[Nhcoll-l] mammal database queries (Roberts, Karen)

Thu Mar 20 19:30:01 EDT 2014

We recognize that we catalog objects that are sometimes whole organisms,
sometimes parts of organisms, sometimes many parts of one organism, or
sometimes groups (lots) of organisms.  We appreciate less that our
cataloged items have a loose relationship to physical reality, and hence no
useful relationship to object-tracking, or to other important attributes of
specimens.  We view our collections as aggregations of cataloged items, and
for many systems, "records" are equated with cataloged items.  That we are
managing objects, not cataloged items, is the underlying problem Karen
describes.

That Karen is tempted to "designate a conceptual parent" ("usually the skin
is designated"), or that Steven must "add an umbrella record," or that AMNH
collections are finding their own independent solutions, all of this is ad
hoc and suggests a fundamental problem.  As early as 1996, Stan Blum
addressed the awkward one-are-really-many problem in a data structure
referred to as the "MVZ Model."

Cataloged items within the MVZ Model are essentially another object,
analogous to the parent/umbrella records mentioned in this discussion, but
so intrinsic is this fact to the overall data structure, that it is not
evident to users of the online implementations of the model
(Arctos<http://arctos.database.museum/>and
MCZbase <http://mczbase.mcz.harvard.edu/>).  A cataloged item is the de
facto parent of one or more objects.  Objects have preparation methods,
conditions, and storage locations.  Objects get sent out on loans, and used
in research.  Nevertheless, cataloged items remain the entities cited in
the scientific output from our collections, and cataloged items are the
usual view that users take in querying collection data.  The data structure
serves two million zoological, botanical, and paleontological records,
originating from 70 collections, from one instance of Oracle at the Texas
Advanced Computing Center <https://www.tacc.utexas.edu/about>, and another
two million records at Harvard.

Gordon Jarrell

Museum of Southwestern Biology

Univeristy of New Mexico, Albuquerque

On Fri, Mar 21, 2014 at 1:18 AM, Thomas J Trombone <trombone at amnh.org>wrote:

