search

International-Data-Spaces-Association / InformationModel

The Information Model of the International Data Spaces implements the IDS reference architecture as an extensible, machine readable and technology independent data model.
Apache License 2.0
61 stars 35 forks source link

Error while loading Ontology to Protege #562

Closed aamir9138 closed 1 year ago

aamir9138 commented 2 years ago

I am getting the error (ERROR 11:03:33 Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error1 for type Class ) when loading the Ontology to Protege 5.5.0 from the below Link.

https://international-data-spaces-association.github.io/InformationModel/docs/serializations/ontology.ttl

JohannesLipp commented 2 years ago

@aamir9138 thanks for reporting this! Could you please try importing the ontology from the following link? At https://w3id.org/idsa/core , you can choose between different serializations including RDF/Turtle: image

One deep-link to the ontology might e.g. be https://international-data-spaces-association.github.io/InformationModel/docs/serializations/ontology.ttl

Our links seem to be the same, could you still please double-check and reply here? Thank you.

aamir9138 commented 2 years ago

@JohannesLipp I tried the above mentioned serialization options. RDF/XML and TTL both give the same errors. other format have warnings only but our Terminology service currently supports only .ttl, .owl and .obo format. image

JohannesLipp commented 2 years ago

Thank you very much! @PHochmann please reproduce/investigate this, thank you.

PHochmann commented 2 years ago

I can reproduce this even though I don't understand where the error comes from. E.g.WARN 09:53:04 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/action in punning not allowed [Declaration(AnnotationProperty(<https://w3id.org/idsa/core/action>)), Declaration(ObjectProperty(<https://w3id.org/idsa/core/action>))] does not make sense since ids:action is only declared once as an ObjectProperty in model/contract/Rule.ttl

PHochmann commented 2 years ago

Output when importing newest serialization into Protege 5.5.0:

