[Nhcoll-l] Digital objects vs. physical objects in collection management databases and how to manage them

Tue Aug 25 17:30:05 EDT 2020

Zach

Thanks for this articulation of your process.  With regard to the issues you raise (which are similar to issues raised in other replies I have received):

  1.  Space – not sure this is a valid reason for using preps given that there are other mechanisms of tagging individuals in a lot rather than separating them out as you indicate – wrapping in cheesecloth or tagging.  Also, imaged individuals can usually be discerned simply by visual inspection of distinguishing characteristics – fin damage, body shape, size, etc.
  2.  Searching - not sure this is a valid reason either given that it is just as easy to search a database for those records that have attachments as searching for preps.  You could add metadata about the attachment that could facilitate searching for various kinds of attachments in the same manner.
  3.  Data integration – These attachments are still published to the aggregators as associated with the occurrence record through extensions or otherwise, even though they are not preps.  See this example from my collection where Genbank sequences, images and citations are all published as part of the record of this tissue - https://www.gbif.org/occurrence/656980275.  CT scans would similarly be included as linkages to Morphosource.

I am still stuck thinking that an image or a CT scan is simply a digital representation of a specimen and not a prep in the traditional sense but maybe I am thinking too narrowly.  I have yet to see a compelling argument for preps.  For instance, if you were to scan a publication or field notebook, would this represent a separate “prep” of the publication or field note page or is it simply a digital representation of the same thing?  Is the distinction that more information can be gleaned from a CT scan than can be gleaned from the specimen itself without dissection?  Is that true of an image?  What more information is available besides coloration from an image taken while alive or shortly after euthanizing?  I am still worried by the possible confusion with collection stats and digital representations being counted as specimens.  I am also worried about the process of publishing data to aggregators where currently digital media are published as part of an Audubon core extension and not as occurrences (which they would be as preps).

Still mulling this over in my brain but it would be great if we had some community consensus as to how to treat these things – which there currently is not given the replies I have been receiving.  I will admit that some of my thinking is driven by the Specify data model that we use for our collections.  I would be interested in hearing how other CMS’s deal with these or is it similarly all over the map.

Andy

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Andy Bentley
Ichthyology Collection Manager
University of Kansas
Biodiversity Institute
Dyche Hall
1345 Jayhawk Boulevard
Lawrence, KS, 66045-7561
USA

Tel: (785) 864-3863
Fax: (785) 864-5335
Email: abentley at ku.edu<mailto:abentley at ku.edu>
http://ichthyology.biodiversity.ku.edu<http://ichthyology.biodiversity.ku.edu/>

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From: "zrandall at flmnh.ufl.edu" <zrandall at flmnh.ufl.edu>
Date: Tuesday, August 25, 2020 at 3:22 PM
To: "SchindelD at si.edu" <schindeld at si.edu>, Andrew Bentley <abentley at ku.edu>, "nhcoll-l at mailman.yale.edu" <nhcoll-l at mailman.yale.edu>
Subject: RE: Digital objects vs. physical objects in collection management databases and how to manage them

Hi Andy,

This is a great topic. We produce a large amount of 2D images (live and preserved) and CT data for our fish collection here at UF. We treat these data as prep types for a collection object. A major reason for this approach and not separating lots is to conserve collection space. Given the rate that we are imaging our specimens, we wouldn’t be able to also support our future growth of newly acquired collections. Additionally, we see the value of having image data as prep types so that the collection object can be the one stop for all “metadata” including from other individuals from the same lot. For example, although we try to CT scan individuals from tissued lots to increase data value, we usually don’t scan the individuals that were tissued because it would be a loss in morphological data captured (e.g. missing fins, epaxial tissue, etc.).  One catalog number to rule them all. Guess we’re a bunch of lumpers at heart.

Our system for tracking down the imaged individual in a lot is still being improved (luckily we rarely get those types of requests). When possible, we image lots with only one individual. If we image lots with several individuals, then we wrap that individual with cheese cloth and/or include tag(s).

Adding these media as prep types in Specify allows us to query the number of multimedia that we have, similarly to tissues. This number only include files existing in Specify, since derivatives and raw data are a whole other can of worms.

