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

Thu Apr 24 15:00:07 CDT 2014

Hi Jose,

I don't think you're na?ve at all!  What you describe is very much in line with what I have in mind as well.  Where it becomes a little bit murky is with respect to the issue of static vs. dynamic datasets as I discussed in my previous post.  If an dataset is to be published, and especially if a persistent, actionable identifier (like a DOI) is assigned to it, we need clear standards of practice for what information may change over time (e.g., clearly-denoted additional relevant data that becomes available after the dataset snapshot is "published"), and what is expected to remain unchanged (static).

The model you outline is very much in keeping with our ideas when we started thinking about this notion of data snapshots.  The reality is, all science is dynamic -- and this is particularly true of taxonomy and regional checklists.  There is literally no end to the change (ultimately because evolution keeps happening in the case of organisms, and species change their distributions over time in the case of regional checklists*).  When ink-on-paper was the primary mode of information exchange among scientists, the ink-on-paper documents were, de-facto, the snapshopts.  To find a comprehensive list of species from a particular place (for example), you needed to find the most recent comprehensive published checklist, then find all the subsequent publications that recorded other taxa from the region.  

With online databases, we have the opportunity to keep them very-much alive and dynamic (literally on a minute-by-minute basis).  What we need is a mechanism for citing this sort of information in a simple and straightforward way.

Aloha,
Rich

*Even if you don't believe in "dispersalism", continents still move.....

> -----Original Message-----
> From: Jose Fernandez Triana [mailto:jftriana at uoguelph.ca]
> Sent: Thursday, April 24, 2014 9:09 AM
> To: Richard Pyle
> Cc: Mary Barkworth; Taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] Showing the importance of natural history collections
> and the networks they are building
> 
> Hi all,
> 
> I second most of the ideas mentioned by Richard and would like to briefly
> expand on the possibilities opened by the Biodiversity Data Journal (BDJ). [I
> may be biased in the sense that I am also working on a checklist to be
> published by the BDJ at some point later this year -not on fishes but on
> braconid parasitoid wasps].
> 
> Richard has mentioned some of the advantages of snap-shot result-sets
> directly into a publication. Besides allowing for future updates to be added as
> new publications (new versions of the original checklist, if you want to
> consider), the use of journals such as BDJ would allow for the publication of
> an incomplete(*) set of data now, with the chance of keeping adding new
> info as successive papers/versions of that dataset come in the future. I think
> most of the taxonomic community has not fully realized the potential of
> this... I may not be the best to explain this in an attractive or clear way -but
> will try anyways.
> 
> Here in the Canadian National Collection of Insects (CNC) I have seen many
> colleagues working for years (10, 20 or more years) in compiling lists or
> catalogs of particular groups. The final product ends being published after so
> many years of efforts -but in the meantime, there is nothing available for
> others; and, if something happens to the person doing that work, then the
> whole corpus of knowledge is lost, or mostly. Most of the researchers doing
> that do not want to publish anything too preliminary (it "looks" as poor
> science, or lousy work... should not one strive to do the work on its entirety?
> they would say). Also, there is the delicate point of sharing "too much" and
> then seeing as others take credit for your work...
> 
> But, what if one publishes the information as it is now in this "dynamic style"
> that is now provided/allowed by the BDJ? Then one wins at least five things:
> 1) Sharing with the wider community the information as it is now, so the
> information is less likely to be lost (or become obsolete, as Richard
> mentioned); 2) The author who had that information still gets the credit (and
> "protection" of his/her data in the sense that there is now a published paper
> under his/her authorship); 3) New versions can/will deal with the incomplete
> (or plainly wrong) data that the original paper would have; 4) Publishing such
> a list/catalog would likely encourage others workers in the field to
> add/improve such list/catalog down the road -generally speaking, we have
> seen in this list what happens with some groups...; 5) The data from
> collections, which until that point was sitting mostly unused and
> unappreciated, can now be credited to the particular collection (as Mary
> stated when starting this thread). I see so many positive feedback
> opportunities here! But I may be naive.
> 
> We are more and more immersed in a digital, online universe -either we like
> it or not, it does not really matter. We now see live broadcasts of pretty
> much anything -from scientist space-walking to singers stripping on stage...
> What if we start doing the same with our taxonomic work? (I am NOT
> referring to the stripping part! ;-)
> 
> For example, what if, instead of waiting 15 years -when I would have a more
> complete(*) checklist of braconid wasps- I go now and start sharing what is
> known at the moment? What if collection records are shared (and
> "protected" via publication) as they are gathered, not when the collection is
> fully digitized? What if we start "broadcasting" our taxonomic work on the
> way (and not just when we arrive to the goal)?
> 
> Just some ideas, I am far from being the best voice or the most
> knowledgeable on the topic. But, as a taxonomist, I am ready to embrace
> more of this.
> 
> And I apologize for some digression and unclear sentences above -but have
> no more time now to polish this comment.
> 
> Cheers,
> Jose
> [(*)- By default, there is no complete checklist or catalog! No matter how
> good it is, there will always be things to be added].
> 
> 
> 
> --
> Jos? L. Fern?ndez-Triana, PhD.
> Research Associate, Canadian National Collection of Insects, and Biodiversity
> Institute of Ontario
> 960 Carling Ave, Ottawa, ON, K1A 0C6
> Phone: 613-759-1034 . Email: jftriana at uoguelph.ca ,
> Jose.Fernandez at agr.gc.ca
> http://www.canacoll.org/Hym/Staff/Triana/Triana.htm
> http://cncbraconidae.blogspot.ca/
> 
> 
> 
> ----- Original Message -----
> From: "Richard Pyle" <deepreef at bishopmuseum.org>
> To: "Mary Barkworth" <Mary.Barkworth at usu.edu>,
> Taxacom at mailman.nhm.ku.edu
> Sent: Thursday, April 24, 2014 1:58:35 PM
> Subject: Re: [Taxacom] Showing the importance of natural history collections
> 	and the networks they are building
> 
> 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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> 
> 
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> Celebrating 27 years of Taxacom in 2014.