Reference

This contains several SeMRA submodules with low-level functionality. You can use these to build your own mapping processing workflows and I/O.

semra.api Module

Semantic Mapping Reasoning Assembler.

Functions

apply_mutations(mappings, mutations, *[, ...])	Apply mutations.
assemble_evidences(mappings, *[, progress])	Assemble evidences.
assert_projection(mappings)	Raise an exception if any entities appear as the subject in multiple mappings.
count_component_sizes(mappings[, ...])	Get a counter where the keys are the set of all prefixes in a weakly connected component.
count_source_target(mappings)	Count pairs of source/target prefixes.
deduplicate_evidence(triple, evidence)	Deduplicate a list of evidences based on their "key" function.
filter_many_to_many(mappings, *[, progress])	Filter out many to many mappings.
filter_mappings(mappings, skip_mappings, *)	Filter out mappings in the second set from the first set.
filter_minimum_confidence(mappings[, cutoff])	Filter mappings below a given confidence.
filter_prefixes(mappings, prefixes, *[, ...])	Filter out mappings whose subject or object are in the given list of prefixes.
filter_self_matches(mappings, *[, progress])	Filter out mappings within the same resource.
filter_subsets(mappings, prefix_to_references)	Filter mappings that don't appear in the given subsets.
flip()	Flip a mapping, if the relation is configured with an inversion.
get_asymmetric_counter(index, priority, *, ...)	Create a symmetric mapping counts counter from a directed index.
get_identifier_index(mappings, *[, ...])	Index which entities in each vocabulary have been mapped.
get_index(mappings, *[, progress, leave])	Aggregate and deduplicate evidences for each core triple.
get_many_to_many(mappings)	Get many-to-many mappings, disregarding predicate type.
get_observed_terms(mappings)	Get the set of terms appearing in each prefix.
get_priority_reference(component, priority)	Get the priority reference from a component.
get_symmetric_counter(index, priority, *, ...)	Create a symmetric mapping counts counter from a directed index.
get_terms(prefixes[, subset_configuration, ...])	Get the set of identifiers for each of the resources.
get_test_evidence([n])	Get test evidence.
get_test_reference([n, prefix])	Get test reference(s).
hydrate_subsets(subset_configuration, *[, ...])	Convert a subset configuration dictionary into a subset artifact.
keep_object_prefixes(mappings, prefixes, *)	Filter out mappings whose objects are not in the given list of prefixes.
keep_prefixes(mappings, prefixes, *[, progress])	Filter out mappings whose subject or object are not in the given list of prefixes.
keep_subject_prefixes(mappings, prefixes, *)	Filter out mappings whose subjects are not in the given list of prefixes.
print_source_target_counts(mappings[, minimum])	Print the counts of source/target prefixes.
prioritize(mappings, priority, *[, progress])	Get a priority star graph.
prioritize_df(mappings, df, *, column[, ...])	Remap a column of a dataframe based on priority mappings.
project()	Ensure that each identifier only appears as the subject of one mapping.
project_dict(mappings, source_prefix, ...)	Get a dictionary from source identifiers to target identifiers.
str_source_target_counts(mappings[, minimum])	Create a table of counts of source/target prefix via tabulate.
summarize_prefixes(mappings)	Get a dataframe summarizing the prefixes appearing in the mappings.
tabulate_index(index)	Create a table of all mappings contained in an index.
unindex(index, *[, progress])	Convert a mapping index into a list of mapping objects.
update_literal_mappings(literal_mappings, ...)	Use a priority mapping to re-write terms with priority groundings.
validate_mappings(mappings, *[, progress])	Validate mappings against the Bioregistry and raise an error on the first invalid.

Classes

Mutation(*, source[, target, confidence, ...])

Represents a mutation operation on a mapping set.

semra.inference Module

Inference functionality for SeMRA.

