Genes¶
For most users, the primary entry point for the CIViC API will be the Genes endpoint. This endpoint allows a user to retrieve information about what genes are in CIViC as well as get lists of variants for specific genes.
Get a list of genes¶
This endpoint returns a listing of genes in CIViC that contain at least one evidence item. Returned gene listings contain variant ids which can be used to query for more detailed variant information. This is an index style endpoint and is paginated by default. You can use the count and page parameters to iterate through all the variants.
HTTP Request Format
GET https://civicdb.org/api/genes
Query Parameters
Parameter |
Default |
Description |
|---|---|---|
page |
1 |
Which page of results to return |
count |
25 |
How many genes to return on a single page |
Example Request
curl https://civicdb.org/api/genes?count=1
Example Response
{
"_meta": {
"current_page": 1,
"per_page": "1",
"total_pages": 332,
"total_count": 332,
"links": {
"next": "https://v1.civicdb.org/api/genes?count=1&page=2",
"previous": null
}
},
"records": [
{
"id": 1,
"name": "ALK",
"entrez_id": 238,
"description": "ALK amplifications, fusions and mutations have been shown to be driving events in non-small cell lung cancer. While crizontinib has demonstrated efficacy in treating the amplification, mutations in ALK have been shown to confer resistance to current tyrosine kinase inhibitors. Second-generation TKI's have seen varied success in treating these resistant cases, and the HSP90 inhibitor 17-AAG has been shown to be cytostatic in ALK-altered cell lines.",
"flagged": false,
"variants": [
{
"name": "CAD::ALK",
"id": 2769,
"evidence_items": {
"accepted_count": 1,
"rejected_count": 0,
"submitted_count": 0
}
},
{
"name": "EML4::ALK L1152R",
"id": 307,
"evidence_items": {
"accepted_count": 1,
"rejected_count": 0,
"submitted_count": 0
}
},
{
"name": "HIP1::ALK I1171N",
"id": 588,
"evidence_items": {
"accepted_count": 1,
"rejected_count": 0,
"submitted_count": 2
}
},
{
"name": "RANBP2::ALK",
"id": 514,
"evidence_items": {
"accepted_count": 1,
"rejected_count": 0,
"submitted_count": 0
}
},
{
"name": "EML4::ALK C1156Y",
"id": 6,
"evidence_items": {
"accepted_count": 4,
"rejected_count": 2,
"submitted_count": 7
}
},
{
"name": "EML4::ALK V1180L",
"id": 528,
"evidence_items": {
"accepted_count": 5,
"rejected_count": 0,
"submitted_count": 0
}
},
{
"name": "Exon 4-11 Deletion",
"id": 550,
"evidence_items": {
"accepted_count": 1,
"rejected_count": 0,
"submitted_count": 0
}
},
{
"name": "Mutation",
"id": 512,
"evidence_items": {
"accepted_count": 1,
"rejected_count": 0,
"submitted_count": 0
}
},
{
"name": "EML4::ALK",
"id": 5,
"evidence_items": {
"accepted_count": 7,
"rejected_count": 0,
"submitted_count": 1
}
},
{
"name": "EML4::ALK S1206Y",
"id": 172,
"evidence_items": {
"accepted_count": 2,
"rejected_count": 0,
"submitted_count": 2
}
},
{
"name": "EML4::ALK and Amplification",
"id": 170,
"evidence_items": {
"accepted_count": 3,
"rejected_count": 0,
"submitted_count": 0
}
},
{
"name": "CLTC::ALK",
"id": 520,
"evidence_items": {
"accepted_count": 3,
"rejected_count": 0,
"submitted_count": 0
}
},
{
"name": "EML4::ALK e2-e20",
"id": 501,
"evidence_items": {
"accepted_count": 2,
"rejected_count": 0,
"submitted_count": 0
}
},
{
"name": "EML4::ALK e6-e20",
"id": 503,
"evidence_items": {
"accepted_count": 7,
"rejected_count": 0,
"submitted_count": 0
}
},
{
"name": "R1275Q",
"id": 9,
"evidence_items": {
"accepted_count": 6,
"rejected_count": 0,
"submitted_count": 3
}
},
{
"name": "F1245V",
"id": 1295,
"evidence_items": {
"accepted_count": 1,
"rejected_count": 1,
"submitted_count": 0
}
},
{
"name": "Alternative Transcript (ATI)",
"id": 839,
"evidence_items": {
"accepted_count": 2,
"rejected_count": 0,
"submitted_count": 2
}
},
{
"name": "I1171T",
"id": 3371,
"evidence_items": {
"accepted_count": 1,
"rejected_count": 0,
"submitted_count": 0
}
},
{
"name": "EML4::ALK I1171S",
"id": 589,
"evidence_items": {
"accepted_count": 1,
"rejected_count": 0,
"submitted_count": 1
}
},
{
