[Nhcoll-l] Unique IDs for museum objects versus specimens
Dirk Neumann
dirk.neumann at zsm.mwn.de
Tue Aug 19 03:03:19 EDT 2014
.... in my opinion, it would be worth enhancing / adapting the Global
Registry of Biological repositories to have as distinct Museum IDs as
possible. Also, with a open system that allows various spellings /
connotations, it is possible to integrate e.g. various projects,
previous museum abbreviations (which should be kept for any reason), etc.
In our fish collection we link voucher IDs & tissue IDs, e.g.
ZSM-PIS-043113 / P-AA-0338
ZSM identifies the collection (based on the museum abbreviations as in
the Eschmeyer Catalog), PIS identifies the section "Pisces" + running
number; tissues are identified by an unambiguous prefix (P= section
identifier, AA = project identifier + running number / scan ID, etc.)
In combination with a GUID or similar identifier, we would be able to
establish a unique identifier that would serve internal and external
(ABS) demands. All further IDs (Scan IDs of DNA-tubes, GenBank numbers,
etc.) should be associated to this master ID, which - ideally -
identifies corresponding vouchers (irrespective if in lot based
containers, sitting on individual pins, or still stuck in unsorted batch
samples).
DNA-samples - as soon as they are extracted - need individual sample
IDs anyway, to allow identification of specimens (regardless of the
system applied, e.g. different barcode-scan IDs, numbering, etc.). This
also applies for bulk extractions of multiple specimens or extractions
out of storage fluids of containers with multiple specimens, as (in most
cases) you need to log & link the resulting sequence to a single
specimen (even though you might want to save money & time while lumping
and processing samples together).
Important in my view is, that the DNA-barcode IDs or any other IDs
created _by researchers_ (= samples are accessioned at a later point.
i.e. after extraction) are 1) unambiguous, 2) correspond to generated
accession files and 3) are used as issued for publication and e.g.
GenBank uploads. This has not always been the case (especially point 2),
and earlier GenBank entries are a good example for this (don't want to
point to others here, just by judging from own experiences from our
DNA-repository).
It might be worth to discuss this in more detail at one of the next
SPNHC meetings (Gainsville and/or Berlin), and perhaps to launch a small
workgroup that could present first ideas open for discussion ?!?
All the best
Dirk
Am 18.08.2014 23:53, schrieb Derek Sikes:
> 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 <mailto: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
> <mailto: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 <http://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
> <tel:314-577-9419>///
>
> *From:*nhcoll-l-bounces at mailman.yale.edu
> <mailto:nhcoll-l-bounces at mailman.yale.edu>
> [mailto: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 <mailto: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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>
> Dirk Neumann
>
>
>
> Tel:+49-89-8107-111 <tel:%2B49-89-8107-111>
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> Bavarian Natural History Collections
>
> The Bavarian State Collection of Zoology
>
> Dirk Neumann, Section Ichthyology / DNA-Lab
>
> Muenchhausenstr. 21
>
> 81247 Munich (Germany)
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--
Dirk Neumann
Tel: 089 / 8107-111
Fax: 089 / 8107-300
email: Dirk.Neumann(a)zsm.mwn.de
Postanschrift:
Staatliche Naturwissenschaftliche Sammlungen Bayerns
Zoologische Staatssammlung München
Dirk Neumann, Sektion Ichthyologie / DNA-Labor
Münchhausenstr. 21
81247 München
Besuchen Sie unsere Sammlung:
http://www.zsm.mwn.de/ich/
---------
Dirk Neumann
Tel: +49-89-8107-111
Fax: +49-89-8107-300
email: Dirk.Neumann(a)zsm.mwn.de
postal address:
Bavarian Natural History Collections
The Bavarian State Collection of Zoology
Dirk Neumann, Section Ichthyology / DNA-Lab
Muenchhausenstr. 21
81247 Munich (Germany)
Visit our section at:
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