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feat: propagating schema metadata
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@DSuveges
DSuveges committed Feb 28, 2025
1 parent e25dedd commit f5dfc76
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Showing 3 changed files with 137 additions and 44 deletions.
164 changes: 123 additions & 41 deletions src/gentropy/assets/schemas/variant_index.json
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Original file line number Diff line number Diff line change
@@ -1,75 +1,99 @@
{
"fields": [
{
"metadata": {},
"metadata": {
"description": "The unique identifier for the variant following schema: {chromosome}-{position}-{referenceAllele}-{alternateAllele}"
},
"name": "variantId",
"nullable": false,
"type": "string"
},
{
"metadata": {},
"metadata": {
"description": "The chromosome on which the variant is located"
},
"name": "chromosome",
"nullable": false,
"type": "string"
},
{
"metadata": {},
"metadata": {
"description": "The position on the chromosome of the variant"
},
"name": "position",
"nullable": false,
"type": "integer"
},
{
"metadata": {},
"metadata": {
"description": "The reference allele for the variant"
},
"name": "referenceAllele",
"nullable": false,
"type": "string"
},
{
"metadata": {},
"metadata": {
"description": "The alternate allele for the variant"
},
"name": "alternateAllele",
"nullable": false,
"type": "string"
},
{
"metadata": {},
"metadata": {
"description": "List predicted or measured effect of the variant based on various methods"
},
"name": "variantEffect",
"nullable": true,
"type": {
"containsNull": true,
"elementType": {
"fields": [
{
"metadata": {},
"metadata": {
"description": "The method name used to predict the effect of the variant"
},
"name": "method",
"nullable": true,
"type": "string"
},
{
"metadata": {},
"metadata": {
"description": "Textual assessment of the variant effect"
},
"name": "assessment",
"nullable": true,
"type": "string"
},
{
"metadata": {},
"metadata": {
"description": "The score of the variant effect"
},
"name": "score",
"nullable": true,
"type": "float"
},
{
"metadata": {},
"metadata": {
"description": "Flagging if the variant effect is considered pathogenic"
},
"name": "assessmentFlag",
"nullable": true,
"type": "string"
},
{
"metadata": {},
"metadata": {
"description": "The target identifier on which the variant effect is interpreted"
},
"name": "targetId",
"nullable": true,
"type": "string"
},
{
"metadata": {},
"metadata": {
"description": "Variant effect normalised between -1 and 1"
},
"name": "normalisedScore",
"nullable": true,
"type": "double"
Expand All @@ -81,7 +105,9 @@
}
},
{
"metadata": {},
"metadata": {
"description": "The sequence ontology identifier of the most severe consequence of the variant based on VEP"
},
"name": "mostSevereConsequenceId",
"nullable": true,
"type": "string"
Expand All @@ -95,7 +121,9 @@
"elementType": {
"fields": [
{
"metadata": {},
"metadata": {
"description": "The sequence ontology identifier of the consequence of the variant based on VEP in the context of the transcript"
},
"name": "variantFunctionalConsequenceIds",
"nullable": true,
"type": {
Expand All @@ -105,13 +133,17 @@
}
},
{
"metadata": {},
"metadata": {
"description": "The amino acide change caused by this variant on this gene"
},
"name": "aminoAcidChange",
"nullable": true,
"type": "string"
},
{
"metadata": {},
"metadata": {
"description": "List of Uniprot identifiers of the gene product"
},
"name": "uniprotAccessions",
"nullable": true,
"type": {
Expand All @@ -121,97 +153,129 @@
}
},
{
"metadata": {},
"metadata": {
"description": "Flagging if the transcript is the canonical transcript for the gene"
},
"name": "isEnsemblCanonical",
"nullable": false,
"type": "boolean"
},
{
"metadata": {},
"metadata": {
"description": "The affected codon in the transcript"
},
