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IDMP-648 add Pluvicto example #469

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IDMP-648 add Pluvicto example #469

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tw-osthus
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Description: Pluvicto example with clinical particulars referenced from FDA and EMA approved PDF documents

@ElisaKendall ElisaKendall changed the title IDMP-648 add Pluvicto example IDMP-648 add Pluvicto example (WIP) Oct 2, 2023
@mereolog mereolog added this to the Release 1.0.0 milestone Oct 5, 2023
@tw-osthus
remove SPAR ontologies
fc7ad62 
Signed-off-by: Thomas Weber <[email protected]>
@tw-osthus
IDMP-648 - add pluvicto example
8011180 
Signed-off-by: Thomas Weber <[email protected]>
@tw-osthus
IDMP-648 - add Pluvicto example
4b69bba 
Signed-off-by: Thomas Weber <[email protected]>
@tw-osthus
Merge branch 'IDMP-648' of https://github.com/edmcouncil/idmp into ID…
927b2b0 
…MP-648

Signed-off-by: Thomas Weber <[email protected]>
@tw-osthus
Merge branch 'master' into IDMP-648
fa127d6
@tw-osthus
IDMP-648 - fix spelling
bdec694 
Signed-off-by: Thomas Weber <[email protected]>
@tw-osthus
IDMP-648 - update FDA document
d07eea2
@tw-osthus
IDMP-648 - change table row/column index datatype to positive integer
a959c95 
Signed-off-by: Thomas Weber <[email protected]>
@tw-osthus
IDMP-648 - update document descriptions
12e1b5e 
Signed-off-by: Thomas Weber <[email protected]>
@tw-osthus
Merge remote-tracking branch 'remotes/origin/IDMP-645' into IDMP-648
5921b71 
fix spelling

Signed-off-by: Thomas Weber <[email protected]>
@tw-osthus
IDMP-648 - add EMA document table 1
fb5e70a 
Signed-off-by: Thomas Weber <[email protected]>
@tw-osthus
IDMP-648 - add pluvicto example to catalog
bcc70da 
Signed-off-by: Thomas Weber <[email protected]>
@tw-osthus
IDMP-648 - add import of SPAR, update EMA document
49eabb5 
Signed-off-by: Thomas Weber <[email protected]>
@tw-osthus
IDMP-648 - update EMA document
31f1cbe
@tw-osthus
Merge branch 'master' into IDMP-648
647a2ca
@tw-osthus
IDMP-648 - add SPAR imports, use ns prefix
cc19edf 
Signed-off-by: Thomas Weber <[email protected]>
@tw-osthus
IDMP-648 - fix ns
7fbc81d 
Signed-off-by: Thomas Weber <[email protected]>
@tw-osthus
IDMP-648 - fix SPAR imports
da59949 
Signed-off-by: Thomas Weber <[email protected]>
@tw-osthus
IDMP-648 - add SPAR imports, fix MedDRA prefix
c75fb47 
Signed-off-by: Thomas Weber <[email protected]>
@tw-osthus
IDMP-648 - fix textual element iri
d821256 
Signed-off-by: Thomas Weber <[email protected]>
@tw-osthus
IDMP-648 - fix textual element IRI
af9059c 
Signed-off-by: Thomas Weber <[email protected]>
@tw-osthus
IDMP-648 - removed parent property has integer value from row and col…
f36662f 
…umn index and span, because it is functional

Signed-off-by: Thomas Weber <[email protected]>
@tw-osthus
IDMP-648 - fix marketing authorization role
b34a09d 
Signed-off-by: Thomas Weber <[email protected]>
tw-osthus and others added 8 commits February 16, 2024 14:46
@tw-osthus
IDMP-648 - add Pluvicto example to MetadataEXT.rdf
0a5874d 
Signed-off-by: Thomas Weber <[email protected]>
@ElisaKendall
IDMP-648 - added namespace and entity declarations to the po ontology…
2f0db8d 
… for better serialization

