Skip to content

Importing ChEBI .owl ontology with n10s.rdf.import.fetch generates incorrect neo4j graph #324

@penguinoctopus

Description

@penguinoctopus

I am trying to import .owl file from official ChEBI website which can be downloaded by:

curl -O https://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl

I am using Neo4j 5.20.0 and the neosemantics .jar found at:

https://github.com/neo4j-labs/neosemantics/releases

logging seems to be set up correctly (I am using slf4j-api-2.0.7.jar and slf4j-simple-2.0.7.jar) and I see no errors when starting neo4j with neo4j start. After running the following commands:

CALL n10s.graphconfig.init();
CALL n10s.rdf.import.fetch("file:///C:/Users/nikit/Downloads/chebi.owl", "RDF/XML");

In neo4j, the ontology is imported fine, no errors, but when I am trying to inspect the nodes and relationships - they are just wrong: it does not have many relationships, node properties that should be there. I asked the ChEBI support and inspected their .owl but on their side everything is fine, so I think it is neosemantics.jar issue here. Just as an example: nodes have no :ChEBI labels (but they should) and no has_role relationships:

https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:46195

I have also asked the question on neo4j forum:

https://community.neo4j.com/t/import-of-chebi-owl-seems-not-correct/68480

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions