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>",
"source": "OpenTargets",
"name": "<string>",
"variant": "<string>",
"rsid": [
"<string>"
],
"study": "<string>",
"neg_log10_pvalue": 123,
"source_url": "<string>",
"class": "<string>",
"method": "<string>",
"label": "<string>",
"version": "October 2022 (22.10)",
"files_filesets": "<string>"
}
]{
"message": "<string>",
"code": "<string>",
"issues": [
{
"message": "<string>"
}
]
}Phenotypes Variants
Retrieve variant-trait pairs from GWAS, SGE, cV2F, and CRISPR screens by phenotypes.
The following parameters can be used to set thresholds on -log10 p_value: gt (>), gte (>=), lt (<), lte (<=). neg_log10_pvalue is only populated for GWAS records; it does not filter out SGE, cV2F, or CRISPR screen edges, which have no p-value field.
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
CRISPR screen:
Query by phenotype identifier
- phenotype_id = NTR_0001118
- method = CRISPR screen
Query by files_fileset
Each files_fileset maps to at most one method, so a method filter is usually not necessary.
- files_fileset = IGVFFI2014OOZP
- method = CRISPR screen
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>",
"source": "OpenTargets",
"name": "<string>",
"variant": "<string>",
"rsid": [
"<string>"
],
"study": "<string>",
"neg_log10_pvalue": 123,
"source_url": "<string>",
"class": "<string>",
"method": "<string>",
"label": "<string>",
"version": "October 2022 (22.10)",
"files_filesets": "<string>"
}
]{
"message": "<string>",
"code": "<string>",
"issues": [
{
"message": "<string>"
}
]
}Query Parameters
CRISPR screen, GWAS, SGE, cV2F GWAS, predicted variant effect on phenotype, protein variant effect, variant effect on phenotype observed data, prediction IGVF, OpenTargets Homo sapiens true, false Response
Successful response
- Option 1
- Option 2
OpenTargets