[Nhcoll-l] Proposing a Preparation extension to Darwin Core - community feedback
Peter T Oboyski
essig.museum at gmail.com
Fri Mar 3 15:16:12 EST 2017
>From the perspective of a terrestrial arthropod collections manager and
researcher, I have been thinking about this issue for some time. How a
specimen was dispatched, processed, and archived makes a big difference in
how it can be used for research. And of course, it could be segregated into
several parts that are treated differently. "It's complicated." But the
better these things can be documented in a standardized way, the more
useful for research. And I like controlled vocabularies, but that would be
a long list across disciplines, and there would need to be an "other"
option.
Suggested fields:
- Killing Method (eg. frozen, cyanide, EtOAc, 95% EtOH, 70% EtOH, ethylene
glycol, propylene glycol, ...)
- Fixative (eg. Formalin, EtOH, ...)
- Preparation (eg. "cleared with KOH, stainied with chlorazol Black & Eosin
Y", " ... Mercurochrome", ...)
- Preparation Notes (eg. "rehydrated in the presence of chlorocresol",
"stored/transported with naphthalene", ...)
- Preservation (eg. 90% EtOH, 70% EtOH, Euparal, Balsam Resin, Hoyer's
solution, ...)
Each of these (and other fields) could have "By" (person) "On Date" (when
it happened). And these fields could apply to separate parts (eg. tissues
sub-sampled for DNA and preserved separately, genitalia dissections with
slide mounts, plants or cultures subdivided among institutions, ...).
Quickly the number of fields proliferates. In a one-to-many relational
system it would not be too difficult to capture in a structured way. But
can GBIF, iDigBio, and others accommodate dimensional data? They generally
work in flat file formats, right?
------------------------------------------------------------
Peter T Oboyski, PhD
Collections Manager & Curatorial Supervisor
Essig Museum of Entomology
1170 Valley Life Science Building
University of California, Berkeley
mailing address:
1101 VLSB, #4780
Berkeley, CA 94720
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510.643.0804 (work phone)
510.847.0360 (cell phone)
--------------------------------------------------------------
On Fri, Mar 3, 2017 at 9:47 AM, Bentley, Andrew Charles <abentley at ku.edu>
wrote:
> Hi all
>
>
>
> During various conversations I have had over the past couple of months in
> my capacity as Specify usability consultant and ichthyology collection
> manager it has become clear to me that one of the major hurdles that is
> experienced with aggregators and sharing of data through Darwin Core is the
> preparation field. Most of the other one-to-many relationships have been
> taken care of (identifications, measurements, collectors, sequences, media
> etc.) through similar extensions or other means leaving preparations as the
> only one left to tackle. Due to the nature of fish collections and our
> propensity to utilize the one-to-many relationship between specimens and
> preparations for all the various preparations we house (ethanol, cleared
> and stained, skeletal, tissue), coupled with the fact that there is only a
> single field in Darwin Core for preparations, mandates that we need to
> concatenate our preparations into a string (or simply not map them) in
> order to be able to map them effectively. As such these concatenations can
> and do include information about preparation type, counts and various other
> pieces of information thus littered the field with a huge amount of unique
> values (160,000 to be exact). With the ever increasing proliferation of
> tissue collections in all disciplines this is becoming a more pressing
> issue for more than just fish collections and is now more widespread across
> all disciplines.
>
>
>
> Given the above, I was thinking of proposing a preparation extension to
> Darwin Core to accommodate this but as a first step would like to get
> feedback from the community as to the perceived need and efficacy for such
> an extension. The extension need not be very complex and would nominally
> include fields for preparation type (controlled vocabulary), count
> (number), prepared by (agent), prepared date and maybe a unique GUID.
> However, the extension would only be useful if the aggregators (GBIF,
> iDigBio etc.) were able to display the data within this extension as part
> of their portal infrastructure thereby increasing the usefulness of the
> records for research purposes. Do you think such an extension would be
> useful? What fields would you like to see included? Question for the
> aggregators – would this data be able to be displayed fore efficient use by
> the ever growing user community?
>
>
>
> Any comments, suggestions, ideas for additional fields etc. are most
> welcome. Please forward to others who may not be on NHCOLL and who may be
> interested.
>
>
>
> Thanks in advance
>
>
>
> Andy
>
>
>
> A : A : A :
> }<(((_°>.,.,.,.}<(((_°>.,.,.,.}<)))_°>
> V V V
> 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
>
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