Index

Symbols

--biolink-release kgx-validate command line option --destination kgx-merge command line option --edge-facet-properties kgx-graph-summary command line option --edge-filters kgx-neo4j-download command line option kgx-neo4j-upload command line option kgx-transform command line option --error-log kgx-graph-summary command line option --graph-name kgx-graph-summary command line option --infores-catalog kgx-transform command line option --input-compression kgx-graph-summary command line option kgx-neo4j-upload command line option kgx-transform command line option kgx-validate command line option --input-format kgx-graph-summary command line option kgx-neo4j-upload command line option kgx-transform command line option kgx-validate command line option --knowledge-sources kgx-transform command line option --merge-config kgx-merge command line option --node-facet-properties kgx-graph-summary command line option --node-filters kgx-neo4j-download command line option kgx-neo4j-upload command line option kgx-transform command line option --output kgx-graph-summary command line option kgx-neo4j-download command line option kgx-transform command line option kgx-validate command line option --output-compression kgx-neo4j-download command line option kgx-transform command line option --output-format kgx-neo4j-download command line option kgx-transform command line option --password kgx-neo4j-download command line option kgx-neo4j-upload command line option --processes kgx-merge command line option kgx-transform command line option --report-format kgx-graph-summary command line option --report-type kgx-graph-summary command line option --source kgx-merge command line option kgx-transform command line option --stream kgx-neo4j-download command line option kgx-neo4j-upload command line option kgx-transform command line option

--transform-config kgx-transform command line option --uri kgx-neo4j-download command line option kgx-neo4j-upload command line option --username kgx-neo4j-download command line option kgx-neo4j-upload command line option --version kgx command line option -b kgx-validate command line option -c kgx-graph-summary command line option kgx-neo4j-upload command line option kgx-transform command line option kgx-validate command line option -d kgx-neo4j-download command line option kgx-transform command line option -e kgx-neo4j-download command line option kgx-neo4j-upload command line option kgx-transform command line option -f kgx-graph-summary command line option kgx-neo4j-download command line option kgx-transform command line option -i kgx-graph-summary command line option kgx-neo4j-upload command line option kgx-transform command line option kgx-validate command line option -k kgx-transform command line option -l kgx-graph-summary command line option kgx-neo4j-download command line option kgx-neo4j-upload command line option -n kgx-graph-summary command line option kgx-neo4j-download command line option kgx-neo4j-upload command line option kgx-transform command line option -o kgx-graph-summary command line option kgx-neo4j-download command line option kgx-transform command line option kgx-validate command line option -p kgx-merge command line option kgx-neo4j-download command line option kgx-neo4j-upload command line option kgx-transform command line option -r kgx-graph-summary command line option -s kgx-neo4j-download command line option kgx-neo4j-upload command line option -u kgx-neo4j-download command line option kgx-neo4j-upload command line option

A

add_all_edges() (in module kgx.graph_operations.graph_merge) add_all_nodes() (in module kgx.graph_operations.graph_merge) add_edge() (kgx.graph.base_graph.BaseGraph method) (kgx.graph.nx_graph.NxGraph method) (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method) add_edge_attribute() (kgx.graph.base_graph.BaseGraph method) (kgx.graph.nx_graph.NxGraph method) add_node() (kgx.graph.base_graph.BaseGraph method) (kgx.graph.nx_graph.NxGraph method) (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method) add_node_attribute() (kgx.graph.base_graph.BaseGraph method) (kgx.graph.nx_graph.NxGraph method) (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method)

add_node_stat() (kgx.graph_operations.summarize_graph.GraphSummary method) analyse_edge() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) (kgx.graph_operations.summarize_graph.GraphSummary method) (kgx.validator.Validator method) analyse_node() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) (kgx.graph_operations.summarize_graph.GraphSummary method) (kgx.validator.Validator method) analyse_node_category() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph.Category method) (kgx.graph_operations.summarize_graph.GraphSummary.Category method) apply_edge_filters() (in module kgx.utils.kgx_utils) apply_filters() (in module kgx.utils.kgx_utils) apply_graph_operations() (in module kgx.utils.kgx_utils) apply_node_filters() (in module kgx.utils.kgx_utils) apply_operations() (in module kgx.cli.cli_utils)

