Skip to main content

Create RDF and JSON-LD from HCA bundles

Project description

Representing HCA Bundles as JSON-LD allows them to be easily converted to RDF and queried using SPARQL. This software, when combined with a graph or triplet store can provide semantic data models that allow for an expressive query interface.


The “bundle_to_rdf” module presents a method for converting HCA bundles to RDF ttl files.

import requests
import bundle_to_rdf

DSS_URL = ""
bundle_uuid = "4be0071d-b36e-4414-a7ee-7b879f60be7c"

r = requests.get("{}/bundles/{}?replica=aws".format(DSS_URL, bundle_uuid))
bundle = r.json()

file_name = bundle_to_rdf.bundle_to_rdf(bundle)

A file is created in the current working directory with a filename following the pattern: {bundle_uuid}.ttl.

This file can then be loaded into a triplet store of your choosing. For an example of usage with BlazeGraph, check out the example-usage.ipynb.


This module should make as few assumptions about the DSS data model as possible. Future developments would use this module as part of a service to either create RDF that can be queried directly, or loaded into a graph store like Blazegraph or Amazon Neptune.


  • Add unit tests, the module currently relies on active connections to the DSS

  • Improve example notebook with biological use cases

  • Demonstrate using the SPARQL and RDF interface to demonstrate tabular representations

  • Integrate into a microservice for generating RDF from bundles on the fly


  • Please add any issues you experience to our Github issue tracker!

  • This software is Open Source, Apache licensed, send in your changes!

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

hca-bundle-jsonld-0.1.2.tar.gz (4.2 kB view hashes)

Uploaded source

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page