IDMP-641 add CDC - PHIN Race and Ethnicity with agencies #451

tw-osthus · 2023-08-14T11:58:35Z

Description:

added CDC, PHIN-VADS to na registries
added Race and Ethnicity vocabulary

Signed-off-by: Thomas Weber <[email protected]>

mereolog

It is not possible to check consistency of https://spec.pistoiaalliance.org/idmp/ontology/ISO/20230814/NorthAmericanJurisdiction/PublicHealthInformationNetwork/ - see below the error thrown by Pellet:

ERROR  12:29:52  An error occurred during reasoning: Unsupported axiom: Ignoring transitivity and/or complex subproperty axioms for hasBroaderEntry.
org.mindswap.pellet.exceptions.UnsupportedFeatureException: Unsupported axiom: Ignoring transitivity and/or complex subproperty axioms for hasBroaderEntry
	at org.mindswap.pellet.RBox.ignoreTransitivity(RBox.java:813) ~[na:na]
	at org.mindswap.pellet.RBox.prepare(RBox.java:612) ~[na:na]
	at org.mindswap.pellet.KnowledgeBase.prepare(KnowledgeBase.java:1776) ~[na:na]
	at org.mindswap.pellet.KnowledgeBase.consistency(KnowledgeBase.java:1969) ~[na:na]
	at org.mindswap.pellet.KnowledgeBase.isConsistent(KnowledgeBase.java:2061) ~[na:na]
	at org.mindswap.pellet.KnowledgeBase.ensureConsistency(KnowledgeBase.java:2075) ~[na:na]
	at org.mindswap.pellet.KnowledgeBase.classify(KnowledgeBase.java:2083) ~[na:na]
	at com.clarkparsia.pellet.owlapiv3.PelletReasoner.precomputeInferences(PelletReasoner.java:1067) ~[na:na]
	at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.precompute(OWLReasonerManagerImpl.java:447) ~[na:na]
	at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner.run(OWLReasonerManagerImpl.java:388) ~[na:na]
	at java.base/java.lang.Thread.run(Unknown Source) ~[na:na]
   WARN  12:29:52  Protege terminated reasoner.

ISO/NorthAmericanJurisdiction/PublicHealthInformationNetwork.rdf

mereolog · 2023-08-21T10:32:57Z

See also #454 (comment) - a similar comment applies here.

Signed-off-by: Thomas Weber <[email protected]>

…hasNarrowerEntry, it does not work with transitive properties Signed-off-by: Thomas Weber <[email protected]>

ISO/NorthAmericanJurisdiction/PublicHealthInformationNetwork.rdf

Signed-off-by: Thomas Weber <[email protected]>

tw-osthus · 2023-09-14T10:55:17Z

needs fix of master branch after merge

mereolog

There is a couple of typos reported in the other comments.

mereolog · 2023-09-15T09:00:10Z

ISO/NorthAmericanJurisdiction/PublicHealthInformationNetwork.rdf

+
+	<owl:NamedIndividual rdf:about="&idmp-phin;VADSCodeSystem-RaceAndEthnicityCDC">
+		<rdfs:label>PHIN-VADS code system - Race and Ethnicity - CDC</rdfs:label>
+		<rdfs:type rdf:resource="&idmp-phin;VADSCodeSystem"/>


This line should read: <rdf:type rdf:resource="&idmp-phin;VADSCodeSystem"/>

mereolog · 2023-09-15T09:01:07Z

ISO/NorthAmericanJurisdiction/PublicHealthInformationNetwork.rdf

+	<owl:Class rdf:about="&idmp-phin;VADSName">
+		<rdfs:subClassOf rdf:resource="&cmns-dsg;Name"/>
+		<rdfs:label>PHIN-VADS name</rdfs:label>
+		<rdf:subClassOf>


This line should read <rdfs:subClassOf>.

mereolog · 2023-09-15T09:01:23Z

ISO/NorthAmericanJurisdiction/PublicHealthInformationNetwork.rdf

+				<owl:allValuesFrom rdf:resource="&idmp-phin;VADSCodeSystem"/>
+			</owl:Restriction>
+		</rdf:subClassOf>
+		<rdf:subClassOf>


This line should read <rdfs:subClassOf>.

