[Taxacom] Software for curating taxonomic/biological/specimen information

Alastair Culham a.culham at reading.ac.uk
Fri Dec 2 03:33:10 CST 2016


We've recently moved the Reading Herbarium data from a local implementation of BRAHMS - to AdLib which is a more general museums database.  This means that all the University collections can share a common platform and the cost of the system and software is met centrally by the University.  It's a commercial system but has good support and data are readily imported and exported. http://alm.axiell.com/solutions/technology/adlib 

Alastair
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Dr Alastair Culham
Centre for Plant Diversity and Systematics
Harborne Building, School of Biological Sciences
University of Reading, Whiteknights, Reading, RG6 6AS
U.K.

Associate Professor of Botany
Curator, Reading University Herbarium (RNG)
Associate Editor, Botanical Journal of the Linnean Society
Programme Director, MSc Plant Diversity
____________________________________________

________________________________________
From: Taxacom [taxacom-bounces at mailman.nhm.ku.edu] on behalf of Chris Grinter [cgrinter at gmail.com]
Sent: 02 December 2016 01:33
To: Doug Yanega
Cc: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Software for curating taxonomic/biological/specimen      information

FMPro has its pros and cons (as do all database systems) - one of its
largest issues being that it's difficult to develop from scratch, expensive
to keep up to date with, and tricky to serve data online. Here at the INHS
we are quickly moving away from it. Since the INHS entomology collection
chose not to upgrade beyond FMP 8.0 years ago (now in v15), we are stuck
operating the database on ancient Windows machines that can run the
original software. If we were to upgrade we would have to purchase several
old versions of FMP to step-wise upgrade our data. Annually licensing File
Maker is very expensive, but you can purchase discounted bundles of
multiple years - plan on spending several thousand dollars for those
software keys. If you want to customize you'll need to also hire a database
manager/programmer as Doug did.

Symbiota is wonderful for data entry and data sharing, however collection
management tools are rough at best. This is in the plans for further
development, but you'd have to discuss with the Symbiota Collections group
for further details. The biggest pro is that you can join SCAN for free to
serve data, or host your own iteration just as the INHS has chosen to do
for a one-time-payment of just about a thousand dollars. The INHS manages
non-entomology collections in FMP and exports CSV files to SCAN for data
access. Paleontology uses Symbiota as its primary database.

The entomology collection is close to fully integrating with TaxonWorks -
an online database designed by the Species File Group (SFG) here at the U
of Illinois. Once we've tested all of the bugs and gotten everything
working we'll have a very powerful and web-based data platform. Integrating
software like barcode readers, geolocate (already added), or any other
open-sourced platform is possible. Matt Yoder from SFG would have to
comment further on the possibility of accepting new collaborations, but it
will eventually be free and open sourced for anyone to use.

Specify also sounds like a great solution, but I have limited experience
with it. In general my bottom line advice would be to discourage any
proprietary database system or one that requires perpetual license fees.

Chris Grinter

Christopher C. Grinter

*Collections Manager of Insects, Illinois Natural History SurveyAssistant
Secretary & Asst. Treasurer, The Lepidopterists' Society*
1816 S Oak Street,
Champaign, IL 61820-0904
cgrinter at gmail.com

On Thu, Dec 1, 2016 at 1:27 PM, Doug Yanega <dyanega at ucr.edu> wrote:

> I'll offer my two cents. Back around 1994, I had a postdoc at the INHS to
> help develop a database for their aquatic insect collection. The database
> was in FileMaker. I learned how to use it, how to design fields and modify
> the interface, how to link relational files, and it was not a difficult
> thing. 22 years later, I still use FileMaker Pro, now to manage a
> collection at UCR containing some 4 million specimens, of which around half
> a million have database records. True, it is not pre-packaged. You have to
> learn how to make it do what you want it to do, but it can do almost
> anything. True, it has some "personality quirks" which take getting used
> to. But it is platform-independent, flexible, powerful, easy to learn and
> use, fairly cheap, and it is extremely well-supported. Over 20 years and
> still going strong, and I have no fear of ever losing our data to
> obsolescence. I've seen most of the other software that's around, and have
> never yet seen anything that I would consider a significant *overall*
> improvement over what FMPro does for me. True, I had to put a fair bit of
> my own time and energy into building the interface, but that's not really a
> drawback; after all, if I decide I need a new or modified data field (e.g.,
> in order to better correspond to Darwin Core standards), or want to add new
> functionality (e.g., displaying images, linking to Google Earth), I can do
> it myself (or with a little help and/or research), sometimes immediately.
>
> I'll add one more thing: since it CAN be customized, FMPro offers the
> potential for different users to develop tools, tricks, and interface
> designs that can be shared with other users, to everyone's collective
> benefit. If someone else using FMPro wanted to see how my database is
> structured, I could easily send them copies of the templates for each of
> the five relational databases that comprise my system (one for localities,
> 3 for taxonomy, and one for specimen records themselves), and vice-versa;
> we could learn from one another, and maybe both come out ahead. I know at
> least a few major collections other than mine use FMPro-based databases
> (e.g., INHS, AMNH), so I'm not alone. But, when discussions like this crop
> up, they ALWAYS focus on pre-packaged specimen management software, so you
> will rarely hear from us. I'd encourage people to consider FMPro as another
> option.
>
> Peace,
>
> --
> Doug Yanega      Dept. of Entomology       Entomology Research Museum
> Univ. of California, Riverside, CA 92521-0314     skype: dyanega
> phone: (951) 827-4315 (disclaimer: opinions are mine, not UCR's)
>              http://cache.ucr.edu/~heraty/yanega.html
>   "There are some enterprises in which a careful disorderliness
>         is the true method" - Herman Melville, Moby Dick, Chap. 82
>
>
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