Best,
Zach
--
Zachary S. Randall
Biological Scientist & Imaging Lab Manager
Florida Museum of Natural History
1659 Museum Road
Gainesville, FL 32611-7800
352-273-1958|Rm. 277

www.zacharyrandall.org
Twitter: @Zach__Randall

From: Nhcoll-l <nhcoll-l-bounces at mailman.yale.edu> On Behalf Of Schindel, David
Sent: Tuesday, August 25, 2020 11:09 AM
To: Bentley, Andrew Charles <abentley at ku.edu>; nhcoll-l at mailman.yale.edu
Subject: Re: [Nhcoll-l] Digital objects vs. physical objects in collection management databases and how to manage them

[External Email]
Hi, Andy,

We've had discussions about this in the Interagency Working Group on Scientific  Collections (IWGSC; see usfsc.nal.usda.gov).  If the digital representations of an object are not published, they would be archival material directly related to the specimen, and therefore part of the collection.  They would be equivalent to field notes, locality maps, audio and video recordings, etc.  lf they are submitted to a public database or other open access data repository (GenBank, CTBase, etc.) then these are publication events that can (and in a perfect world, would be) linked to the specimen record along with scholarly publications in which the specimen is cited.

In both cases, a comprehensively curated system of specimen digitization would allow users to discover and navigate to all these assets.

Best regards and stay well -

David

David E. Schindel, Research Associate
Office of the Provost
Smithsonian Institution
Email: schindeld at si.edu<mailto:schindeld at si.edu>

________________________________
From: Nhcoll-l <nhcoll-l-bounces at mailman.yale.edu<mailto:nhcoll-l-bounces at mailman.yale.edu>> on behalf of Bentley, Andrew Charles <abentley at ku.edu<mailto:abentley at ku.edu>>
Sent: Monday, August 24, 2020 4:16 PM
To: nhcoll-l at mailman.yale.edu<mailto:nhcoll-l at mailman.yale.edu> <nhcoll-l at mailman.yale.edu<mailto:nhcoll-l at mailman.yale.edu>>
Subject: [Nhcoll-l] Digital objects vs. physical objects in collection management databases and how to manage them

External Email - Exercise Caution

Hi all

I am trying to resolve a philosophical conundrum brought on by the ever-increasing mountain of digital data being produces from and associated with natural history collections.  My question is whether digital representations of an object (images, CT scans, etc.) should be treated as preparations of an object in a collections database similar to other physical preparations or treated differently?  For instance, in a fish collection like mine, you have a lot that has a certain number of specimens.  Some of those may be subsequently cleared and stained or have skeletons prepared.  These are traditionally handled as preparations of the original lot with the same catalog number (although in some collections they are treated as separate catalog numbers).  Now, however, you have digital representations of those physical objects such as images, CT scans, etc.  Should these also be treated as preparations or be treated differently - as digital products or linked as attachments to the physical objects?  To me, they are not physical objects but digital representations of the original object.  As such, they are somewhat different to a preparation.  This has implications when totaling traditional counts of objects in a collection as well as when publishing data from a collection to the aggregator community.  In some instances, this may be governed by the data model and business rules of the CMS you are using or by your personal preference.

I would be interested in hearing your views on this and how you handle this in your collection as I am not sure there is any community consensus as to which way to handle these.  I have heard of both methods being used in various collections.

Thanks in advance

Andy

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Andy Bentley

Ichthyology Collection Manager

University of Kansas

Biodiversity Institute

Dyche Hall

1345 Jayhawk Boulevard

Lawrence, KS, 66045-7561

USA

Tel: (785) 864-3863

Fax: (785) 864-5335

Email: abentley at ku.edu<mailto:abentley at ku.edu>

http://ichthyology.biodiversity.ku.edu<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam02.safelinks.protection.outlook.com_-3Furl-3Dhttp-253A-252F-252Fichthyology.biodiversity.ku.edu-252F-26data-3D02-257C01-257Cschindeld-2540si.edu-257C05bb69872c7b4aa324d208d8486a936a-257C989b5e2a14e44efe93b78cdd5fc5d11c-257C0-257C0-257C637338969870562799-26sdata-3D05wkr90YzamCsPVnBhhcDKJXZOvQO4CCkun82aj8z3s-253D-26reserved-3D0%26d%3DDwMFAw%26c%3DsJ6xIWYx-zLMB3EPkvcnVg%26r%3DBsjUEaAzErVnOJA4kXSO_g%26m%3DdjrI-zIT93wiMGeria7qiHeg1OnPwpMDkL1fmqCoeBk%26s%3Dz6APnia86i0F27gg3vvbRfIh_HCwEBpFrZWKVObYaYU%26e%3D&data=02%7C01%7Cabentley%40ku.edu%7C9b20f56ff46a4587b84f08d84934919f%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637339837426191803&sdata=sHT%2BbOrOFfIpCemASxMgK%2BLu%2FJPocbV2PwYpLXCv33E%3D&reserved=0>

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