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Overview

The ImmPort API includes endpoints for:

  • Authentication/Authorization
  • Shared Data

    • Study Data
    • Assay Result Data
    • Controlled Vocabulary or Lookup Tables
    • Study Metadata (Used by UI)
    • Download Files
  • Data Upload

  • Batch Updater

Note

Many of the Shared Data endpoints have been documented using OpenAPI 3.0 and Swagger and can be reviewed here.

Many of the endpoints are password protected and require sending an ImmPort access token to use the endpoint, but several are open and do not require an ImmPort access token. Some of the endpoints support multiple filter critera's for narrowing down the returned data to specific information of interest. Most of the endpoints return data in JSON or TSV format. How to obtain an access tokem, filter criterias and file format topics will be discussed in more detail in the appropriate section.

The Python Examples under the Shared Data API heading, includes several examples of how to use the API endpoints.

Authentication

When an endpoint requires an access token, one can be obtained by sending a request to the authentication endpoint and including the ImmPort username and password.

https://www.immport.org/auth/token

Shell Command

curl -X POST https://www.immport.org/auth/token -d username="REPLACE_WITH_USERNAME" -d password="REPLACE_WITH_PASSWORD"
Results
{
"status" : 200,
"access_token" : "Example-OiJSUzI1NiIsInR5cCI6IkpXVCJ9.eyJleHAiOjE2MjMzNTE5NDMsInVzZXJfbmFtZSI6ImNhbXBqbyIsImF1dGhvcml0aWVzIjpbIlJPTEVfVVNFUiIsIlJPTEVfQ1VSQVRJT05fVVNFUiIsIlJPTEVfQURNSU4iLCJST0xFX0lNTVBPUlRfREFUQV9NQU5BR0VNRU5UX0FETUlOIiwiUk9MRV9VU0VSX0FETUlOSVNUUkFUSU9OX0FETUlOIiwiUk9MRV9TSEFSSU5HX1VTRVIiLCJST0xFX0RBVEFfQlJPV1NFUl9BRE1JTiJdLCJqdGkiOiI1ZjFkMzQ3Mi03MWU5LTQ0ODUtYjQ2Zi0wM2E4MGY2Mjk4NDUiLCJjbGllbnRfaWQiOiJpbW1wb3J0LWF1dGgtdG9rZW4tY2xpZW50Iiwic2NvcGUiOlsiYnJvd3NlIiwiZG93bmxvYWQiXX0.PC9vinTYFffEMvD3UXrOq2X6DuQF_8I3HpfuzHw2EG-j8c9GufCChgRieLhmqJ8_K9ngLe_sHzvyWN6GOofUPDr5AQOGYDxurhDzWhLD58841uOQYEhbZtVF0FcO84Ybi1ld_Zgj0Rhauv2jjvZJj-vakANOndEQtsIVmMSKLcnJ93Zk8_Mxtt35yxphZOizbYMmbq8tOy40vGF4O8yHLGgJS-SEebD7shiE7DoWFW5urKvyU6szIa0sz_i1oUoBJLtVeb3pW_lpgkQ3xo4-lCBgK2SkEvdq5g-So5cUNKzW619Tcznjs68z88droOX3gqu3oHxO4Z5Do824_2lzeA"
}

The token returned is a JWT token. JSON Web Token (JWT) is an open standard (RFC 7519) that defines a compact and self-contained way for securely transmitting information between parties as a JSON object.

The token must be used to initiate a API request that requires authentication within 3600 seconds. After 3600 seconds the token will be invalid and the user will need to get a new token.

Sample API call using Shell Commands

In the following example, an authentication token is saved as an environment variable (token) and passed to the HTTP header in the curl command to retrieve ELISA results data.

The first line is a POST to the authentication URL https://www.immport.org/auth/token with the username and password to get an authentication token. The fgrep command is used search the response for a token and then assign the value of the token to an environment variable named "token".

The second line is a GET on the URL https://immport.org/data/query/result/elisa with the filter parameter studyAccession=SDY2,SDY4. The authentication token ("token") is passed in the HTTP header as shown.

The response will return ELISA result data that belongs to study accessions SDY2 and SDY4 (Check the Results tab below). The default format of the response is JSON. The response will be an array of the specific result type or file path data. The filter conditions are always combined using the AND operator.

The above shell script or any code starting with #!/bin/bash can be copied to a .sh file (e.g. elisadata.sh )and executed at the command prompt of a terminal and the output can be directed to a file. (Please replace the REPLACE_WITH_USERNAME with your username and REPLACE_WITH_PASSWORD with your password.)