mereolog · 2023-09-15T09:01:52Z

ISO/NorthAmericanJurisdiction/PublicHealthInformationNetwork.rdf

+				<owl:onProperty rdf:resource="&cmns-col;isIncludedIn"/>
+				<owl:allValuesFrom rdf:resource="&idmp-phin;VADSCodeSystem"/>
+			</owl:Restriction>
+		</rdf:subClassOf>


This line should read </rdfs:subClassOf>.

mereolog · 2023-09-15T09:02:13Z

ISO/NorthAmericanJurisdiction/PublicHealthInformationNetwork.rdf

+				<owl:onProperty rdf:resource="&cmns-dsg;denotes"/>
+				<owl:allValuesFrom rdf:resource="&idmp-phin;VADSCodeSystemConcept"/>
+			</owl:Restriction>
+		</rdf:subClassOf>


This line should read </rdfs:subClassOf>.

mereolog · 2023-09-15T09:20:58Z

ERROR 11:19:45 An error occurred during reasoning: Cannot do reasoning with inconsistent ontologies!

Reason for inconsistency: Literal value "https://phinvads.cdc.gov/vads/ViewCodeSystem.action?id=2.16.840.1.113883.6.238"^^string does not belong to datatype anyURI.
org.mindswap.pellet.exceptions.InconsistentOntologyException: Cannot do reasoning with inconsistent ontologies!
Reason for inconsistency: Literal value "https://phinvads.cdc.gov/vads/ViewCodeSystem.action?id=2.16.840.1.113883.6.238"^^string does not belong to datatype anyURI

mereolog · 2023-09-15T09:22:23Z

AboutIDMPDev.rdf

+        <owl:imports rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/ISO/NorthAmericanJurisdiction/CommonTerminologyCriteriaForAdverseEvents/"/>
+        <owl:imports rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/ISO/NorthAmericanJurisdiction/PublicHealthInformationNetwork/"/>


These two ontologies should be "registered" in AboutIDMPDev-ReferenceIndividuals.rdf as well because all and only ontologies "registered" there are subject to hygiene tests.

Signed-off-by: Thomas Weber <[email protected]>

ISO/NorthAmericanJurisdiction/PublicHealthInformationNetwork.rdf

Signed-off-by: Thomas Weber <[email protected]>

Signed-off-by: Elisa Kendall <[email protected]>

…value domain from ISO 21090 Signed-off-by: Elisa Kendall <[email protected]>

…D, further defined the code for the code set, replaced min 1 cardinality restrictions with some values from for improved performance, completed other concepts and corrected spelling Signed-off-by: Elisa Kendall <[email protected]>

Signed-off-by: Elisa Kendall <[email protected]>

ElisaKendall

Approved with the changes made.

tw-osthus added 2 commits August 14, 2023 13:54

add CDC - PHIN Race and Ethnicity with agencies

07bd18b

Signed-off-by: Thomas Weber <[email protected]>

Merge branch 'master' into IDMP-641

70bead1

tw-osthus requested review from mereolog and ElisaKendall August 21, 2023 08:04

mereolog requested changes Aug 21, 2023

View reviewed changes

ISO/NorthAmericanJurisdiction/PublicHealthInformationNetwork.rdf Outdated Show resolved Hide resolved

tw-osthus added 4 commits August 21, 2023 12:46

add PHIN classification scheme

782c31a

Signed-off-by: Thomas Weber <[email protected]>

Merge branch 'master' into IDMP-641

e543c1f

merge master and update catalog

707892b

Signed-off-by: Thomas Weber <[email protected]>

removed min 0 cardinality restriction on mvf:hasBroaderEntry and mvf:…

d079f99

…hasNarrowerEntry, it does not work with transitive properties Signed-off-by: Thomas Weber <[email protected]>

tw-osthus requested a review from mereolog August 21, 2023 11:13

mereolog requested changes Aug 21, 2023

View reviewed changes

ISO/NorthAmericanJurisdiction/PublicHealthInformationNetwork.rdf Outdated Show resolved Hide resolved

