And Specify seeks a solution to
> disambiguate "Containers" from specimens.
>
>
>
> But unique identifiers referring to museum objects or specimens are not
> "dumb" in the same way that they are for localities, collection events,
> taxa, etc. They refer to physical objects located in a collection that bear
> a label with that unique identifier. That unique identifier is thus part of
> the object retrieval process for collection users, in addition to being for
> data retrieval.
>
>
>
> So can we envision a system where the unique identifier for the 77th
> specimen on a microscope slide can also be used as part of the object
> retrieval process? Or have we decided that, given a unique identifier for
> the 77th specimen, I'm better off having to go to the database to reference
> the museum object's ID before heading into the compactors? Does anyone have
> a significant objection to the decimal INST-123456.077 to uniquely refer to
> the 77th specimen in/on museum object INST-123456?
>
>
>
> Thanks for the continued discussion!
>
>
>
> Colin
>
>
>
>
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