B

BaseGraph (class in kgx.graph.base_graph)

build_cliques() (in module kgx.graph_operations.clique_merge) build_export_row() (in module kgx.utils.kgx_utils)

C

camelcase_to_sentencecase() (in module kgx.utils.kgx_utils) check_all_categories() (in module kgx.graph_operations.clique_merge) check_categories() (in module kgx.graph_operations.clique_merge) check_edge_filter() (kgx.source.graph_source.GraphSource method) (kgx.source.json_source.JsonSource method) (kgx.source.jsonl_source.JsonlSource method) (kgx.source.neo_source.NeoSource method) (kgx.source.obograph_source.ObographSource method) (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method) (kgx.source.source.Source method) (kgx.source.sssom_source.SssomSource method) (kgx.source.trapi_source.TrapiSource method) (kgx.source.tsv_source.TsvSource method) check_node_filter() (kgx.source.graph_source.GraphSource method) (kgx.source.json_source.JsonSource method) (kgx.source.jsonl_source.JsonlSource method) (kgx.source.neo_source.NeoSource method) (kgx.source.obograph_source.ObographSource method) (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method) (kgx.source.source.Source method) (kgx.source.sssom_source.SssomSource method) (kgx.source.trapi_source.TrapiSource method) (kgx.source.tsv_source.TsvSource method) clear() (kgx.graph.base_graph.BaseGraph method) (kgx.graph.nx_graph.NxGraph method)

clear_errors() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) (kgx.graph_operations.summarize_graph.GraphSummary method) (kgx.transformer.Transformer method) (kgx.validator.Validator method) clear_graph_metadata() (kgx.source.graph_source.GraphSource method) (kgx.source.json_source.JsonSource method) (kgx.source.jsonl_source.JsonlSource method) (kgx.source.neo_source.NeoSource method) (kgx.source.obograph_source.ObographSource method) (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method) (kgx.source.source.Source method) (kgx.source.sssom_source.SssomSource method) (kgx.source.trapi_source.TrapiSource method) (kgx.source.tsv_source.TsvSource method) clique_merge() (in module kgx.graph_operations.clique_merge) close_connection() (in module kgx.utils.kgx_utils) consolidate_edges() (in module kgx.graph_operations.clique_merge) contract() (in module kgx.utils.kgx_utils) (kgx.prefix_manager.PrefixManager method) count() (kgx.source.neo_source.NeoSource method) create_connection() (in module kgx.utils.kgx_utils) create_constraint_query() (kgx.sink.neo_sink.NeoSink static method) create_constraints() (kgx.sink.neo_sink.NeoSink method) curie_lookup() (in module kgx.utils.graph_utils) CurieLookupService (class in kgx.curie_lookup_service) current_time_in_millis() (in module kgx.utils.kgx_utils)

D

degree() (kgx.graph.base_graph.BaseGraph method) (kgx.graph.nx_graph.NxGraph method)

dereify() (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method)

E

edges() (kgx.graph.base_graph.BaseGraph method) (kgx.graph.nx_graph.NxGraph method) edges_iter() (kgx.graph.base_graph.BaseGraph method) (kgx.graph.nx_graph.NxGraph method)

elect_leader() (in module kgx.graph_operations.clique_merge) expand() (in module kgx.utils.kgx_utils) (kgx.prefix_manager.PrefixManager method)

F

finalize() (kgx.sink.graph_sink.GraphSink method) (kgx.sink.json_sink.JsonSink method) (kgx.sink.jsonl_sink.JsonlSink method) (kgx.sink.neo_sink.NeoSink method) (kgx.sink.parquet_sink.ParquetSink method) (kgx.sink.rdf_sink.RdfSink method) (kgx.sink.sink.Sink method) (kgx.sink.tsv_sink.TsvSink method)

fold_predicate() (in module kgx.graph_operations) format_biolink_category() (in module kgx.utils.kgx_utils) format_edge_filter() (kgx.source.neo_source.NeoSource static method) format_node_filter() (kgx.source.neo_source.NeoSource static method)

