[Nhcoll-l] Multiple numbers

Fri Mar 11 19:11:31 EST 2016

... also if you consider DNA & tissue collections, it is hardly feasible 
to maintain original lot or specimen accession numbers, especially on 
pre-numbered (eg 2D barcoded) tubes or tissues/DNAs that have been 
shared/received from researchers outside the own institution.

While in vertebrates maintaining the "original" accession ID for any 
subsamples, parts, or preparations inside one institution might be 
feasible, this gets extremely difficult if samples of the same 
individuum are shared among different institutions or collections (eg 
our bird hides are still in ZSM, while the skeletons are stored in a 
separate, archaeozoological collection as reference material).

Ideally, you would wish to keep the same ID for all parts derived out of 
the original specimens, but practically you would wish to have an 
integrated data and collection management system that allows "to keep" 
on track (ideally with GUIDs as explained by Doug). This surely has 
special relevance in insect collections, where individualisation 
typically happens during extraction in the DNA lab, but not during 
accession of specimens or cataloguing of insect drawers.

However, it is of fundamental importance - also because of the 
provenance of samples needs to be clear under ABS aspects during any 
downstream sharing of samples, either internal or external - that the 
"origin" of samples and all derivatives remains clearly traceable.

An integrated and flexible system using unique IDs and GUILDs (which is 
basically a lot based approached as mentioned by Andy combined with an 
additional layer that allows to relate "insect drawers" with x species 
from y locations but also subsequent tissue subsamples, original DNA 
extracts, aliquots of the same extraction, repeated extractions of same 
tissues etc.) is surely the best approach to handle the scenario Paul 
described in his original post/question. This also allows to manage 
external tissues which are only curated but have to be stored under 
their original (external) IDs/field numbers/barcodes...

Adding pre- or suffixes (for specific collections, eg PIS for pisces, 
HERP for herps, MAM for mammals) helps to tackle issues with overlapping 
numbers in different collections inside the same institution. This also 
works for specific projects, as long as these additions are clearly 
defined and consistently managed (eg ZSM-PIS-00001 for a fish specimen, 
ZSM-OTO-001 for a otolith of a completely different, not preserved fish, 
ZSM-YOY-001 for fish larvae; all numbers were inherited from earlier 
"historic" collections).

My two cents ..

