[eml-dev] taxonRankValue for species names
Ken Ramsey
kramsey at jornada-vmail.nmsu.edu
Tue Sep 4 10:19:22 PDT 2012
Hi Matt,
Is this what you meant?
<taxonomicClassification>
<taxonRankName>Genus</taxonRankName>
<taxonRankValue>Aristida</taxonRankValue>
<taxonomicClassification>
<taxonRankName>Species</taxonRankName>
<taxonRankValue>Aristida purpurea</taxonRankValue>
</taxonomicClassification>
<taxonomicClassification>
<taxonRankName>Subspecies</taxonRankName>
<taxonRankValue>Aristida purpurea var. nealleyi</taxonRankValue>
</taxonomicClassification>
</taxonomicClassification>
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
-------------------------------
>>> Matt Jones <jones at nceas.ucsb.edu> 9/4/2012 10:21 AM >>>
Add it in at the subspecies rank level.
Matt
On Tue, Sep 4, 2012 at 8:18 AM, Ken Ramsey
<kramsey at jornada-vmail.nmsu.edu>wrote:
> 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
> >>
> >>
> >> _______________________________________________
> >> Eml-dev mailing list
> >> Eml-dev at ecoinformatics.org
> >> http://lists.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/eml-dev
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