Named alleles

[apriltuesday]

Better diff of test output here

Example named-allele evidence:

{
  "datasourceId": "pharmgkb",
  "datasourceVersion": "2024-01-05",
  "datatypeId": "clinical_annotation",
  "studyId": "1448104189",
  "evidenceLevel": "2A",
  "literature": [
    "16338275",
    "17329992",
    "26389554",
    "26389554",
    "27286724",
    "17178267",
    "17502774",
    "17502774",
    "21589866",
    "28723731",
    "28723731",
    "32302325"
  ],
  "genotype": "*6",
  "genotypeAnnotationText": "Patients carrying the CYP2B6*6 allele in combination with a normal or decreased function allele may have decreased clearance of methadone as compared to patients with two normal function alleles. However, conflicting evidence has been reported. Other genetic and clinical factors may also affect methadone metabolism. This annotation only covers the pharmacokinetic relationship between CYP2B6 and methadone and does not include evidence about clinical outcomes.",
  "directionality": "Decreased function",
  "drugFromSource": "methadone",
  "drugFromSourceId": "CHEBI_6807",
  "pgxCategory": "metabolism/pk",
  "phenotypeText": "Heroin Dependence",
  "phenotypeFromSourceId": "EFO_0004240",
  "haplotypeId": "CYP2B6*6",
  "haplotypeFromSourceId": "PA165818762",
  "targetFromSourceId": "ENSG00000197408"
}

[tcezard]

The changes looks ok.
The current model (if kept as is) would have to thoroughly explain though because it is a bit confusing.
The new haplotypeId seems to make sense since the named alleles represent haplotypes but in some case it won't match. (haplotypeId: GSTT1 non-null/non-null). Maybe we should discuss with OT to have a more appropriate name
For the genotype, it is similarly ambiguous although more often wrong than right.

The options are:

• Changing the name to something that reflect the heterogenicity of the data
• Document the heterogenicity in the field's description.

[apriltuesday]

Updates to schema as per this thread