Index

Symbols

--author_id sssom-filter command line option --author_label sssom-filter command line option --by-columns sssom-sort command line option --by-rows sssom-sort command line option --clean-prefixes sssom-parse command line option --comment sssom-annotate command line option sssom-filter command line option --confidence sssom-filter command line option --config sssom-sparql command line option --creator_id sssom-annotate command line option sssom-filter command line option --creator_label sssom-annotate command line option sssom-filter command line option --curation_rule sssom-filter command line option --curation_rule_text sssom-filter command line option --curie_map sssom-annotate command line option --default-confidence sssom-ptable command line option --embedded-mode sssom-parse command line option --extension_definitions sssom-annotate command line option --fields sssom-correlations command line option sssom-crosstab command line option --graph sssom-sparql command line option --input-format sssom-parse command line option sssom-rewire command line option --inverse-factor sssom-ptable command line option --inverse-map sssom-invert command line option --issue_tracker sssom-annotate command line option --issue_tracker_item sssom-filter command line option --license sssom-annotate command line option sssom-filter command line option --limit sssom-sparql command line option --mapping-file sssom-rewire command line option --mapping-predicate-filter sssom-parse command line option --mapping_cardinality sssom-filter command line option --mapping_date sssom-annotate command line option sssom-filter command line option --mapping_justification sssom-filter command line option --mapping_provider sssom-annotate command line option sssom-filter command line option --mapping_set_description sssom-annotate command line option --mapping_set_id sssom-annotate command line option --mapping_set_source sssom-annotate command line option --mapping_set_title sssom-annotate command line option --mapping_set_version sssom-annotate command line option --mapping_source sssom-filter command line option --mapping_tool sssom-annotate command line option sssom-filter command line option --mapping_tool_version sssom-annotate command line option sssom-filter command line option --mappings sssom-annotate command line option --match_string sssom-filter command line option --merge-inverted sssom-invert command line option --metadata sssom-cliquesummary command line option sssom-parse command line option --no-clean-prefixes sssom-parse command line option --no-merge-inverted sssom-invert command line option --no-object-labels sssom-sparql command line option --no-strict-clean-prefixes sssom-parse command line option --no-update-justification sssom-invert command line option --non-embedded-mode sssom-parse command line option --object-labels sssom-sparql command line option --object_category sssom-filter command line option --object_id sssom-filter command line option --object_label sssom-filter command line option --object_match_field sssom-annotate command line option sssom-filter command line option --object_preprocessing sssom-annotate command line option sssom-filter command line option --object_source sssom-annotate command line option sssom-filter command line option --object_source_version sssom-annotate command line option sssom-filter command line option --object_type sssom-annotate command line option sssom-filter command line option --other sssom-annotate command line option sssom-filter command line option --output sssom-annotate command line option sssom-cliquesummary command line option sssom-convert command line option sssom-correlations command line option sssom-crosstab command line option sssom-dedupe command line option sssom-diff command line option sssom-dosql command line option sssom-filter command line option sssom-invert command line option sssom-merge command line option sssom-parse command line option sssom-ptable command line option sssom-reconcile-prefixes command line option sssom-remove command line option sssom-rewire command line option sssom-sort command line option sssom-sparql command line option --output-directory sssom-partition command line option sssom-split command line option

