VRS 2.0 Schema Modifications for VariationDescriptors

Step 1: Drop the "canonical_variation" item in the descriptor, and move all of its contained items ("id", "type", and "canonical_context") up a level.

Step 2: Change the type from "CanonicalVariationDescriptor" to "CanonicalVariation"

Step 3: Add a "digest" item to the top level containing just the digest portion of the CanonicalVariation "id" item at the top level.

Step 4: Change to outer level "id" field (in the form of ["id": "cgterms:VariationDescriptor_567576.2022-03-30"] to be of the form ["identifier": "clinvar:567576.2022-03-30]

There are other annotations contained in the sample mockup Larry provided: `{

"id": "ga4gh:CLV.yi7FnYRVHoVQzRebAXh_CQ0Syy8O_ezL",
"type": "CanonicalVariation",

"label": "NM_004360.5(CDH1):c.376_382dup (p.His128fs)",
"description": "NM_004360.5(CDH1):c.376_382dup (p.His128fs)",

"canonical_context": {

    "id": "ga4gh:VA.e64Sf4vI4oQGSTzIL1lWlm4hDnGniJHL",
    "type": "Allele",

    -- this allele is also decoratable... but we are not showing that here...

    "location": {

        "id": "ga4gh:SL.HQWgJ_9cBc9_T0hyAq1z3wdIjgrvivdo",
        "type": "SequenceLocation",

        -- this location is also decoratable... but we are not showing that here...

        "start": {
            "type": "Number",
            "value": 68801874
        },
        "end": {
            "type": "Number",
            "value": 68801888
        },

        -- we also need to convert this sequence_id into a 'sequence' object so that it too can be decoratable... TBD
        "sequence_id": "ga4gh:SQ.yC_0RBj3fgBlvgyAuycbzdubtLxq-rE0"

    },
    "state": {
        "type": "LiteralSequenceExpression",
        "sequence": "CCGCCCCCCGCCCCCCGCCCC"
    }

},

-- we need a new attribute or method for tagging equivalent xrefs, in clinvar that would involve a versioned clinvar variation id.
"identifier": "clinvar:567576.2022-03-30",
"xrefs": [
    "https://www.ncbi.nlm.nih.gov/clinvar/567576",
    "https://identifiers.org/clinvar:567576"
],

-- we may need to revisit the VariationMember structure to make sure these are expressable as Variations... TBD
"members": [
    {
        "type": "VariationMember",
        "expressions": [
            {
                "type": "Expression",
                "syntax": "hgvs.g",
                "value": "NG_008021.1:g.69584CCGCCCC[3]"
            }
        ]
    },
    {
        "type": "VariationMember",
        "expressions": [
            {
                "type": "Expression",
                "syntax": "hgvs.c",
                "value": "NM_001317184.2:c.376_382dup"
            }
        ]
    },
    {
        "type": "VariationMember",
        "expressions": [
            {
                "type": "Expression",
                "syntax": "hgvs.c",
                "value": "NM_004360.5(CDH1):c.369_375CCGCCCC[3]"
            }
        ]
    },
    {
        "type": "VariationMember",
        "expressions": [
            {
                "type": "Expression",
                "syntax": "hgvs.g",
                "value": "NC_000016.9:g.68835778CCGCCCC[3]"
            }
        ]
    },
    {
        "type": "VariationMember",
        "expressions": [
            {
                "type": "Expression",
                "syntax": "hgvs.p",
                "value": "NP_001304113.1:p.His128fs"
            }
        ]
    },
    {
        "type": "VariationMember",
        "expressions": [
            {
                "type": "Expression",
                "syntax": "hgvs.c",
                "value": "NM_001317186.2:c.-1451CCGCCCC[3]"
            }
        ]
    },
    {
        "type": "VariationMember",
        "expressions": [
            {
                "type": "Expression",
                "syntax": "hgvs.c",
                "value": "NM_001317185.2:c.-1247CCGCCCC[3]"
            }
        ]
    },
    {
        "type": "VariationMember",
        "expressions": [
            {
                "type": "Expression",
                "syntax": "spdi",
                "value": "NC_000016.10:68801874:CCGCCCCCCGCCCC:CCGCCCCCCGCCCCCCGCCCC"
            }
        ]
    },
    {
        "type": "VariationMember",
        "expressions": [
            {
                "type": "Expression",
                "syntax": "hgvs.p",
                "value": "NP_004351.1:p.His128fs"
            }
        ]
    },
    {
        "type": "VariationMember",
        "expressions": [
            {
                "type": "Expression",
                "syntax": "hgvs.c",
                "value": "NM_004360.5:c.376_382dup"
            }
        ]
    },
    {
        "type": "VariationMember",
        "expressions": [
            {
                "type": "Expression",
                "syntax": "hgvs.g",
                "value": "NC_000016.10:g.68801875CCGCCCC[3]"
            }
        ]
    },
    {
        "type": "VariationMember",
        "expressions": [
            {
                "type": "Expression",
                "syntax": "hgvs.g",
                "value": "LRG_301:g.69584CCGCCCC[3]"
            }
        ]
    }
]

