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OntologyYaml

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OntologyYaml

What it is

  • Utility for translating an RDFLib Graph containing ontology classes, object properties, and individuals into a YAML-friendly Python dict structure.
  • Designed to extract classes (notably BFO), ABI individuals, and their relations, then normalize common URI prefixes.

Public API

class OntologyYaml

  • __init__(triple_store_service: ITripleStoreService)
    • Stores a triple store service dependency (currently not used by the static translation method).
  • @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 = [])
    • Translates an RDFLib Graph into a YAML-ready dictionary with keys:
      • prefixes
      • classes
      • entities

class Translator

  • translate(graph, class_colors_mapping, top_level_class, display_relations_names, yaml_properties)
    • Orchestrates translation by loading triples/classes/properties/individuals and producing YAML data via create_yaml(...).
  • Other methods exist but are internal helpers (no leading underscore consistency, but intended for internal use):
    • load_triples(g)
    • load_classes()
    • compute_class_levels(cls_id)
    • load_object_properties()
    • load_individuals()
    • map_oprop_labels()
    • create_yaml(class_color, display_relations_names, yaml_properties)
    • get_linked_classes(cls_id, rel_type=None) (used internally for domain/range expression trees)

Configuration/Dependencies

  • Requires:
    • rdflib (Graph, URIRef, RDF, RDFS, OWL)
    • pydash as _
    • naas_abi_core.logger
    • naas_abi_core.services.triple_store.TripleStorePorts.ITripleStoreService
  • Prefix normalization performed in output:
    • xsd, abi, bfo, cco
  • Notes on data expectations in the RDF graph:
    • Classes are detected via rdf:type owl:Class
    • Object properties via rdf:type owl:ObjectProperty (labels used to find relation predicates on individuals)
    • Individuals via rdf:type owl:NamedIndividual
    • Individuals are only emitted as YAML entities if their URI contains "/abi/"

Usage

from rdflib import Graph
from naas_abi_core.utils.OntologyYaml import OntologyYaml
 
g = Graph()
# Populate `g` with ontology + individuals data...
 
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 AttributeError unless Translator is fixed or externally patched to have __triple_store_service.
  • Default argument class_colors_mapping: dict = {} is mutable.
  • Only the first subclassOf entry is used when emitting a class is_a relation (subclass[0]).
  • Relation extraction for individuals depends on object property labels (rdfs:label); it then looks for those label strings as keys in the individual’s predicate-mapped dict (i.e., the label must match the mapped predicate name in self.mapping output).

Graph View