--output-format sssom-convert command line option sssom-rewire command line option --precedence sssom-rewire command line option --predicate_id sssom-filter command line option --predicate_label sssom-filter command line option --predicate_modifier sssom-filter command line option --prefix sssom-sparql command line option --prefix-map-mode sssom-parse command line option --publication_date sssom-annotate command line option sssom-filter command line option --query sssom-dosql command line option --quiet sssom command line option --reconcile sssom-merge command line option --reconcile-prefix-file sssom-reconcile-prefixes command line option --remove-map sssom-remove command line option --replace-multivalued sssom-annotate command line option --reviewer_id sssom-filter command line option --reviewer_label sssom-filter command line option --see_also sssom-annotate command line option sssom-filter command line option --similarity_measure sssom-filter command line option --similarity_score sssom-filter command line option --statsfile sssom-cliquesummary command line option --strict-clean-prefixes sssom-parse command line option --subject-prefix sssom-invert command line option --subject_category sssom-filter command line option --subject_id sssom-filter command line option --subject_label sssom-filter command line option --subject_match_field sssom-annotate command line option sssom-filter command line option --subject_preprocessing sssom-annotate command line option sssom-filter command line option --subject_source sssom-annotate command line option sssom-filter command line option --subject_source_version sssom-annotate command line option sssom-filter command line option --subject_type sssom-annotate command line option sssom-filter command line option --transpose sssom-correlations command line option sssom-crosstab command line option --update-justification sssom-invert command line option --url sssom-sparql command line option --validation-types sssom-validate command line option --verbose sssom command line option --version sssom command line option -C sssom-parse command line option -c sssom-sparql command line option -d sssom-partition command line option sssom-split command line option -E sssom-parse command line option -e sssom-sparql command line option -F sssom-parse command line option -f sssom-correlations command line option sssom-crosstab command line option -g sssom-sparql command line option -I sssom-parse command line option sssom-rewire command line option -k sssom-sort command line option -l sssom-sparql command line option -m sssom-cliquesummary command line option sssom-parse command line option sssom-rewire command line option -O sssom-convert command line option sssom-rewire command line option -o sssom-annotate command line option sssom-cliquesummary command line option sssom-convert command line option sssom-correlations command line option sssom-crosstab command line option sssom-dedupe command line option sssom-diff command line option sssom-dosql command line option sssom-filter command line option sssom-invert command line option sssom-merge command line option sssom-parse command line option sssom-ptable command line option sssom-reconcile-prefixes command line option sssom-remove command line option sssom-rewire command line option sssom-sort command line option sssom-sparql command line option -P sssom-invert command line option sssom-sparql command line option -p sssom-parse command line option sssom-reconcile-prefixes command line option -Q sssom-dosql command line option -q sssom command line option -R sssom-merge command line option -r sssom-sort command line option -s sssom-cliquesummary command line option -t sssom-correlations command line option sssom-crosstab command line option -V sssom-validate command line option -v sssom command line option -W sssom-ptable command line option

_

__format__() (sssom.constants.SchemaValidationType method)

__new__() (sssom.constants.SSSOMSchemaView static method)

A

add_default_confidence() (in module sssom.util), [1] annotate_file() (in module sssom.io), [1]

are_params_slots() (in module sssom.util), [1] assign_default_confidence() (in module sssom.util), [1] augment_metadata() (in module sssom.util), [1]

C

check_all_prefixes_in_curie_map() (in module sssom.validators) check_strict_curie_format() (in module sssom.validators) clean_context() (sssom.util.MappingSetDataFrame method), [1] clean_prefix_map() (sssom.util.MappingSetDataFrame method), [1] collapse() (in module sssom.util), [1] combined_dataframe (sssom.util.MappingSetDiff attribute), [1] common_tuples (sssom.util.MappingSetDiff attribute) compare_dataframes() (in module sssom.util), [1] CompositeMatching (sssom.constants.SEMAPV attribute)

convert_file() (in module sssom.io), [1] converter (sssom.sparql_util.EndpointConfig attribute) (sssom.sssom_document.MappingSetDocument attribute) (sssom.util.MappingSetDataFrame attribute) ConverterHint (in module sssom.context), [1] create_entity() (in module sssom.util), [1] CrossSpeciesBroadMatch (sssom.constants.SEMAPV attribute) CrossSpeciesExactMatch (sssom.constants.SEMAPV attribute) CrossSpeciesNarrowMatch (sssom.constants.SEMAPV attribute)

D

dataframe_to_ptable() (in module sssom.util), [1] deal_with_negation() (in module sssom.util), [1] df (sssom.util.MappingSetDataFrame attribute)

dict (sssom.constants.SSSOMSchemaView property) double_slots (sssom.constants.SSSOMSchemaView property) dynamically_generate_sssom_options() (in module sssom.cli), [1]