G

generate_edge_identifiers() (in module kgx.utils.kgx_utils) generate_edge_key() (in module kgx.utils.kgx_utils) generate_graph_stats() (in module kgx.graph_operations.summarize_graph) generate_meta_knowledge_graph() (in module kgx.graph_operations.meta_knowledge_graph) generate_unwind_edge_query() (kgx.sink.neo_sink.NeoSink static method) generate_unwind_node_query() (kgx.sink.neo_sink.NeoSink static method) generate_uuid() (in module kgx.utils.kgx_utils) get_all_prefixes() (kgx.validator.Validator static method) get_ancestors() (in module kgx.utils.graph_utils) get_biolink_ancestors() (in module kgx.utils.kgx_utils) get_biolink_element() (in module kgx.utils.kgx_utils) (in module kgx.utils.rdf_utils) (kgx.sink.rdf_sink.RdfSink method) (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method) get_biolink_property_types() (in module kgx.utils.kgx_utils) get_cache() (in module kgx.utils.kgx_utils) get_category() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) (kgx.graph_operations.summarize_graph.GraphSummary method) (kgx.source.obograph_source.ObographSource method) get_category_curie_by_index() (kgx.graph_operations.summarize_graph.GraphSummary.Category class method) get_category_curie_from_index() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph.Category class method) get_category_from_equivalence() (in module kgx.graph_operations.clique_merge) get_category_via_superclass() (in module kgx.utils.graph_utils) get_cid() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph.Category method) (kgx.graph_operations.summarize_graph.GraphSummary.Category method) get_clique_category() (in module kgx.graph_operations.clique_merge) get_count() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph.Category method) (kgx.graph_operations.summarize_graph.GraphSummary.Category method) get_count_by_id_prefixes() (kgx.graph_operations.summarize_graph.GraphSummary.Category method) get_count_by_source() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph.Category method) get_curie_lookup_service() (in module kgx.utils.kgx_utils) get_default_model_version() (kgx.validator.Validator class method) get_edge() (kgx.graph.base_graph.BaseGraph method) (kgx.graph.nx_graph.NxGraph method) get_edge_attributes() (kgx.graph.base_graph.BaseGraph static method) (kgx.graph.nx_graph.NxGraph static method) get_edge_count_by_predicate() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) get_edge_count_by_source() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) get_edge_mapping_count() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) get_edge_stats() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) get_edges() (kgx.source.neo_source.NeoSource method) get_errors() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) (kgx.graph_operations.summarize_graph.GraphSummary method) (kgx.transformer.Transformer method) (kgx.validator.Validator method) get_facet_counts() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph static method) (kgx.graph_operations.summarize_graph.GraphSummary method) get_graph_summary() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) (kgx.graph_operations.summarize_graph.GraphSummary method) get_id_prefixes() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph.Category method) (kgx.graph_operations.summarize_graph.GraphSummary.Category method) get_infores_catalog() (kgx.source.graph_source.GraphSource method) (kgx.source.json_source.JsonSource method) (kgx.source.jsonl_source.JsonlSource method) (kgx.source.neo_source.NeoSource method) (kgx.source.obograph_source.ObographSource method) (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method) (kgx.source.source.Source method) (kgx.source.sssom_source.SssomSource method) (kgx.source.trapi_source.TrapiSource method) (kgx.source.tsv_source.TsvSource method) (kgx.transformer.Transformer method)

