Gene¶
Referenced schema · Source · Dereferenced version
A gene concept, with the sequence locations of its MANE Select transcript and protein product.
Fields¶
| Field | Type | Required | Description |
|---|---|---|---|
id |
string matching ^gene:hgnc:\d+$ |
yes | |
conceptType |
always Gene |
yes | |
name |
string | yes | |
primary_coding_id |
string matching ^coding:[a-z]+:.+$ |
yes | Foreign key to codings.id. |
mappings |
array of string matching ^map:.+::.+$ |
yes | |
cds_start |
integer at least 0 | yes | |
location |
string | yes | |
location_sortable |
string | yes | |
protein_product |
string matching ^ga4gh:SL.[A-Za-z0-9_-]{32}$ |
yes | Foreign key to sequence_locations.id. |
protein_product_exons |
array of string matching ^ga4gh:SL.[A-Za-z0-9_-]{32}$ |
yes | |
transcript |
string matching ^ga4gh:SL.[A-Za-z0-9_-]{32}$ |
yes | Foreign key to sequence_locations.id. |
transcript_exons |
array of string matching ^ga4gh:SL.[A-Za-z0-9_-]{32}$ |
yes |
JSON Schema¶
Full JSON Schema
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://moalmanac.org/schemas/referenced/genes.schema.json",
"title": "Gene",
"description": "A gene concept, with the sequence locations of its MANE Select transcript and protein product.",
"type": "object",
"properties": {
"id": {
"type": "string",
"pattern": "^gene:hgnc:\\d+$"
},
"conceptType": {
"const": "Gene"
},
"name": {
"type": "string"
},
"primary_coding_id": {
"type": "string",
"pattern": "^coding:[a-z]+:.+$",
"description": "Foreign key to `codings.id`."
},
"mappings": {
"type": "array",
"items": {
"type": "string",
"pattern": "^map:.+::.+$",
"description": "Foreign key to `mappings.id`."
}
},
"cds_start": {
"type": "integer",
"minimum": 0
},
"location": {
"type": "string"
},
"location_sortable": {
"type": "string"
},
"protein_product": {
"type": "string",
"pattern": "^ga4gh:SL\\.[A-Za-z0-9_-]{32}$",
"description": "Foreign key to `sequence_locations.id`."
},
"protein_product_exons": {
"type": "array",
"items": {
"type": "string",
"pattern": "^ga4gh:SL\\.[A-Za-z0-9_-]{32}$",
"description": "Foreign key to `sequence_locations.id`."
}
},
"transcript": {
"type": "string",
"pattern": "^ga4gh:SL\\.[A-Za-z0-9_-]{32}$",
"description": "Foreign key to `sequence_locations.id`."
},
"transcript_exons": {
"type": "array",
"items": {
"type": "string",
"pattern": "^ga4gh:SL\\.[A-Za-z0-9_-]{32}$",
"description": "Foreign key to `sequence_locations.id`."
}
}
},
"required": [
"id",
"conceptType",
"name",
"primary_coding_id",
"mappings",
"cds_start",
"location",
"location_sortable",
"protein_product",
"protein_product_exons",
"transcript",
"transcript_exons"
],
"additionalProperties": false
}