INFO 12:59:37 OWL API Version: 4.5.9.2019-02-01T07:24:44Z
INFO 12:59:44 ------------------------------- Loading Ontology -------------------------------
INFO 12:59:44 Loading ontology from file:/home/philipph/Downloads/ontology(1).ttl
INFO 12:59:45 Unparsed triple: _:genid-nodeid-node1g4a9ubbox17 -> http://www.w3.org/2002/07/owl#unionOf -> _:genid-nodeid-node1g4a9ubbox18
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/action in punning not allowed [Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/action>))](https://w3id.org/idsa/core/action%3E))), Declaration(ObjectProperty(<[https://w3id.org/idsa/core/action>))]](https://w3id.org/idsa/core/action%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/rightOperandReference in punning not allowed [Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/rightOperandReference>))](https://w3id.org/idsa/core/rightOperandReference%3E))), Declaration(ObjectProperty(<[https://w3id.org/idsa/core/rightOperandReference>))]](https://w3id.org/idsa/core/rightOperandReference%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/accrualPeriodicity in punning not allowed [Declaration(DataProperty(<[https://w3id.org/idsa/core/accrualPeriodicity>))](https://w3id.org/idsa/core/accrualPeriodicity%3E))), Declaration(ObjectProperty(<[https://w3id.org/idsa/core/accrualPeriodicity>))]](https://w3id.org/idsa/core/accrualPeriodicity%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/latitude in punning not allowed [Declaration(DataProperty(<[https://w3id.org/idsa/core/latitude>))](https://w3id.org/idsa/core/latitude%3E))), Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/latitude>))]](https://w3id.org/idsa/core/latitude%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/corporateHomepage in punning not allowed [Declaration(DataProperty(<[https://w3id.org/idsa/core/corporateHomepage>))](https://w3id.org/idsa/core/corporateHomepage%3E))), Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/corporateHomepage>))]](https://w3id.org/idsa/core/corporateHomepage%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/postDuty in punning not allowed [Declaration(ObjectProperty(<[https://w3id.org/idsa/core/postDuty>))](https://w3id.org/idsa/core/postDuty%3E))), Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/postDuty>))]](https://w3id.org/idsa/core/postDuty%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/pipEndpoint in punning not allowed [Declaration(ObjectProperty(<[https://w3id.org/idsa/core/pipEndpoint>))](https://w3id.org/idsa/core/pipEndpoint%3E))), Declaration(DataProperty(<[https://w3id.org/idsa/core/pipEndpoint>))]](https://w3id.org/idsa/core/pipEndpoint%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/operator in punning not allowed [Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/operator>))](https://w3id.org/idsa/core/operator%3E))), Declaration(ObjectProperty(<[https://w3id.org/idsa/core/operator>))]](https://w3id.org/idsa/core/operator%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/source in punning not allowed [Declaration(DataProperty(<[https://w3id.org/idsa/core/source>))](https://w3id.org/idsa/core/source%3E))), Declaration(ObjectProperty(<[https://w3id.org/idsa/core/source>))]](https://w3id.org/idsa/core/source%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/recipientAgent in punning not allowed [Declaration(ObjectProperty(<[https://w3id.org/idsa/core/recipientAgent>))](https://w3id.org/idsa/core/recipientAgent%3E))), Declaration(DataProperty(<[https://w3id.org/idsa/core/recipientAgent>))]](https://w3id.org/idsa/core/recipientAgent%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/familyName in punning not allowed [Declaration(DataProperty(<[https://w3id.org/idsa/core/familyName>))](https://w3id.org/idsa/core/familyName%3E))), Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/familyName>))]](https://w3id.org/idsa/core/familyName%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/and in punning not allowed [Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/and>))](https://w3id.org/idsa/core/and%3E))), Declaration(ObjectProperty(<[https://w3id.org/idsa/core/and>))]](https://w3id.org/idsa/core/and%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/accessed in punning not allowed [Declaration(DataProperty(<[https://w3id.org/idsa/core/accessed>))](https://w3id.org/idsa/core/accessed%3E))), Declaration(ObjectProperty(<[https://w3id.org/idsa/core/accessed>))]](https://w3id.org/idsa/core/accessed%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/issued in punning not allowed [Declaration(DataProperty(<[https://w3id.org/idsa/core/issued>))](https://w3id.org/idsa/core/issued%3E))), Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/issued>))]](https://w3id.org/idsa/core/issued%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/temporalResolution in punning not allowed [Declaration(DataProperty(<[https://w3id.org/idsa/core/temporalResolution>))](https://w3id.org/idsa/core/temporalResolution%3E))), Declaration(ObjectProperty(<[https://w3id.org/idsa/core/temporalResolution>))]](https://w3id.org/idsa/core/temporalResolution%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/prohibition in punning not allowed [Declaration(ObjectProperty(<[https://w3id.org/idsa/core/prohibition>))](https://w3id.org/idsa/core/prohibition%3E))), Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/prohibition>))]](https://w3id.org/idsa/core/prohibition%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/data in punning not allowed [Declaration(ObjectProperty(<[https://w3id.org/idsa/core/data>))](https://w3id.org/idsa/core/data%3E))), Declaration(DataProperty(<[https://w3id.org/idsa/core/data>))]](https://w3id.org/idsa/core/data%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/corporateEmailAddress in punning not allowed [Declaration(DataProperty(<[https://w3id.org/idsa/core/corporateEmailAddress>))](https://w3id.org/idsa/core/corporateEmailAddress%3E))), Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/corporateEmailAddress>))]](https://w3id.org/idsa/core/corporateEmailAddress%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/usageDuration in punning not allowed [Declaration(DataProperty(<[https://w3id.org/idsa/core/usageDuration>))](https://w3id.org/idsa/core/usageDuration%3E))), Declaration(ObjectProperty(<[https://w3id.org/idsa/core/usageDuration>))]](https://w3id.org/idsa/core/usageDuration%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/xone in punning not allowed [Declaration(ObjectProperty(<[https://w3id.org/idsa/core/xone>))](https://w3id.org/idsa/core/xone%3E))), Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/xone>))]](https://w3id.org/idsa/core/xone%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/requester in punning not allowed [Declaration(DataProperty(<[https://w3id.org/idsa/core/requester>))](https://w3id.org/idsa/core/requester%3E))), Declaration(ObjectProperty(<[https://w3id.org/idsa/core/requester>))]](https://w3id.org/idsa/core/requester%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/issuerConnector in punning not allowed [Declaration(ObjectProperty(<[https://w3id.org/idsa/core/issuerConnector>))](https://w3id.org/idsa/core/issuerConnector%3E))), Declaration(DataProperty(<[https://w3id.org/idsa/core/issuerConnector>))]](https://w3id.org/idsa/core/issuerConnector%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/memberParticipant in punning not allowed [Declaration(ObjectProperty(<[https://w3id.org/idsa/core/memberParticipant>))](https://w3id.org/idsa/core/memberParticipant%3E))), Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/memberParticipant>))]](https://w3id.org/idsa/core/memberParticipant%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/emailAddress