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Taxonomy Fixes #655

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@jwaspin jwaspin commented Feb 21, 2024

  • Code formatting
  • app/services/itis.js added taxonAuthor and updateDate to itis response object
  • app/pods/components/object/md-taxonomy/collection/template.hbs added Identification References and changes Voucher to Vouchers since it's an array and removed modifications from system list
  • app/pods/components/object/md-taxonomy/collection/system/template.hbs wrapped citation in Classification Authority and reordered Modifications after Classification Authority
  • app/pods/components/object/md-taxonomy/collection/system/preview/template.hbs removed Modifications from system list preview
  • app/pods/components/control/md-itis/template.hbs added taxonAuthor and updateDate to the results description

Moving to v1.4.0
Add 'Classification Authority' wrapper.
Reorder 'Modifications' to come after 'Classification Authority'.
@jwaspin jwaspin linked an issue Feb 21, 2024 that may be closed by this pull request
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@jwaspin jwaspin marked this pull request as ready for review March 28, 2024 21:01
@jwaspin jwaspin requested a review from hmaier-fws March 28, 2024 21:04
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@jwaspin I think we're going to have to do a bit of fine tuning before merging this in.

@dwalt there were a few things that I saw as potentially being vague in the ITIS species information that is displayed by http://23.23.4.125:8001/. The two things I noticed with the displayed species information are:

  • Updated: date
    • This is actually the date that the ITIS record was last modified. It has no bearing on information related to the species naming or classification. In the case of "Viburnum nudum" this is actually the date when the ITIS record was updated to reflect that the "jurisdictionalOriginList" was updated to indicate that the plant is native to Canada. I recommend that we either rename this field to "Last ITIS update" (or something similar), or delete it. I'm OK with any of those options.
  • Classifier: taxonAuthor
    • When I first saw this I wasn't really sure what it was (I once worked with a plant Taxonomist to build an Arctic species database and was indoctrinated into the world of taxonomy and systematics). As I mentioned in a comment to issue Taxonomy ITIS Species Classifier #529, species names (nomenclature) are not the same as species classification (taxonomy). For example, Viburnum nudum is currently "classified" within the Family "Adoxaceae", however, it was previously "classified" under the "Caprifoliaceae" family. The entire Genus was reclassified, but the taxonomic authority (author) remained the same. I recommend that we just call this "Taxon Author" to align with general convention and the ITIS usage.

And if we're going to make changes, I would also recommend that we update the placeholder text for the "modifications" box (see #528) to use the actual definition for the "Classification_System_Modifications" from the Content Standard for Digital Geospatial Metadata Part 1: Biological Data Profile which defines the attribute as "A description of any modifications or exceptions made to the classification system or authority used." (p. 1-22).

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dwalt commented Apr 4, 2024

@hmaier-fws
Date: In my testing on Pacific Walrus, I got two dates: 1815, type=adopted description=Illiger; 2024-4-3 type=transmitted description=Taxa imported from ITIS. This is what I would have expected and is a successful data retrieve in my opinion. I acknowledge there is history of reclassification that is way too convoluted to cite. My thought was to cite the original classifier and leave it at that. I think this is what you meant by Taxon Author, but please confirm.

Modifications: Technically it would be in better alignment with the standard that defined Taxonomy for metadata, I would concede. But, in the interest of clarity for authors, I find the FGDC usage unclear and limiting. In use I have seen an interest to cite an ornithology authority in addition to ITIS because it has identified a recent classification change that ITIS has not yet accepted due to their backlog. Another use case is a novel sub-species not yet accepted by an authority. The FGDC definition does not really cover these cases, and are judgements made by the observer.

@jwaspin jwaspin marked this pull request as draft April 15, 2024 22:52
@jwaspin jwaspin marked this pull request as ready for review April 16, 2024 15:14
@jwaspin jwaspin marked this pull request as draft May 7, 2024 21:01
@jwaspin jwaspin changed the base branch from develop to fix/677-fix-data-quality May 17, 2024 17:29
@jwaspin jwaspin deleted the branch fix/677-fix-data-quality July 3, 2024 00:08
@jwaspin jwaspin closed this Jul 3, 2024
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Taxonomy ITIS Species Classifier Taxonomy Modifications
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