Index

Symbols

--build-docker semra-landscape command line option --include-wikidata semra-build command line option --no-include-wikidata semra-build command line option --only semra-landscape command line option --prune-sssom semra-build command line option --readme-only semra-landscape command line option --refresh-processed semra-landscape command line option --refresh-raw semra-build command line option semra-landscape command line option

--refresh-source semra-build command line option semra-landscape command line option --skip-below semra-build command line option --test semra-build command line option --upload semra-build command line option semra-landscape command line option --verbose semra-landscape command line option --version semra command line option --write-labels semra-build command line option -v semra-landscape command line option

A

all (AssembleReturnType attribute) ANATOMY_CONFIGURATION (in module semra.landscape.anatomy) apply_mutations() (in module semra.api)

assemble() (in module semra.pipeline) assemble_evidences() (in module semra.api) AssembleReturnType (class in semra.pipeline) assert_projection() (in module semra.api)

B

BEN_REFERENCE (in module semra.vocabulary)

BROAD_MATCH (in module semra.vocabulary)

C

CELL_CONFIGURATION (in module semra.landscape.cell) CHAIN_MAPPING (in module semra.vocabulary) CHARLIE (in module semra.vocabulary) cli() (Configuration method) CLOSE_MATCH (in module semra.vocabulary) COMPLEX_CONFIGURATION (in module semra.landscape.complex) CONCEPT_NODES_HEADER (in module semra.io.neo4j_io)

ConfidenceMixin (class in semra.struct) Configuration (class in semra.pipeline) configuration_path (Configuration attribute) count_component_sizes() (in module semra.api) count_source_target() (in module semra.api) curie (KeyedMixin attribute) CURIE_TO_JUSTIFICATION (in module semra.rules) CURIE_TO_RELATION (in module semra.rules)

D

DB_XREF (in module semra.vocabulary) deduplicate_evidence() (in module semra.api)

DERIVED_PREDICATE (in module semra.io.neo4j_io) DIRECTIONLESS (in module semra.rules) DISEASE_CONFIGURATION (in module semra.landscape.disease)

E

EDGES_HEADER (in module semra.io.neo4j_io) EDGES_SUPPLEMENT_HEADER (in module semra.io.neo4j_io) ensure_zenodo() (Configuration method) EQUIVALENT_TO (in module semra.vocabulary) EVIDENCE_NODES_HEADER (in module semra.io.neo4j_io)

evidence_type (ReasonedEvidenceKey attribute) EvidenceMixin (class in semra.struct) EXACT_MATCH (in module semra.vocabulary) explanation (EvidenceMixin attribute) (ReasonedEvidence attribute)

F

filter_many_to_many() (in module semra.api) filter_mappings() (in module semra.api) filter_minimum_confidence() (in module semra.api) filter_prefixes() (in module semra.api) filter_self_matches() (in module semra.api) filter_subsets() (in module semra.api) FLIP (in module semra.rules) flip() (in module semra.api) from_bioontologies() (in module semra.io) from_cache_df() (in module semra.io)

from_digraph() (in module semra.io) from_jsonl() (in module semra.io) from_multidigraph() (in module semra.io) from_pickle() (in module semra.io) from_prefixes() (Configuration class method) from_pyobo() (in module semra.io) FROM_SET_PREDICATE (in module semra.io.neo4j_io) from_sssom() (in module semra.io) from_sssom_df() (in module semra.io) from_triple() (Mapping class method)

G

GENE_CONFIGURATION (in module semra.landscape.gene) GENERALIZATIONS (in module semra.rules) get_asymmetric_counter() (in module semra.api) get_cli() (Configuration method) get_confidence() (ConfidenceMixin method) (Mapping method) (MappingSet method) (ReasonedEvidence method) (SimpleEvidence method) get_hydrated_subsets() (Configuration method) get_identifier_index() (in module semra.api)

get_index() (in module semra.api) get_many_to_many() (in module semra.api) get_mappings() (Configuration method) get_observed_terms() (in module semra.api) get_priority_reference() (in module semra.api) get_raw_mappings() (in module semra.pipeline) get_reference() (KeyedMixin method) get_sssom_df() (in module semra.io) get_symmetric_counter() (in module semra.api) get_terms() (in module semra.api) get_test_evidence() (in module semra.api) get_test_reference() (in module semra.api)

H

HAS_AUTHOR_PREDICATE (in module semra.io.neo4j_io) HAS_EVIDENCE_PREDICATE (in module semra.io.neo4j_io) has_primary (Mapping attribute) has_priority_path() (Configuration method) has_processed_path() (Configuration method)

has_raw_path() (Configuration method) has_secondary (Mapping attribute) has_tertiary (Mapping attribute) hexdigest() (KeyedMixin method) hydrate_subsets() (in module semra.api)

I

IMPRECISE (in module semra.rules) infer_chains() (in module semra.inference) infer_dbxref_mutations() (in module semra.inference) infer_generalizations() (in module semra.inference) infer_mutations() (in module semra.inference)

infer_mutual_dbxref_mutations() (in module semra.inference) infer_priority() (Configuration class method) infer_reversible() (in module semra.inference) Input (class in semra.pipeline) INVERSION_MAPPING (in module semra.vocabulary)

J

justification (ReasonedEvidenceKey attribute)

JUSTIFICATIONS (in module semra.rules)

