Gilda Adapter

Command Line Examples

Use the gilda selector:

$ runoak -i gilda: COMMAND [COMMAND-ARGUMENTS-AND-OPTIONS]

Currently ontology sub-selectors are not supported

Annotation

$ runoak -i gilda: annotate -W "cell cortex"

Code

class oaklib.implementations.gilda.GildaImplementation(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, grounder: gilda.Grounder = None, **_kwargs)[source]

Perform named entity normalization on text strings with Gilda [gyori2021].

[gyori2021]

Benjamin M Gyori, Charles Tapley Hoyt, Albert Steppi (2021) Gilda: biomedical entity text normalization with machine-learned disambiguation as a service, Bioinformatics Advances, Volume 2, Issue 1, 2022, vbac034,