get_input_file_types() (in module kgx.cli.cli_utils) get_leader_by_annotation() (in module kgx.graph_operations.clique_merge) get_leader_by_prefix_priority() (in module kgx.graph_operations.clique_merge) get_leader_by_sort() (in module kgx.graph_operations.clique_merge) get_name() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph.Category method) (kgx.graph_operations.summarize_graph.GraphSummary method) (kgx.graph_operations.summarize_graph.GraphSummary.Category method) get_node() (kgx.graph.base_graph.BaseGraph method) (kgx.graph.nx_graph.NxGraph method) get_node_attributes() (kgx.graph.base_graph.BaseGraph static method) (kgx.graph.nx_graph.NxGraph static method) get_node_count_by_category() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) get_node_stats() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) (kgx.graph_operations.summarize_graph.GraphSummary method) get_nodes() (kgx.source.neo_source.NeoSource method) get_number_of_categories() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) get_output_file_types() (in module kgx.cli.cli_utils) get_pages() (kgx.source.neo_source.NeoSource method) get_parents() (in module kgx.utils.graph_utils) get_predicate_count() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) get_prefix() (kgx.prefix_manager.PrefixManager static method) get_prefix_prioritization_map() (in module kgx.utils.kgx_utils) get_reference() (kgx.prefix_manager.PrefixManager static method) get_report_format_types() (in module kgx.cli.cli_utils) get_required_edge_properties() (kgx.validator.Validator static method) get_required_node_properties() (kgx.validator.Validator static method) get_sink() (kgx.transformer.Transformer method) get_source() (kgx.transformer.Transformer method) get_the_validator() (kgx.validator.Validator class method) get_toolkit() (in module kgx.utils.kgx_utils) (kgx.validator.Validator class method) get_total_edge_counts_across_mappings() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) get_total_edges_count() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) get_total_node_counts_across_categories() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) get_total_nodes_count() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) get_type_for_property() (in module kgx.utils.kgx_utils) get_validating_toolkit() (kgx.validator.Validator method) get_validation_model_version() (kgx.validator.Validator method) graph_summary() (in module kgx.cli.cli_utils) GraphEntityType (class in kgx.utils.kgx_utils) GraphSink (class in kgx.sink.graph_sink) GraphSource (class in kgx.source.graph_source) GraphSummary (class in kgx.graph_operations.summarize_graph) GraphSummary.Category (class in kgx.graph_operations.summarize_graph) gs_default() (in module kgx.graph_operations.summarize_graph)

H

has_edge() (kgx.graph.base_graph.BaseGraph method) (kgx.graph.nx_graph.NxGraph method)

has_node() (kgx.graph.base_graph.BaseGraph method) (kgx.graph.nx_graph.NxGraph method)

I

in_edges() (kgx.graph.base_graph.BaseGraph method) (kgx.graph.nx_graph.NxGraph method) infer_category() (in module kgx.utils.rdf_utils) INPUTS kgx-graph-summary command line option kgx-neo4j-upload command line option kgx-transform command line option kgx-validate command line option

is_curie() (kgx.prefix_manager.PrefixManager static method) is_iri() (kgx.prefix_manager.PrefixManager static method) is_null() (in module kgx.utils.kgx_utils)

J

json_object() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph.Category method) (kgx.graph_operations.summarize_graph.GraphSummary.Category method) JsonlSink (class in kgx.sink.jsonl_sink)

JsonlSource (class in kgx.source.jsonl_source) JsonSink (class in kgx.sink.json_sink) JsonSource (class in kgx.source.json_source)

K

kgx command line option --version kgx-graph-summary command line option --edge-facet-properties --error-log --graph-name --input-compression --input-format --node-facet-properties --output --report-format --report-type -c -f -i -l -n -o -r INPUTS kgx-merge command line option --destination --merge-config --processes --source -p kgx-neo4j-download command line option --edge-filters --node-filters --output --output-compression --output-format --password --stream --uri --username -d -e -f -l -n -o -p -s -u kgx-neo4j-upload command line option --edge-filters --input-compression --input-format --node-filters --password --stream --uri --username -c -e -i -l -n -p -s -u INPUTS kgx-transform command line option --edge-filters --infores-catalog --input-compression --input-format --knowledge-sources --node-filters --output --output-compression --output-format --processes --source --stream --transform-config -c -d -e -f -i -k -n -o -p INPUTS

