Usage

sssom_pydantic.api Module

This is a placeholder for putting the main code for your module.

Functions

hash_mapping(mapping, converter)	Hash the entire SSSOM semantic mapping record.
hash_mapping_to_reference(mapping, converter)	Hash a mapping into a reference.
hash_triple(mapping, converter)	Return a triples sameness identifier.
hash_triple_to_reference(mapping, converter)	Return a mapping sameness identifier as a reference.
standardize_mappings(mappings, *[, converter])	Standardize mappings against the Bioregistry.

Classes

ExtensionDefinition(*, slot_name[, ...])	A processed extension definition.
ExtensionDefinitionRecord(*, slot_name[, ...])	An extension definition that can be readily dumped to SSSOM.
MappingSet(*, id[, confidence, description, ...])	A processed representation of a mapping set.
MappingSetRecord(*[, curie_map, ...])	Represents a mapping set, readily serializable for usage in SSSOM TSV.
MappingTool(*[, reference, name, version])	Represents metadata about a mapping tool.
SemanticMapping(*, subject, predicate, ...)	Represents most fields for SSSOM.

Class Inheritance Diagram

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sssom_pydantic.io Module

I/O operations for SSSOM.

Functions

append(mappings, path, *[, metadata, ...])	Append processed records.
append_unprocessed(records, path, *[, ...])	Append records to the end of an existing file.
format(path, *[, metadata_path, metadata, ...])	Lint a file.
lint(*args, **kwargs)	Run the formatter.
read(...)	Read and process SSSOM from TSV.
read_iterable(path_or_url, *[, ...])	Read and process SSSOM from TSV in an iterable way.
read_unprocessed(path_or_url, *[, ...])	Read SSSOM TSV into unprocessed records.
record_to_semantic_mapping(record, converter, *)	Parse a record into a mapping.
row_to_record(row, *[, propagatable])	Parse a row from a SSSOM TSV file, unprocessed.
row_to_semantic_mapping(row, converter, *[, ...])	Get a semantic mapping from a row.
to_dataframe(mappings)	Construct a pandas dataframe that represents the SSSOM TSV format.
write(mappings, path, *[, metadata, ...])	Write semantic mappings as SSSOM TSV.
write_metadata(metadata, file)	Write SSSOM metadata for the top of a TSV.
write_unprocessed(records, path, *[, ...])	Write unprocessed records.

Classes

CachedSemanticMappings(path, *[, force, cache])	Make a function lazily cache SSSOM.
ParseError(line_number, exception, stage)	An error during SSSOM parsing and processing that causes a row to be unrecoverable.
SemanticMappingPack(mappings, converter, ...)	The results of reading and processing a SSSOM TSV file.

Class Inheritance Diagram

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sssom_pydantic.models Module

Models for SSSOM.

Classes

ExpandedRecord(*[, record_id, ...])	Represents an SSSOM record (i.e., a row in a SSSOM TSV file) expanded with URIs.
Record(*[, record_id, subject_label, ...])	Represents an SSSOM record (i.e., a row in a SSSOM TSV file).

Class Inheritance Diagram

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sssom_pydantic.process Module

Utilities for working with semantic mappings.

Functions

curate(mapping, /, authors, mark[, ...])	Curate a mapping.
estimate_confidence(mappings, *[, ...])	Estimate the confidence of a subject-predicate-triple based on multiple evidences.
exclude_negative(mappings)	Exclude negative mappings.
exclude_unsure(mappings)	Exclude usunre mappings.
filter_by_confidence(mappings, cutoff)	Filter by confidence.
get_canonical_tuple(mapping)	Get the canonical tuple from a mapping entry.
invert(mapping, *, converter[, ...])	Invert a mapping.
invert_broad_matches(mappings, *, converter)	Invert broad matches into narrow matches.
invert_by_object_prefix(mappings, ...[, ...])	Invert mappings with the given object prefix.
invert_by_prefix_pair(mappings, ...[, ...])	Invert mappings with the given subject and object (SO) prefixes.
invert_by_subject_prefix(mappings, ...[, ...])	Invert mappings with the given subject prefix.
invert_narrow_matches(mappings, *, converter)	Invert narrow matches into broad matches.
merge_manual_curations(mappings, *, converter)	Merge manually curated mappings.
publish(mapping, /, *[, exists_action, date])	Add a publication date to the mapping.
remove_redundant_external(mappings, *others)	Remove mappings with same S/O pairs in other given mappings.
remove_redundant_internal(mappings, *[, ...])	Remove redundant mappings.
review(mapping, reviewers, *[, score, date, ...])	Review a mapping and produce a new record.

Classes

InvalidExistsActionError(value)

An error for an invalid exists action.

Class Inheritance Diagram

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sssom_pydantic.query Module

Tools for filtering mappings.

Functions

count_entities(mappings)	Count appearances of subjects and objects.
count_prefix_pairs(mappings)	Count subject/object prefix pairs.
count_unique_entities(mappings)	Count the number of unique entities appearing in the subjects and objects of mappings.
filter_mappings(mappings, query, *[, ...])	Filter mappings based on a query.
get_mappings(mappings[, query, limit, ...])	Get a sequence of mappings.
paginate_mappings(mappings, *[, sort, ...])	Paginate mappings with sort, offset, and limit operations.
sort_mappings(mappings, sort)	Sort mappings.

Classes

Query(*[, triple_id, query, subject_query, ...])

A query over semantic mappings.

Class Inheritance Diagram

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