Diabetes Epigenome Atlas Application Programming Interface (API)

The Diabetes Genome Atlas API provides programmatic access to Diabetes Genome Atlas portal and drives data query and submission functionality. The Diabetes Genome Atlas API uses JSON and standard HTTP verbs for communication with the portal.

There are several third-party tools that can be used with Diabetes Genome Atlas REST API, we have tested following tools that can be used for communicating with our portal:

Tool

Description

JSON Formatter

Web browser plugin for Safari

JSONVIEW

Web browser plugin for Chrome and Firefox

Restlet

Web browser plugin for Chrome

Curl

Command line tool

Postman REST Client

Tool for API development

 

Diabetes Genome Atlas Accession Ids

Every object (e.g., experiment, annotation, biosamples, antibodies, data file etc.) have unique accession TSTXXXXXXXX ids.  API request – response can be made to retrieve specific individual, group or mashup of these objects.

Search and Retrieval Examples

Web browser JSON pretty-printer plugin

JSON pretty-printer plugin for web browser can be used to view page as JSON.  In order to view page as JSON add ?format=json to the URL

Example: To request metadata for experiment TSTSR112545:

http://www.t2depigenome.org/experiments/TSTSR112545/?format=json

 

Curl

Prerequisite:  json.tool provides command line interface to validate and pretty-print JSON

Installation for OS X and Linux:

$ pip install jsontool

The following is an example of a request to annotation endpoint using annotation id, that retrieves annotation metadata:

$ curl –L -H "Accept: application/json" http://www.t2depigenome.org/annotations/TSTSR027410/ | python -m json.tool > 13-state_model_liver.json

 Sample Output:

The following is an example of a request to annotation endpoint using annotation id, that retrieves annotation metadata:

curl -L -H "Accept: application/json" http://www.t2depigenome.org/search/?searchTerm=RRBS | python -m json.tool > RRBS

Retrieval of all ATAC-seq experiments in TSV format

curl -L "Accept: application/json" 'www.t2depigenome.org/report.tsv?type=Experiment&searchTerm=ATAC-seq'

Programmatic access to metadata

T2DREAM_metadata_access.py script abstracts the GET request for metadata retrieval. It takes metadata type and accession id and returns metadata in JSON format.

The following metadata endpoints are available from Diabetes Epienome Atlas API to access metadata programmatically

Metadata Endpoints (--type)

Description

experiment

Includes assay metadata, replicate information and data files

annotation

Metadata for an annotation set

files

Metadata for a data file (e.g., fastq, bigwig, bed, bam, bigBed,  tagAlign, sra)

biosamples

Metadata for biosamples

antibodies

Metadata for antibodies

target

metadata for target gene

 

The REST-API codebase is available on  Diabetes Epigenome Atlas REST API GitHub Repository

Prerequisite: python modules - argparse , json, requests

Example: Download antibody metadata

python T2DREAM_metadata_access.py --accession TSTAB000404 --type antibodies

Truncated output