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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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[phaleron-patho]: Subclasses for Long-bone Anatomical Regions of Interest Specifications #180

Open cuboideum opened 1 year ago

cuboideum commented 1 year ago

@zarquon42b requests that the anatomical regions of interest specifications representing long bones which are needed for the Phaleron Size & Shape module should be structured by subclasses reflecting the tabs in the AnthroGraph Phaleron App. This is necessary for implementation of the ontology extension in AnthroGraph.

zarquon42b commented 1 year ago

Size&Shape ROISpecs are missing subclass statements linking the respective roispecs to the overarching classes to be addressed in each tab. Expected behavior: The following query is supposed to give all ROIspecs associated with upper limbs, it also fails for LowerLimbs. However the following query does not yield those classes:

 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
    SELECT $value WHERE  {
    $value rdfs:subClassOf* <http://w3id.org/rdfbones/ext/phaleron-patho/UpperLimbLongBoneAROISpecification> .
}
zarquon42b commented 1 year ago

Additionally, PhaleronSkullAROISpecification needs to be somehow nested under <http://w3id.org/rdfbones/ext/phaleron-patho/AROISpecification> because for the forms we need to select all classes that are a subClassOf another class. For PhaleronSkullAROISpecification there is no such a class for 2 reasons

  1. using $value rdfs:subClassOf* PhaleronSkullAROISpecification will yield the correct class but in case of longbones will also deliver the overarching classes which is nonsense
  2. using $value rdfs:subClassOf <http://w3id.org/rdfbones/ext/phaleron-patho/AROISpecification> will yield the other dozen of subclasses we actually do not want.

Solution: Make an additional class such as: PhaleronSkullAROISpecification => subClassOf => myNewClass => subClassOf => AROISpecification

cuboideum commented 1 year ago

https://github.com/RDFBones/Phaleron-Pathologies/pull/14 implements the following hierarchy:

The subclasses of 'Phaleron regional anatomical region of interest specification' define what should be selectable in individual tabs within AnthroGraph.

Note that the classes representing specifications for the upper and lower limbs, respectively, have yet another subclass each, for metacarpals and metatarsals. The skull class does not have any subclasses. @zarquon42b: Is this a problem for implementation in AnthroGraph?

cuboideum commented 1 year ago

Pull request https://github.com/AnthroGraph/Phaleron-AppOntology/pull/26 ports the changes implemented with https://github.com/RDFBones/Phaleron-Pathologies/pull/14 to the Phaleron App Ontology.

@zarquon42b Please accept if workable and close this issue.

zarquon42b commented 1 year ago

Please add intermediate classes for all collection of regions (Upper/Lower/Skull). Even for Skull where there is only one "collective" class. This is necessary to have the same hierarchical depth and to query the containing ROIs (modelled as subclasses) via: $value rdfs:subClassOf dummy:collectiveClass .

E.g. like

SELECT $value WHERE  {
$value rdfs:subClassOf <http://w3id.org/rdfbones/ext/phaleron-patho/UpperLimbLongBoneAROISpecification> .
}

which currently does not work for PhaleronSkullAROISpecification

cuboideum commented 1 year ago

Pull request https://github.com/AnthroGraph/Phaleron-AppOntology/pull/26 is updated by commit https://github.com/AnthroGraph/Phaleron-AppOntology/pull/26/commits/d5fe8fc5f8963f6745b1a11ba33e657bd0262343 to address https://github.com/RDFBones/RDFBones-O/issues/180#issuecomment-1535890746 above.

@zarquon42b: Does this work for you?

cuboideum commented 1 year ago

@zarquon42b: Can this issue be closed?