Signed-off-by: Elisa Kendall <[email protected]>
@ElisaKendall
IDMP-648 - corrected IRIs for the po ontology and updated metadata to…
c742847 
… exclude those that are unused and do not resolve properly

Signed-off-by: Elisa Kendall <[email protected]>
@tw-osthus
IDMP-648 - add SNOMED ontology, fix labels, fixed and removed unused …
59fd948 
…SPAR namespaces

Signed-off-by: Thomas Weber <[email protected]>
@ElisaKendall
Merge branch 'master' of https://github.com/edmcouncil/idmp into IDMP…
70026d1 
…-648 and addressed conflicts

Signed-off-by: Elisa Kendall <[email protected]>
@ElisaKendall
Merge branch 'master' of https://github.com/edmcouncil/idmp into IDMP…
bcb779b 
…-648
@mereolog
Merge branch 'master' into IDMP-648
38e39f8
@mereolog
catalog file in Examples updated
0239387 
Signed-off-by: mereolog <[email protected]>
mereolog
mereolog requested changes Apr 19, 2024
View reviewed changes
EXT/Examples/PluvictoExample.rdf Outdated
<idmp-mprd:hasUndesirableEffectAsSymptomConditionEffect rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/ISO/MedicalDictionaryForRegulatoryActivities/term/LLT/10029354"/>
<idmp-mprd:hasUndesirableEffectAsSymptomConditionEffect rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/ISO/MedicalDictionaryForRegulatoryActivities/term/LLT/10033661"/>
<idmp-mprd:hasUndesirableEffectAsSymptomConditionEffect rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/ISO/MedicalDictionaryForRegulatoryActivities/term/LLT/10043554"/>
<idmp-mprd:hasUndesirableEffectAsSymptomConditionEffect rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/ISO/MedicalDictionaryForRegulatoryActivities/term/LLT/Anaemia"/>
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https://spec.pistoiaalliance.org/idmp/ontology/ISO/MedicalDictionaryForRegulatoryActivities/term/LLT/Anaemia does have a type declared.

@mereolog
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Reason for inconsistency foundy by openllet:

Individual https://spor.ema.europa.eu/v1/lists/100000000006/terms/100000073049 has more than 1 values for property https://www.omg.org/spec/MVF/MultipleVocabularyFacility/hasTextualName violating the cardinality restriction.

@tw-osthus
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@mereolog I know of this inconsistency. This is why I have created the ticket on MVF hasTexutalName to discuss with Elisa

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mereolog commented May 6, 2024

@tw-osthus could you resolve the merge conflict?

@tw-osthus tw-osthus requested a review from mereolog May 7, 2024 09:46
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mereolog commented May 9, 2024

As of now we have these issues:

======================================= run consistency check at level: warning
 - AboutIDMPDev-ReferenceIndividuals.rdf : [https://spec.pistoiaalliance.org/idmp/ontology/AboutIDMPDev-ReferenceIndividuals/]
	ERROR: consistency check at level "warning" was timed out after "1h"
======================================= run consistency check at level: error
 - AboutIDMPProd-ReferenceIndividuals.rdf : [https://spec.pistoiaalliance.org/idmp/ontology/AboutIDMPProd-ReferenceIndividuals/]

   missingImports
	iri                 cause
	---                 -----
	http://purl.org/co  OWLOntologyCreationIOException: java.io.FileNotFoundException: https://dwellonit.sourceforge.net/co

	Ontology "AboutIDMPProd-ReferenceIndividuals.rdf" is consistent.

I am not sure how to progress from here.

@mereolog
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@tw-osthus would you mind resolving the merge conflicts?

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@ElisaKendall ElisaKendall Awaiting requested review from ElisaKendall

@mereolog mereolog Awaiting requested review from mereolog

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@tw-osthus @mereolog @ElisaKendall