Test implementation of eml-based species lists for LTER

[Rich Williams]

I'm curious about the specification of a two-part scientific name in the
species element (or more correctly in the taxonRankValue of the
taxonomicClassification element with taxonRankName of Species).  Is this
standard practice for EML?  I was expecting to just see the species name in
there, and not see the Genus value duplicated.  If the species always
actually contains a two-part scientific name, is there then a requirement
that the first word of the species be equal to the genus, is the genus is
present?

Rich

> -----Original Message-----
> From: eml-dev-admin at ecoinformatics.org
> [mailto:eml-dev-admin at ecoinformatics.org]On Behalf Of Matt Jones
> Sent: Tuesday, April 13, 2004 12:05 PM
> To: Wade Sheldon
> Cc: James Brunt; eml-dev at ecoinformatics.org
> Subject: Re: Test implementation of eml-based species lists for LTER
>
>
> Wade,
>
> Looks great.  You're on the leading edge yet again :)  I think using EML
> to exchange this sort of information is a great idea.  It would also be
> good to do the literature citation information this way because once
> people get used to exchanging EML it should be easy to implement.
>
> A couple of comments about the taxonomic EML you generated:
>
> 1) When you list several taxa that share parent taxa (e.g., they are in
> the same Class), we had intended that you could nest two subtrees
> underneath the last identical rank, so that the EML representation is
> more compact.  This means, for example, that many species would be
> clustered in each genus, many genera in each family, etc up the tree.
> The only reason that I can see to separate them is if different
> taxonomicClassification systems apply (e.g., a different authority was
> used for identifications, circumscriptions, or names), and then they
> should be in different taxonomicCoverage elements.  But if they were all
> identified using the same system, then creating one tree instead of many
> I think is better.  Are there reasons you did it as you did?
>
> 2) You didn't include a taxonomicSystem element.  Although optional, I
> think this is a very important element.  It lets the user understand how
> you did identifications, and provides citations for field guides,
> taxonomic mongraphs, etc. that were used in identifying and classifying
> the organisms.  The more people do synthetic work, the more important
> this information is.  Bob Morris wrote an interesting email about the
> pitfalls of species lists to the seek-taxon list that you might find
> useful and interesting.  It was part of a larger thread where we were
> discussing species lists in general and their utility over the long
> term, especially with regard to species names versus species concepts.
> Here's the links that I think are most relevant:
>
> Species lists:
> http://www.ecoinformatics.org/pipermail/seek-taxon/2004-March/000160.html
>
> and the background for that email:
> http://www.ecoinformatics.org/pipermail/seek-taxon/2004-March/000159.html
>
> Thanks again, Wade.
>
> Matt
>
>
> Wade Sheldon wrote:
> > Matt and James,
> >
> > This week I have been making some changes to how we display taxonomic
> > records on the web. As part of this process, I decided to spend
> a little
> > time following through on a proposal I made during our last IMExec
> > meeting to test eml as a format for dissemination of species lists
> > within LTER. As a candidate document style I "trumped up" a
> species list
> > data set containing the species list in taxonomicCoverage format, with
> > appropriate title, abstract, keywords, project descriptors, etc.
> > relevant to the purpose. I also included temporalCoverage information
> > indicating the date the list was generated.
> >
> > If you are interested in looking over my test implementation, you can
> > generate various species lists in eml format using the web forms at:
> > http://gce-lter.marsci.uga.edu/lter/asp/db/all_species_lists.asp
> >
> > I don't currently plan to maintain versioned copies of the species list
> > (or sub-lists) in our site data catalog, so the packageID
> information is
> > basically notional; however, we could certainly do so at some point if
> > there were interest so I left it in. I am primarily throwing
> this out as
> > a candidate schema for cross-site exchange of taxonomic information. We
> > will be working on a "eml best practices" document for LTER in the next
> > 1-2 months, and I thought it would be good to consider recommendations
> > for documentation of non-tabular data as well as conventional tabular
> > data sets. Exchange/submission of bibliographic citations and personnel
> > lists are other potential uses of eml we discussed.
> >
> > Comments or recommendations would be appreciated.
> >
> > --Wade Sheldon, GCE
>
> --
> -------------------------------------------------------------------
> Matt Jones                                     jones at nceas.ucsb.edu
> http://www.nceas.ucsb.edu/    Fax: 425-920-2439    Ph: 907-789-0496
> National Center for Ecological Analysis and Synthesis (NCEAS)
> University of California Santa Barbara
> Interested in ecological informatics? http://www.ecoinformatics.org
> -------------------------------------------------------------------
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