Ontology-Verifier

A RDF Ontology verifier and ontology trouble shooter for CASE/UCO.

What it does

Ontology-Verifier takes output of a tool (JSON/JSON-LD/XML/etc...) and attempts to verify it aligns with a RDF based ontology (OWL/N3/ttl). Any entry in the tool's output that is NOT in the Ontology (specified via CLI) will display an error. CLI arugments can be added to cause a debugger to start so you may explore the graph to view where things went wrong.

How it works

Verifier.py will read in an RDF vocabulary defined via -g (glossary) to check a custom tool's output against via -i. The Python library rdflib is used to turn the RDF schema into tripples which are then broken into three lists; subject, predicate and object. Finally, each element of the tools ouput within the tool's subject and predicate are checked againast the glossary's subject and predicate to confirm the existence of these RDF elements. If an element is found or not found it is displayed to the user. BNodes are skipped as they have no appropriate label in RDF and should not be used to verify an ontology.

Why not SPARQL?

In order to facilitate a broad range of ontologies and custom tool outputs, SPARQL queries are not used for verification. CASE/UCO allow for robust flexibility and this tool aims to compliment this approach.

Installation

sudo pip install -r requirements.txt 

Unit Tests

The ontology verifier is heavily reliant on 3rd pary libraries, primarily RDFlib. RDFLib is under heavy development. To ensure compatability with new releases unit tests have been written to check for consistency.

Run Unit Tests

cd tests;
python test_verifier.py;

Usage

CLI Usage

• -g: Define the RDF schema (aka glossary) in use for your ontology.

• -gf: Define the format the schema is in. By default verifier will try to auto-guess based on extension. However, if additional plugins are installed it is best practice to manually specify it.

• -i: The external tool's output you want to verify the ontology against.

• -if: Define RDF schema for tool data that's being injested.

• --debug: Break on errors that occur within --verify.

• -tg: Print subject, predicate, object for each graph within tool schema.

• -gg: Print subject, predicate, object for each graph within glossary schema.

CLI Example

• Check for inconsistencies between graphs:

verify.py -g case.ttl -gf turtle -i output.json-ld -if json-ld --verify=1

• Check for inconsistencies between graphs with color output:

verify.py -g case.ttl -gf turtle -i output.json-ld -if json-ld --verify=1 --color=1

• Enter debug mode. This will cause a PDB session to open when an inconsistency is met. This can be useful for manually navigating the RDF graph in Python.:

verify.py -g case.ttl -gf turtle -i output.json-ld -if json-ld --verify=1 --debug=1

• Print all graphs for tool's schema.

verify.py -g case.ttl -gf turtle -i output.json-ld -if json-ld -tg=1

• Print all graphs for ontology's schema.

verify.py -g case.ttl -gf turtle -i output.json-ld -if json-ld -gg=1

Submitting an Issue

If/when you run into an issue with a given RDF schema format or the verifier.py script, please open an issue with the error and as much technical detail as you can provide.