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RDFBones / RDFBones-O

An RDF ontology for research data from physical anthropology and related fields of expertise.
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[AgeEstimation] Different phaleron-ae namespaces #189

Closed zarquon42b closed 10 months ago

zarquon42b commented 10 months ago

There are some classes under two distinct namespaces: I.e. the class AgeEstimationProcess exists as

  1. <http://w3id.org/rdfbones/anthrograph/app/phaleron-ae/AgeEstimationProcess>
  2. <http://w3id.org/rdfbones/ext/phaleron-ae/AgeEstimationProcess>

The problem is that the sex specific subclasses are defined within the first (wrong) namespace. However the second seems to be the correct one.

The problem also exists for AgeEstimationDataset and PubicAgeEstimationDatasetSection

Code to find stuff in the wrong namespace: 

PREFIX paeapp: <http://w3id.org/rdfbones/anthrograph/app/phaleron-ae/>
SELECT *  WHERE {
  ?s ?p ?o.
  FILTER( STRSTARTS(str(?s), str(paeapp:)) )
  }
cuboideum commented 10 months ago

The correct prefix is the second, http://w3id.org/rdfbones/ext/phaleron-ae/. I need to eliminate the other one.

zarquon42b commented 10 months ago

But dont forget to update all subclass statements that are linked to the erroneous ones!

cuboideum commented 10 months ago

Pull request https://github.com/AnthroGraph/Phaleron-AppOntology/pull/40 fixes the issue in the Phaleron app ontology.

cuboideum commented 10 months ago

Commit https://github.com/AnthroGraph/Phaleron-AppOntology/commit/338b7c9e87be1bfb271be09c2121bd1f2333878e merges the changes into the robot branch of the Phaleron app ontology.

zarquon42b commented 10 months ago

But dont forget to update all subclass statements that are linked to the erroneous ones!

... unfortunately this is now the case.

SELECT * WHERE { ?ageProcess rdfs:subClassOf* <http://w3id.org/rdfbones/ext/phaleron-ae/AgeEstimationDataset> }

Only yields: http://w3id.org/rdfbones/anthrograph/app/phaleron-app/FemaleAgeEstimationDataset

PubicAgeEstimationDatasetSection and AgeEstimationProcess lack the indeterminate versions of the subclasses.

zarquon42b commented 10 months ago

Also the superclasses are a mess: superclass of <http://w3id.org/rdfbones/anthrograph/app/phaleron-app/IndeterminateSexPubicAgeEstimationDatasetSection> is <http://w3id.org/rdfbones/ext/phaleron-ae/AgeEstimationProcess/PubicAgeEstimationDatasetSection> instead of <http://w3id.org/rdfbones/ext/phaleron-ae/PubicAgeEstimationDatasetSection> (without the AgeEstimationProcess in the URI)

Same problem with

In all cases the namespace part of the superclass is wrong (additional string).

cuboideum commented 10 months ago

https://github.com/RDFBones/RDFBones-O/issues/189#issuecomment-1711856598 is fixed with commit https://github.com/AnthroGraph/Phaleron-AppOntology/commit/1f18f2301efca95a5279a51a03a4a1a5e1086393.

cuboideum commented 10 months ago

https://github.com/RDFBones/RDFBones-O/issues/189#issuecomment-1711902983 is also fixed by these changes.

cuboideum commented 10 months ago

Issue fixed with commit https://github.com/AnthroGraph/Phaleron-AppOntology/commit/1060b29609d7e5473e269ae10e3cba5fb4c153cd.

zarquon42b commented 10 months ago

No, it is still not fixed.

  1. PubicAgeEstimationDatasetSection is still missing the subclass IndeterminatePubicAgeEstimationDatasetSection
  2. SpecimenOfBiologicalSexRole is missing the subclass IndeterminateSpecimenRole
cuboideum commented 10 months ago

Pull request https://github.com/AnthroGraph/Phaleron-AppOntology/pull/42 fixes request 1. in the Phaleron app ontology.

zarquon42b commented 10 months ago

Almost there. SpecimenOfBiologicalSexRole is still missing the subclass IndeterminateSpecimenRole

cuboideum commented 10 months ago

Commit https://github.com/AnthroGraph/Phaleron-AppOntology/commit/f5fac10573346dfe3563d7a585c3704762fd4445 updates the Phaleron-AgeEstimation submodule of the Phaleron app ontology which fixes request 2. and closes the issue.

zarquon42b commented 10 months ago

Not so hasty, young man. The statement <http://w3id.org/rdfbones/ext/phaleron-ae/SpecimenOfIndeterminateSexRole> <http://w3id.org/rdfbones/anthrograph/app/phaleron-app/sexBasedContext> "ind" . is now missing.

cuboideum commented 10 months ago

Request from comment https://github.com/RDFBones/RDFBones-O/issues/189#issuecomment-1714162845 is fixed in the Phaleron app ontology with pull request https://github.com/AnthroGraph/Phaleron-AppOntology/pull/43.

cuboideum commented 10 months ago

Changes from pull request https://github.com/AnthroGraph/Phaleron-AppOntology/pull/43 are ported to the robot branch of the Phaleron app ontology with commit https://github.com/AnthroGraph/Phaleron-AppOntology/commit/db3f2a60c876dc68ae1629a0bbb271b21acbb760.

This fixes the issue.