Functions

infer_chains(mappings, *[, backwards, ...])	Apply graph-based reasoning over mapping chains to infer new mappings.
infer_dbxref_mutations(mappings, pairs[, ...])	Upgrade database cross-references into exact matches for the given pairs.
infer_generalizations(mappings, *[, progress])	Apply generalization rules.
infer_mutations(mappings, pairs, ...[, progress])	Infer mappings with alternate predicates for the given prefix pairs.
infer_mutual_dbxref_mutations(mappings, prefixes)	Upgrade database cross-references into exact matches for the given pairs.
infer_reversible(mappings, *[, progress])	Extend the mapping list with flipped mappings.

semra.rules Module

Constants and rules for inference.

Variables

CURIE_TO_JUSTIFICATION	A mapping from CURIEs to mapping justifications
CURIE_TO_RELATION	A mapping from CURIEs to reference objects for mapping predicates
DIRECTIONLESS	Which predicates are directionless
FLIP	A mapping of inverse relationships that can be applied when inversting mappings
GENERALIZATIONS	Rules for relaxing a more strict predicate to a more loose one, see https://mapping-commons.github.io/sssom/chaining-rules/#generalisation-rules
IMPRECISE	A set of mappings that are not considered as precise
JUSTIFICATIONS	A list of references that can be used as mapping justifications in SSSOM
RELATIONS	A list of mapping predicates suggested by SSSOM.
TRANSITIVE	Which predicates are transitive? This excludes the imprecise onces
TWO_STEP	Two step chain inference rules

semra.vocabulary Module

Vocabulary used in SeMRA.

Variables

BEN_REFERENCE	Extends curies.NamableReference to normalize the prefix against the Bioregistry.
BROAD_MATCH	A reference to skos:broadMatch
CHAIN_MAPPING	A reference to semapv:MappingChaining that can be used as a mapping justification, see also semra.rules.JUSTIFICATIONS.
CHARLIE	A reference to Charles Tapley Hoyt, the author of SeMRA
CLOSE_MATCH	A reference to skos:closeMatch
DB_XREF	A reference to oboInOwl:hasDbXref
EQUIVALENT_TO	A reference to owl:equivalentTo
EXACT_MATCH	A reference to skos:exactMatch
INVERSION_MAPPING	A reference to semapv:MappingInversion that can be used as a mapping justification, see also semra.rules.JUSTIFICATIONS.
KNOWLEDGE_MAPPING	A reference to semapv:BackgroundKnowledgeBasedMatching that can be used as a mapping justification, see also semra.rules.JUSTIFICATIONS.
LEXICAL_MAPPING	A reference to semapv:LexicalMatchingProcess that can be used as a mapping justification, see also semra.rules.JUSTIFICATIONS.
MANUAL_MAPPING	A reference to semapv:ManualMappingCuration that can be used as a mapping justification, see also semra.rules.JUSTIFICATIONS.
NARROW_MATCH	A reference to skos:narrowMatch
REPLACED_BY	A reference to IAO:0100001 (term replaced by)
SUBCLASS	A reference to rdfs:subClassOf
UNSPECIFIED_MAPPING	A reference to semapv:UnspecifiedMatchingProcess that can be used as a mapping justification, see also semra.rules.JUSTIFICATIONS.

semra.constants Module

Constants for SeMRA.

Variables

SEMRA_EVIDENCE_PREFIX	The prefix used in CURIEs representing evidences
SEMRA_MAPPING_PREFIX	The prefix used in CURIEs representing mappings
SEMRA_MAPPING_SET_PREFIX	The prefix used in CURIEs representing mappings sets
SEMRA_NEO4J_CONCEPT_LABEL	The label used for nodes representing concepts (i.e., entities) in SeMRA's Neo4j export
SEMRA_NEO4J_EVIDENCE_LABEL	The label used for nodes representing evidences in SeMRA's Neo4j export
SEMRA_NEO4J_MAPPING_LABEL	The label used for nodes representing mappings in SeMRA's Neo4j export
SEMRA_NEO4J_MAPPING_SET_LABEL	The label used for nodes representing mapping sets in SeMRA's Neo4j export