all the best
Dirk

Am 11.03.2016 um 13:14 schrieb Rogers, Steve:
> Often you are left at the whims of earlier collection managers. For my bird collection we have separate skin, skeleton, fluid, egg, nest, and even flat skin numbering systems and each had to be given an acronym indicating the series it belonged to since you cannot have six number "1's" in you collection. The Darwin Core has a field "related catalog number" which is where we put in other internal catalog numbers for example a schmoo + skeleton + boneless spread wing, and they also have a field "other catalogue numbers" where we record the numbers other museums had assigned birds we got in exchange from other museums, for example https://urldefense.proofpoint.com/v2/url?u=http-3A__portal.vertnet.org_o_cm_birds-3Fid-3Dp101712&d=AwIFAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=CLFZJ3fvGSmDp7xK1dNZfh6uGV_h-8NVlo3fXNoRNzI&m=4rcN__6y2ghaZeUEkcIxT2ollYf1q2-dwMIWk_Z4Km4&s=Bf2_L37xpaZn06M89lFdPzqXAjaADMlGTZwrNouvWWU&e=  which was formerly AMNH 205566.
>
> In the Herp collection I also care for, the early managers had a separate amphibian collection starting with number 1, but then started with number 1 twice in the separate reptile catalogs, later using a single numbering system in reptiles, but didn't start a unified amphibian and reptile numbers system until catalogue number 10,001. I was the very lucky person in the 1980's who had to string and hand-write herp tags for about 25,000 or more specimens in the series then identified as R, P and S series because of computerization. There were some 'lot' catalogued groups of specimens, and an alphabetic letter following the official catalogue number. For example R-3106, which had been tagged in a series 3106-A, 3106-B, up to 3106-GG, had to be retagged R 3106A, R 3106B, etc. That numbering system was left over from years ago as we exchanged both 3106-Y through 3106 DD and separately 3106EE through GG. https://urldefense.proofpoint.com/v2/url?u=https-3A__www.idigbio.org_portal_rec
>   ords_f41de187-2D79b1-2D4693-2Da032-2D11c7cc7de076&d=AwIFAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=CLFZJ3fvGSmDp7xK1dNZfh6uGV_h-8NVlo3fXNoRNzI&m=4rcN__6y2ghaZeUEkcIxT2ollYf1q2-dwMIWk_Z4Km4&s=rADSLeuOBsfjDxVlqeLK_Am99nHELvoltKpP4VKwPUM&e=
>
> It is all good fun..
>
> Stephen P. Rogers (Mr.)
> Collection Manager of Section of Birds
> and Section of Amphibians and Reptiles
> Carnegie Museum of Natural History
> 4400 Forbes Avenue
> Pittsburgh PA 15213-4080
> Phone: 412-622-3255 or 3258
> Email: rogerss at CarnegieMNH.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.carnegiemnh.org_birds_index.html&d=AwIFAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=CLFZJ3fvGSmDp7xK1dNZfh6uGV_h-8NVlo3fXNoRNzI&m=4rcN__6y2ghaZeUEkcIxT2ollYf1q2-dwMIWk_Z4Km4&s=5a16xwI1fYTdm2A434qh5JjKrQL7TTbeLdOle2YDUbg&e=
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.carnegiemnh.org_herps_index.html&d=AwIFAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=CLFZJ3fvGSmDp7xK1dNZfh6uGV_h-8NVlo3fXNoRNzI&m=4rcN__6y2ghaZeUEkcIxT2ollYf1q2-dwMIWk_Z4Km4&s=qUvD-KYKTWoq2ezxXyM4mco7WY4TWWd5K2ECsGu--1E&e=
>
> -----Original Message-----
> From: nhcoll-l-bounces at mailman.yale.edu [mailto:nhcoll-l-bounces at mailman.yale.edu] On Behalf Of Thomas J Trombone
> Sent: Thursday, March 10, 2016 3:00 PM
> To: Kevin Winker
> Cc: NH-COLL listserv (nhcoll-l at mailman.yale.edu)
> Subject: Re: [Nhcoll-l] Multiple numbers
>
> If we started numbering from scratch, I'd agree, Kevin. But we started in 1883 :)
>
> __________________
> Thomas J. Trombone
> Data Manager
> Division of Vertebrate Zoology - Ornithology American Museum of Natural History Central Park West @ 79th Street New York, NY 10024-5192
>
> Phone: (212) 313-7783
> Email: trombone at amnh.org
> URL: https://urldefense.proofpoint.com/v2/url?u=http-3A__research.amnh.org_ornithology_&d=AwIGaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=CLFZJ3fvGSmDp7xK1dNZfh6uGV_h-8NVlo3fXNoRNzI&m=v-Rg3vDcZRzhwEF1YxVm73UdVpR4LlRjluGWO3zOjm0&s=4f5V78Eit_oT7No2TLGHClOiu0_CGAMW-0yIvuRuYxk&e=
>
>
> -----Original Message-----
> From: Kevin Winker [mailto:kevin.winker at alaska.edu]
> Sent: Thursday, 10 March 2016 2:56 PM
> To: Thomas J Trombone
> Cc: NH-COLL listserv (nhcoll-l at mailman.yale.edu)
> Subject: Re: [Nhcoll-l] Multiple numbers
>
> We use one number for all preserved parts (each individual bird gets one number). Thus each part is easily linked to the voucher and other preserved parts. My brain doesn't handle hierarchical database relations with multiple different numbers very well.
>
> Best, K.
>
> On 3/10/16, Thomas J Trombone <trombone at amnh.org> wrote:
>> Andy's post reminds me that I should have added: our
>> multiple-catalog-number system works fine in our database (KE EMu)
>> because each bird is assigned its own catalog record (record
>> type="Specimen/Lot") and each preparation is assigned a child catalog
>> record (record type = "Preparation.") It is the child preparation
>> records that bear the catalog numbers, so the multiple numbers can be
>> easily stored, output, queried for, etc. And the records are of course
