curl --request GET \
--url https://catalog-api-dev.demo.igvf.org/api/phenotypes/variantsimport 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>"
}
]
}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
curl --request GET \
--url https://catalog-api-dev.demo.igvf.org/api/phenotypes/variantsimport 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
GWAS, SGE, cV2F GWAS, predicted variant effect on phenotype, protein variant effect observed data, prediction IGVF, OpenTargets Homo sapiens true, false Response
Successful response
- Option 1
- Option 2