LiteralMapping

class LiteralMapping(*, reference: R, predicate: Reference = NamedReference(prefix='oboInOwl', identifier='hasRelatedSynonym', name='has related synonym'), text: str, language: LanguageAlpha2 | None = None, type: Reference | None = None, provenance: list[Reference] = <factory>, contributor: Reference | None = None, comment: str | None = None, source: str | None = None, date: date | None = None, taxon: Reference | None = None)[source]

Bases: BaseModel, Generic[R]

A data model for literal mappings.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

Attributes Summary

`curie`	Get the reference's CURIE.
`date_str`	Get the date as a string.
`model_config`	Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
`name`	Get the reference's (optional) name.

Methods Summary

`from_gilda`(-> ~ssslm.model.LiteralMapping)	Construct a synonym from a `gilda` term.
`from_row`(-> ~ssslm.model.LiteralMapping)	Parse a dictionary representing a row in a TSV.
`get_all_references`()	Get all references made by this object.
`to_gilda`()	Get this synonym as a `gilda` term.

Attributes Documentation

curie: Get the reference’s CURIE.

date_str: Get the date as a string.

model_config = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

name: Get the reference’s (optional) name.

Methods Documentation

classmethod from_gilda(term: gilda.Term, *, reference_cls: type[R] = None) → LiteralMapping[source]

classmethod from_gilda(term: gilda.Term, *, reference_cls: None = None) → LiteralMapping[NamableReference]

Construct a synonym from a gilda term.

Parameters:

term – A Gilda term
reference_cls – the class to use to instantiate references

Returns:

A literal mapping object

Warning

Gilda’s data model is less detailed, so resulting synonym objects will not have detailed curation provenance

classmethod from_row(row: dict[str, Any], *, names: Mapping[Reference, str] | None = None, reference_cls: type[R] = None) → LiteralMapping[source]
classmethod from_row(row: dict[str, Any], *, names: Mapping[Reference, str] | None = None, reference_cls: None = None) → LiteralMapping[NamableReference]: Parse a dictionary representing a row in a TSV.

get_all_references() → set[Reference][source]: Get all references made by this object.

to_gilda() → gilda.Term[source]

Get this synonym as a gilda term.

Returns:: An object that can be indexed by Gilda for NER and grounding