>> linked together for easy retrieval. Thus a bird consisting of skeleton
>> and tissues preparations would occupy three database records: one for
>> the bird (with taxonomic & locality info) and one each for the
>> skeleton and tissue (with preparation and storage info specific to
>> each.)
>>
>> Best,
>> Tom
>>
>> __________________
>> Thomas J. Trombone
>> Data Manager
>> Division of Vertebrate Zoology - Ornithology American Museum of
>> Natural History Central Park West @ 79th Street New York, NY
>> 10024-5192
>> Phone: (212) 313-7783
>> Email: trombone at amnh.org
>> URL:
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__research.amnh.org_
>> ornithology_&d=AwIFAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=CLFZJ3fvGSmDp7xK1dNZf
>> h6uGV_h-8NVlo3fXNoRNzI&m=atYFurC0tZdoHVb_e6YhioB24vdJ9HJS1h9P3pF60aA&s
>> =-_by7_ImZiuzTKqj3hkaedDhFrk2qkGiwwa1FGzpoB4&e=
>>
>>
>> From: nhcoll-l-bounces at mailman.yale.edu
>> [mailto:nhcoll-l-bounces at mailman.yale.edu] On Behalf Of Thomas J
>> Trombone
>> Sent: Thursday, 10 March 2016 2:04 PM
>> To: NH-COLL listserv (nhcoll-l at mailman.yale.edu)
>> Subject: Re: [Nhcoll-l] Multiple numbers
>>
>> Hi Paul,
>>
>> Funny you should use birds as your example, as the AMNH Ornithology
>> Department does just this. Since our collection's inception we have
>> assigned different catalog numbers to the various elements derived
>> from the same bird, and in fact now have five independent catalog
>> number series: skins, skeletons, alcohol specimens, tissue samples,
>> and egg/nest sets. A bird may be represented by one or more numbers in
>> any of those series (depending on which preparations exist in our
>> collection) and the numbers are entirely independent of one another.,
>> i.e., skin 800,000 may correspond to skeleton
>> 30,000 and to tissue 20,000.
>>
>> We considered moving away from this system a few years ago but decided
>> for the sake of expediency that it was best to maintain it. For one
>> thing, the different numbers have appeared in publications over the
>> years. Moreover, we had no interest in physically renumbering existing
>> specimens to match a new unified approach.
>>
>> Personally, I think it's best to go with a single catalog number per
>> organism or lot if you have the choice. A drawback to our current
>> approach is that there is no single number series that applies to
>> every bird in our collection. That is to say, a bird specimen
>> consisting of simply a skin might be described by AMNH SKIN 800,000,
>> while a specimen consisting of only a skeleton may be AMNH 30,000
>> (which is an entirely different bird than the one numbered AMNH SKIN
>> 30,000.) And a bird consisting of a skeleton and a tissue sample might be described by AMNH SKEL 30,000 *and* AMNH DOT 20,000.
>> Of course you run into an analogous problem involving suffixes with a
>> single-number system, but at least you can say for sure which bird a
>> given integer refers to: the number 5,000 would apply to only one
>> bird, whereas at AMNH that number has been used five times, for an
>> unrelated skin, skeleton, alc, tissue, and egg/nest.
>>
>> My two cents.
>>
>> Tom
>>
>> __________________
>> Thomas J. Trombone
>> Data Manager
>> Division of Vertebrate Zoology - Ornithology American Museum of
>> Natural History Central Park West @ 79th Street New York, NY
>> 10024-5192
>>
>> Phone: (212) 313-7783
>> Email: trombone at amnh.org<mailto:trombone at amnh.org>
>> URL:
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__research.amnh.org_
>> ornithology_&d=AwIFAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=CLFZJ3fvGSmDp7xK1dNZf
>> h6uGV_h-8NVlo3fXNoRNzI&m=atYFurC0tZdoHVb_e6YhioB24vdJ9HJS1h9P3pF60aA&s
>> =-_by7_ImZiuzTKqj3hkaedDhFrk2qkGiwwa1FGzpoB4&e=
>>
>>
>> From:
>> 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
>> Callomon,Paul
>> Sent: Thursday, 10 March 2016 1:28 PM
>> To: NH-COLL listserv
>> (nhcoll-l at mailman.yale.edu<mailto:nhcoll-l at mailman.yale.edu>)
>> Subject: [Nhcoll-l] Multiple numbers
>>
>> Colleagues:
>>
>> In some collections, individual components of a lot that are stored in
>> a particular medium (for example: the empty dry shell, frozen tissue
>> snip and alcohol-preserved body from the same snail or the dry skin
>> and fluid-preserved guts of a single bird) each get different catalog numbers.
>> The question: All other things being equal, is it better collections
>> management practice for all parts of a single lot to have the same
>> catalog number (perhaps with different states of preservation
>> indicated separately or as prefixes/suffixes)?
>> A "lot" is defined as all specimens collected at the same time in the
>> same place. This can be a single bird or a hundred pond snails.
>>
>> How do you handle this in your collection?
>>
>> 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<mailto:callomon at ansp.org> Tel 215-405-5096 - Fax
>> 215-299-1170
>>
>
> --
> Kevin Winker
> University of Alaska Museum
> 907 Yukon Drive
> Fairbanks, AK 99775
>
> NOTE NEW EMAIL ADDRESS: kevin.winker at alaska.edu _______________________________________________
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