tw-osthus added 9 commits August 25, 2023 12:55

fix corrupted datatype iris

e4a5bf5

Signed-off-by: Thomas Weber <[email protected]>

fix content source annotation

b9b0847

Signed-off-by: Thomas Weber <[email protected]>

Merge branch 'master' into IDMP-641

077242d

add ontology to about IDMP dev

4a28fb2

Signed-off-by: Thomas Weber <[email protected]>

fix datatype for cmns-txt:hasTextValue

b0ef32b

Signed-off-by: Thomas Weber <[email protected]>

aligned with pattern

40da81b

Signed-off-by: Thomas Weber <[email protected]>

PHIN-VADS code system is subclass of code system

16f9456

Signed-off-by: Thomas Weber <[email protected]>

fix url

35603c2

Signed-off-by: Thomas Weber <[email protected]>

Merge branch 'master' into IDMP-641

d9e10e5

tw-osthus requested a review from mereolog September 14, 2023 10:54

Merge branch 'master' into IDMP-641

3e2129f

mereolog requested changes Sep 15, 2023

View reviewed changes

mereolog reviewed Sep 15, 2023

View reviewed changes

tw-osthus added 2 commits September 15, 2023 11:47

fix typos and register ontology in reference individuals

6f1c7fa

Signed-off-by: Thomas Weber <[email protected]>

fix inferencing

358aaf1

Signed-off-by: Thomas Weber <[email protected]>

mereolog reviewed Sep 18, 2023

View reviewed changes

ISO/NorthAmericanJurisdiction/PublicHealthInformationNetwork.rdf Outdated Show resolved Hide resolved

tw-osthus and others added 4 commits September 18, 2023 10:56

fix IRI

9836368

Signed-off-by: Thomas Weber <[email protected]>

IDMP-641 - corrected IRIs in declarations for the PHIN ontology

a40bd43

Signed-off-by: Elisa Kendall <[email protected]>

IDMP-641 - revised the definition of a value set to be a subclass of …

9131f54

…value domain from ISO 21090 Signed-off-by: Elisa Kendall <[email protected]>

ElisaKendall previously approved these changes Sep 20, 2023

View reviewed changes

ElisaKendall requested a review from mereolog September 20, 2023 03:48

IDMP-641 - corrected typo

49b03c4

Signed-off-by: Elisa Kendall <[email protected]>

ElisaKendall dismissed their stale review via 49b03c4 September 20, 2023 03:56

ElisaKendall self-requested a review September 20, 2023 03:56

ElisaKendall added 2 commits September 19, 2023 21:00

IDMP-641 - addressed missing metadata and removed unneeded catalog file

12e554b

Signed-off-by: Elisa Kendall <[email protected]>

IDMP-641 - eliminated punning issue

2a18258

Signed-off-by: Elisa Kendall <[email protected]>

ElisaKendall approved these changes Sep 20, 2023

View reviewed changes

mereolog approved these changes Sep 20, 2023

View reviewed changes

mereolog merged commit b490221 into master Sep 20, 2023
6 checks passed

mereolog deleted the IDMP-641 branch September 20, 2023 14:59

mereolog added this to the Release 0.5.0 milestone Sep 22, 2023

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IDMP-641 add CDC - PHIN Race and Ethnicity with agencies #451

IDMP-641 add CDC - PHIN Race and Ethnicity with agencies #451

tw-osthus commented Aug 14, 2023

mereolog left a comment

mereolog commented Aug 21, 2023

tw-osthus commented Sep 14, 2023

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mereolog Sep 15, 2023

mereolog Sep 15, 2023

mereolog Sep 15, 2023

mereolog Sep 15, 2023

mereolog Sep 15, 2023

tw-osthus Sep 15, 2023

mereolog commented Sep 15, 2023

mereolog Sep 15, 2023

tw-osthus Sep 15, 2023

ElisaKendall left a comment

		<owl:imports rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/ISO/NorthAmericanJurisdiction/CommonTerminologyCriteriaForAdverseEvents/"/>
		<owl:imports rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/ISO/NorthAmericanJurisdiction/PublicHealthInformationNetwork/"/>

IDMP-641 add CDC - PHIN Race and Ethnicity with agencies #451

IDMP-641 add CDC - PHIN Race and Ethnicity with agencies #451

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tw-osthus commented Aug 14, 2023

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mereolog commented Aug 21, 2023

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