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feature request #8180

Add property term "Presence/Absence" to CDM default terms

Added by Patrick Plitzner 7 months ago. Updated about 2 months ago.

Status:
Closed
Priority:
Highest
Category:
cdm
Target version:
Start date:
03/15/2019
Due date:
% Done:

100%

Severity:
normal
Tags:

Description

When describing a specimen via Characters (almost) all structures may or may not exist. To be able to describe if a structure is missing we can create a Character consisting of the respective structure combined with the "Presence/Absence" property.

The property is categorical allowing 2 states: present/absent

These states should also be added to the CDM default terms

Note: In the additivity ontology CDM data base we already imported those terms from the TDWG terms wiki:

So this ticket may be seen as obsolete if we do not want to add those terms to the default terms.


Related issues

Blocks Edit - feature request #8178: Auto-create absence/presence character for every structure Rejected 03/14/2019

Associated revisions

Revision b0a48ddf (diff)
Added by Andreas Müller about 2 months ago

ref #8180 Add Presence state vocabulary to default terms

Revision 749e8fb4 (diff)
Added by Andreas Müller about 2 months ago

ref #8180 Add vocabulary to test data

Revision 03335762 (diff)
Added by Andreas Müller about 2 months ago

ref #8180 fix incorrect UUID in test data

Revision 0a788123 (diff)
Added by Andreas Müller about 2 months ago

ref #8180 ... and update test data in other projects

Revision b3fbf38e (diff)
Added by Andreas Müller about 2 months ago

ref #8180 ... and again try to fix the test data

History

#1 Updated by Patrick Plitzner 7 months ago

#2 Updated by Andreas Müller 7 months ago

  • Status changed from New to In Progress
  • Priority changed from New to Highest

#3 Updated by Andreas Müller 6 months ago

  • Target version changed from Release 5.6 to Release 5.7

#4 Updated by Andreas Müller 6 months ago

  • Target version changed from Release 5.7 to Release 5.8

#5 Updated by Andreas Müller 3 months ago

  • Target version changed from Release 5.8 to Release 5.9

#6 Updated by Patrick Plitzner 3 months ago

  • Description updated (diff)
  • Status changed from In Progress to Feedback

#7 Updated by Andreas Müller 3 months ago

Hallo,

ich sehe gerade das folgende Terme doppelt vorkommen in der Ontologie:

"REPLACE (uri, 'https://terms.tdwg.org/wiki/ft:','')"
"absent"
"aestivation"
"aging"
"divisions"
"False"
"folding"
"generative"
"presence"
"present"
"series"
"smell"
"vernation"

Gibt es dafür einen Grund? Ich halte es für problematisch, wenn Terme mit gleichem Identifier (URI) in unterschiedlichen Vokabularen gespeichert werden. Da stimmt dann tendenziell was nicht. Allerdings müssen wir in diesem Zusammenhang vielleicht nochmal besprechen, was unsere Vokabulare in diesem Fall für eine Semantik haben.

Das scheint mir sogar eine sehr grunsätzliche Frage im Bezug auf Terme, die aus externen Vokabularen kommen. Es ist noch ungeklärt, was wir machen, wenn wir nur einzelne Terme aus solchen Vokabularen ins CDM übernehmen wollen. Im CDM gehören Terme ja obligat zu einem Vokabular, so dass das schwierig wird.

Das müssen wir weiter diskutieren. Dafür würde ich zunächst aber erstmal die Duplikate verstehen wollen und ob diese richtig verwendet wurden.

Viele Grüße,
Andreas M.

P.S: Besonders wichtig ist hier der Fall present/absent der ja einen Spezialfall darstellt, der extrem häufig verwendet wird (zumindest im Hintergrund). Da ist auf jeden Fall notwendig zu klären, ob die Terme, die sowohl im Presence Vokabular als auch im Quantity Vokabular vorkommen das gleiche bedeuten und man sie beide braucht.

#8 Updated by Andreas Müller 3 months ago

Query for above request:

SELECT REPLACE (uri, 'https://terms.tdwg.org/wiki/ft:','') 
FROM DefinedTermBase dtb
WHERE dtb.uri IS NOT NULL
GROUP BY dtb.uri
HAVING COUNT(*) > 1

#9 Updated by Andreas Müller 3 months ago

  • Status changed from Feedback to In Progress
  • Target version changed from Release 5.9 to Release 5.10

As the current solution works for additivity maybe we should postpone creating the two new terms until the above question is answered and until we better know how to handle terms from external vocabularies in CDM.
At least as long as we have not decided to replace the current terms by pure CDM terms with the same meaning (maybe the current "presence" vocabulary is meant to be something like this but then the term uris are not correct)

#10 Updated by Andreas Müller 2 months ago

  • Target version changed from Release 5.10 to Release 5.9

#11 Updated by Andreas Müller about 2 months ago

  • Status changed from In Progress to Resolved
  • Assignee changed from Andreas Müller to Patrick Plitzner
  • % Done changed from 0 to 50

#12 Updated by Patrick Plitzner about 2 months ago

  • Status changed from Resolved to Closed
  • Assignee changed from Patrick Plitzner to Andreas Müller
  • % Done changed from 50 to 100

Terms and vocabulary are available in the taxeditor and replace possible existing presence/absence terms.

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