This is a sample file that is in the current form (i.e. Version 1.0 form) - but it is not the variant.

{ "description": "NM_004360.5(CDH1):c.376_382dup (p.His128fs)", "type": "CanonicalVariationDescriptor", "xrefs": [ "https://www.ncbi.nlm.nih.gov/clinvar/567576", "https://identifiers.org/clinvar:567576" ], "canonical_variation": { "id": "ga4gh:CLV.yi7FnYRVHoVQzRebAXh_CQ0Syy8O_ezL", "type": "CanonicalVariation", "canonical_context": { "id": "ga4gh:VA.e64Sf4vI4oQGSTzIL1lWlm4hDnGniJHL", "type": "Allele", "location": { "id": "ga4gh:SL.HQWgJ_9cBc9_T0hyAq1z3wdIjgrvivdo", "type": "SequenceLocation", "sequence_id": "ga4gh:SQ.yC_0RBj3fgBlvgyAuycbzdubtLxq-rE0", "start": { "type": "Number", "value": 68801874 }, "end": { "type": "Number", "value": 68801888 } }, "state": { "type": "LiteralSequenceExpression", "sequence": "CCGCCCCCCGCCCCCCGCCCC" } } }, "label": "NM_004360.5(CDH1):c.376_382dup (p.His128fs)", "id": "cgterms:VariationDescriptor_567576.2022-03-30", "members": [ { "type": "VariationMember", "expressions": [ { "type": "Expression", "syntax": "hgvs.g", "value": "NG_008021.1:g.69584CCGCCCC[3]" } ] }, { "type": "VariationMember", "expressions": [ { "type": "Expression", "syntax": "hgvs.c", "value": "NM_001317184.2:c.376_382dup" } ] }, { "type": "VariationMember", "expressions": [ { "type": "Expression", "syntax": "hgvs.c", "value": "NM_004360.5(CDH1):c.369_375CCGCCCC[3]" } ] }, { "type": "VariationMember", "expressions": [ { "type": "Expression", "syntax": "hgvs.g", "value": "NC_000016.9:g.68835778CCGCCCC[3]" } ] }, { "type": "VariationMember", "expressions": [ { "type": "Expression", "syntax": "hgvs.p", "value": "NP_001304113.1:p.His128fs" } ] }, { "type": "VariationMember", "expressions": [ { "type": "Expression", "syntax": "hgvs.c", "value": "NM_001317186.2:c.-1451CCGCCCC[3]" } ] }, { "type": "VariationMember", "expressions": [ { "type": "Expression", "syntax": "hgvs.c", "value": "NM_001317185.2:c.-1247CCGCCCC[3]" } ] }, { "type": "VariationMember", "expressions": [ { "type": "Expression", "syntax": "spdi", "value": "NC_000016.10:68801874:CCGCCCCCCGCCCC:CCGCCCCCCGCCCCCCGCCCC" } ] }, { "type": "VariationMember", "expressions": [ { "type": "Expression", "syntax": "hgvs.p", "value": "NP_004351.1:p.His128fs" } ] }, { "type": "VariationMember", "expressions": [ { "type": "Expression", "syntax": "hgvs.c", "value": "NM_004360.5:c.376_382dup" } ] }, { "type": "VariationMember", "expressions": [ { "type": "Expression", "syntax": "hgvs.g", "value": "NC_000016.10:g.68801875CCGCCCC[3]" } ] }, { "type": "VariationMember", "expressions": [ { "type": "Expression", "syntax": "hgvs.g", "value": "LRG_301:g.69584CCGCCCC[3]" } ] } ] }

clingen-data-model / genegraph

VRS 2.0 Schema Modifications for VariationDescriptors #761