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

John Longino jacklongino at gmail.com
Thu Dec 1 11:20:01 CST 2016


I don’t mean to imply that the public are cows. Just following the silage metaphor. In agriculture, cows are valuable and the ultimate purpose.


On Dec 1, 2016, at 10:12 AM, Richard Rabeler <rabeler at umich.edu> wrote:

> Dear John:
> 
> I love the following sentence in your e-mail:  
> 
> "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."
> 
> A great analogy that I will like use (with attribution!!) in the future.
> 
> Sincerely,
> 
> Rich Rabeler, 
> Senior Collection Manager
> Associate Research Scientist
> University of Michigan Herbarium
> 
> On Thu, Dec 1, 2016 at 11:54 AM, John Longino <jacklongino at gmail.com> wrote:
> 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
> >>>>>
> >>>>> _______________________________________________
> >>>>> Taxacom Mailing List
> >>>>> Taxacom at mailman.nhm.ku.edu
> >>>>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fma
> >>>>> ilman.nhm.ku.edu%2Fcgi-bin%2Fmailman%2Flistinfo%2Ftaxacom&data=01%
> >>>>> 7C01%7Cagosti%40amnh.org%7C5b921a9e8a424939b53308d419db4d98%7Cbe00
> >>>>> 03e8c6b9496883aeb34586974b76%7C1&sdata=6GYwtWX2Op82V5yrh%2Bul%2BeS
> >>>>> xRE5ByYrypyzax43qMV8%3D&reserved=0
> >>>>> The Taxacom Archive back to 1992 may be searched at:
> >>>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftaxa
> >>>> com.markmail.org&data=01%7C01%7Cagosti%40amnh.org%7C5b921a9e8a424939
> >>>> b53308d419db4d98%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=QUiIPF
> >>>> F1Jhfs1s9%2Ff0v1DoLScJenNjfO5kj2oRbHtpI%3D&reserved=0
> >>>>> Injecting Intellectual Liquidity for 29 years.
> >>>> _______________________________________________
> >>>> Taxacom Mailing List
> >>>> Taxacom at mailman.nhm.ku.edu
> >>>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmail
> >>>> man.nhm.ku.edu%2Fcgi-bin%2Fmailman%2Flistinfo%2Ftaxacom&data=01%7C01
> >>>> %7Cagosti%40amnh.org%7C5b921a9e8a424939b53308d419db4d98%7Cbe0003e8c6
> >>>> b9496883aeb34586974b76%7C1&sdata=6GYwtWX2Op82V5yrh%2Bul%2BeSxRE5ByYr
> >>>> ypyzax43qMV8%3D&reserved=0 The Taxacom Archive back to 1992 may be
> >>>> searched at:
> >>>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftaxa
> >>>> com.markmail.org&data=01%7C01%7Cagosti%40amnh.org%7C5b921a9e8a424939
> >>>> b53308d419db4d98%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=QUiIPF
> >>>> F1Jhfs1s9%2Ff0v1DoLScJenNjfO5kj2oRbHtpI%3D&reserved=0
> >>>>
> >>>> Injecting Intellectual Liquidity for 29 years.
> >>>>
> >>> _______________________________________________
> >>> Taxacom Mailing List
> >>> Taxacom at mailman.nhm.ku.edu
> >>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmailma
> >>> n.nhm.ku.edu%2Fcgi-bin%2Fmailman%2Flistinfo%2Ftaxacom&data=01%7C01%7Ca
> >>> gosti%40amnh.org%7C5b921a9e8a424939b53308d419db4d98%7Cbe0003e8c6b94968
> >>> 83aeb34586974b76%7C1&sdata=6GYwtWX2Op82V5yrh%2Bul%2BeSxRE5ByYrypyzax43
> >>> qMV8%3D&reserved=0 The Taxacom Archive back to 1992 may be searched
> >>> at:
> >>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftaxaco
> >>> m.markmail.org&data=01%7C01%7Cagosti%40amnh.org%7C5b921a9e8a424939b533
> >>> 08d419db4d98%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=QUiIPFF1Jhfs
> >>> 1s9%2Ff0v1DoLScJenNjfO5kj2oRbHtpI%3D&reserved=0
> >>>
> >>> Injecting Intellectual Liquidity for 29 years.
> >>>
> >> _______________________________________________
> >> Taxacom Mailing List
> >> Taxacom at mailman.nhm.ku.edu
> >> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmailman.nhm.ku.edu%2Fcgi-bin%2Fmailman%2Flistinfo%2Ftaxacom&data=01%7C01%7Cagosti%40amnh.org%7C5b921a9e8a424939b53308d419db4d98%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=6GYwtWX2Op82V5yrh%2Bul%2BeSxRE5ByYrypyzax43qMV8%3D&reserved=0
> >> The Taxacom Archive back to 1992 may be searched at: https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftaxacom.markmail.org&data=01%7C01%7Cagosti%40amnh.org%7C5b921a9e8a424939b53308d419db4d98%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=QUiIPFF1Jhfs1s9%2Ff0v1DoLScJenNjfO5kj2oRbHtpI%3D&reserved=0
> >>
> >> Injecting Intellectual Liquidity for 29 years.
> >> _______________________________________________
> >> Taxacom Mailing List
> >> Taxacom at mailman.nhm.ku.edu
> >> http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> >> The Taxacom Archive back to 1992 may be searched at: http://taxacom.markmail.org
> >>
> >> Injecting Intellectual Liquidity for 29 years.
> >
> >
> > --
> > ___________________________________________________________________________________
> >
> > Dr. Dagmar Triebel
> >
> > Head of the IT Center
> > Staatliche Naturwissenschaftliche Sammlungen Bayerns
> >
> > Senior Curator of Fungi and Algae
> > Botanische Staatssammlung München
> > Menzinger Straße 67
> > 80638 München, Germany
> >
> > Tel   ++49-089-17861-252
> > Fax   ++49-089-17861-193
> > Email triebel at bsm.mwn.de
> >
> > http://www.snsb.info
> > http://www.snsb.info/staff_triebel.html
> >
> > Mailing lists:
> > https://lists.lrz.de/mailman/listinfo/dwb-info  (DWB software updates)
> > https://lists.lrz.de/mailman/listinfo/snsb-dwb-maintenance  (SNSB maintenance work)
> > ___________________________________________________________________________________
> >
> > _______________________________________________
> > Taxacom Mailing List
> > Taxacom at mailman.nhm.ku.edu
> > http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> > The Taxacom Archive back to 1992 may be searched at: http://taxacom.markmail.org
> >
> > Injecting Intellectual Liquidity for 29 years.
> 
> 
> ************************************************
> 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
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> The Taxacom Archive back to 1992 may be searched at: http://taxacom.markmail.org
> 
> Injecting Intellectual Liquidity for 29 years.
> 


************************************************
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















More information about the Taxacom mailing list