kgx-validate command line option --biolink-release --input-compression --input-format --output -b -c -i -o INPUTS kgx.cli.cli_utils module kgx.curie_lookup_service module kgx.graph.base_graph module kgx.graph.nx_graph module kgx.graph_operations.clique_merge module kgx.graph_operations.graph_merge module kgx.graph_operations.meta_knowledge_graph module kgx.graph_operations.summarize_graph module kgx.prefix_manager module kgx.sink.graph_sink module kgx.sink.json_sink module kgx.sink.jsonl_sink module kgx.sink.neo_sink module kgx.sink.parquet_sink module kgx.sink.rdf_sink module kgx.sink.sink module kgx.sink.tsv_sink module kgx.source.graph_source module kgx.source.json_source module kgx.source.jsonl_source module kgx.source.neo_source module kgx.source.obograph_source module kgx.source.owl_source module kgx.source.rdf_source module kgx.source.source module kgx.source.sssom_source module kgx.source.trapi_source module kgx.source.tsv_source module kgx.transformer module kgx.utils.graph_utils module kgx.utils.kgx_utils module kgx.utils.rdf_utils module kgx.validator module

L

load_edge() (kgx.source.neo_source.NeoSource method) (kgx.source.sssom_source.SssomSource method) (kgx.source.trapi_source.TrapiSource method) load_edges() (kgx.source.neo_source.NeoSource method) (kgx.source.sssom_source.SssomSource method) load_graph() (kgx.source.owl_source.OwlSource method) load_node() (kgx.source.neo_source.NeoSource method) (kgx.source.sssom_source.SssomSource method) (kgx.source.trapi_source.TrapiSource method)

load_nodes() (kgx.source.neo_source.NeoSource method) load_ontologies() (kgx.curie_lookup_service.CurieLookupService method) log_error() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) (kgx.graph_operations.summarize_graph.GraphSummary method) (kgx.transformer.Transformer method) (kgx.validator.Validator method)

M

merge() (in module kgx.cli.cli_utils) merge_all_graphs() (in module kgx.graph_operations.graph_merge) merge_edge() (in module kgx.graph_operations.graph_merge) merge_graphs() (in module kgx.graph_operations.graph_merge) merge_node() (in module kgx.graph_operations.graph_merge) MetaKnowledgeGraph (class in kgx.graph_operations.meta_knowledge_graph) MetaKnowledgeGraph.Category (class in kgx.graph_operations.meta_knowledge_graph) mkg_default() (in module kgx.graph_operations.meta_knowledge_graph) module kgx.cli.cli_utils kgx.curie_lookup_service kgx.graph.base_graph kgx.graph.nx_graph kgx.graph_operations.clique_merge kgx.graph_operations.graph_merge kgx.graph_operations.meta_knowledge_graph kgx.graph_operations.summarize_graph kgx.prefix_manager kgx.sink.graph_sink kgx.sink.json_sink kgx.sink.jsonl_sink kgx.sink.neo_sink kgx.sink.parquet_sink kgx.sink.rdf_sink kgx.sink.sink kgx.sink.tsv_sink kgx.source.graph_source kgx.source.json_source kgx.source.jsonl_source kgx.source.neo_source kgx.source.obograph_source kgx.source.owl_source kgx.source.rdf_source kgx.source.source kgx.source.sssom_source kgx.source.trapi_source kgx.source.tsv_source kgx.transformer kgx.utils.graph_utils kgx.utils.kgx_utils kgx.utils.rdf_utils kgx.validator

N

neo4j_download() (in module kgx.cli.cli_utils) neo4j_upload() (in module kgx.cli.cli_utils) NeoSink (class in kgx.sink.neo_sink) NeoSource (class in kgx.source.neo_source) nodes() (kgx.graph.base_graph.BaseGraph method) (kgx.graph.nx_graph.NxGraph method)

nodes_iter() (kgx.graph.base_graph.BaseGraph method) (kgx.graph.nx_graph.NxGraph method) number_of_edges() (kgx.graph.base_graph.BaseGraph method) (kgx.graph.nx_graph.NxGraph method) number_of_nodes() (kgx.graph.base_graph.BaseGraph method) (kgx.graph.nx_graph.NxGraph method) NxGraph (class in kgx.graph.nx_graph)

