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larrybabblarrybabb
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convert 2.0.0-snapshot.2025-02 branch to 2.0 release ready branch (#638)
* convert 2.0.0-snapshot.2025-02 branch to 2.0 release ready branch * update sm + fix schema ids to 2.0.0
1 parent 2a77d5f commit 42398be

26 files changed

+103
-103
lines changed

‎.gitmodules

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@@ -1,4 +1,4 @@
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[submodule "submodules/gks-core"]
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path = submodules/gks-core
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url = https://github.com/ga4gh/gks-core.git
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branch = 1.0.0-snapshot.2025-02
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branch = 1.0

‎.requirements.txt

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@@ -3,7 +3,7 @@ jsonschema
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referencing
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ipython
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pyyaml
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ga4gh.gks.metaschema==0.3.1
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ga4gh.gks.metaschema==0.3.2
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sphinx ~= 7.2
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sphinx-rtd-theme ~= 1.2
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jupyterlab

‎schema/vrs/json/Adjacency

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{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/Adjacency",
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"$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/Adjacency",
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"title": "Adjacency",
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"type": "object",
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"maturity": "trial use",
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"type": "array",
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"ordered": false,
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"items": {
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"$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.4/json/Extension"
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"$ref": "/ga4gh/schema/gks-core/1.0.0/json/Extension"
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},
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"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
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"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
@@ -53,7 +53,7 @@
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"type": "array",
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"ordered": false,
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"items": {
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/Expression"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/Expression"
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}
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},
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"type": {
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"items": {
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"oneOf": [
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{
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/SequenceLocation"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/SequenceLocation"
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},
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{
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"$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.4/json/iriReference"
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"$ref": "/ga4gh/schema/gks-core/1.0.0/json/iriReference"
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}
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],
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"not": {
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"description": "The sequence found between adjoined sequences.",
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"oneOf": [
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{
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/LengthExpression"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/LengthExpression"
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},
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{
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/LiteralSequenceExpression"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/LiteralSequenceExpression"
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},
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{
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/ReferenceLengthExpression"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/ReferenceLengthExpression"
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}
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]
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},

‎schema/vrs/json/Allele

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@@ -1,6 +1,6 @@
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{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/Allele",
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"$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/Allele",
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"title": "Allele",
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"type": "object",
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"maturity": "trial use",
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"type": "array",
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"ordered": false,
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"items": {
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"$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.4/json/Extension"
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"$ref": "/ga4gh/schema/gks-core/1.0.0/json/Extension"
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},
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"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
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"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
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"type": "array",
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"ordered": false,
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"items": {
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/Expression"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/Expression"
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}
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},
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"type": {
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"location": {
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"oneOf": [
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{
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/SequenceLocation"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/SequenceLocation"
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},
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{
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"$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.4/json/iriReference"
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"$ref": "/ga4gh/schema/gks-core/1.0.0/json/iriReference"
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}
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],
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"description": "The location of the Allele"
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"description": "An expression of the sequence state",
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"oneOf": [
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{
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/LengthExpression"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/LengthExpression"
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},
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{
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/LiteralSequenceExpression"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/LiteralSequenceExpression"
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},
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{
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/ReferenceLengthExpression"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/ReferenceLengthExpression"
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}
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]
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}

‎schema/vrs/json/CisPhasedBlock

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{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/CisPhasedBlock",
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"$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/CisPhasedBlock",
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"title": "CisPhasedBlock",
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"type": "object",
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"maturity": "trial use",
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"type": "array",
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"ordered": false,
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"items": {
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"$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.4/json/Extension"
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"$ref": "/ga4gh/schema/gks-core/1.0.0/json/Extension"
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},
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"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
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"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
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"type": "array",
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"ordered": false,
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"items": {
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/Expression"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/Expression"
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}
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},
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"type": {
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"items": {
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"oneOf": [
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{
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/Allele"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/Allele"
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},
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{
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"$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.4/json/iriReference"
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"$ref": "/ga4gh/schema/gks-core/1.0.0/json/iriReference"
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}
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]
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},
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"description": "A list of Alleles that are found in-cis on a shared molecule."
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},
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"sequenceReference": {
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/SequenceReference",
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/SequenceReference",
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"description": "An optional Sequence Reference on which all of the in-cis Alleles are found. When defined, this may be used to implicitly define the `sequenceReference` attribute for each of the CisPhasedBlock member Alleles."
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}
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},

