triplifier 2.0.0

Python port of the Triplifier tool.

Triplifier

This repository creates the tooling project for the Triplifier.

Python package

The Python code is packaged for distribution. You can install it from GitHub Packages:

pip install triplifier

After installation the triplifier command is available to run the tool.

References

• Soest J van, Choudhury A, Gaikwad N, Sloep M, Dumontier M, Dekker A (2019) Annotation of Existing Databases using Semantic Web Technologies: Making Data more FAIR. CEUR-WS, Edinburgh, pp 94–101

Run as command-line tool

The basic configuration for the Python port can be run with the following command:

triplifier -c triplifier.yaml

The YAML configuration file contains the database connection information using SQLAlchemy style URLs.

SQLite database file

db:
  url: sqlite:///my.db
  user: user
  password: pass

Postgres database file

db:
  url: "postgresql://postgres:postgres@localhost:5432/my_database"

Optional arguments

By default, the tool will generate an ontology file (ontology.owl) and a turtle file containing the materialized triples (output.ttl) relative to the execution folder. To change this, the following additional arguments can be used:

• -o <output_path_for_materialized_triples_file>
• -t <output_path_for_ontology_file>
• -c <configuration_file>
• -b <base_uri_for_ontology>
• --ontologyAndOrData <ontology|data>

The --ontologyAndOrData option allows running only the ontology extraction (ontology) or only the data materialization (data) given an ontology file. If omitted, both steps are executed.

Annotations using the result

An example of annotations (and insertions) can be found in the following repository:

• https://gitlab.com/UM-CDS/fair/data/maastro-rectum