Bug: Assigning a blank node an rdf:nodeID can lead to duplicates in LDTab

[ckindermann]

Consider the following example (adapted from UBERON), in which an existential restriction is assigned rdf:nodeID="genid3" that gets referenced three times in the class description of obo:UBERON_0037447:

XML example

 <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0037447">
       <owl:equivalentClass>
           <owl:Class>
               <owl:intersectionOf rdf:parseType="Collection">
                   <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0000060"/>
                   <owl:Restriction rdf:nodeID="genid3">
                       <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
                       <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001333"/>
                   </owl:Restriction>
               </owl:intersectionOf>
           </owl:Class>
       </owl:equivalentClass>
       <rdfs:subClassOf>
           <owl:Class>
               <owl:intersectionOf rdf:parseType="Collection">
                   <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0000060"/>
                   <owl:Restriction rdf:nodeID="genid3">
                       <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
                       <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001333"/>
                   </owl:Restriction>
               </owl:intersectionOf>
           </owl:Class>
       </rdfs:subClassOf>
       <rdfs:subClassOf rdf:nodeID="genid3"/>
  </owl:Class>
  <owl:Restriction rdf:nodeID="genid3">
      <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
      <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001333"/>
  </owl:Restriction>

Executing ldtab import results in JSON objects where the values associated with the blank node with rdf:nodeID="genid3" are repeated the same number of times the blank node is referenced. For example, the object of the LDTab triple representing <rdfs:subClassOf rdf:nodeID="genid3"/> looks as follows:

JSON representation in LDTab

{
  "owl:onProperty": [
    {
      "datatype": "_IRI",
      "object": "obo:BFO_0000050"
    },
    {
      "datatype": "_IRI",
      "object": "obo:BFO_0000050"
    },
    {
      "datatype": "_IRI",
      "object": "obo:BFO_0000050"
    }
  ],
  "owl:someValuesFrom": [
    {
      "datatype": "_IRI",
      "object": "obo:UBERON_0001333"
    },
    {
      "datatype": "_IRI",
      "object": "obo:UBERON_0001333"
    },
    {
      "datatype": "_IRI",
      "object": "obo:UBERON_0001333"
    }
  ],
  "rdf:type": [
    {
      "datatype": "_IRI",
      "object": "owl:Restriction"
    },
    {
      "datatype": "_IRI",
      "object": "owl:Restriction"
    },
    {
      "datatype": "_IRI",
      "object": "owl:Restriction"
    }
  ]
}

This bug does not seem to be present when using ldtab import -s.

The bug is also not present when removing rdf:nodeID="genid3".

I suspect the bug to be located in one of these functions:

• in rdf_model.clj:
  • get-blank-node-objects
  • get-blanknode-dependencies
• in thin2thick:
  • node-2-thick-map