hca-bundle-jsonld 0.1.2

Create RDF and JSON-LD from HCA bundles

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.

Usage

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

import requests
import bundle_to_rdf

DSS_URL = "https://dss.dev.data.humancellatlas.org/v1"
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)
print(file_name)

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.

Development

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.

TODO

• 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

Contributing

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

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