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Should edge_id's use the core_predicate when there is no qualified_predicate? #397

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ecwood opened this issue Jul 10, 2024 · 0 comments
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question Further information is requested sar-look Marks an issue that Steve needs to examine

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@ecwood
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ecwood commented Jul 10, 2024

While investigating biolink:causes for Unsecret Agent, I realized that edges without qualified predicates do not have a biolink predicate in their edge_id. For example:

{
  "negated": "False",
  "primary_knowledge_source": "infores:semmeddb",
  "relation_label": "causes",
  "subject": "UMLS:C1608383",
  "source_predicate": "SEMMEDDB:causes",
  "update_date": "2021-12-01 13:50:27",
  "predicate": "biolink:causes",
  "domain_range_exclusion": "False",
  "publications_info": "{'PMID:34846163': {'object score': '888', 'publication date': '2021 Nov 30', 'sentence': 'Identifying the most-expressed    var     gene sequences in whole-blood clinical samples without the need for extensive processing or generating sample-specific reference genome data is critical for understanding the role of PfEMP1s in malaria pathogenesis.', 'subject score': '916'}}",
  "predicate_label": "causes",
  "id": "UMLS:C1608383---SEMMEDDB:causes---None---None---None---UMLS:C0024530---SEMMEDDB:",
  "publications": [
    "PMID:34846163"
  ],
  "object": "UMLS:C0024530"
}

In contrast:

{
  "negated": "False",
  "primary_knowledge_source": "infores:drugbank",
  "qualified_object_aspect": "degradation",
  "qualified_predicate": "biolink:causes",
  "relation_label": "degradation",
  "subject": "DRUGBANK:DB06752",
  "source_predicate": "DRUGBANK:degradation",
  "predicate": "biolink:affects",
  "domain_range_exclusion": "False",
  "publications_info": "{'sentence': 'Heparin binding'}",
  "predicate_label": "degradation",
  "id": "DRUGBANK:DB06752---DRUGBANK:degradation---biolink:causes---degradation---None---UniProtKB:P13727---identifiers_org_registry:drugbank",
  "object": "UniProtKB:P13727"
}

@saramsey do you have any thoughts?

@ecwood ecwood added sar-look Marks an issue that Steve needs to examine question Further information is requested labels Jul 10, 2024
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