[eml-dev] taxonRankValue for species names
Ken Ramsey
kramsey at jornada-vmail.nmsu.edu
Tue Sep 4 11:29:04 PDT 2012
Hi Matt,
That is what I was trying to get at.
I can see the value of using only the variety name (<taxonRankValue>var. nealleyi</taxonRankValue>), but it seems to have the same problem mentioned previously regarding the use of a binomial instead of only the species. By extension of the binomial discussion, shouldn't we specify the rank value for the subspecies as follows?
<taxonRankValue>Aristida purpurea var. nealleyi</taxonRankValue>
I cannot speak to the differences between using the term variety or subspecies for the rank name. Personally, I think we should choose one and stick with it until a better alternative presents itself.
I agree there are similar problems with authorities which we (Jornada LTER) typically include within our site species list. ITIS links the name of the genus, species, and variety to the taxonomic reference that displays the scientific name including the authority which is itself a link to a listing of other species using that authority. I assume this is to avoid issues relating to changes in species authorities over time.
I think we should recommend that within EML. the rank value (Aristida, Aristida purpurea, Aristida purpurea var. nealleyi) be included without authority and that the specificity would be determined by the rank name (Genus = Aristida, Species = Aristida purpurea, Subspecies = 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
-------------------------------
>>> Matt Jones <jones at nceas.ucsb.edu> 9/4/2012 11:32 AM >>>
Almost. The nesting wasn't quite right. It should be:
<taxonomicClassification>
<taxonRankName>Genus</taxonRankName>
<taxonRankValue>Aristida</taxonRankValue>
<taxonomicClassification>
<taxonRankName>Species</taxonRankName>
<taxonRankValue>Aristida purpurea</taxonRankValue>
<taxonomicClassification>
<taxonRankName>Subspecies</taxonRankName>
<taxonRankValue>Aristida purpurea var. nealleyi</taxonRankValue>
</taxonomicClassification>
</taxonomicClassification>
</taxonomicClassification>
Of course, this then begs the question as to what the proper rank is, and
whether the subspecies/variant should include the species binomial or not,
and whether it should include the 'var.'. Folks over on TDWG argue about
this (and authority name strings) incessantly.
For the rank, should it be "Subspecies" or "Vairant"?
For the variant rank value, should it be:
<taxonRankValue>Aristida purpurea var. nealleyi</taxonRankValue>
or
<taxonRankValue>nealleyi</taxonRankValue>
or
<taxonRankValue>var. nealleyi</taxonRankValue>
Matt
On Tue, Sep 4, 2012 at 9:19 AM, Ken Ramsey
<kramsey at jornada-vmail.nmsu.edu>wrote:
> 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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