Info

Welcome to the generated Dolphin API.

This procedure describes the API of the DOmain Logo Protein for Human INformation (Dolphin). The system was developed using the Laravel framework. Its interoperability with external infrastructures is made possible via a REST API system. The database is developed in PostgreSQL.

Annotations

API to annotate missense variants in protein domain.

Variants annotation

To use this query, a protein missense mutation and an ID are required. The ID should to be one of those four options : "gene", "uniprot", "ensembl" and "refseq".
The "frequencies" option will add gnomAD and Dolphin frequencies to the results.

Example request:

curl -X GET \
    -G "https://dolphin.mmg-gbit.eu/api/VariantAnnotation?variation=G560V&ensembl=ENST00000316623" \
    -H "Content-Type: application/json" \
    -H "Accept: application/json"

const url = new URL(
    "https://dolphin.mmg-gbit.eu/api/VariantAnnotation"
);

let params = {
    "variation": "G560V",
    "ensembl": "ENST00000316623",
};
Object.keys(params)
    .forEach(key => url.searchParams.append(key, params[key]));

let headers = {
    "Content-Type": "application/json",
    "Accept": "application/json",
};

fetch(url, {
    method: "GET",
    headers: headers,
})
    .then(response => response.json())
    .then(json => console.log(json));

$client = new \GuzzleHttp\Client();
$response = $client->get(
    'https://dolphin.mmg-gbit.eu/api/VariantAnnotation',
    [
        'headers' => [
            'Content-Type' => 'application/json',
            'Accept' => 'application/json',
        ],
        'query' => [
            'variation'=> 'G560V',
            'ensembl'=> 'ENST00000316623',
        ],
    ]
);
$body = $response->getBody();
print_r(json_decode((string) $body));

Example response (200):

{
    "gene": "FBN1",
    "variation": "G560V",
    "frequencies": "1",
    "entry_name": [
        "A0A1B1PFX5_HUMAN",
        "A0A6I8PL22_HUMAN",
        "F6U495_HUMAN",
        "FBN1_HUMAN",
        "H0YN80_HUMAN",
        "H0YND0_HUMAN",
        "L8E6V0_HUMAN",
        "L8E775_HUMAN",
        "Q75N88_HUMAN",
        "Q75N89_HUMAN"
    ],
    "hgvsp.3": "p.GLY560VAL",
    "results": [
        {
            "entry_name": "FBN1_HUMAN",
            "pfid": "PF07645",
            "pos_in_logo": 208,
            "AA": {
                "aa_ref": "G",
                "aa_alt": "V"
            },
            "score": {
                "score_ref": 2.531,
                "score_alt": -4.781,
                "score_delta": -7.312
            },
            "name_dom": "EGF_CA",
            "name_complete": "Calcium-binding EGF domain",
            "frequencies": {
                "GnomAD_AF": 0,
                "Dolphin_AF": 2.3873e-5
            },
            "acmg": "PM1;"
        }
    ]
}

Example response (422):

{
    "message": "Process Failed",
    "status": false,
    "data": [],
    "errors": {
        "gene": [
            "The selected gene is invalid."
        ]
    }
}

HTTP Request

GET api/VariantAnnotation

Query Parameters