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KRR-Oxford / OWL2Vec-Star

Embedding OWL ontologies
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Blank nodes generated #5

Closed ferzcam closed 2 years ago

ferzcam commented 2 years ago

When calling the class OntologyProjection with include_literals=True, some triples with blank nodes are generated. Those blank nodes do not seem to be used somewhere else, so I wondered if such triples are being used at some point or can just be ignored.

ernestojimenezruiz commented 2 years ago

Hi Fernando, This is happening calling just OntologyProjection right? I think I will need the input ontology to reproduce the problem. Thanks Ernesto

ferzcam commented 2 years ago

Hi. Yes, it happens with OntologyProjection. I have tried with goslim_yeast.owl and go.owl, both from the Gene Ontology. An example with goslim_yeast could be the following: For the annotation axiom

    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0005085"/>
        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
        <owl:annotatedTarget>Reactome:R-HSA-170979</owl:annotatedTarget>
        <rdfs:label>(Frs2)C3G stimulates nucleotide exchange on Rap1</rdfs:label>
    </owl:Axiom>

These two triples are generated:

('GO:0005085', 'http://www.geneontology.org/formats/oboInOwl#hasDbXref', 'Reactome:R-HSA-170979') ('199', 'rdfs:label', '(Frs2)C3G stimulates nucleotide exchange on Rap1')

But in the second triple, the node 199 (that may change in different runs) seems not to be used anywhere else.

ernestojimenezruiz commented 2 years ago

I see, interesting, the problem here is that the rdfs:label annotation is over an axiom/triple (this case another annotation).

We were not directly considering these cases, so the triple ends-up being isolated. I guess owlready creates this blank-node with id 199 and possibly does the reification to annotate an axiom/triple.

Best Ernesto

El vie, 11 feb 2022 a las 12:47, Fernando Zhapa @.***>) escribió:

Hi. Yes, it happens with OntologyProjection. I have tried with goslim_yeast.owl and go.owl, both from the Gene Ontology. An example with goslim_yeast could be the following: For the annotation axiom

<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0005085"/>
    <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
    <owl:annotatedTarget>Reactome:R-HSA-170979</owl:annotatedTarget>
    <rdfs:label>(Frs2)C3G stimulates nucleotide exchange on Rap1</rdfs:label>
</owl:Axiom>

These two triples are generated:

('GO:0005085', 'http://www.geneontology.org/formats/oboInOwl#hasDbXref', 'Reactome:R-HSA-170979') ('199', 'rdfs:label', '(Frs2)C3G stimulates nucleotide exchange on Rap1')

But in the second triple, the node 199 (that may change in different runs) seems not to be used anywhere else.

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ferzcam commented 2 years ago

I see, so those extra triples can be ignored. Thank you very much.