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

Thu Mar 20 10:18:27 EDT 2014

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<mailto: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

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E steven.vandermije at naturalis.nl<mailto:steven.vandermije at naturalis.nl>, I www.naturalis.nl<http://www.naturalis.nl/>

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Message: 3
Date: Tue, 18 Mar 2014 17:40:40 +1100
From: "Roberts, Karen" <karoberts at museum.vic.gov.au<mailto:karoberts at museum.vic.gov.au>>
Subject: [Nhcoll-l]  mammal database queries
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>>
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        <AB0EB33C73AD494EBB8D722C00B3F6BB1A9182A129 at RAKALI.mv.vic.gov.au<mailto:AB0EB33C73AD494EBB8D722C00B3F6BB1A9182A129 at RAKALI.mv.vic.gov.au>>
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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

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