"name": "codons",
"nullable": true,
"type": "string"
},
{
"metadata": {},
"metadata": {
"description": "The distance of the variant from the transcript"
},
"name": "distanceFromFootprint",
"nullable": true,
"type": "long"
},
{
"metadata": {},
"metadata": {
"description": "The distance of the variant from the transcription start site"
},
"name": "distanceFromTss",
"nullable": true,
"type": "long"
},
{
"metadata": {},
"metadata": {
"description": "The appris annotation of the transcript"
},
"name": "appris",
"nullable": true,
"type": "string"
},
{
"metadata": {},
"metadata": {
"description": "MANE annotation of the transcript"
},
"name": "maneSelect",
"nullable": true,
"type": "string"
},
{
"metadata": {},
"metadata": {
"description": "Ensembl gene identifier"
},
"name": "targetId",
"nullable": true,
"type": "string"
},
{
"metadata": {},
"metadata": {
"description": "VEP predicted impact of the variant on the transcript"
},
"name": "impact",
"nullable": true,
"type": "string"
},
{
"metadata": {},
"metadata": {
"description": "Loss of function prediction based on LOFTEE"
},
"name": "lofteePrediction",
"nullable": true,
"type": "string"
},
{
"metadata": {},
"metadata": {
"description": "SIFT prediction of the variant impact on the transcript"
},
"name": "siftPrediction",
"nullable": true,
"type": "float"
},
{
"metadata": {},
"metadata": {
"description": "Polyphen prediction of the variant impact on the transcript"
},
"name": "polyphenPrediction",
"nullable": true,
"type": "float"
},
{
"metadata": {},
"metadata": {
"description": "Score based on VEP consequence"
},
"name": "consequenceScore",
"nullable": true,
"type": "float"
},
{
"metadata": {},
"metadata": {
"description": "The index of the transcript in the list of transcripts around the gene"
},
"name": "transcriptIndex",
"nullable": true,
"type": "integer"
},
{
"metadata": {},
"metadata": {
"description": "The HGNC gene symbol of the gene"
},
"name": "approvedSymbol",
"nullable": true,
"type": "string"
},
{
"metadata": {},
"metadata": {
"description": "Biotype of the transcript"
},
"name": "biotype",
"nullable": true,
"type": "string"
},
{
"metadata": {},
"metadata": {
"description": "The Ensembl transcript identifier"
},
"name": "transcriptId",
"nullable": true,
"type": "string"
Expand All @@ -223,7 +287,9 @@
}
},
{
"metadata": {},
"metadata": {
"description": "The list of rsIds for the variant"
},
"name": "rsIds",
"nullable": true,
"type": {
Expand All @@ -233,7 +299,9 @@
}
},
{
"metadata": {},
"metadata": {
"description": "HGVS identifier of the variant"
},
"name": "hgvsId",
"nullable": true,
"type": "string"
Expand All @@ -249,37 +317,49 @@
"name": "populationName",
"type": "string",
"nullable": true,
"metadata": {}
"metadata": {
"description": "Name of the population"
}
},
{
"name": "alleleFrequency",
"type": "double",
"nullable": true,
"metadata": {}
"metadata": {
"description": "The frequency of the alternate allele in the population"
}
}
]
},
"containsNull": true
},
"nullable": true,
"metadata": {}
"metadata": {
"description": "The allele frequencies of the variant in different populations"
}
},
{
"metadata": {},
"metadata": {
"description": "The list of cross-references for the variant in different databases"
},
"name": "dbXrefs",
"nullable": true,
"type": {
"containsNull": true,
"elementType": {
"fields": [
{
"metadata": {},
"metadata": {
"description": "Identifier of the variant in the given database"
},
"name": "id",
"nullable": true,
"type": "string"
},
{
"metadata": {},
"metadata": {
"description": "Name of the database"
},
"name": "source",
"nullable": true,
"type": "string"
Expand All @@ -291,7 +371,9 @@
}
},
{
"metadata": {},
"metadata": {
"description": "Short summary of the variant effect"
},
"name": "variantDescription",
"nullable": true,
"type": "string"
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