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update documentation for species binomials #250

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mbjones opened this issue Mar 12, 2017 · 2 comments
Closed

update documentation for species binomials #250

mbjones opened this issue Mar 12, 2017 · 2 comments

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@mbjones
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@mbjones mbjones commented Mar 12, 2017


Author Name: Margaret O'Brien (Margaret O'Brien)
Original Redmine Issue: 5704, https://projects.ecoinformatics.org/ecoinfo/issues/5704
Original Date: 2012-09-04
Original Assignee: Matt Jones


The EML documentation needs an update to reflect correct practice when including a taxonomic species name. Taxonomically speaking, the 'species name' is a genus and the specific epithet. But looking at it from a strictly hierarchical node structure the specific epithet looks and acts like the other nodes. However a node 'alterniflora' has no taxon rank by itself.

LTER already reccommends this construction in its Best Practices, but actual implementations are inconsistent, perhaps because of the normative documentation.

Another note: The normative docs also seem to refer to "Acer rubrum" as the 'common name' of Red Maple, which is incorrect..

Here is an example of 2 implementations sent to eml-dev (from Wade Sheldon):

with binomial:

Genus Spartina Species Spartina alterniflora

without binomial:

Genus Spartina Species alterniflora

Here is the text from the EML 2.1.1 normative docs:
(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."

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@mbjones mbjones commented Mar 12, 2017


Original Redmine Comment
Author Name: Redmine Admin (Redmine Admin)
Original Date: 2013-03-27T21:31:24Z


Original Bugzilla ID was 5704

@mbjones mbjones added this to the Unspecified milestone Mar 12, 2017
@mbjones mbjones modified the milestones: EML2.2.0, Unspecified Apr 22, 2017
@mbjones mbjones added this to TODO in EML 2.2.0 Release Apr 22, 2017
@mbjones mbjones removed the Category: eml label Jul 24, 2017
@mbjones mbjones moved this from TODO to High priority in EML 2.2.0 Release Oct 3, 2017
@mbjones mbjones added the next label Oct 30, 2017
@mobb mobb added the documentation label Jul 13, 2018
@mobb mobb added in progress and removed next labels Jul 24, 2018
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@mobb mobb commented Aug 16, 2018

The primary issue appears to have been already fixed. here is current text:

            'Acer rubrum' would be an example of a species rank value with the 
            common name of 'Red Maple'. </doc:example>```

I updated 2 things:
1.  added quotes and capitalization to the common name
2. removed the sentence from the example that recommended including all ranks. with the addition of external refs (issue #141), this is no longer necessary - in fact we might want to recommend the opposite. 
mobb added a commit that referenced this issue Aug 16, 2018
@mobb mobb added needs-review and removed in progress labels Aug 16, 2018
@mbjones mbjones closed this Nov 21, 2018
@mbjones mbjones removed the needs-review label Nov 21, 2018
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