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TRAPI validation issues with new Multiomics KPs #877

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colleenXu opened this issue Oct 1, 2024 · 1 comment
Open

TRAPI validation issues with new Multiomics KPs #877

colleenXu opened this issue Oct 1, 2024 · 1 comment
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external Requires fixes to an external service

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@colleenXu
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colleenXu commented Oct 1, 2024

Related to #865

@gglusman

(TRAPI "orange" errors don't prevent ARS from using BTE's response)

TRAPI "orange" error on edge-attribute's attribute_type_id

Examples from Multiomics drug-approvals

Noticed in https://arax.ci.transltr.io/?r=a2607f33-0e13-402c-a0fb-5282f7540ad3 (see BTE's TRAPI validation).

  • approval
		=> Edge has a value that is not a CURIE for attribute_type_id
			$ infores:dailymed -> infores:multiomics-drugapprovals -> infores:biothings-explorer
				# approval
				- edge_id: 
					CHEBI:5384[biolink:SmallMolecule]--biolink:treats->MONDO:0005147[biolink:Disease]
					CHEBI:188719[biolink:SmallMolecule]--biolink:treats->MONDO:0005147[biolink:Disease]
					CHEBI:40237[biolink:SmallMolecule]--biolink:treats->MONDO:0005147[biolink:Disease]

Examples from Multiomics clinical-trials

Noticed in https://arax.ci.transltr.io/?r=a2607f33-0e13-402c-a0fb-5282f7540ad3 (see BTE's TRAPI validation).

  • subject_boxed_warning
  • biolink:supporting_study_metadata
			$ infores:clinicaltrials -> infores:aact -> infores:multiomics-clinicaltrials -> infores:biothings-explorer
				# subject_boxed_warning
				- edge_id: 
					CHEBI:135922[biolink:SmallMolecule]--biolink:treats->MONDO:0005147[biolink:Disease]
					CHEBI:85078[biolink:SmallMolecule]--biolink:treats->MONDO:0005147[biolink:Disease]
					CHEBI:82720[biolink:SmallMolecule]--biolink:treats->MONDO:0005147[biolink:Disease]
		=> Edge is not permitted to have an 'abstract' attribute_type_id
			$ infores:clinicaltrials -> infores:aact -> infores:multiomics-clinicaltrials -> infores:biothings-explorer
				# biolink:supporting_study_metadata
				- edge_id: 
					UNII:GFX7QIS1II[biolink:MolecularMixture]--biolink:treats->MONDO:0005147[biolink:Disease]
					UNII:GFX7QIS1II[biolink:MolecularMixture]--biolink:treats->MONDO:0005147[biolink:Disease]
					UNII:GFX7QIS1II[biolink:MolecularMixture]--biolink:in_clinical_trials_for->MONDO:0005147[biolink:Disease]

@colleenXu colleenXu added the external Requires fixes to an external service label Oct 1, 2024
@gglusman
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gglusman commented Oct 1, 2024

Thanks! Better modeling of this is in progress w/Matt & Sierra.

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