#!/bin/bash

export token=`curl -X POST https://www.immport.org/auth/token -d username="REPLACE_WITH_USERNAME" -d password="REPLACE_WITH_PASSWORD" 2>&1  | fgrep '"access_token"' | sed -e 's/^.*"access_token":"//;s/".*$//'`

curl -k -H "Authorization: bearer $token" "https://www.immport.org/data/query/result/elisa?studyAccession=SDY2,SDY4"
Results
[ {
  "resultId" : 89390,
  "ageEvent" : "Age at enrollment",
  "ageEventSpecify" : null,
  "ageUnit" : "Years",
  "ancestralPopulation" : null,
  "analytePreferred" : null,
  "analyteReported" : "VZVQual",
  "armAccession" : "ARM235",
  "armName" : "Healthy controls",
  "biosampleAccession" : "BS476749",
  "biosampleType" : "Other",
  "biosampleSubtype" : null,
  "clinical" : "Y",
  "comments" : "negative qualitative result",
  "ethnicity" : "Not Hispanic or Latino",
  "experimentAccession" : "EXP8311",
  "expsampleAccession" : "ES474813",
  "gender" : "Male",
  "maxSubjectAge" : 1.00,
  "measurementTechnique" : "ELISA",
  "minSubjectAge" : 1.00,
  "plannedVisitAccession" : "PV1518",
  "race" : "White",
  "raceSpecify" : null,
  "repositoryAccession" : null,
  "repositoryName" : null,
  "species" : "Homo sapiens",
  "strain" : null,
  "studyAccession" : "SDY2",
  "studyTitle" : "Immune Response to Varicella Vaccination in Subjects with Atopic Dermatitis Compared to Nonatopic Controls",
  "studyTimeCollected" : 1.00,
  "studyTimeCollectedUnit" : "Days",
  "subjectAccession" : "SUB106751",
  "subjectPhenotype" : "non atopic dermititis",
  "unitPreferred" : null,
  "unitReported" : "-1: neg 1: pos",
  "valuePreferred" : -1.0,
  "valueReported" : "-1",
  "treatmentAccession" : null,
  "studyTimeT0EventSpecify" : null,
  "studyTimeT0Event" : "Not Specified"
}, {
  "resultId" : 89391,
  "ageEvent" : "Age at enrollment",
  "ageEventSpecify" : null,
  "ageUnit" : "Years",
  "ancestralPopulation" : null,
  "analytePreferred" : null,
  "analyteReported" : "VZVQual",
  "armAccession" : "ARM235",
  "armName" : "Healthy controls",
  "biosampleAccession" : "BS476750",
  "biosampleType" : "Other",
  "biosampleSubtype" : null,
  "clinical" : "Y",
  "comments" : "negative qualitative result",
  "ethnicity" : "Not Hispanic or Latino",
  "experimentAccession" : "EXP8311",
  "expsampleAccession" : "ES474814",
  "gender" : "Female",
  "maxSubjectAge" : 1.00,
  "measurementTechnique" : "ELISA",
  "minSubjectAge" : 1.00,
  "plannedVisitAccession" : "PV1518",
  "race" : "White",
  "raceSpecify" : null,
  "repositoryAccession" : null,
  "repositoryName" : null,
  "species" : "Homo sapiens",
  "strain" : null,
  "studyAccession" : "SDY2",
  "studyTitle" : "Immune Response to Varicella Vaccination in Subjects with Atopic Dermatitis Compared to Nonatopic Controls",
  "studyTimeCollected" : 1.00,
  "studyTimeCollectedUnit" : "Days",
  "subjectAccession" : "SUB106784",
  "subjectPhenotype" : "non atopic dermititis",
  "unitPreferred" : null,
  "unitReported" : "-1: neg 1: pos",
  "valuePreferred" : -1.0,
  "valueReported" : "-1",
  "treatmentAccession" : null,
  "studyTimeT0EventSpecify" : null,
  "studyTimeT0Event" : "Not Specified"
},........   

Tools for communicating with the ImmPort Data Query API

Many third-party tools can be used for communicating with the API and for visualizing API calls. 1G Examples of tools for communicating with the API:

Tool Type
Curl Command line tool
HTTPie Command line tool
Postman REST Client App for Google Chrome and OS X
DHC REST Client Google Chrome extension
Google Chrome Google Chrome web browser
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