in punning not allowed [Declaration(DataProperty(<[https://w3id.org/idsa/core/emailAddress>))](https://w3id.org/idsa/core/emailAddress%3E))), Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/emailAddress>))]](https://w3id.org/idsa/core/emailAddress%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/authService in punning not allowed [Declaration(DataProperty(<[https://w3id.org/idsa/core/authService>))](https://w3id.org/idsa/core/authService%3E))), Declaration(ObjectProperty(<[https://w3id.org/idsa/core/authService>))]](https://w3id.org/idsa/core/authService%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/longitude in punning not allowed [Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/longitude>))](https://w3id.org/idsa/core/longitude%3E))), Declaration(DataProperty(<[https://w3id.org/idsa/core/longitude>))]](https://w3id.org/idsa/core/longitude%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/referringConnector in punning not allowed [Declaration(DataProperty(<[https://w3id.org/idsa/core/referringConnector>))](https://w3id.org/idsa/core/referringConnector%3E))), Declaration(ObjectProperty(<[https://w3id.org/idsa/core/referringConnector>))]](https://w3id.org/idsa/core/referringConnector%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/preDuty in punning not allowed [Declaration(ObjectProperty(<[https://w3id.org/idsa/core/preDuty>))](https://w3id.org/idsa/core/preDuty%3E))), Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/preDuty>))]](https://w3id.org/idsa/core/preDuty%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/or in punning not allowed [Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/or>))](https://w3id.org/idsa/core/or%3E))), Declaration(ObjectProperty(<[https://w3id.org/idsa/core/or>))]](https://w3id.org/idsa/core/or%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/permission in punning not allowed [Declaration(ObjectProperty(<[https://w3id.org/idsa/core/permission>))](https://w3id.org/idsa/core/permission%3E))), Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/permission>))]](https://w3id.org/idsa/core/permission%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/primarySite in punning not allowed [Declaration(ObjectProperty(<[https://w3id.org/idsa/core/primarySite>))](https://w3id.org/idsa/core/primarySite%3E))), Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/primarySite>))]](https://w3id.org/idsa/core/primarySite%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/assigner in punning not allowed [Declaration(ObjectProperty(<[https://w3id.org/idsa/core/assigner>))](https://w3id.org/idsa/core/assigner%3E))), Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/assigner>))]](https://w3id.org/idsa/core/assigner%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/assetSource in punning not allowed [Declaration(DataProperty(<[https://w3id.org/idsa/core/assetSource>))](https://w3id.org/idsa/core/assetSource%3E))), Declaration(ObjectProperty(<[https://w3id.org/idsa/core/assetSource>))]](https://w3id.org/idsa/core/assetSource%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/constraint in punning not allowed [Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/constraint>))](https://w3id.org/idsa/core/constraint%3E))), Declaration(ObjectProperty(<[https://w3id.org/idsa/core/constraint>))]](https://w3id.org/idsa/core/constraint%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/obligation in punning not allowed [Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/obligation>))](https://w3id.org/idsa/core/obligation%3E))), Declaration(ObjectProperty(<[https://w3id.org/idsa/core/obligation>))]](https://w3id.org/idsa/core/obligation%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/memberPerson in punning not allowed [Declaration(ObjectProperty(<[https://w3id.org/idsa/core/memberPerson>))](https://w3id.org/idsa/core/memberPerson%3E))), Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/memberPerson>))]](https://w3id.org/idsa/core/memberPerson%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/proxyAuthentication in punning not allowed [Declaration(ObjectProperty(<[https://w3id.org/idsa/core/proxyAuthentication>))](https://w3id.org/idsa/core/proxyAuthentication%3E))), Declaration(DataProperty(<[https://w3id.org/idsa/core/proxyAuthentication>))]](https://w3id.org/idsa/core/proxyAuthentication%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/rightOperand in punning not allowed [Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/rightOperand>))](https://w3id.org/idsa/core/rightOperand%3E))), Declaration(ObjectProperty(<[https://w3id.org/idsa/core/rightOperand>))]](https://w3id.org/idsa/core/rightOperand%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/senderAgent in punning not allowed [Declaration(ObjectProperty(<[https://w3id.org/idsa/core/senderAgent>))](https://w3id.org/idsa/core/senderAgent%3E))), Declaration(DataProperty(<[https://w3id.org/idsa/core/senderAgent>))]](https://w3id.org/idsa/core/senderAgent%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/givenName in punning not allowed [Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/givenName>))](https://w3id.org/idsa/core/givenName%3E))), Declaration(DataProperty(<[https://w3id.org/idsa/core/givenName>))]](https://w3id.org/idsa/core/givenName%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/unit in punning not allowed [Declaration(ObjectProperty(<[https://w3id.org/idsa/core/unit>))](https://w3id.org/idsa/core/unit%3E))), Declaration(DataProperty(<[https://w3id.org/idsa/core/unit>))](https://w3id.org/idsa/core/unit%3E))), Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/unit>))]](https://w3id.org/idsa/core/unit%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/assignee in punning not allowed [Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/assignee>))](https://w3id.org/idsa/core/assignee%3E))), Declaration(ObjectProperty(<[https://w3id.org/idsa/core/assignee>))]](https://w3id.org/idsa/core/assignee%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/phoneNumber in punning not allowed [Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/phoneNumber>))](https://w3id.org/idsa/core/phoneNumber%3E))), Declaration(DataProperty(<[https://w3id.org/idsa/core/phoneNumber>))]](https://w3id.org/idsa/core/phoneNumber%3E))])
WARN 12:59:45 Illegal redeclarations of entities: reuse of entity https://w3id.org/idsa/core/homepage in punning not allowed [Declaration(DataProperty(<[https://w3id.org/idsa/core/homepage>))](https://w3id.org/idsa/core/homepage%3E))), Declaration(AnnotationProperty(<[https://w3id.org/idsa/core/homepage>))]](https://w3id.org/idsa/core/homepage%3E))])
WARN 12:59:45 Annotation property domain axiom turned to data property domain after parsing. This could introduce errors if the original domain was an anonymous expression: _:genid-nodeid-node1g4a9ubbox17 is the new domain.
WARN 12:59:45 Annotation property range axiom turned to data property range after parsing. This could introduce errors if the original range was an anonymous expression: http://www.w3.org/2001/XMLSchema#dateTimeStamp is the new domain.
INFO 12:59:45 Finished loading file:/home/philipph/Downloads/ontology(1).ttl
INFO 12:59:45 Loading for ontology and imports closure successfully completed in 711 ms
INFO 12:59:45 Updated document format class from: org.semanticweb.owlapi.formats.RioTurtleDocumentFormat to: org.semanticweb.owlapi.formats.TurtleDocumentFormat
INFO 12:59:45
JohannesLipp commented 2 years ago

