The T2DREAM API provides programmatic access to T2DREAM portal and drives data query and submission functionality. The T2DREAM API uses JSON and standard HTTP verbs for communication with the portal.
There are several third-party tools that can be used with T2DREAM 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 |
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.
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.t2dream-demo.org/experiments/TSTSR112545/?format=json
Prerequisite: json.tool provides command line interface to validate and pretty-print JSON
Installation for OS X and Linux:
$ pip install jsontool
Example of a request to annotation endpoint using annotation id, that retrieves annotation metadata:
$ curl –L -H "Accept: application/json" http://www.t2dream-demo.org/annotations/TSTSR027410/ | python -m json.tool > 13-state_model_liver.json
Example of a request to match objects that match RRBS:
curl -L -H "Accept: application/json" http://www.t2dream-demo.org/search/?searchTerm=RRBS | python -m json.tool > RRBS
Retrieval of all ATAC-seq experiments in TSV format:
curl -L "Accept: application/json" 'www.t2dream-demo.org/report.tsv?type=Experiment&searchTerm=ATAC-seq'
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 T2DREAM 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 T2DREAM REST API GitHub Repository
Prerequisite: python modules - argparse , json, requests
Example: Download antibody metadata
python2 T2DREAM_metadata_access.py --accession TSTAB000404 --type antibodies
Truncated output
