Test implementation of eml-based species lists for LTER

Matt Jones jones at nceas.ucsb.edu
Tue Apr 13 12:46:43 PDT 2004 

Hi Rich,

Yeah, that is accepted practice for EML.  It derived from the same 
practice which was established for this same set of fields for the NBII 
Biological Data Profile (BDP).  Feedback for the said that the species 
part of a binomial epithet is *never* written without the genus part of 
the binomial, and the subspecies part is *never* written without the 
species and genus part.  A number of established taxonomists objected 
strongly to having a field for species which did not include the Genus, 
even though the Genus was above it in a field. Soo...the Biological Data 
WOrking Group agreed to modify the BDP to require that the Species rank 
include the whole binomial, and that Subspecies rank includes the whole 
trinomial.

EML strives to be compatible with the BDP, so we simply adopted there 
conventions, although not without substantial debate over about a year. 
  Nevertheless, I think it is a poor design, but I kind of feel stuck 
with it.  Maybe if everyone using EML were to agree that it could or 
should be just a monomial, then we could change it in a future version 
of EML (we can of course generate the needed binomials and trinomials 
from the individual components as needed to generate BDP metadata. 
Comments appreciated.

Matt

Rich Williams wrote:
> 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
>>-------------------------------------------------------------------
>>_______________________________________________
>>eml-dev mailing list
>>eml-dev at ecoinformatics.org
>>http://www.ecoinformatics.org/mailman/listinfo/eml-dev

-- 
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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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