[Nhcoll-l] Unique IDs for museum objects versus specimens
Graham, Eileen
GrahamE at si.edu
Tue Aug 19 17:20:25 EDT 2014
All,
To chime in about GRBio - the registry is designed to catalog unique institution codes, in addition to providing general information about the collections and primary contacts. We have a few overlapping codes, but are currently working with those institutions to try and sort out the duplicates. For institutions that are not currently registered, if they register their institution using a code that is already in the system then they will be prompted to choose a different code.
We are in the process of expanding GRBio to encompass all scientific collections. GRSciColl will allow for the registry of collections across the full scope of scientific disciplines. More to come as that timeline is worked out. Or better yet, if you'd like to add yourself to the GRSciColl mailing list, please sign up here<http://www.grscicoll.org/>.
Thanks,
Eileen
Eileen Graham, Program Manager
Scientific Collections International
e: grahame at si.edu<mailto:grahame at si.edu>
p: 202-633-0256
t: @sci_coll<https://twitter.com/sci_coll>
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From: nhcoll-l-bounces at mailman.yale.edu [mailto:nhcoll-l-bounces at mailman.yale.edu] On Behalf Of Dirk Neumann
Sent: Tuesday, August 19, 2014 3:03 AM
To: nhcoll-l at mailman.yale.edu
Subject: Re: [Nhcoll-l] Unique IDs for museum objects versus specimens
.... 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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natural history collections to ensure their continuing value to
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NHCOLL-L is brought to you by the Society for the Preservation of
Natural History Collections (SPNHC), an international society whose
mission is to improve the preservation, conservation and management of
natural history collections to ensure their continuing value to
society. See http://www.spnhc.org for membership information.
--
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:
http://www.zsm.mwn.de/ich/
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