[eml-dev] taxonRankValue for species names

[Ken Ramsey]

Hi Everyone,

How would you deal with varieties or sub-species (e.g., Aristida purpurea var. nealleyi)? 

Ken




-------------------------------
Ken Ramsey
Data Manager
Jornada LTER Project
New Mexico State University
2995 Knox Street, suite 200
Box 30003, MSC 3JER
Las Cruces, NM 88003
(575)646-7918 (office)
(575)646-5889 (fax)
kramsey at jornada-vmail.nmsu.edu
-------------------------------
>>> Margaret O'Brien <mob at msi.ucsb.edu> 9/4/2012 9:46 AM >>>
Hi Wade -
I agree with James.
For your code (and assuming it is for use with LTER datasets), I would 
assume that the input conforms to our Best Practices. Code that can 
detect the difference between the species binomial and the species 
fragment is a friendly touch, but I think that looking for a space 
character might be a little unreliable. One could also argue that 
accommodating bad practice is not a particularly good idea (despite 
what's in the normative docs), but that is a somewhat unpopular point of 
view.

There are many areas where the normative docs are not quite in line with 
best practices. I will enter your email in as a bug so that it can be 
fixed in some future release.

Margaret

-----------
Margaret O'Brien
Information Management
Santa Barbara Coastal LTER
Marine Science Institute, UCSB
Santa Barbara, CA 93106
805-893-2071 (voice)
http://sbc.lternet.edu 

On 9/3/12 8:47 PM, James Brunt wrote:
> I was taught - admittedly long ago - that, taxonomically speaking, the
> 'species name' must include the genus and the specific epithet. While
> looking at it from a strictly hierarchical node structure the specific
> epithet looks and acts like the other nodes. However, taxonomically the
> node 'alterniflora' has no taxon rank by itself. I guess I'd prefer to
> see the binomial 'species name' concept retained in our metadata if
> there is no confounding reason why it shouldn't be so.
>
> The is also a mistake in the normative docs if they are referring to
> Acer rubrum as the 'common name' of Red Maple.
>
> My two bits.
>
> James
>
> James W. Brunt
> Chief Information Officer
> Long Term Ecological Research Network
> LTER Network Office
> Department of Biology MSC03 2020
> 1 University of New Mexico
> Albuquerque, NM 87131-0001
> 505 277 2535
> jbrunt at LTERnet.edu 
> OpenPGP-Id: 1024D/4E657C39
>
> On 9/3/2012 10:51 AM, Wade Sheldon wrote:
>> Hi folks,
>>
>> I've been working on an XSL that extracts selected content from an EML
>> document to annotate parsed data sets in MATLAB, and I came across some
>> inconsistencies in encoding of taxonomicCoverage elements for species
>> names from different EML implementers. Specifically, some authors use
>> the species binomial, and some do not, i.e.
>>
>> with binomial:
>>
>> <taxonomicClassification>
>>     <taxonRankName>Genus</taxonRankName>
>>     <taxonRankValue>Spartina</taxonRankValue>
>>     <taxonomicClassification>
>>        <taxonRankName>Species</taxonRankName>
>>        <taxonRankValue>Spartina alterniflora</taxonRankValue>
>>     </taxonomicClassification>
>> </taxonomicClassification>
>>
>> vs.
>>
>> without binomial:
>>
>> <taxonomicClassification>
>>     <taxonRankName>Genus</taxonRankName>
>>     <taxonRankValue>Spartina</taxonRankValue>
>>     <taxonomicClassification>
>>        <taxonRankName>Species</taxonRankName>
>>        <taxonRankValue>alterniflora</taxonRankValue>
>>     </taxonomicClassification>
>> </taxonomicClassification>
>>
>>
>> When I first started producing EML back in 2003 I used the species name
>> without genus, but Matt Jones and Dan Higgins suggested I use the
>> species binomial instead. We also included that recommendation in the
>> LTER EML best practices
>> (http://im.lternet.edu/sites/im.lternet.edu/files/emlbestpractices-2.0-FINAL-20110801_0.pdf).
>>
>>
>> However, the normative docs for EML 2.1.1
>> (http://knb.ecoinformatics.org/software/eml/eml-2.1.1/eml-coverage.html)
>> seem to suggest the opposite approach:
>>
>> "The name representing the taxonomic rank of the taxon being described.
>> The values included may be referenced from an authoritative source such
>> as the Integrated Taxonomic Information System (ITIS)in the U.S.
>> (http://www/itis.usda.gov) and in Canada
>> (http://sis.agr.gc.ca/pls/itisca/taxaget). Also, Species2000 is another
>> source of taxonomic information, found at (http://www.sp2000.org)
>> Example(s):
>> Acer would be an example of a genus rank value, and rubrum would be an
>> example of a species rank value, together indicating the common name of
>> red maple. It is recommended to start with Kingdom and include ranks
>> down to the most detailed level possible."
>>
>> For now I'm revising the XSL to check for species-only using a contains
>> node test on a space character, but handling both cases is a pain
>> considering the nesting, so it would be better to standardize on one
>> approach.
>>
>> Thoughts?
>>
>> Wade Sheldon
>> GCE-LTER
>>
>>
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