O

ObographSource (class in kgx.source.obograph_source) out_edges() (kgx.graph.base_graph.BaseGraph method) (kgx.graph.nx_graph.NxGraph method)

OwlSource (class in kgx.source.owl_source)

P

ParquetSink (class in kgx.sink.parquet_sink) parse() (kgx.source.graph_source.GraphSource method) (kgx.source.json_source.JsonSource method) (kgx.source.jsonl_source.JsonlSource method) (kgx.source.neo_source.NeoSource method) (kgx.source.obograph_source.ObographSource method) (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method) (kgx.source.sssom_source.SssomSource method) (kgx.source.trapi_source.TrapiSource method) (kgx.source.tsv_source.TsvSource method) parse_header() (kgx.source.sssom_source.SssomSource method)

parse_meta() (kgx.source.obograph_source.ObographSource method) parse_source() (in module kgx.cli.cli_utils) PrefixManager (class in kgx.prefix_manager) prepare_data_dict() (in module kgx.utils.kgx_utils) prepare_input_args() (in module kgx.cli.cli_utils) prepare_output_args() (in module kgx.cli.cli_utils) prepare_top_level_args() (in module kgx.cli.cli_utils) process() (kgx.transformer.Transformer method) process_predicate() (in module kgx.utils.rdf_utils) (kgx.sink.rdf_sink.RdfSink method) (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method)

R

RdfSink (class in kgx.sink.rdf_sink) RdfSource (class in kgx.source.rdf_source) read_edge() (kgx.source.json_source.JsonSource method) (kgx.source.jsonl_source.JsonlSource method) (kgx.source.obograph_source.ObographSource method) (kgx.source.trapi_source.TrapiSource method) (kgx.source.tsv_source.TsvSource method) read_edges() (kgx.source.graph_source.GraphSource method) (kgx.source.json_source.JsonSource method) (kgx.source.jsonl_source.JsonlSource method) (kgx.source.obograph_source.ObographSource method) (kgx.source.trapi_source.TrapiSource method) (kgx.source.tsv_source.TsvSource method) read_edges_jsonl() (kgx.source.trapi_source.TrapiSource method) read_node() (kgx.source.json_source.JsonSource method) (kgx.source.jsonl_source.JsonlSource method) (kgx.source.obograph_source.ObographSource method) (kgx.source.trapi_source.TrapiSource method) (kgx.source.tsv_source.TsvSource method)

read_nodes() (kgx.source.graph_source.GraphSource method) (kgx.source.json_source.JsonSource method) (kgx.source.jsonl_source.JsonlSource method) (kgx.source.obograph_source.ObographSource method) (kgx.source.trapi_source.TrapiSource method) (kgx.source.tsv_source.TsvSource method) read_nodes_jsonl() (kgx.source.trapi_source.TrapiSource method) reify() (kgx.sink.rdf_sink.RdfSink method) relabel_nodes() (kgx.graph.base_graph.BaseGraph static method) (kgx.graph.nx_graph.NxGraph static method) remap_edge_property() (in module kgx.graph_operations) remap_node_identifier() (in module kgx.graph_operations) remap_node_property() (in module kgx.graph_operations) remove_edge() (kgx.graph.base_graph.BaseGraph method) (kgx.graph.nx_graph.NxGraph method) remove_node() (kgx.graph.base_graph.BaseGraph method) (kgx.graph.nx_graph.NxGraph method) remove_null() (in module kgx.utils.kgx_utils) remove_singleton_nodes() (in module kgx.graph_operations)

