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task #7369

closed

Handle taxonomically valueless taxa correctly

Added by Andreas Müller over 3 years ago. Updated 4 months ago.

Status:
Closed
Priority:
Priority13
Category:
cdmadapter
Target version:
Start date:
04/25/2018
Due date:
% Done:

100%

Estimated time:
0.50 h
Severity:
normal
Tags:

Description

Currently 268 taxa in E+M have an IsExcludedMarker with IsExcludedExtension "not accepted: taxonomically valueless local or singular biotype" or "provisional: probably a taxonomically valueless local or singular biotype"

In the BM dataportal this is shown as the taxon status (e.g. http://ww2.bgbm.org/EuroPlusMed/PTaxonDetail.asp?NameCache=Rubus%20trachyadenes&PTRefFk=7300000 ).

These taxa do not have parent taxa.

We need to decide how to store this information.

Solutions:

1) Adding 2 marker types and the information as markers
2) Using extensions or annotations with the given full text
3) extend the doubtful flag to an enumeration to allow multiple states like "doubtful","taxonomically valueless","probably taxonomically valueless", ...

Also we need to decide if these taxa should be included in the taxon tree somehow.

Currently only those taxa having synonyms or misapplied names are attached to the tree (as root taxa) - need to check why.

taxa in BM

SELECT  n.FullNameCache,  pt.*
FROM  PTaxon AS pt INNER JOIN Name n ON n.NameId = pt.PTNameFk
WHERE (pt.IsExcludedExtension IS NOT NULL) OR (pt.IsExcludedMarker = 1)
ORDER BY pt.IsExcludedExtension

Note: These taxa may have synonyms and 1x even a misapplied name

SELECT  acc.FullNameCache, syn.FullNameCache syn,  rel.RelPTaxonId, rel.RelQualifierFk, pt.PTNameFk, pt.PTRefFk, pt.Detail, pt.RIdentifier, pt.IdInSource, pt.StatusFk, pt.DoubtfulFlag, pt.NamePhrase, pt.UseNameCacheFlag, pt.Created_When, pt.Updated_When, 
                         pt.Created_Who, pt.Updated_Who, pt.Notes, pt.PublishFlag, pt.TreeIndex, pt.IndexNameString, pt.InMCLArea, pt.FamilyCache, pt.LastScrutinyFk, pt.SpeciesExpertFk, pt.IsExcludedMarker, pt.IsExcludedExtension, 
                         pt.UUID
FROM            PTaxon AS pt INNER JOIN
                         RelPTaxon AS rel ON rel.PTNameFk2 = pt.PTNameFk AND rel.PTRefFk2 = pt.PTRefFk
                         INNER JOIN Name syn ON syn.NameID = rel.PTNameFk1
                         INNER JOIN Name acc ON acc.NameId = rel.PTNameFk2
WHERE  (pt.IsExcludedExtension IS NOT NULL) OR (pt.IsExcludedMarker = 1)
ORDER BY pt.IsExcludedExtension, acc.FullNameCache

In the publication script they are all set to publish = 1

Also have in mind that they need to be exported to PESI.


Related issues

Precedes Edit - feature request #8285: Handle taxonomically valueless taxa in data portalNewAndreas Kohlbecker04/26/201804/26/2018

Actions
Actions #1

Updated by Andreas Müller over 3 years ago

  • Description updated (diff)
Actions #2

Updated by Andreas Müller over 3 years ago

  • Description updated (diff)
Actions #3

Updated by Andreas Müller over 3 years ago

  • Description updated (diff)
Actions #4

Updated by Andreas Müller over 3 years ago

first implementation with markers now available

Actions #5

Updated by Andreas Müller over 3 years ago

  • Status changed from New to In Progress
  • Priority changed from New to Highest
  • % Done changed from 0 to 40
Actions #6

Updated by Andreas Müller over 3 years ago

  • Estimated time set to 2.00 h
Actions #7

Updated by Andreas Müller over 3 years ago

  • Description updated (diff)
Actions #8

Updated by Andreas Müller over 3 years ago

  • Description updated (diff)
Actions #9

Updated by Andreas Müller over 3 years ago

  • Description updated (diff)
Actions #11

Updated by Andreas Müller over 3 years ago

  • Description updated (diff)
Actions #12

Updated by Andreas Müller over 3 years ago

  • Target version changed from Euro+Med Portal Release to Euro+Med Migration
Actions #13

Updated by Andreas Müller over 3 years ago

  • Description updated (diff)
Actions #14

Updated by Andreas Müller over 3 years ago

  • Subject changed from [E+M] Handle taxonomically valueless taxa correctly to ERS: Handle taxonomically valueless taxa correctly
  • Priority changed from Highest to Priority13
Actions #15

Updated by Andreas Müller over 3 years ago

ERS (2015-08-15):

zum Thema Rubus lässt sich sagen:

die 19 Taxa, die im Baum direkt unter Plantae included sind (so sieht es jedenfalls aus), gehören zu einer Gruppe von insgesamt 232 Rubus-Taxa. Die anderen scheinen als orphaned importiert worden zu sein, warum diese 19 nicht orphaned sind, verstehe ich nicht. Ich sehe keinen Unterschied zu den anderen Rubus dieser Gruppe.

Hintergrund: diese Taxa sollen zwar über die Suche gefunden werden, aber nicht Bestandteil des Taxon Tree sein, also über das Browsen nicht zu finden sein. So ist es im Berlin-Model implementiert: Diese Arten haben keine Eltern, sondern hängen "in der Luft", sind aber akzeptiert. Wenn man also im Portal danach sucht, erhält man den Namen und die Verbreitung angezeigt, zusammen mit der Nachricht NOT ACCEPTED: TAXONOMICALLY VALUELESS LOCAL OR SINGULAR BIOTYPE

etwa Rubus abietinus Sudre http://ww2.bgbm.org/EuroPlusMed/PTaxonDetail.asp?NameCache=Rubus%20abietinus&PTRefFk=7300000

Wenn ich es richtig verstehe, werden ja orphaned taxa im CDM eigentlich nicht unterstützt, oder? Jedenfalls kann man sie mit dem EDITor zwar finden, aber nicht editieren (da erhält man eine Fehlermeldung). Insofern ist die jetzt für die 19 Taxa implementierte Lösung, sie allesamt direkt unter Plantae zu hängen, gar nicht so schlecht, denn sie sollen eben nicht neben den anderen Rubus-Taxa stehen. Jedenfalls wüsste ich nicht, was man sonst mit ihnen machen soll. Eventuell kann man sie innerhalb der Plantae unter eine Zwischenstufe hängen wie "Rubus biotypes" oder so ähnlich.

Actions #16

Updated by Andreas Müller over 2 years ago

Actions #17

Updated by Andreas Müller over 2 years ago

  • Tags changed from euro+med to euro+med, pesi
  • Subject changed from ERS: Handle taxonomically valueless taxa correctly to Handle taxonomically valueless taxa correctly
  • Status changed from In Progress to Resolved
  • % Done changed from 40 to 90
  • Estimated time changed from 2.00 h to 0.50 h

The taxa are now all exported to a common root taxon "Valueless". They can be moved somewhere else after import if necessary.

We still need to implement how they should show up in the data portal.

Actions #18

Updated by Andreas Müller 4 months ago

  • Status changed from Resolved to Closed
  • % Done changed from 90 to 100

An example for a "valueless" taxon in CDM is https://www.europlusmed.org/cdm_dataportal/taxon/6a572ecd-f989-44a2-96ce-54d8141b3c0d.

Final work needs to be done in dataportal, handled by #8285

Actions

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