"name": "F1174L",
"id": 8,
"evidence_items": {
"accepted_count": 9,
"rejected_count": 0,
"submitted_count": 3
}
},
{
"name": "STRN::ALK",
"id": 2218,
"evidence_items": {
"accepted_count": 1,
"rejected_count": 0,
"submitted_count": 0
}
},
{
"name": "ALK Fusion G1269A",
"id": 552,
"evidence_items": {
"accepted_count": 4,
"rejected_count": 0,
"submitted_count": 0
}
},
{
"name": "ALK Fusion G1202R",
"id": 171,
"evidence_items": {
"accepted_count": 6,
"rejected_count": 0,
"submitted_count": 3
}
},
{
"name": "ALK Fusion I1171",
"id": 527,
"evidence_items": {
"accepted_count": 7,
"rejected_count": 0,
"submitted_count": 3
}
},
{
"name": "EML4::ALK G1269A",
"id": 308,
"evidence_items": {
"accepted_count": 2,
"rejected_count": 0,
"submitted_count": 6
}
},
{
"name": "EML4::ALK L1196M",
"id": 7,
"evidence_items": {
"accepted_count": 4,
"rejected_count": 0,
"submitted_count": 11
}
},
{
"name": "F1245C",
"id": 549,
"evidence_items": {
"accepted_count": 2,
"rejected_count": 0,
"submitted_count": 0
}
},
{
"name": "EML4::ALK e20-e20",
"id": 500,
"evidence_items": {
"accepted_count": 4,
"rejected_count": 0,
"submitted_count": 0
}
},
{
"name": "Fusion",
"id": 499,
"evidence_items": {
"accepted_count": 31,
"rejected_count": 2,
"submitted_count": 10
}
},
{
"name": "ALK Fusion F1245C",
"id": 551,
"evidence_items": {
"accepted_count": 3,
"rejected_count": 0,
"submitted_count": 0
}
},
{
"name": "EML4::ALK C1156Y-L1198F",
"id": 352,
"evidence_items": {
"accepted_count": 2,
"rejected_count": 0,
"submitted_count": 1
}
},
{
"name": "NPM::ALK",
"id": 513,
"evidence_items": {
"accepted_count": 3,
"rejected_count": 1,
"submitted_count": 0
}
},
{
"name": "EML4::ALK T1151INST",
"id": 173,
"evidence_items": {
"accepted_count": 4,
"rejected_count": 0,
"submitted_count": 1
}
}
],
"aliases": [
"ALK1",
"ALK",
"NBLST3",
"CD246"
],
"updated_at": "2017-03-06T00:00:15.358Z",
"type": "gene"
}
]
}
Get details for a specific gene¶
This endpoint retrieves details about a specific gene.
Note that the default behavior of this endpoint is to use internal CIViC ids. If you want to use Entrez ids or gene symbols, you need to specify the identifier_type parameter.
HTTP Request Format
GET https://civicdb.org/api/genes/:id
Query Parameters
Parameter |
Valid Values |
Description |
|---|---|---|
identifier_type |
|
Type of gene identifier used in your query |
Example Request
curl https://civicdb.org/api/genes/AXL?identifier_type=entrez_symbol
Example Response
{
"id": 533,
"name": "AXL",
"entrez_id": 558,
"description": "",
"flagged": false,
"variants": [
{
"name": "EXPRESSION",
"id": 651,
"evidence_items": {
"accepted_count": 1,
"rejected_count": 0,
"submitted_count": 0
}
}
],
"aliases": [
"AXL",
"UFO",
"Tyro7",
"JTK11",
"ARK"
],
"updated_at": "2015-09-03T20:09:41.304Z",
"type": "gene",
"lifecycle_actions": {},
"sources": [],
"provisional_values": {},
"errors": {}
}
Get several genes at once via an identifier¶
The endpoint can be used to fetch overview information for multiple genes at the same time. It supports the same identifier_types as the detail endpoint.
HTTP Request Format
GET https://civicdb.org/api/genes/:id1,:id2
Query Parameters
Parameter |
Valid Values |
Description |
|---|---|---|
identifier_type |
|
Type of gene identifier used in your query |
Example Request
curl https://civicdb.org/api/genes/AXL,CDK2?identifier_type=entrez_symbol
Example Response
[
{
"id": 533,
"name": "AXL",
"entrez_id": 558,
"description": "",
"flagged": false,
"variants": [
{
"name": "EXPRESSION",
"id": 651,
"evidence_items": {
"accepted_count": 1,
"rejected_count": 0,
"submitted_count": 0
}
}
],
"aliases": [
"ARK",
"UFO",
"Tyro7",
"JTK11",
"AXL"
],
"updated_at": "2015-09-03T20:09:41.304Z",
"type": "gene"
},
{
"id": 906,
"name": "CDK2",
"entrez_id": 1017,
"description": "",
"flagged": false,
"variants": [
{
"name": "CYTOPLASMIC EXPRESSION",
"id": 1283,
"evidence_items": {
"accepted_count": 0,
"rejected_count": 0,
"submitted_count": 1
}
}
],
"aliases": [
"p33(CDK2)",
"CDKN2",
"CDK2"
],
"updated_at": "2017-02-09T21:58:24.886Z",
"type": "gene"
}
]