OK so we are not getting errors. But we can reproduce the warnings, got it. I investigated the ontology source file and found that the mentioned properties are indeed defined more than once.

@lcomet Could you please investigate why for instance accrualPeriodicity is defined as ObjectProperty and DatatypePropert?

Please also investigate, why <https://w3id.org/idsa/core/action> is defined as both ObjectPropert and AnnotationProperty.

Thank you very much!

lcomet commented 1 year ago

@JohannesLipp After verification and testing of some scenarios, the summary of my findings is the following:

  1. ids:accrualPeriodicity is defined in DigitalContent.ttl as a owl:DatatypeProperty and a owl:subPropertyOf dct:accrualPeriodicity (up to version 4.1.0 of our ontology)
  2. The definition in point 1. is creating the following effect: ids:accrualPeriodicity is treated as an Object Property, and dct:accrualPeriodicity as a Data Property, which can also be observed by opening the DigitalContent.ttl file in Protégé
  3. Once we apply changes from the Refactor IDS Model process , in which we removed redundant definitions this behaviour shouldn't persist. As tested locally by removing the redundant ids:accrualPeriodicity definition.
  4. Rerunning the serialization process at this point is not going to help, as we are taking the files from the last release in the repository.
  5. Similar illegal redefinition messages refer to similar local definitions by referring to external properties.

For more details about the evaluation process regarding this issue, please see the following document: IDS-InfoModel-Issue-562.pdf

JohannesLipp commented 1 year ago

Thank you @lcomet !

tl;dr: The upcoming version 5 (and also already the current develop branch) solve this issue.