Usage

ssslm.model Module

A data model for synonyms.

Functions

append_literal_mapping(literal_mapping, path)	Append a literal mapping to an existing file.
df_to_literal_mappings(...)	Get mapping objects from a dataframe.
get_prefixes(literal_mapping_index)	Get all prefixes appearing in a literal mapping index or iterable of literal mappings.
group_literal_mappings(literal_mappings)	Aggregate literal mappings by reference.
lint_literal_mappings(path, *[, delimiter, ...])	Lint a literal mappings file.
literal_mappings_to_df(literal_mappings)	Get a pandas dataframe from the literal mappings.
literal_mappings_to_gilda(literal_mappings, *)	Convert literal mappings to gilda terms.
read_gilda_terms(...)	Read Gilda terms from a file.
read_literal_mappings(...)	Load literal mappings from a file.
remap_literal_mappings(literal_mappings, ...)	Use a priority mapping to re-write terms with priority groundings.
write_gilda_terms(literal_mappings, path, *)	Write Gilda terms to a file.
write_literal_mappings(literal_mappings, path, *)	Write literal mappings to a path.

Classes

LiteralMapping(*, reference, predicate, ...)	A data model for literal mappings.
LiteralMappingTuple(text, curie, name, ...)	Represents rows in a spreadsheet.

Variables

DEFAULT_PREDICATE	The default synonym type predicate was chosen based on the OBO standard - when you don't specify a scope, this is what it infers
PREDICATES	A set of permissible predicates
GildaErrorPolicy	The error policy when converting to/from gilda terms
LiteralMappingIndex	An index from the reference to a list of mappings that use the reference
R	Type variable.
Writer	Valid writers

ssslm.io Package

I/O for SSSLM.

Functions

read_skos(-> list[~ssslm.model.LiteralMapping])

Read literal mappings from a SKOS.

ssslm.ner Module

NER utilities build on literal mappings.

Functions

make_grounder(...)	Get a grounder from literal mappings.
read_annotations(-> list[~ssslm.ner.Annotation])	Read annotations from a TSV file.
write_annotations(annotations, path)	Write annotations to a TSV file.

Classes

Annotation(*, text, start, end, match)	Data about an annotation.
Annotator()	An interface for something that can annotate.
GLiNERGrounder(matcher, *[, model, threshold])	An annotator that works via gliner.
GildaGrounder(grounder, *[, reference_cls])	A grounder and annotator that uses gilda as a backend.
GildaMatcher(grounder, *[, reference_cls])	A matcher that uses gilda as a backend.
Grounder()	A combine matcher and annotator.
Match(*, reference, score)	A match from NER.
Matcher()	An interface for a named entity normalizer.
PandasTargetType(*values)	How should pandas columns be filled.
SpacyGrounder(matcher, spacy_model)	An annotator that works via spacy.
WrappedMatcher(*, matcher)	A matcher that wraps another matcher, allowing for composition.

Variables

GLINER_DEFAULT	The default model used for GLiNER.
GrounderHint	A type for an object can be coerced into a SSSLM-backed grounder via make_grounder()

Class Inheritance Diagram

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