Short term hierarchy enhancement for SKOS vocabularies including multiple Concept Schemes

[jonquet]

Problem

When a SKOS vocabulary contains several skos:ConceptScheme AgroPortal build the hierarchy tree displaying at the root all the concepts with a skos:topConceptOf declaration.

For instance INRAETHES in stageportal (see discussion #233)

Requirement

We already require (for metadata extraction, but also as a good practice) that ONE skos:ConceptScheme (that would be the main one, including the other ones) be also declared owl:Ontology. This allow to consider the concept scheme as the main object and grab the metadata annotation properties.

Proposed solution

Display in the hierarchy tree only the top concepts of the main concept scheme (i.e. the one which is alos declared owl:ontology).

[syphax-bouazzouni]

Some context and references

• Adding the ontology IRI: In the generating RDF step of the ontology process we add the following triple "http://bioportal.bioontology.org/ontologies/URI owl:versionInfo " (we can found in the code here https://github.com/ontoportal-lirmm/owlapi_wrapper/blob/268aad5e8831d3f83ee12ae195e52afb526d180e/src/main/java/org/stanford/ncbo/oapiwrapper/OntologyParser.java#L146). Than this ontology is used for extracting the meta
• Fetching the roots on an ontology: for the case of SKOS we are fetching the roots concepts by fetching all the top Concepts using this SPARQL query

Solution

Change the SPARQL query that is fetching the top Concept from

SELECT DISTINCT ?root WHERE {
GRAPH #{self.id.to_ntriples} {
  ?x #{RDF::SKOS[:hasTopConcept].to_ntriples} ?root .
}}

To

SELECT DISTINCT ?root WHERE {
GRAPH #{self.id.to_ntriples} {
  #{self.ontology_uri.to_ntriples} #{RDF::SKOS[:hasTopConcept].to_ntriples} ?root .
}}

With this new query the fetched top concepts will be only from the owl:Ontology

[syphax-bouazzouni]

Done in testportal

[saubin78]

brilliant! Thanks a lot Syphax!

[syphax-bouazzouni]

Fixed with https://github.com/ontoportal-lirmm/ontologies_linked_data/issues/22