E

EndpointConfig (class in sssom.sparql_util) ensure_converter() (in module sssom.context), [1]

entity_reference_slots (sssom.constants.SSSOMSchemaView property) EntityPair (class in sssom.util), [1] extract_iris() (in module sssom.io), [1]

F

filter_file() (in module sssom.io), [1] filter_out_prefixes() (in module sssom.util), [1] filter_prefixes() (in module sssom.util), [1] filter_redundant_rows() (in module sssom.util), [1] from_alignment_minidom() (in module sssom.parsers), [1] from_mapping_set() (sssom.util.MappingSetDataFrame class method), [1]

from_mapping_set_document() (sssom.util.MappingSetDataFrame class method), [1] from_mappings() (sssom.util.MappingSetDataFrame class method), [1] from_obographs() (in module sssom.parsers), [1] from_sssom_dataframe() (in module sssom.parsers), [1] from_sssom_json() (in module sssom.parsers), [1] from_sssom_rdf() (in module sssom.parsers), [1]

G

generate_mapping_set_id() (in module sssom.constants) get_all_prefixes() (in module sssom.util), [1] get_converter() (in module sssom.context), [1] get_default_metadata() (in module sssom.constants) get_dict_from_mapping() (in module sssom.util), [1] get_file_extension() (in module sssom.util), [1] get_metadata_and_prefix_map() (in module sssom.io), [1] get_parsing_function() (in module sssom.parsers), [1]

get_prefix_from_curie() (in module sssom.util), [1] get_prefixes_used_in_metadata() (in module sssom.util), [1] get_prefixes_used_in_table() (in module sssom.util), [1] get_row_based_on_hierarchy() (in module sssom.util), [1] get_src() (in module sssom.cliques), [1] get_writer_function() (in module sssom.writers), [1] graph (sssom.sparql_util.EndpointConfig attribute) group_mappings() (in module sssom.util), [1] group_values() (in module sssom.cliques), [1]

I

include_object_labels (sssom.sparql_util.EndpointConfig attribute) inject_metadata_into_df() (in module sssom.util), [1] INPUT sssom-annotate command line option sssom-cliquesummary command line option sssom-convert command line option sssom-correlations command line option sssom-crosstab command line option sssom-dedupe command line option sssom-filter command line option sssom-invert command line option sssom-parse command line option sssom-ptable command line option sssom-reconcile-prefixes command line option sssom-remove command line option sssom-rewire command line option sssom-sort command line option sssom-split command line option sssom-validate command line option

INPUTS sssom-diff command line option sssom-dosql command line option sssom-merge command line option sssom-partition command line option instance (sssom.constants.SSSOMSchemaView attribute) invert_mappings() (in module sssom.util), [1] is_multivalued_slot() (in module sssom.util), [1]

J

JsonSchema (sssom.constants.SchemaValidationType attribute)

K

KEY_FEATURES (in module sssom.util), [1]

L

LexicalMatching (sssom.constants.SEMAPV attribute) LexicalSimilarityThresholdMatching (sssom.constants.SEMAPV attribute)

limit (sssom.sparql_util.EndpointConfig attribute) LogicalReasoning (sssom.constants.SEMAPV attribute)

M

ManualMappingCuration (sssom.constants.SEMAPV attribute) mapping_enum_keys (sssom.constants.SSSOMSchemaView property) mapping_set (sssom.sssom_document.MappingSetDocument attribute), [1] mapping_set_slots (sssom.constants.SSSOMSchemaView property) mapping_slots (sssom.constants.SSSOMSchemaView property) MappingChaining (sssom.constants.SEMAPV attribute) MappingInversion (sssom.constants.SEMAPV attribute) MappingReview (sssom.constants.SEMAPV attribute) MappingSetDataFrame (class in sssom.util), [1] MappingSetDiff (class in sssom.util), [1] MappingSetDocument (class in sssom.sssom_document), [1] merge() (sssom.util.MappingSetDataFrame method), [1] merge_msdf() (in module sssom.util), [1] metadata (sssom.util.MappingSetDataFrame attribute) MetadataType (in module sssom.constants)

