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add biolink prefix to qualified_predicate #206

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@andrewsu andrewsu commented Aug 9, 2024

In NCATSTranslator/Feedback#914, BTE is producing a result that fails TRAPI validation. The detailed validation error is:

		Critical:
		* Trapi:
		=> Schema validation error
			$ global
				# v1.5.0
				- component | json_path | reason: 
					KnowledgeGraph | $.edges.inferred-CHEBI:26216-affects-UniProtKB:Q8N6C7.qualifiers[0].qualifier_type_id | 'qualified_predicate' does not match '^biolink:[a-z][a-z_]*$'

The relevant section of the TRAPI is

                        "inferred-CHEBI:26216-affects-UniProtKB:Q8N6C7": {
                            "subject": "CHEBI:26216",
                            "object": "UniProtKB:Q8N6C7",
                            "predicate": "biolink:affects",
                            "sources": [
                                  [snip]
                            ],
                            "attributes": [
                                  [snip]
                            ],
                            "qualifiers": [
                                {
                                    "qualifier_type_id": "qualified_predicate",
                                    "qualifier_value": "causes"
                                },
                                {
                                    "qualifier_type_id": "object_aspect_qualifier",
                                    "qualifier_value": "activity_or_abundance"
                                },
                                {
                                    "qualifier_type_id": "object_direction_qualifier",
                                    "qualifier_value": "increased"
                                }
                            ]
                        },

I believe this PR would fix this error, but would like @colleenXu or @tokebe to review...

@andrewsu andrewsu requested review from tokebe and colleenXu August 9, 2024 16:11
@tokebe
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tokebe commented Aug 9, 2024

This will not fix the problem, templateGroup qualifiers are only used for matching. This commit should fix the issue.

@tokebe tokebe closed this Aug 9, 2024
@andrewsu andrewsu deleted the andrewsu-patch-1 branch August 9, 2024 16:54
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2 participants