‎schema/vrs/json/CopyNumberChange

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{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/CopyNumberChange",
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"$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/CopyNumberChange",
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"title": "CopyNumberChange",
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"type": "object",
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"maturity": "draft",
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"type": "array",
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"ordered": false,
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"items": {
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"$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.4/json/Extension"
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"$ref": "/ga4gh/schema/gks-core/1.0.0/json/Extension"
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},
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"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
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"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
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"type": "array",
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"ordered": false,
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"items": {
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/Expression"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/Expression"
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}
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},
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"type": {
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"location": {
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"oneOf": [
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{
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/SequenceLocation"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/SequenceLocation"
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},
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{
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"$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.4/json/iriReference"
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"$ref": "/ga4gh/schema/gks-core/1.0.0/json/iriReference"
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}
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],
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"description": "The location of the subject of the copy change."
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},
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"copyChange": {
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"description": "MUST use a `primaryCode` representing one of \"EFO:0030069\" (complete genomic loss), \"EFO:0020073\" (high-level loss), \"EFO:0030068\" (low-level loss), \"EFO:0030067\" (loss), \"EFO:0030064\" (regional base ploidy), \"EFO:0030070\" (gain), \"EFO:0030071\" (low-level gain), \"EFO:0030072\" (high-level gain).",
78-
"$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.4/json/MappableConcept"
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"$ref": "/ga4gh/schema/gks-core/1.0.0/json/MappableConcept"
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}
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},
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"required": [

‎schema/vrs/json/CopyNumberCount

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{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/CopyNumberCount",
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"$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/CopyNumberCount",
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"title": "CopyNumberCount",
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"type": "object",
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"maturity": "trial use",
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"type": "array",
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"ordered": false,
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"items": {
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"$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.4/json/Extension"
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"$ref": "/ga4gh/schema/gks-core/1.0.0/json/Extension"
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},
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"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
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"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
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"type": "array",
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"ordered": false,
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"items": {
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/Expression"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/Expression"
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}
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},
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"type": {
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"location": {
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"oneOf": [
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{
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/SequenceLocation"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/SequenceLocation"
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},
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{
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"$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.4/json/iriReference"
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"$ref": "/ga4gh/schema/gks-core/1.0.0/json/iriReference"
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}
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],
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"description": "The location of the subject of the copy count."
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},
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"copies": {
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"oneOf": [
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{
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/Range"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/Range"
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},
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{
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"type": "integer"

‎schema/vrs/json/DerivativeMolecule

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{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/DerivativeMolecule",
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"$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/DerivativeMolecule",
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"title": "DerivativeMolecule",
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"type": "object",
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"maturity": "draft",
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"type": "array",
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"ordered": false,
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"items": {
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"$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.4/json/Extension"
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"$ref": "/ga4gh/schema/gks-core/1.0.0/json/Extension"
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},
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"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
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"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
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"type": "array",
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"ordered": false,
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"items": {
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/Expression"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/Expression"
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}
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},
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"type": {
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"items": {
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"oneOf": [
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{
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/Allele"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/Allele"
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},
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{
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/CisPhasedBlock"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/CisPhasedBlock"
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},
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{
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/Terminus"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/Terminus"
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},
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{
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/TraversalBlock"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/TraversalBlock"
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},
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{
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"$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.4/json/iriReference"
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"$ref": "/ga4gh/schema/gks-core/1.0.0/json/iriReference"
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}
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]
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},

‎schema/vrs/json/Expression

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{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/Expression",
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"$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/Expression",
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"title": "Expression",
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"type": "object",
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"maturity": "trial use",
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"type": "array",
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"ordered": false,
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"items": {
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"$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.4/json/Extension"
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"$ref": "/ga4gh/schema/gks-core/1.0.0/json/Extension"
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},
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"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
2020
"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."

‎schema/vrs/json/LengthExpression

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{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/LengthExpression",
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"$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/LengthExpression",
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"title": "LengthExpression",
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"type": "object",
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"maturity": "draft",
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"type": "array",
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"ordered": false,
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"items": {
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"$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.4/json/Extension"
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"$ref": "/ga4gh/schema/gks-core/1.0.0/json/Extension"
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},
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"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
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"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
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"description": "The length of the sequence.",
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"oneOf": [
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{
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/Range"
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/Range"
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},
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{
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"type": "integer"

‎schema/vrs/json/LiteralSequenceExpression

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{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/LiteralSequenceExpression",
3+
"$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/LiteralSequenceExpression",
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"title": "LiteralSequenceExpression",
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"type": "object",
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"maturity": "trial use",
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"type": "array",
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"ordered": false,
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"items": {
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"$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.4/json/Extension"
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"$ref": "/ga4gh/schema/gks-core/1.0.0/json/Extension"
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},
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"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
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"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
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"default": "LiteralSequenceExpression"
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},
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"sequence": {
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"$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.4/json/sequenceString",
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"$ref": "/ga4gh/schema/vrs/2.0.0/json/sequenceString",
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"description": "the literal sequence"
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}
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},

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