[Taxacom] Showing the importance of natural history collections and the networks they are building

[Richard Pyle]

Hi Mary,

I have LONG supported this notion.  One of the problems, though, is that
very few databases allow future users to see what the database contained on
the date on which it was accessed.  In an ideal world, all online databases
would include a parameter "asOfDate" or something similar, where users can
pass in a particular date and see what the database consisted of as of that
date.  For some systems (which maintain robust edit logs or "audit trails",
or maintain explicit versioning), it would be possible to do this; but for
many systems it would not.

Recognizing this issue, about ten years ago we conceived of a system where
users of our online databases could select an option to "publish" a full
snapshot of the query results they examined.  The idea would be for a user
to construct a query of the database and get a result-set back, then upon
deciding that this result-set is the one to be cited, there would be a
button that "published" the result set as an XML file (which could be
represented as a styled PDF or converted to Excel, complete with its own
title, authorship [jointly the person constructing the query, and the
database owner], full data set, and its own "references" section that cited
the original sources of the data).  This XML file would then be permanently
archived for future access, and would be the digital object cited in the
work for which it was generated.

We never followed through with the development of that concept (budget
issues, different priorities, etc.); but there may yet be some value in
doing it.  For example, perhaps there could be an automated system that
allowed users of online databases to snap-shot result-sets directly into a
publication venue such as the Biodiversity Data Journal.

Speaking of that journal, we are planning to publish a regional checklist
(fishes of the Northwestern Hawaiian Islands) in BDJ that changes the way
such regional checklists are created.  Basically, we build an evidence-based
checklist of occurrence records for within-scope taxa at within-scope
region, and store this in a database.  The checklist is annotated and
curated by the authors, who vet all the data, flag dubious records, confirm
taxonomic identifications, etc.  The checklist is then published in a highly
structured form (ala BDJ), with a link back to the database.  The link would
then go to a page that displays everything as it appeared in the published
version, as well as all data that were altered or added since the moment of
publication.  The "vetted" (published) records would be formatted clearly to
distinguish from all the un-vetted, "raw" data that became available
following the publication.  That way people who come to that website could
see the full content of what was published, *AND* all of the new information
that has become available since the time it was published.  Eventually, when
there is enough new information, it would be vetted again and a new-snapshot
generated and published (in the form of a "revised" checklist, or
new-records paper, or whatever).  The idea is to be able to clearly show the
full dataset as it was snapshot-published, and also give acces to
up-to-the-moment additional data; thus avoiding the current problem with
regional checklists, which is that they become obsolete the moment they are
published.

In any case, I fully support the idea of more consistent and deliberate
citation of online data systems in the "references" section of publications,
and I'd like to see us move even beyond that to a standard system that
allows people to immediately compare what was available at the time the
dataset was cited to what is currently in the dataset now.

Aloha,
Rich

> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Mary Barkworth
> Sent: Thursday, April 24, 2014 6:49 AM
> To: (Taxacom at mailman.nhm.ku.edu)
> Subject: [Taxacom] Showing the importance of natural history collections
and
> the networks they are building
> 
> The other day I reviewed a paper that stated it drew information from lots
of
> databases and networks but to find out which one had to go to the authors'
> web site and click on a pull-down list. That started me thinking of how to
get
> more recognition for collections, databases, and networks.
> Suggestion: Collections, databases, and networks that contributed
> significantly to development of any paper, poster, pamphlet, report etc.
> should be cited in the references section (the old "Literature cited"
section).
> We should do this ourselves, ask other authors to do so when reviewing
> papers, and promote the idea at meetings we go to in which people make
> use of collections data - whether of environmental consultants,
politicians, or
> ecologists. Having collections and networks (and floras consulted too)
listed
> in the reference section would mean that publishers will start marking
them
> up and search engines may find them, all of which would, I suspect, make
it
> easier to show how fundamental collections and networks are to today's
> research.  Below I have some suggested formats for networks that I use.
> 1.       SEINet Network. 2014+. Provider of records from over 60 US
herbaria.
> Accessed via http://ngpherbaria.org<http://ngpherbaria.org/>, 23 April
2014.
> 2.       NGPHerbaria.org. 2014+. Portal to records from over 60 US
herbaria.
> Accessed via http://ngpherbaria.org<http://ngpherbaria.org/>, 23 April
2014.
> 3.       Intermountainbiota.org. 2014+. For records to herbaria of Utah
State
> University's campuses. Accessed via
> http<http://ngpherbaria.org/>://intermountainbiota.org<http://ngpherbari
> a.org/>, 23 April 2014.
> 4.       BHSC. 2014+. Records from the herbarium of Black Hills State
University.
> Accessed via http://swbiodiversity.org/, 23 April 2014
> 5.       Intermountain Herbarium. 2014+. Records from the herbarium of
Utah
> State University, Logan Campus. Accessed via https://www.idigbio.org/ 23
> April 2014
> Logically, one could also ask to see herbaria from which one borrowed
> specimens listed in the References cited rather than (or in addition to)
> acknowledgments.
> I am a plant person. I would think that the same approach would serve
other
> natural history collections and networks but perhaps not.
> Comments welcome.
> Mary
> 
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