module sssom, [1] sssom.cli, [1] sssom.cliques, [1] sssom.constants sssom.context, [1] sssom.io, [1] sssom.parsers, [1] sssom.rdf_util sssom.sparql_util sssom.sssom_document, [1] sssom.util, [1] sssom.validators sssom.writers, [1] multivalued_slots (sssom.constants.SSSOMSchemaView property)

O

object_entity (sssom.util.EntityPair attribute)

P

pandas_set_no_silent_downcasting() (in module sssom.util), [1] parse() (in module sssom.util), [1] parse_alignment_xml() (in module sssom.parsers), [1] parse_file() (in module sssom.io), [1] parse_obographs_json() (in module sssom.parsers), [1] parse_sssom_json() (in module sssom.parsers), [1] parse_sssom_rdf() (in module sssom.parsers), [1]

parse_sssom_table() (in module sssom.parsers), [1] predicates (sssom.sparql_util.EndpointConfig attribute) predmap (sssom.sparql_util.EndpointConfig attribute) prefix_map (sssom.sssom_document.MappingSetDocument property), [1] (sssom.util.MappingSetDataFrame property), [1] PrefixMapCompleteness (sssom.constants.SchemaValidationType attribute) print_linkml_report() (in module sssom.validators)

Q

query_mappings() (in module sssom.sparql_util)

R

raise_for_bad_path() (in module sssom.util), [1] reconcile_prefix_and_data() (in module sssom.util), [1] remove_mappings() (sssom.util.MappingSetDataFrame method), [1]

remove_unmatched() (in module sssom.util), [1] rewire_graph() (in module sssom.rdf_util) run_sql_query() (in module sssom.io), [1]

S

safe_compress() (in module sssom.util), [1] SchemaValidationType (class in sssom.constants) SemanticSimilarityThresholdMatching (sssom.constants.SEMAPV attribute) SEMAPV (class in sssom.constants) Shacl (sssom.constants.SchemaValidationType attribute) slots (sssom.constants.SSSOMSchemaView property) sort_df_rows_columns() (in module sssom.util), [1] sort_sssom() (in module sssom.util), [1] Sparql (sssom.constants.SchemaValidationType attribute) split_dataframe() (in module sssom.parsers), [1] split_dataframe_by_prefix() (in module sssom.parsers), [1] split_file() (in module sssom.io), [1] split_into_cliques() (in module sssom.cliques), [1] sssom module, [1] sssom command line option --quiet --verbose --version -q -v sssom-annotate command line option --comment --creator_id --creator_label --curie_map --extension_definitions --issue_tracker --license --mapping_date --mapping_provider --mapping_set_description --mapping_set_id --mapping_set_source --mapping_set_title --mapping_set_version --mapping_tool --mapping_tool_version --mappings --object_match_field --object_preprocessing --object_source --object_source_version --object_type --other --output --publication_date --replace-multivalued --see_also --subject_match_field --subject_preprocessing --subject_source --subject_source_version --subject_type -o INPUT sssom-cliquesummary command line option --metadata --output --statsfile -m -o -s INPUT sssom-convert command line option --output --output-format -o -O INPUT sssom-correlations command line option --fields --output --transpose -f -o -t INPUT sssom-crosstab command line option --fields --output --transpose -f -o -t INPUT sssom-dedupe command line option --output -o INPUT sssom-diff command line option --output -o INPUTS sssom-dosql command line option --output --query -o -Q INPUTS sssom-filter command line option --author_id --author_label --comment --confidence --creator_id --creator_label --curation_rule --curation_rule_text --issue_tracker_item --license --mapping_cardinality --mapping_date --mapping_justification --mapping_provider --mapping_source --mapping_tool --mapping_tool_version --match_string --object_category --object_id --object_label --object_match_field --object_preprocessing --object_source --object_source_version --object_type --other --output --predicate_id --predicate_label --predicate_modifier --publication_date --reviewer_id --reviewer_label --see_also --similarity_measure --similarity_score --subject_category --subject_id --subject_label --subject_match_field --subject_preprocessing --subject_source --subject_source_version --subject_type -o INPUT

