fix(datamodel): restructured genomic variants and interpretations tables #5088
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Wait for #5095 before merging |
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davidruvolo51
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mswertz
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davidruvolo51
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davidruvolo51
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Jul 19, 2025
data/_demodata/applications/patient_registry/Genomic variants.csv
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data/_demodata/applications/patient_registry/Variant interpretation analyses.csv
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data/_demodata/applications/patient_registry/Variant interpretations.csv
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| Genomic variants,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C17248,Beacon v2 GenomicVariation see also https://www.ga4gh.org/product/categorical-variation-catvar/,Patient registry | ||
| Genomic variants,,id,string,1,TRUE,,,,,,"http://purl.obolibrary.org/obo/NCIT_C164813,bc2:variantInternalId",A unique identifier maintained by an authoritative database that represents a genetic variation. E.g. 20:2447955..2447958c>g,Patient registry | ||
| Genomic variants,,alternative ids,string_array,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C90353,A backup sequence of characters used to identify an entity,Patient registry | ||
| Genomic variants,,variant status,ontology,,,CatalogueOntologies,Status,,,,http://semanticscience.org/resource/SIO_000033,"An characterisation of the variant that indicates the state or progress (e.g., confirmed, to be verified, etc.)",Patient registry |
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See comment above. Still not sure if this is genius or strange. Maybe we should go with genius, but then we need some evidence linked from either inside (a variant interpretation refback) or external (e.g. a URI to clinvar)
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What are the main changes you did
This PR is part of molgenis/GCC#1084.
Variant interpretationsHow to test
PATIENT_REGISTRYtemplate and load the demo dataVariant interpretations,Interpretation consensus,Variant interpretation analysesChecklist