[Nhcoll-l] Automating desirability

Thu Aug 8 17:44:58 EDT 2024

Hi Paul,

Thank you for starting this conversation. I've been thinking about this a
lot myself as we get so many more specimens than what we are capable of
processing or storing, even if we only take "parts" as vouchers (e.g.,
tissue samples)! While I do not have a decision tool, I have been working
on a shiny application <https://nhm-birds.shinyapps.io/lacm_birds/> that
quickly summarizes our collection data that can help with some of these
decisions. For instance, if you type in "Corvus corax" (Common Raven) in
the species field and go on to the "Count data tab", one could infer that
it wouldn't hurt to add some study skins from specimens collected in
December but maybe not in March. The benefit of this app is that the mobile
version works pretty well too so I can always quickly access the database
on the go. I have written up a short post
<https://younghasuh.com/blog/shiny-start/> on how to get started for such
an application if you were to apply it to your collection and make some of
those changes most relevant to your system.
[image: image.png]

Please let me know if you have any questions!

Best,
Young

--
Young Ha Suh, Ph.D.
Ornithology Collections Manager
Natural History Museum of Los Angeles County
900 Exposition Blvd
Los Angeles, CA 90007
[she/her]

On Fri, Jul 19, 2024, 9:32 AM Shoobs, Nate <shoobs.1 at osu.edu> wrote:

> Paul, See https: //www. researchgate.
> net/post/Should-natural-history-museums-keep-large-series-of-common-species
> and the attached paper which was spawned from the discussion have some
> interesting perspectives. I recently formalized our policy
> 
>
> Paul,
>
> See
>
>
> https://www.researchgate.net/post/Should-natural-history-museums-keep-large-series-of-common-species
> <https://urldefense.com/v3/__https://www.researchgate.net/post/Should-natural-history-museums-keep-large-series-of-common-species__;!!Ljrh0eb5atLX!uBgU_APyf08zX6HLkLhckelYYx3zlWXp-NXszHENWA-pPf1NqXG-mW1FoPwdr28VA341CeB9v_9d$>
>
> and the attached paper which was spawned from the discussion have some
> interesting perspectives.
>
>
>
> I recently formalized our policy here at OSUM.
>
>    - I have made it a policy that I do not catalogue new marine material
>    unless it is of special interest to staff/faculty. This represents a
>    conscious decision to limit growth of the collection along a major axis,
>    but it saves a significant amount of my time, because we don’t have any
>    marine malacologists in our department, and the collection is already weak
>    in that area.
>
>
>    - We cull lots of bivalves pretty aggressively, and put the culled
>    specimens in an uncatalogued collection that we use for education/exchange
>    with other institutions. We don’t cull vouchers, new taxa to the
>    collection, or rare species.
>
> In order of priority, we catalogue / accept the following, regardless of
> how many specimens we have already:
>
>    1. Specimens that are vouchers for scientific papers and state-funded
>    surveys (this is our principal mandate as a collection, our funding is tied
>    to it.)
>    2. Specimens of recently extinct species
>    3. Specimens of species which are new to the collection
>    4. Specimens of federally threatened or endangered species
>    5. Specimens from countries other than the U.S.
>    6. Specimens from combinations of time and place that do not occur in
>    the collection already, regardless of how many specimens of that species we
>    already have.
>       - Time interval is 1 year. Space interval is based on watershed.
>       So, if we don’t have a specimen from that watershed in that year, the lot
>       gets added to the queue.
>       - Lots in this category (i.e. unremarkable lots of things we
>       already have many specimens of) will often be culled down to 1 or 2
>       specimens unless a large series hasn’t been collected in a while (this is a
>       subjective decision but can be quickly seen in the database)
>
>
>
> We are newly using a Specify 7 database, which makes it easy to save
> queries that cover the above situations for checking things out before
> cataloguing.
>
>
>
> -N
>
> --
>
> [image: The Ohio State University]
> *Nathaniel F. Shoobs*
> Curator of Mollusks
> College of Arts & Sciences Dept. of Evolution, Ecology, and Organismal
> Biology
> Museum of Biological Diversity, 1315 Kinnear Rd, Columbus, OH 43212
> 614-688-1342 (Office)
> mbd.osu.edu
> <https://urldefense.com/v3/__http://mbd.osu.edu__;!!Ljrh0eb5atLX!uBgU_APyf08zX6HLkLhckelYYx3zlWXp-NXszHENWA-pPf1NqXG-mW1FoPwdr28VA341CTCjqMTg$>
>
>
>
> *From: *Nhcoll-l <nhcoll-l-bounces at mailman.yale.edu> on behalf of
> Callomon,Paul <prc44 at drexel.edu>
> *Date: *Friday, July 19, 2024 at 11:36 AM
> *To: *NH-COLL listserv (nhcoll-l at mailman.yale.edu) <
> nhcoll-l at mailman.yale.edu>
> *Subject: *[Nhcoll-l] FW: Automating desirability
>
> Folks, We are working on a large-scale project to deal with the backlog of
> incoming material to our collection that has built up over several decades.
> As part of this, we are aiming to build sets of criteria and cascading
> binary decision points
>
> Folks,
>
>
>
> We are working on a large-scale project to deal with the backlog of
> incoming material to our collection that has built up over several decades.
> As part of this, we are aiming to build sets of criteria and cascading
> binary decision points that will eventually allow personnel with no
> training in taxonomy to use an automated system to assess whether a
> particular specimen lot should be cataloged or not. This would become a
> plug-in to our database, so that workers could go directly from a label to
> a decision to data input.
>
>
>
> Examples of binaries include: How many do we already have / from that
> country / from that specific locality / from that time frame. Other
> possible criteria include, for example, “Lot size” (large lots from a
> single collecting event may be more useful for analysis than single
> specimens), “Unique or recognized collector name,” “rarity in museum
> collections versus abundance in nature” (not an easy one, though
> aggregators and resources like iNaturalist are making this possible).
>
>
>
> Resulting decisions would be Catalog/Do not catalog/Set aside. Material in
> the last set would then be reviewed by taxonomists as happens now, but with
> suitably refined algorithms correctly assigning the common stuff it would
> hopefully be a small proportion of the total. All collections face a
> decline in the numbers of in-house people who can make these decisions off
> the tops of their heads, and in addition to creating new career pathways
> into taxonomy we also need to automate those parts of our jobs that safely
> can be. Collections like ours are facing a deluge of new material as a
> whole generation of collectors manifests impermanence – we have accepted
> 17,000 lots in a single family via just two donations in the last few
> years, for example.
>
>
>
> So to an ask: In this developmental phase we are looking for any papers
> published on related subjects, and particularly the creation and use of
> algorithms in operations like this. If you know of any papers that deal
> with “transforming taxonomically informed decisions into binary algorithms”
> or “how can existing databases can proactively assign a relative value to
> an incoming lot” even tangentially or in nominally unrelated fields, please
> pass the reference on.
>
>
>
> *Paul Callomon*
> *Collection Manager, Malacology and General Invertebrates*
> ------------------------------
>
> *Academy of Natural Sciences of Drexel University, Philadelphia*
> *callomon at ansp.org* <callomon at ansp.org>* Tel 215-405-5096 - Fax
> 215-299-1170*
>
>
>
>
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