>  Hi Karen,
>
>
>
> In the AMNH Vertebrate Zoology KE EMu database we also use a conceptual
> parent "Organism" record in our Catalog module which has child
> "Preparation" records. The parent record is the only record that links to
> the Taxonomy and the Collecting Events modules (among others.) The child
> Preparation records are each of a type specific to a particular department.
> For example, in my own department (Ornithology) we have five pre-defined
> types of Preparation record: skin; skeleton; fluid (i.e., stored in
> alcohol); tissue sample; egg/nest set. The particular types of Preparation
> records used by another department would be different. Ichthyology in
> particular implemented a slightly different version of this model, where
> the parent record does not refer to a single organism but instead to a
> "Lot" of fish, and each Preparation record corresponds to some subset of
> that lot that has been treated in a particular way (e.g., 50 individuals
> stored in ethanol vs. 10 individuals cleared and stained and stored in
> glycerin.)
>
>
>
> In some departments the catalog number appears in the parent record. In
> Ornithology we have a historical practice of numbering each of our
> collections independently, so we have a different catalog number in each
> Preparation record. The parent/child model allows us to easily retrieve and
> sort records by catalog number, which would not be quite as simple if all
> the numbers were embedded in a single record.
>
>
>
> The model allows each Preparation record to be loaned independently of the
> other related preparations from a given specimen, and also allows storage
> location and inventory status to be recorded independently for each
> preparation.
>
>
>
> Our preparation type classification scheme is not terribly standardized,
> but in Ornithology we aim for an arrangement such as you describe: a
> top-level category designating the type of specimen in broadest terms
> (skin; feathers; toe pad sample; etc.) and a lower-level description (flat
> skin and wing; spread wing; tail only; etc.) In other departments the more
> descriptive term is used at the top level and the subsequent level
> describes the condition of the specimen (Damaged; Disarticulated;
> Dissected; etc.)
>
>
>
> I find the conceptual parent model works well for us as it allows
> flexibility in data retrieval and reporting, and accurately reflects the
> very separate nature of our various collections while easily maintaining
> the relationship of all preparations derived from a given individual
> organism. However the model does complicate things to a degree. Data entry
> using the EMu client is a bit more cumbersome, as one must create the
> parent record first and then create the child records as needed. Similarly,
> importing data requires a few extra steps. And query time can be affected
> when one runs a query on Preparation records based on a value in the
> related Parent records, because the sub-query must run first, and EMu could
> use some query optimization enhancements in this situation. Nonetheless the
> benefits outweigh the costs for Vertebrate Zoology in my estimation. Having
> said that, our Division of Invertebrate Zoology is about to adopt EMu and
> has opted not to implement the parent/child model, though our Division of
> Paleontology plans to use it in order to reflect the relationship between
> their fossils, molds and casts.
>
>
>
> Happy to follow up on or off list.
>
>
>
> 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: http://research.amnh.org/ornithology/
>
>
>
> *From:* nhcoll-l-bounces at mailman.yale.edu [mailto:
> nhcoll-l-bounces at mailman.yale.edu] *On Behalf Of *Steven van der Mije
> *Sent:* Tuesday, 18 March 2014 3:37 AM
> *To:* nhcoll-l at mailman.yale.edu
> *Subject:* [Nhcoll-l] mammal database queries (Roberts, Karen)
>
>
>
> Dear Karen,
>
>
>
> at Naturalis we also describe our mammal specimens in multiple records,
> but we also add an umbrella record (called *virtual specimen*) probably
> similar to your conceptual parent, to group together the different records
> for the specimen. Furthermore the records get the same registrationnumber,
> only differentiated by a suffix (.a,.b, etc.), so can be filtered or
> searched with the same registration number.
>
> We have a preparation type classification, for some collections this is
> very detailed (palaeontolgy for instance). In mammals I try to keep it as
> broad as possible, so the term would be *skull* or *cranium *(searchable
> with the thesaurus) and we have a description field for additional remarks
> (for instance *only right mandible)*.
>
>
>
> Best wishes,
>
>
>    Steven van der Mije
>
> hoofd collectie vertebraten / senior collectiebeheerder vogels en
> zoogdieren
>
> head of vertebrate collections / collection manager birds and mammals
>
>
>
>   T 071-5687536, M 06-45336594
> Darwinweg 2, Postbus 9517, 2300 RA Leiden
> E steven.vandermije at naturalis.nl, I www.naturalis.nl<http://www.naturalis.nl/>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 18 Mar 2014 17:40:40 +1100
> From: "Roberts, Karen" <karoberts at museum.vic.gov.au>
> Subject: [Nhcoll-l]  mammal database queries
> To: "nhcoll-l at mailman.yale.edu" <nhcoll-l at mailman.yale.edu>
> Message-ID:
>         <AB0EB33C73AD494EBB8D722C00B3F6BB1A9182A129 at RAKALI.mv.vic.gov.au>
> Content-Type: text/plain; charset="us-ascii"
>
> Hello colleagues,
>
> I've recently been having some issues with the way mammal specimen
> collection data is recorded in our database and I was wondering how others
> organise their collection data.
>
> My issues revolve around being able to record different preparation types
> in a simple manner that enables easy retrieval of data relating to 1) how
> many individuals of that species we have 2) how many of a certain
> preparation type we have, and 3) what the location of the different prep
> types is. At the moment I can achieve all these, but not always in an easy
> way.
>
> We use KE EMu and use a multiple record method of recording different prep
> types as only one location can be linked to each record (our institution
> uses a barcode based location system). Therefore, a skin, skull and fluid
> prep from one individual will need to be recorded three times - so that
> separate location data can be added - and linked to the main record,
> usually the skin is designated. Associated tissue samples are also linked
> to the main record, but they have completely different catalogue numbering
> so there isn't a straight forward way to search that brings up all records
> for one individual (same goes for older specimens where different parts of
> a single individual specimen were originally registered with different
> catalogue numbers). Many of these things I probably can't change but I'm
> hoping I can improve things a little and it's nice to know how others
> manage similar problems.
>
>
> So my specific questions for the list are:
>
> 1. In the case of specimens with more than one preparation type, how do
> you record these - in one record or multiple?
>
> 2. How do you record locations for different parts of a single individual
> specimen (if you do at all)?
>
> 3. Do you have a generic preparation type classification that is
> supplemented by additional information? Eg. 'skull' as a prep type
> description but then another field that indicates whether it is a complete
> skull with mandibles or just a partial cranium.
>
> 4. For those that use KE Emu or similar systems, do you use the conceptual
> parent method of grouping multiple associated records? I wasn't keen on it,
> but I am starting to think it may be more practical.
>
>
> Thank you all for your input and thoughts (happy to hear from non-mammal
> people too!).
>
> Karen
>
>
>
>
>
>
>
> Karen Roberts, PhD
> Collection Manager, Vertebrates
> Museum Victoria, GPO Box 666, Melbourne VIC 3001, Australia
>
> e: karoberts at museum.vic.gov.au<mailto:karoberts at museum.vic.gov.au>
> web: http://museumvictoria.com.au/
>
>
>
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-- 
Gordon Jarrell
Museum of Southwestern Biology
University of New Mexico
Albuquerque, NM 87131-0001
mobile: 505-506-2145
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