Skip to content

babelon

Details
GitHub monarch-initiative/babelon
Language Python
Description A format for language profiles for ontologies

Dependencies

External Dependencies

Package Version
python ^3.9
click *
importlib-metadata >=4.8.0
rdflib >=6.3.2
jsonasobj2 ^1.0.4
xmltodict ^0.13.0
pandas ^2.0.2
oaklib ^0.5.9
tabulate ^0.9.0
llm ^0.13.1
python-dotenv ^1.0.1
curies ^0.7.7
sssom ^0.4.4
linkml-runtime ^1.7.1
linkml ^1.7.4

Documentation

DOI

Babelon - A simple standard for managing ontology translations and language profiles

Editors: - @matentzn - @LLTommy - @mellybelly - @drseb - Anyone that wants to be on here.

Provisional documentation here.

Babelon is simple standard for managing ontology translations and language profiles. Profiles are managed a simple TSV files, for example:

source source_version source_language translation_language subject_id predicate_id source_value translation_value translator translation_date translation_confidence translation_precision translation_type
http://purl.obolibrary.org/obo/hp.owl http://purl.obolibrary.org/obo/hp/releases/2021-04-13/hp.owl en de HP:0001945 rdfs:label Fever Fieber https://orcid.org/0000-0002-1373-XXXX 2021-05-21 0.95 exact HumanCurated
http://purl.obolibrary.org/obo/hp.owl http://purl.obolibrary.org/obo/hp/releases/2021-04-13/hp.owl en de HP:0002615 oio:exactSynonym Low blood pressure Niedriger Blutdruck https://orcid.org/0000-0002-1373-XXXX 2021-05-21 0.9 exact HumanCurated

The goal of Babelon is to capture the minimum data required to enable the following use cases:

  • Translate a profile into RDF to enable seamless integration of alternative language alongside the primary ones.
  • Support all properties for translation, including labels, synonyms and definitions.
  • Capture important metadata such as confidence and precision of translation.
  • Enable cross-language editing. For example:
  • Notify language profile maintainers of new terms or changed labels
  • Notify the core ontology teams of changes to translations, with a potential to suggest updating ones own annotations or adding new synonyms.

As a first use case for the format, we see to capture the French language translations of the Human Phenotype Ontology by the Orphanet team and use them to provide versioned language profiles of HPO.

Editors

# in new environment
pip install poetry
poetry install
make translations

Acknowledgements

This cookiecutter project was developed from the monarch-project-template template and will be kept up-to-date using cruft.