S

sanitize_category() (kgx.sink.neo_sink.NeoSink static method) sanitize_import() (in module kgx.utils.kgx_utils) save() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) (kgx.graph_operations.summarize_graph.GraphSummary method) (kgx.transformer.Transformer method) sentencecase_to_camelcase() (in module kgx.utils.kgx_utils) sentencecase_to_snakecase() (in module kgx.utils.kgx_utils) set_biolink_model() (kgx.validator.Validator class method) set_edge_attributes() (kgx.graph.base_graph.BaseGraph static method) (kgx.graph.nx_graph.NxGraph static method) set_edge_filter() (kgx.source.graph_source.GraphSource method) (kgx.source.json_source.JsonSource method) (kgx.source.jsonl_source.JsonlSource method) (kgx.source.neo_source.NeoSource method) (kgx.source.obograph_source.ObographSource method) (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method) (kgx.source.source.Source method) (kgx.source.sssom_source.SssomSource method) (kgx.source.trapi_source.TrapiSource method) (kgx.source.tsv_source.TsvSource method) set_edge_filters() (kgx.source.graph_source.GraphSource method) (kgx.source.json_source.JsonSource method) (kgx.source.jsonl_source.JsonlSource method) (kgx.source.neo_source.NeoSource method) (kgx.source.obograph_source.ObographSource method) (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method) (kgx.source.source.Source method) (kgx.source.sssom_source.SssomSource method) (kgx.source.trapi_source.TrapiSource method) (kgx.source.tsv_source.TsvSource method) set_edge_properties() (kgx.sink.tsv_sink.TsvSink method) set_edge_provenance() (kgx.source.graph_source.GraphSource method) (kgx.source.json_source.JsonSource method) (kgx.source.jsonl_source.JsonlSource method) (kgx.source.neo_source.NeoSource method) (kgx.source.obograph_source.ObographSource method) (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method) (kgx.source.source.Source method) (kgx.source.sssom_source.SssomSource method) (kgx.source.trapi_source.TrapiSource method) (kgx.source.tsv_source.TsvSource method) set_node_attributes() (kgx.graph.base_graph.BaseGraph static method) (kgx.graph.nx_graph.NxGraph static method) set_node_filter() (kgx.source.graph_source.GraphSource method) (kgx.source.json_source.JsonSource method) (kgx.source.jsonl_source.JsonlSource method) (kgx.source.neo_source.NeoSource method) (kgx.source.obograph_source.ObographSource method) (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method) (kgx.source.source.Source method) (kgx.source.sssom_source.SssomSource method) (kgx.source.trapi_source.TrapiSource method) (kgx.source.tsv_source.TsvSource method) set_node_filters() (kgx.source.graph_source.GraphSource method) (kgx.source.json_source.JsonSource method) (kgx.source.jsonl_source.JsonlSource method) (kgx.source.neo_source.NeoSource method) (kgx.source.obograph_source.ObographSource method) (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method) (kgx.source.source.Source method) (kgx.source.sssom_source.SssomSource method) (kgx.source.trapi_source.TrapiSource method) (kgx.source.tsv_source.TsvSource method)