sssom-help command line option SUBCOMMAND sssom-invert command line option --inverse-map --merge-inverted --no-merge-inverted --no-update-justification --output --subject-prefix --update-justification -o -P INPUT sssom-merge command line option --output --reconcile -o -R INPUTS sssom-parse command line option --clean-prefixes --embedded-mode --input-format --mapping-predicate-filter --metadata --no-clean-prefixes --no-strict-clean-prefixes --non-embedded-mode --output --prefix-map-mode --strict-clean-prefixes -C -E -F -I -m -o -p INPUT sssom-partition command line option --output-directory -d INPUTS sssom-ptable command line option --default-confidence --inverse-factor --output -o -W INPUT sssom-reconcile-prefixes command line option --output --reconcile-prefix-file -o -p INPUT sssom-remove command line option --output --remove-map -o INPUT sssom-rewire command line option --input-format --mapping-file --output --output-format --precedence -I -m -O -o INPUT sssom-sort command line option --by-columns --by-rows --output -k -o -r INPUT sssom-sparql command line option --config --graph --limit --no-object-labels --object-labels --output --prefix --url -c -e -g -l -o -P sssom-split command line option --output-directory -d INPUT sssom-validate command line option --validation-types -V INPUT sssom.cli module, [1] sssom.cliques module, [1] sssom.constants module sssom.context module, [1] sssom.io module, [1] sssom.parsers module, [1] sssom.rdf_util module sssom.sparql_util module sssom.sssom_document module, [1] sssom.util module, [1] sssom.validators module sssom.writers module, [1] SSSOMSchemaView (class in sssom.constants) standardize_references() (sssom.util.MappingSetDataFrame method), [1] StrictCurieFormat (sssom.constants.SchemaValidationType attribute) SUBCOMMAND sssom-help command line option subject_entity (sssom.util.EntityPair attribute) summarize_cliques() (in module sssom.cliques), [1]

T

to_digraph() (in module sssom.cliques), [1] to_fhir_json() (in module sssom.writers), [1] to_json() (in module sssom.writers), [1] to_mapping_set() (sssom.util.MappingSetDataFrame method), [1] to_mapping_set_dataframe() (in module sssom.util), [1]

to_mapping_set_document() (in module sssom.parsers), [1] (sssom.util.MappingSetDataFrame method), [1] to_mappings() (sssom.util.MappingSetDataFrame method), [1] to_ontoportal_json() (in module sssom.writers), [1] to_owl_graph() (in module sssom.writers), [1] to_rdf_graph() (in module sssom.writers), [1]

U

unique_tuples1 (sssom.util.MappingSetDiff attribute) unique_tuples2 (sssom.util.MappingSetDiff attribute)

UnspecifiedMatching (sssom.constants.SEMAPV attribute) url (sssom.sparql_util.EndpointConfig attribute)

V

validate() (in module sssom.validators) validate_file() (in module sssom.io), [1] validate_json_schema() (in module sssom.validators)

validate_shacl() (in module sssom.validators) validate_sparql() (in module sssom.validators) view (sssom.constants.SSSOMSchemaView property)

W

with_converter() (sssom.util.MappingSetDataFrame class method), [1] write_fhir_json() (in module sssom.writers), [1] write_json() (in module sssom.writers), [1] write_ontoportal_json() (in module sssom.writers), [1]

write_owl() (in module sssom.writers), [1] write_rdf() (in module sssom.writers), [1] write_table() (in module sssom.writers), [1] write_tables() (in module sssom.writers), [1]