Phenotypes Variants

curl --request GET \
  --url https://catalog-api-dev.demo.igvf.org/api/phenotypes/variants

import requests

url = "https://catalog-api-dev.demo.igvf.org/api/phenotypes/variants"

response = requests.get(url)

print(response.text)

const options = {method: 'GET'};

fetch('https://catalog-api-dev.demo.igvf.org/api/phenotypes/variants', options)
  .then(res => res.json())
  .then(res => console.log(res))
  .catch(err => console.error(err));

[
  {
    "phenotype_id": "<string>",
    "phenotype_term": "<string>",
    "p_value": 123,
    "beta": 123,
    "beta_ci_lower": 123,
    "beta_ci_upper": 123,
    "oddsr_ci_lower": 123,
    "oddsr_ci_upper": 123,
    "lead_chrom": "<string>",
    "lead_pos": 123,
    "lead_ref": "<string>",
    "lead_alt": "<string>",
    "direction": "<string>",
    "name": "<string>",
    "variant": "<string>",
    "rsid": [
      "<string>"
    ],
    "study": "<string>",
    "neg_log10_pvalue": 123,
    "source": "OpenTargets",
    "source_url": "<string>",
    "class": "<string>",
    "method": "<string>",
    "label": "<string>",
    "version": "October 2022 (22.10)"
  }
]

{
  "message": "<string>",
  "code": "<string>",
  "issues": [
    {
      "message": "<string>"
    }
  ]
}

API Reference

Phenotypes Variants

Retrieve variant-trait pairs from GWAS, SGE, and cV2F by phenotypes.

The following parameters can be used to set thresholds on -log10 p_value: gt (>), gte (>=), lt (<), lte (<=).

Set verbose = true to retrieve full info on the studies.

At least one of these fields is required: phenotype_id, phenotype_name, method, or files_fileset.

The limit parameter controls the page size and can not exceed 100.

Pagination is 0-based.

Examples by method

These examples are grouped by method; use the method filter to return data from a specific method.

GWAS:

Single result

phenotype_id = EFO_0010325
method = GWAS

Group results

neg_log10_pvalue = gte:5
method = GWAS

SGE:

Query by phenotype identifier

phenotype_id = NCIT_C16407
method = SGE

Query by files_fileset

Each files_fileset maps to at most one method, so a method filter is usually not necessary.

files_fileset = IGVFFI3125FMNW
method = SGE

cV2F:

query by phenotype identifier

phenotype_id = GO_0003674
method = cV2F

query by files_fileset

Each files_fileset maps to at most one method, so a method filter is usually not necessary.

files_fileset = IGVFFI3063JRLI
method = cV2F

Phenotypes Variants

curl --request GET \
  --url https://catalog-api-dev.demo.igvf.org/api/phenotypes/variants

import requests

url = "https://catalog-api-dev.demo.igvf.org/api/phenotypes/variants"

response = requests.get(url)

print(response.text)

const options = {method: 'GET'};

fetch('https://catalog-api-dev.demo.igvf.org/api/phenotypes/variants', options)
  .then(res => res.json())
  .then(res => console.log(res))
  .catch(err => console.error(err));

[
  {
    "phenotype_id": "<string>",
    "phenotype_term": "<string>",
    "p_value": 123,
    "beta": 123,
    "beta_ci_lower": 123,
    "beta_ci_upper": 123,
    "oddsr_ci_lower": 123,
    "oddsr_ci_upper": 123,
    "lead_chrom": "<string>",
    "lead_pos": 123,
    "lead_ref": "<string>",
    "lead_alt": "<string>",
    "direction": "<string>",
    "name": "<string>",
    "variant": "<string>",
    "rsid": [
      "<string>"
    ],
    "study": "<string>",
    "neg_log10_pvalue": 123,
    "source": "OpenTargets",
    "source_url": "<string>",
    "class": "<string>",
    "method": "<string>",
    "label": "<string>",
    "version": "October 2022 (22.10)"
  }
]

{
  "message": "<string>",
  "code": "<string>",
  "issues": [
    {
      "message": "<string>"
    }
  ]
}

Query Parameters

phenotype_id

string

phenotype_name

string

neg_log10_pvalue

string

method

enum<string>

Available options:

GWAS,

SGE,

cV2F

label

enum<string>

Available options:

GWAS,

predicted variant effect on phenotype,

protein variant effect

class

enum<string>

Available options:

observed data,

prediction

files_fileset

string

source

enum<string>

Available options:

IGVF,

OpenTargets

organism

enum<string>

default:Homo sapiens

Available options:

Homo sapiens

verbose

enum<string>

default:false

Available options:

true,

false

page

number

default:0

limit

number

Response

Successful response

Option 1
Option 2

phenotype_id

string | null

required

phenotype_term

string | null

required

p_value

number | null

required

beta

number | null

required

beta_ci_lower

number | null

required

beta_ci_upper

number | null

required

oddsr_ci_lower

number | null

required

oddsr_ci_upper

number | null

required

lead_chrom

string | null

required

lead_pos

number | null

required

lead_ref

string | null

required

lead_alt

string | null

required

direction

string | null

required

name

string

required

variant

required

rsid

string[] | null

study

neg_log10_pvalue

number | null

source

string

default:OpenTargets

source_url

string | null

class

string | null

method

string | null

label

string | null

version

string

default:October 2022 (22.10)

Diseases Variants Phenotypes Coding Variants

Overview

Endpoints

Phenotypes Variants

Query Parameters

Response