duchenne.json does not conform to specification

[cmungall]

I am using the experimental linkml rendering of phenopackets which has more rigorous validation that protobuf

It finds an error with:

https://github.com/phenopackets/phenopacket-tools/blob/gh-pages/examples/phenopackets/duchenne.json

specifically the variantInterpretation

phenopacket-tools/examples/phenopackets/duchenne.json

Lines 76 to 116 in 2cb8966

	"variantInterpretation": {
	"acmgPathogenicityClassification": "PATHOGENIC",
	"variationDescriptor": {
	"variation": {
	"copyNumber": {
	"allele": {
	"sequenceLocation": {
	"sequenceId": "refseq:NC_000023.11",
	"sequenceInterval": {
	"startNumber": {
	"value": "31774144"
	},
	"endNumber": {
	"value": "31785736"
	}
	}
	}
	},
	"number": {
	"value": "1"
	}
	}
	},
	"geneContext": {
	"valueId": "HGNC:2928",
	"symbol": "DMD"
	},
	"expressions": [{
	"syntax": "hgvs.c",
	"value": "NM_004006.3:c.7310-11543_7359del"
	}, {
	"syntax": "transcript_reference",
	"value": "NM_004006.3"
	}],
	"moleculeContext": "genomic",
	"allelicState": {
	"id": "GENO:0000134",
	"label": "hemizygous"
	}
	}
	}

lacks an id as specified in the comments here https://phenopacket-schema.readthedocs.io/en/latest/variant.html

[cmungall]

also:

• retinoblastoma
• holoprosencephaly5

[ielis]

Hi @cmungall
thanks for pointing this out. Yes, the code that works with VRS-like is a weak spot of the library/app.
We may need to adjust the builders on the go as I am having serious trouble with understanding the VRS specification. I am coming from a VCF/HGVS world and I am not sure how one can map variant types commonly encountered in those nomenclatures.

In #150 I reworked the examples to ensure they are valid according to phenopacket-tools base validator.