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!
1 maintainer
Metadata
1 maintainer
Release files for hca-bundle-jsonld 0.1.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| hca-bundle-jsonld-0.1.2.tar.gz | 4.2 kB | Without provenance | Details |
Release files / hca-bundle-jsonld-0.1.2.tar.gz
| Download URL | hca-bundle-jsonld-0.1.2.tar.gz |
|---|---|
| Size | 4.2 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
852a7e6f429fa375f4c7c5ad09ac252fc54ae92a8b295b53e15eabb3be1c0ee9
|
|
BLAKE2b-256 checksum How to use checksums |
625cedc8a14034d1a15301d4782f8b3fe2e1cd144c451f5b81d8978f1aede473
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
Security for hca-bundle-jsonld 0.1.2
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