K

keep_object_prefixes() (in module semra.api) keep_prefixes() (in module semra.api) keep_subject_prefixes() (in module semra.api) key() (KeyedMixin method) (Mapping method) (MappingSet method) (ReasonedEvidence method) (SimpleEvidence method)

KeyedMixin (class in semra.struct) KNOWLEDGE_MAPPING (in module semra.vocabulary)

L

LEXICAL_MAPPING (in module semra.vocabulary)

license (MappingSetKey attribute)

M

MANUAL_MAPPING (in module semra.vocabulary) Mapping (class in semra.struct) MAPPING_NODES_HEADER (in module semra.io.neo4j_io) mapping_set (ReasonedEvidence attribute) mapping_set_names (EvidenceMixin attribute) (ReasonedEvidence attribute) (SimpleEvidence attribute) MAPPING_SET_NODES_HEADER (in module semra.io.neo4j_io) MappingSet (class in semra.struct) MappingSetKey (class in semra.struct) model_config (Configuration attribute) (Input attribute) (Mapping attribute) (MappingSet attribute) (Mutation attribute), [1] (ReasonedEvidence attribute) (SimpleEvidence attribute) module semra.api semra.constants semra.database semra.inference semra.io semra.io.neo4j_io semra.landscape semra.landscape.anatomy semra.landscape.cell semra.landscape.complex semra.landscape.disease semra.landscape.gene semra.pipeline semra.rules semra.struct semra.vocabulary

Mutation (class in semra.api) (class in semra.pipeline)

N

name (MappingSetKey attribute)

NARROW_MATCH (in module semra.vocabulary) none (AssembleReturnType attribute)

P

print_source_target_counts() (in module semra.api) prioritize() (in module semra.api) prioritize_df() (in module semra.api) priority (AssembleReturnType attribute) priority_counts_path (Configuration attribute) priority_graph_path (Configuration attribute) priority_jsonl_path (Configuration attribute) priority_pickle_path (Configuration attribute) priority_sssom_path (Configuration attribute) process_raw_mappings() (in module semra.pipeline) processed_counts_path (Configuration attribute)

processed_graph_path (Configuration attribute) processed_jsonl_path (Configuration attribute) processed_landscape_histogram_path (Configuration attribute) processed_landscape_upset_path (Configuration attribute) processed_neo4j_name (Configuration attribute) processed_neo4j_path (Configuration attribute) processed_pickle_path (Configuration attribute) processed_sssom_path (Configuration attribute) project() (in module semra.api) project_dict() (in module semra.api) purl (MappingSetKey attribute)

R

raw_counts_path (Configuration attribute) raw_graph_path (Configuration attribute) raw_jsonl_path (Configuration attribute) raw_neo4j_name (Configuration attribute) raw_neo4j_path (Configuration attribute) raw_pickle_path (Configuration attribute) raw_sssom_path (Configuration attribute) read_priority_mappings() (Configuration method)

read_processed_mappings() (Configuration method) read_raw_mappings() (Configuration method) readme_path (Configuration attribute) ReasonedEvidence (class in semra.struct) ReasonedEvidenceKey (class in semra.struct) RELATIONS (in module semra.rules) REPLACED_BY (in module semra.vocabulary) rest (ReasonedEvidenceKey attribute)

S

semra command line option --version semra-build command line option --include-wikidata --no-include-wikidata --prune-sssom --refresh-raw --refresh-source --skip-below --test --upload --write-labels semra-landscape command line option --build-docker --only --readme-only --refresh-processed --refresh-raw --refresh-source --upload --verbose -v semra.api module semra.constants module semra.database module semra.inference module semra.io module semra.io.neo4j_io module

semra.landscape module semra.landscape.anatomy module semra.landscape.cell module semra.landscape.complex module semra.landscape.disease module semra.landscape.gene module semra.pipeline module semra.rules module semra.struct module semra.vocabulary module SEMRA_EVIDENCE_PREFIX (in module semra.constants) SEMRA_MAPPING_PREFIX (in module semra.constants) SEMRA_MAPPING_SET_PREFIX (in module semra.constants) SEMRA_NEO4J_CONCEPT_LABEL (in module semra.constants) SEMRA_NEO4J_EVIDENCE_LABEL (in module semra.constants) SEMRA_NEO4J_MAPPING_LABEL (in module semra.constants) SEMRA_NEO4J_MAPPING_SET_LABEL (in module semra.constants) should_apply_to() (Mutation method), [1] SimpleEvidence (class in semra.struct) source_summary_path (Configuration attribute) stats_path (Configuration attribute) str_source_target_counts() (in module semra.api) SUBCLASS (in module semra.vocabulary) summarize_prefixes() (in module semra.api)

T

tabulate_index() (in module semra.api) to_digraph() (in module semra.io) to_multidigraph() (in module semra.io)

TRANSITIVE (in module semra.rules) triple (Mapping attribute) TWO_STEP (in module semra.rules)

U

unindex() (in module semra.api) UNSPECIFIED_MAPPING (in module semra.vocabulary)

update_literal_mappings() (in module semra.api) upload_zenodo() (Configuration method)

V

validate_mappings() (in module semra.api)

version (MappingSetKey attribute)

W

write_jsonl() (in module semra.io) write_neo4j() (in module semra.io)

write_pickle() (in module semra.io) write_sssom() (in module semra.io)

Z

zenodo_url() (Configuration method)