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

Thu Apr 24 14:19:01 CDT 2014

Surely we can learn from past mistakes and do this properly. Citations are meaningless unless they are counted, and the way to do this efficiently is with identifiers such as DOIs, not developing some arbitrary way of citing databases or datasets. Mint DOIs for collections, mint DOIs for datasets (GBIF is heading down this route), make data a first class citizen by making it trivially easy to cite. Don't moan about people not citing data if you haven't made it easy for them to do so. If you value your data, make it easy to cite - give it a DOI. 

Regards

Rod

Sent from my iPhone

> On 24 Apr 2014, at 19:34, "Richard Pyle" <deepreef at bishopmuseum.org> wrote:
> 
> 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
>> 
>> _______________________________________________
>> Taxacom Mailing List
>> Taxacom at mailman.nhm.ku.edu
>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>> The Taxacom Archive back to 1992 may be searched at:
>> http://taxacom.markmail.org
>> 
>> Celebrating 27 years of Taxacom in 2014.
> 
> 
> _______________________________________________
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> The Taxacom Archive back to 1992 may be searched at: http://taxacom.markmail.org
> 
> Celebrating 27 years of Taxacom in 2014.