MONDO:0000432 Self-Loop JSON Loading

[iimpulse]

MONDO:0000432

Bug/Typo/Error description
When loading the simple base graph with our internal ontology load phenol we fail to parse the graph to due a self referencing loop.

Self-loop edge: Relationship [source=MONDO:0000432, target=MONDO:0000432, id=361, relationshipType=RelationshipType{id='http://purl.obolibrary.org/obo/RO_0004029', label='disease has feature'}]',

https://orcid.org/0000-0002-2157-3591

[matentzn]

Which file are you using?

[matentzn]

This is the cycle:

[Term]
id: MONDO:0000432
....
relationship: disease_has_feature MONDO:0000432 {source="MONDO:Wikidata"} ! lymphoplasmacytic lymphoma

MONDO:0000432 is a phenotypic feature of itself.

• Add QC check to ensure this does not happen again add qc check for cycles #7961
• Fix by removing the disease_has_feature MONDO:0000432 assertion remove assertion causing cycle #7960

[matentzn]

Here is the qc check that need to be added:

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix IAO: <http://purl.obolibrary.org/obo/IAO_>
prefix MONDO: <http://purl.obolibrary.org/obo/MONDO_>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix oio: <http://www.geneontology.org/formats/oboInOwl#>
prefix def: <http://purl.obolibrary.org/obo/IAO_0000115>
prefix owl: <http://www.w3.org/2002/07/owl#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX RO: <http://purl.obolibrary.org/obo/RO_>


SELECT ?entity ?property ?value 

WHERE
{
  VALUES ?property { RO:0004003 RO:0004029 }
  ?entity rdfs:subClassOf [
        owl:onProperty ?property ;
        owl:someValuesFrom ?entity
      ] .
  BIND ("Self cycle detected" as ?value)
} 

@twhetzel can you take this on? This is a real bug and should be fixed before the release I think!

[twhetzel]

Sure, I can do this.