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Bug #2210

Displaying taxonomic information imported from table

Added by Veronique Connolly about 15 years ago. Updated almost 8 years ago.

Status:
Resolved
Priority:
Normal
Assignee:
Category:
morpho - general
Target version:
Start date:
09/28/2005
Due date:
% Done:

0%

Estimated time:
Bugzilla-Id:
2210

Description

When you import taxonomic information from several columns of a table, the
information displayed in the data package is in alphabetical order rather than
in taxonomic rank order. For example, if the table you are importing info from
has one column that contains the genus name and another column the species
epithet, what will be displayed in the data package is a list of the genus names
and species epithets in alphabetical order (even though you selected "genus" as
the taxon category for the 1st column and "species" for the 2nd column). This
kind of list wouldn't make sense since for a given species, the genus name and
the species epithet would be separated.

When you use the NDPW to provide taxonomic info, if you enter text under the
"Name" columns for Rank = Genus and for Rank = Species, what gets displayed in
the data package is the genus name followed by the species epithet. This is the
way it should appear when you import taxonomic info from a table.

History

#1 Updated by Matt Jones about 15 years ago

I think there is a fundamental misunderstanding about the use of the EML
taxonomicCoverage fields here that is leading to this problem in how Morpho is
importing the taxon information. In EML (and the BDP, as they are the same), a
Genus or higher level value in the taxonRankValue field should be a monomial,
while a Species-level rank should ALWAYS be at least a binomial. For example...

For Genus Ursus, you should have:
<taxonRankName>Genus</taxonRankName>
<taxonRankValue>Ursus</taxonRankValue>

For Species Ursus arctos you have:
<taxonRankName>Species</taxonRankName>
<taxonRankValue>Ursus arctos</taxonRankValue>

Note how it is a binomial!

So the following construct is NOT VALID in EML because the species value is not
a binomial:
<taxonomicClassification>
<taxonRankName>Genus</taxonRankName>
<taxonRankValue>Ursus</taxonRankValue>
</taxonomicClassification>
<taxonomicClassification>
<taxonRankName>Species</taxonRankName>
<taxonRankValue>arctos</taxonRankValue>
</taxonomicClassification>

In Morpho, when we are importing taxonomic data from a table, a 'Genus' column
can be imported into taxonRankValue fields as a monomial, but it is not right to
import the monomial 'arctos' value from a column into a Species rank. Instead,
we need to concatenate the Genus and species info from the two columns and put
the concatenated value into the taxonRankValue field.

This example in the BDP shows this doen correctly, but the EML spec gives a
misleading example and should probably be corrected and be more specific about
how to handle species binomials and trinomials, etc.

#2 Updated by ben leinfelder almost 8 years ago

I am updating the EML documentation (embedded in the eml-coverage.xsd source) to use species binomial in the red maple example:

'Acer' would be an example of a genus rank value, and 'Acer rubrum' would be an example of a species rank value with the common name of red maple.

#3 Updated by Redmine Admin over 7 years ago

Original Bugzilla ID was 2210

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