[Nhcoll-l] Digital objects vs. physical objects in collection management databases and how to manage them
Randall, Zachary
zrandall at flmnh.ufl.edu
Wed Aug 26 15:49:41 EDT 2020
I should clarify that our 2D image data (photographs) are added as prep types as well as collection object attachments. Our CT data is currently only added as prep types since it’s all freely accessible on MorphoSource (MS). We have the RSS feed from MS integrated with our collection IPT making the scans discoverable to aggregators. However, currently we don’t have a link yet between MS and our collection database. If you currently search our online database the only way you’ll know we have CT data is because it’s listed as a prep type. We intend to also include a collection object attachment for CT and is something we are currently working on. For the attachment we want to avoid hosting duplicated data that is already on MS, while at the same time identifying our institution as being the home repository for the raw CT data.
In the end we try to use a combination of prep type and collection object attachment as a means to make the data discoverable. We are definitely looking forward to future methods on how to support and convey this digital media.
Also, I’m interested to know how other institutions have tied data hosted on MS into their local database. Please email me if you'd like to share your methods (since it's a different thread topic).
Here is an example of one of our collection records on iDigBio that has a 2D image and CT data:
https://www.idigbio.org/portal/records/1dfa5b41-bf10-414a-925b-9dad7b2e8958
Same record on our online-database:
http://specifyportal.flmnh.ufl.edu/fishes/ (catalog number 160521)
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 Sadie Mills <Sadie.Mills at niwa.co.nz>
Sent: Tuesday, August 25, 2020 8:30 PM
To: nhcoll-l at mailman.yale.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]
Here at the NIWA Invertebrate Collection in our Specify database we have the specimen images as attributes of our collection object. We store the image files in our NIWA-wide image management database (An Atlas database), which creates a unique asset ID for the image that can be shared via a public link. We copy these Atlas asset IDs for each associated image into individual “specimen image” fields in the “Collection Object Attribute” table. These fields are link fields that are programmed to go to our Atlas image database public link. So we can have multiple asset IDs per collection object.
We also have a yes/no tickbox labelled as “Photo” on the “preparation” table so that we can use that to flag if we have a photo of that particular preparation. Usually we would register a separate lot as the photo voucher, but we don’t always do this if the individual is pretty distinct looking in the group of multiple specimens.
Cheers,
Sadie
From: Nhcoll-l <nhcoll-l-bounces at mailman.yale.edu> On Behalf Of Dean Pentcheff
Sent: Wednesday, 26 August 2020 11:03 AM
To: nhcoll-l at mailman.yale.edu
Subject: Re: [Nhcoll-l] Digital objects vs. physical objects in collection management databases and how to manage them
Speaking from a perspective coming from managing diverse marine invertebrates: we would consider any digital products as being derivatives (and hence "filed with" or linked to) the original specimen. Linking an image or a CT scan back to a specimen (to be precise: to a specimen record distinguished by a unique specimenID) would be treated just like linking a molecular sequencing extract back to a specimen record.
The workflow that often goes with marine invertebrates has led us away from the "prep" concept (which seems to come naturally for vertebrate collections where there are a roughly fixed number of kinds of preps for specimens) to a parent/child concept. A "specimen" can be an unsorted lot (multi-phyletic), or a jar of individuals assumed to be the same species, or one critter in a jar. The moment an individual (or sub-lot) is removed or distinguished in some way, it gets a new specimenID that is linked as a "child" of the "parent" specimen record. That process can continue (all the worms from an unsorted lot could be given their own specimenID as a lot, and then individuals pulled from the worm jar could each get their own specimenID when they're isolated for sequencing). The idea is that anything you will want to refer to individually later (in a publication, etc.) should get its own specimenID.
Now, having said that, and thinking about images, CT scans, and molecular extracts, I hypothesize that I think about those in a way very similar to the way vertebrate people think about "preps". An image never gets its own specimenID, but always points to a specimenID (yes, there's an imageID for the image record, but that's just the identifier for the image record and does not pretend to be anything else). The same is true for molecular extracts, and would be for CT scans if we had any. Each of those derived products (images, extracts, CT scans) would probably get its own table in a database, since there are properties unique to it that are irrelevant to the others. But they exist as derivatives of the specimen identified by its specimenID (and use that specimenID to maintain the linkage). It seems to me that this is analogous to the "prep" idea, which has a defined set of physical derivatives that can come from a specimen, each one of which may have its own properties. Some of these derivatives (images, CT scans) are electronic-only, and some are physical (molecular extract), but they're treated similarly as defined derivatives of specimens.
A field we maintain in the specimen table is "specimen exists (yes/no)". We have situations where there are derivative products but no physical specimen remains in the collection: when the specimen was consumed for molecular analysis, for example. But that same system would accommodate a situation where there never was a physical specimen, but there only ever was an image, for example. We're mostly specimen-based (not so much observation-based), so in practice almost all the situations like that existing in our case are situations where we started with a physical specimen.
