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

John Longino jacklongino at gmail.com
Thu Dec 1 10:54:16 CST 2016


I have a similar problem with Biota on a Mac, and am looking for an upgrade solution now.

Biota was perfect for a small project or individual curator (http://viceroy.eeb.uconn.edu/biota/). Key functionality for me is to work constantly with real barcodes on real specimens, where there is no uniformity to the specimen codes. I need to be able to scan barcodes with CASENT, UNSM, FMNH, INBIO, etc. prefixes, find those records, change data values (identifications, notes, ownership, location). I can easily export the whole thing as a big flatfile and send it to an aggregator like gbif (via AntWeb in my case).

It seems to me that most collections software is designed for institutions, and often has at its core a conflation of ownership and unique specimen identifiers, such that only an institution’s prefix is allowed. If a variable physical specimen identifier is allowed, it is as some ancillary field without the same degree of functionality. 

I use this database constantly for rapidly selecting subsets of records and exporting subsets of data, for various ecological analyses. It is hard or me to imagine a web-based CMS that gives me the same fluidity.

I am totally in favor of getting specimen content out to the public, but there is value in having a silo to prepare high-quality silage before distributing it to the cows. Silos have gotten a bad rap, but silos are great for creating high-quality content. Every silo I know (coming from an agricultural background) has a door and an ultimate purpose of distributing its contents. There should be some more options for small-scale operations, “within-silo” collections software, something in between an excel spreadsheet and something big like Specify.

Jack Longino


On Dec 1, 2016, at 5:35 AM, Dagmar Triebel <triebel at bsm.mwn.de> wrote:

> Hi,
> 
> you might also download and test Diversity Workbench software, see under http://diversityworkbench.net/Portal/Diversity_Workbench
> 
> Best
> 
> Dagmar Triebel
> 
> 
> 
> Am 01.12.2016 um 13:18 schrieb Donat Agosti:
>> Here one more link to a (fresh of the press) report covering Colleting Management Systems from EU BON.
>> 
>> Ronquist F, Skyttner M, Kõljalg U, Röppert D, Penev L, Stoev P, Peer I, Stein M, Calabuig I, Agosti D, Kempa M 2016. Deliverable 1.3 (D1.3): Systems for mobilizing and managing collection-based data (specimen + DNA-data) fully integrated. EU BON, Museum für Naturkunde - Leibniz Institute for Research on Evolution and Biodiversity, Berlin Germany. doi: 10.5281/zenodo.189960 https://doi.org/10.5281/zenodo.189960
>> 
>> 
>> Donat
>> 
>> -----Original Message-----
>> From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Tony Rees
>> Sent: Thursday, December 1, 2016 12:15 PM
>> To: Scott Thomson <scott.thomson321 at gmail.com>
>> Cc: taxacom <taxacom at mailman.nhm.ku.edu>
>> Subject: Re: [Taxacom] Software for curating taxonomic/biological/specimen information
>> 
>> Hi,
>> 
>> You might also enquire with the Atlas of Living Australia (ALA) since they state that they are supporting the BioLink software for some users:
>> 
>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ala.org.au%2Fabout-the-atlas%2Four-data-providers%2Fsystems-supported-by-the-atlas%2F&data=01%7C01%7Cagosti%40amnh.org%7C5b921a9e8a424939b53308d419db4d98%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=4Cgyrw8WbdoWbgRga6ycCO4EOLHTBtA9XHqKuQKh8zQ%3D&reserved=0
>> 
>> Regards - Tony
>> 
>> Tony Rees, New South Wales, Australia
>> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fabout.me%2FTonyRees&data=01%7C01%7Cagosti%40amnh.org%7C5b921a9e8a424939b53308d419db4d98%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=fzcTrNZxTE5GI4ZBrcrcUfsgxJh4YX7TIK5jkRUcJBI%3D&reserved=0
>> 
>> On 1 December 2016 at 20:10, Scott Thomson <scott.thomson321 at gmail.com>
>> wrote:
>> 
>>> Hi,
>>> 
>>> I would agree with Lynn on Specify.
>>> 
>>> However, if you wish send my your CSIRO software and I can see if it
>>> can work in Windows 10, either by hacking it or another means. Though
>>> there are a lot of programs that do not function under Win10. It may
>>> be simply a missing library in 10, in which case installing the
>>> library into 10 will get the program working. It will depend on the
>>> reasons. If CSIRO no longer supports it it may be better to be rid of
>>> it, up to you. Windows is not as retro as it used to be.
>>> 
>>> Cheers, Scott
>>> 
>>> On Dec 1, 2016 5:50 AM, "Lynn Raw" <lynn at afriherp.org> wrote:
>>> 
>>>> Barry,
>>>> 
>>>> You might like to look into Specify  ( http://specifyx.
>>> specifysoftware.org
>>>> ) as a possible solution. I have no connection with this software
>>>> other than as a user who makes use of only a small fraction of its
>>> capabilities.
>>>> Regards,
>>>> 
>>>> Lynn Raw
>>>> 
>>>>> On 1 Dec 2016, at 04:36, Barry Roth <barry_roth at yahoo.com> wrote:
>>>>> 
>>>>> Colleagues,
>>>>> For over a decade I have used the CSIRO program BioLink to curate
>>>> taxonomic, specimen, biogeographic, and bibliographic information.
>>>> CSIRO long ago stopped supporting the program, but I have found it
>>>> useful and
>>> by
>>>> now have committed a great amount of information to the system.  My
>>>> most recent change of computers, however, has got me into Windows
>>>> 10, on which BioLink will not run -- unless I am missing some hack
>>>> that will allow it
>>> to
>>>> do so.
>>>>> Do you have any suggestion for another piece of software that
>>>>> would
>>> work
>>>> for these same tasks?  I back up the BioLink content into a giant
>>>> Excel spreadsheet regularly so the data is literally preserved, but
>>>> this or course does not have the relational aspects of BioLink nor
>>>> its reporting capabilities.  I need to be able to track collection
>>>> specimens (and institutions, or course), with their usual data;
>>>> localities
>>> georeferenced;
>>>> a flexible taxonomy that can be edited (e.g. by drag-and-drop) as
>>>> science marches ahead; references; and pretty much all the types of
>>>> information that practical taxonomy requires us to manage.
>>>>> An alternative that would not require me to enter all my saved
>>>> information piecemeal would be best, of course.
>>>>> All thoughts welcome,
>>>>> Barry
>>>>> 
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>> 
>> Injecting Intellectual Liquidity for 29 years.
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>> Injecting Intellectual Liquidity for 29 years.
> 
> 
> -- 
> ___________________________________________________________________________________
> 
> Dr. Dagmar Triebel
> 
> Head of the IT Center
> Staatliche Naturwissenschaftliche Sammlungen Bayerns
> 
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************************************************
John T. (Jack) Longino
Professor and Associate Chair, Department of Biology
257 S 1400 E, University of Utah
Salt Lake City, UT 84112

Longino Ant Lab at https://sites.google.com/site/longinoantlab/
Project ADMAC at https://sites.google.com/site/admacsite/home















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