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OntologyYaml

What it is​

Utilities to translate an RDFLib Graph (ontology + individuals) into a YAML-ready Python dict containing:

  • namespace prefixes
  • a set of selected classes (BFO by default + classes referenced by ABI individuals)
  • entities (individuals under the /abi/ namespace) with relations and selected data properties

Public API​

class OntologyYaml​

  • __init__(triple_store_service: ITripleStoreService)
    • Stores a triple store service (note: currently not used by the static conversion entrypoint).
  • @staticmethod rdf_to_yaml(graph, class_colors_mapping: dict = {}, top_level_class: str = "http://purl.obolibrary.org/obo/BFO_0000001", display_relations_names: bool = True, yaml_properties: list = []) -> dict
    • Converts an RDF graph to a YAML-like dictionary using an internal Translator.

class Translator​

Intended internal implementation used by OntologyYaml.rdf_to_yaml.

  • translate(graph, class_colors_mapping, top_level_class, display_relations_names, yaml_properties) -> dict
    • Orchestrates parsing and YAML structure creation.
  • Other methods are internal helpers (not prefixed with _ consistently, but effectively internal to the workflow):
    • load_triples(g), load_classes(), compute_class_levels(cls_id), load_object_properties(), load_individuals(), map_oprop_labels(), create_yaml(...)
    • get_linked_classes(cls_id, rel_type=None) for resolving OWL list constructs used in domain/range expressions (unionOf, intersectionOf, complementOf).

Configuration/Dependencies​

  • Python packages
    • rdflib (Graph, URIRef, and vocab terms RDF, RDFS, OWL)
    • pydash (imported as _)
  • Project dependencies
    • naas_abi_core.logger
    • naas_abi_core.services.triple_store.TripleStorePorts.ITripleStoreService

Usage​

from rdflib import Graph
from naas_abi_core.utils.OntologyYaml import OntologyYaml

g = Graph()
# Populate `g` with ontology triples and individuals...

yaml_data = OntologyYaml.rdf_to_yaml(g)

print(yaml_data.keys())  # dict_keys(['prefixes', 'classes', 'entities'])

Caveats​

  • OntologyYaml.rdf_to_yaml() instantiates Translator() with no arguments, but Translator.__init__ references self.__triple_store_service.get_schema_graph() even though __triple_store_service is not defined in Translator. As written, calling rdf_to_yaml() will raise an exception unless Translator is modified or __triple_store_service is injected some other way.
  • Only predicates present in an internal URI-to-name mapping are kept when loading triples; all other predicates are ignored.
  • Only individuals whose URI contains "/abi/" are emitted as entities.
  • Class inclusion in output:
    • all BFO classes ("BFO_" in URI) are included by default
    • additional classes are pulled in only if they are on the type chain of emitted ABI individuals (walking is_a via the first subclassOf).
  • The function mutates the provided class_colors_mapping by adding random colors for newly encountered classes.