-Dean
--
Dean Pentcheff
pentcheff at gmail.com<mailto:pentcheff at gmail.com>
pentcheff at nhm.org<mailto:dpentche at nhm.org>
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On Tue, Aug 25, 2020 at 2:30 PM Bentley, Andrew Charles <abentley at ku.edu<mailto:abentley at ku.edu>> wrote:
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<https://urldefense.proofpoint.com/v2/url?u=https-3A__aus01.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Fwww.gbif.org-252Foccurrence-252F656980275-26data-3D02-257C01-257Csadie.mills-2540niwa.co.nz-257C86ec6c523f324a04b20b08d8494b1a4f-257C41caed736a0c468aba499ff6aafd1c77-257C0-257C0-257C637339934272691270-26sdata-3DWR-252B8x-252FU5-252BbX3BsHOBw93dIcOWP9DpKlKDPLYACXpc-252Fk-253D-26reserved-3D0&d=DwMGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=bCj30vsHhpXdIkMcApjSJm56alV4bPghffnioNsekNk&m=3d00XzK0KRM4K1W8nS84wf0R6vh7onvZ1-xzh7gRh2g&s=jBO7vXgJGBWCmuGH2u0qtlHiiITv_Seuzl3cb-IoelQ&e=>. 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<https://urldefense.proofpoint.com/v2/url?u=https-3A__aus01.safelinks.protection.outlook.com_-3Furl-3Dhttp-253A-252F-252Fichthyology.biodiversity.ku.edu-252F-26data-3D02-257C01-257Csadie.mills-2540niwa.co.nz-257C86ec6c523f324a04b20b08d8494b1a4f-257C41caed736a0c468aba499ff6aafd1c77-257C0-257C0-257C637339934272701263-26sdata-3D86Tbu44VoiQc2dQj-252BKILyE2GpZLyc3Gdsp919rsH2-252BY-253D-26reserved-3D0&d=DwMGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=bCj30vsHhpXdIkMcApjSJm56alV4bPghffnioNsekNk&m=3d00XzK0KRM4K1W8nS84wf0R6vh7onvZ1-xzh7gRh2g&s=uLIiiaOf4rQYRlCwuPs4FbFxqZVJuT3iMT933ygKc8E&e=>
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From: "zrandall at flmnh.ufl.edu<mailto:zrandall at flmnh.ufl.edu>" <zrandall at flmnh.ufl.edu<mailto:zrandall at flmnh.ufl.edu>>
Date: Tuesday, August 25, 2020 at 3:22 PM
To: "SchindelD at si.edu<mailto:SchindelD at si.edu>" <schindeld at si.edu<mailto:schindeld at si.edu>>, Andrew Bentley <abentley at ku.edu<mailto:abentley at ku.edu>>, "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: 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<https://urldefense.proofpoint.com/v2/url?u=https-3A__aus01.safelinks.protection.outlook.com_-3Furl-3Dhttp-253A-252F-252Fwww.zacharyrandall.org-252F-26data-3D02-257C01-257Csadie.mills-2540niwa.co.nz-257C86ec6c523f324a04b20b08d8494b1a4f-257C41caed736a0c468aba499ff6aafd1c77-257C0-257C0-257C637339934272711256-26sdata-3DDrKZChoxDX1jMoLZhWMwwFXMRCDkNW41vJNtTUnT4-252F4-253D-26reserved-3D0&d=DwMGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=bCj30vsHhpXdIkMcApjSJm56alV4bPghffnioNsekNk&m=3d00XzK0KRM4K1W8nS84wf0R6vh7onvZ1-xzh7gRh2g&s=xOoWkSCn8alFvC_fvhVz7LOy6JIffuIGF7ihNWq0PV8&e=>
Twitter: @Zach__Randall
From: Nhcoll-l <nhcoll-l-bounces at mailman.yale.edu<mailto: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<mailto:abentley at ku.edu>>; nhcoll-l at mailman.yale.edu<mailto: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<https://urldefense.proofpoint.com/v2/url?u=https-3A__aus01.safelinks.protection.outlook.com_-3Furl-3Dhttp-253A-252F-252Fusfsc.nal.usda.gov-252F-26data-3D02-257C01-257Csadie.mills-2540niwa.co.nz-257C86ec6c523f324a04b20b08d8494b1a4f-257C41caed736a0c468aba499ff6aafd1c77-257C0-257C0-257C637339934272711256-26sdata-3D0qnHc2sjvCpuhJJor5snd9sTQHMriqSEZS-252BFZr8S4Tk-253D-26reserved-3D0&d=DwMGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=bCj30vsHhpXdIkMcApjSJm56alV4bPghffnioNsekNk&m=3d00XzK0KRM4K1W8nS84wf0R6vh7onvZ1-xzh7gRh2g&s=OLbPa0vd81TOH4_r9I6AXq6TilZEHYeslYWGYLYO4TA&e=>). 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>
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To ensure compliance with legal requirements and to maintain cyber security standards, NIWA's IT systems are subject to ongoing monitoring, activity logging and auditing. This monitoring and auditing service may be provided by third parties. Such third parties can access information transmitted to, processed by and stored on NIWA's IT systems
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