Simple OBO Adapter

About

This is an alternative to Pronto / OBO Files Adapter for loading OBO Format files

Initialization

To ensure use of simpleobo when specifying a selector, use the simpleobo scheme:

runoak -i simpleobo:path/to/file.obo COMMAND [COMMAND-OPTIONS]

Code

class oaklib.implementations.simpleobo.simple_obo_implementation.SimpleOboImplementation(resource: ~oaklib.resource.OntologyResource = None, strict: bool = False, _multilingual: bool = None, autosave: bool = <factory>, exclude_owl_top_and_bottom: bool = <factory>, ontology_metamodel_mapper: ~oaklib.mappers.ontology_metadata_mapper.OntologyMetadataMapper | None = None, _converter: ~curies.api.Converter | None = None, auto_relax_axioms: bool = None, cache_lookups: bool = False, property_cache: ~oaklib.utilities.keyval_cache.KeyValCache = <factory>, _edge_index: ~oaklib.indexes.edge_index.EdgeIndex | None = None, _entailed_edge_index: ~oaklib.indexes.edge_index.EdgeIndex | None = None, _prefix_map: ~typing.Mapping[str, str] | None = None, functional_writer: <module 'funowl.writers.FunctionalWriter' from '/home/runner/.cache/pypoetry/virtualenvs/oaklib-5bvmowLS-py3.9/lib/python3.9/site-packages/funowl/writers/FunctionalWriter.py'> = None, obo_document: ~oaklib.implementations.simpleobo.simple_obo_parser.OboDocument = None, _relationship_index_cache: ~typing.Dict[str, ~typing.List[~typing.Tuple[str, str, str]]] = None, _alt_id_to_replacement_map: ~typing.Dict[str, ~typing.List[str]] = None, _uses_legacy_properties: bool = None, **_kwargs)[source]

Simple OBO-file backed implementation

This implementation is incomplete and is intended primarily as a Patcher implementation

This can be abandoned when pronto is less strict