From ISA JSON to ISA JSON-LD (RDF): Dataset Maturity Level 3



Recipe Overview
Reading Time
15 minutes
Executable Code
Yes
Difficulty
Moving to a semantically typed version - ISA-JSON-LD
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Recipe Type
Hands-on
Audience
Principal Investigator, Data Manager, Data Scientist
Maturity Level & Indicator
DSM-2-C6
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Abstract:

The goal of this tutorial is to show how to go from an ISA document to an equivalent RDF representation using python tools, but also to highlight some limitations of existing libraries and point to alternative options to complete a meaningful conversion to RDF Turtle format.

This notebook mainly highlights the new functionality coming with ISA-API rc10.3 latest release which allows converting ISA-JSON to ISA-JSON-LD, with the choice of 3 popular ontological frameworks for semantic anchoring. These are:

  • obofoundry, a set of interoperable ontologies for the biological domain.

  • schema.org, the search engine orientated ontology developed by companies such as Yandex, Bing,Google

  • wikidata, a set of semantic concepts backing wikipedia and wikidata resources.

These frameworks have been chosen for interoperability.

This notebook has a companion notebook which goes over the exploration of the resulting RDF representations using a set of SPARQL queries. Check it out here

Let’s get started

We do so by getting all necessary ISA tools and importing the latest module for conversion to JSON-LD from ISA-JSON.

import os
import json
from json import load
import datetime
import isatools
from isatools.convert.json2jsonld import ISALDSerializer

1. Loading an ISA-JSON document in memory with json.load() function

Prior to invoking the ISALDserializer function, we need to do three things.

  • First, pass an url or a path to the ISA JSON instance to convert to JSON-LD

  • Second, select the ontology framework used for the semantic conversion. One may choose from the following 3 options:

  • Third, choose if to rely on embedding the @context file in the output or relying on url to individual contexts. By default, the converter will embed the all in one context information. The reason for this is the lack of support for JSON-LD 1.1 specifications in many of the python libraries supported RDF parsing (e.g. RDFlib)

instance_path = os.path.join("./output/BII-S-3-synth/", "isa-new_ids.json")

with open(instance_path, 'r') as instance_file:
        instance = load(instance_file)
        instance_file.close()

2. Transforming ISA-JSON to ISA JSON-LD with ISALDserializer function

# we now invoke the ISALDSerializer function

ontology = "isaterms"

serializer = ISALDSerializer(instance)
serializer.set_ontology(ontology)
serializer.set_instance(instance)

json_ld_content = serializer.output

Now that the conversion is performed, we can write the resulting ISA-JSON-LD to file:

3. Writing ISA JSON-LD to file

isa_json_ld_path = os.path.join("./output/BII-S-3-synth/", "isa-new_ids-BII-S-3-ld-" + ontology + "-v1.json")

with open(isa_json_ld_path, 'w') as outfile:
    json.dump(json_ld_content,  outfile, ensure_ascii=False, indent=4)

4. Converting ISA-JSONLD instance to RDF Turtle using python RDFlib library

Note

Python RDFlib version should be at last 6.0.2

from rdflib import Graph

graph = Graph()
graph.parse(isa_json_ld_path)

print(f"Graph g has {len(graph)} statements.")

# Write turtle file
rdf_path=os.path.join("./output/BII-S-3-synth/", "isa-new_ids-BII-S-3-ld-" + ontology + "-v3.ttl")
with open(rdf_path, 'w') as rdf_file:
        rdf_file.write(graph.serialize(format='turtle'))

Authors

Authors

Name

ORCID

Affiliation

Type

ELIXIR Node

Contribution

Philippe Rocca-Serra

University of Oxford

Writing - Original Draft

Dominique Batista

University of Oxford

Writing - Original Draft
Creating a community annotation compliant ISA descriptor: Dataset Maturity Level 2 Packaging ISA as a Research Object (RO) - Dataset Maturity Level 4