set_node_properties() (kgx.sink.tsv_sink.TsvSink method) set_node_property_predicates() (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method) set_node_provenance() (kgx.source.graph_source.GraphSource method) (kgx.source.json_source.JsonSource method) (kgx.source.jsonl_source.JsonlSource method) (kgx.source.neo_source.NeoSource method) (kgx.source.obograph_source.ObographSource method) (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method) (kgx.source.source.Source method) (kgx.source.sssom_source.SssomSource method) (kgx.source.trapi_source.TrapiSource method) (kgx.source.tsv_source.TsvSource method) set_predicate_mapping() (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method) set_prefix_map() (kgx.prefix_manager.PrefixManager method) (kgx.source.graph_source.GraphSource method) (kgx.source.json_source.JsonSource method) (kgx.source.jsonl_source.JsonlSource method) (kgx.source.neo_source.NeoSource method) (kgx.source.obograph_source.ObographSource method) (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method) (kgx.source.source.Source method) (kgx.source.sssom_source.SssomSource method) (kgx.source.trapi_source.TrapiSource method) (kgx.source.tsv_source.TsvSource method) set_property_types() (kgx.sink.rdf_sink.RdfSink method) set_provenance_map() (kgx.source.graph_source.GraphSource method) (kgx.source.json_source.JsonSource method) (kgx.source.jsonl_source.JsonlSource method) (kgx.source.neo_source.NeoSource method) (kgx.source.obograph_source.ObographSource method) (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method) (kgx.source.source.Source method) (kgx.source.sssom_source.SssomSource method) (kgx.source.trapi_source.TrapiSource method) (kgx.source.tsv_source.TsvSource method) set_reverse_predicate_mapping() (kgx.sink.rdf_sink.RdfSink method) set_reverse_prefix_map() (kgx.sink.graph_sink.GraphSink method) (kgx.sink.json_sink.JsonSink method) (kgx.sink.jsonl_sink.JsonlSink method) (kgx.sink.neo_sink.NeoSink method) (kgx.sink.parquet_sink.ParquetSink method) (kgx.sink.rdf_sink.RdfSink method) (kgx.sink.sink.Sink method) (kgx.sink.tsv_sink.TsvSink method) (kgx.source.json_source.JsonSource method) (kgx.source.jsonl_source.JsonlSource method) (kgx.source.obograph_source.ObographSource method) (kgx.source.sssom_source.SssomSource method) (kgx.source.trapi_source.TrapiSource method) (kgx.source.tsv_source.TsvSource method) Sink (class in kgx.sink.sink) snakecase_to_sentencecase() (in module kgx.utils.kgx_utils) sort_categories() (in module kgx.graph_operations.clique_merge) Source (class in kgx.source.source) SssomSource (class in kgx.source.sssom_source) summarize_graph() (in module kgx.graph_operations.meta_knowledge_graph) (in module kgx.graph_operations.summarize_graph) (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) (kgx.graph_operations.summarize_graph.GraphSummary method) summarize_graph_edges() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) (kgx.graph_operations.summarize_graph.GraphSummary method) summarize_graph_nodes() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) (kgx.graph_operations.summarize_graph.GraphSummary method)

T

transform() (in module kgx.cli.cli_utils) (kgx.transformer.Transformer method) transform_source() (in module kgx.cli.cli_utils) Transformer (class in kgx.transformer)

TrapiSource (class in kgx.source.trapi_source) triple() (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method) TsvSink (class in kgx.sink.tsv_sink) TsvSource (class in kgx.source.tsv_source)

U

unfold_node_property() (in module kgx.graph_operations) update_edge() (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method) update_edge_attribute() (kgx.graph.base_graph.BaseGraph method) (kgx.graph.nx_graph.NxGraph method) update_node() (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method)

update_node_attribute() (kgx.graph.base_graph.BaseGraph method) (kgx.graph.nx_graph.NxGraph method) update_node_categories() (in module kgx.graph_operations.clique_merge) update_prefix_map() (kgx.prefix_manager.PrefixManager method) update_reverse_prefix_map() (kgx.prefix_manager.PrefixManager method) uriref() (kgx.sink.rdf_sink.RdfSink method)

V

validate() (in module kgx.cli.cli_utils) (kgx.validator.Validator method) validate_categories() (kgx.validator.Validator method) validate_edge() (kgx.source.graph_source.GraphSource method) (kgx.source.json_source.JsonSource method) (kgx.source.jsonl_source.JsonlSource method) (kgx.source.neo_source.NeoSource method) (kgx.source.obograph_source.ObographSource method) (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method) (kgx.source.source.Source method) (kgx.source.sssom_source.SssomSource method) (kgx.source.trapi_source.TrapiSource method) (kgx.source.tsv_source.TsvSource method) validate_edge_predicate() (kgx.validator.Validator method) validate_edge_properties() (kgx.validator.Validator method) validate_edge_property_types() (kgx.validator.Validator method)

validate_edge_property_values() (kgx.validator.Validator method) validate_edges() (kgx.validator.Validator method) validate_node() (kgx.source.graph_source.GraphSource method) (kgx.source.json_source.JsonSource method) (kgx.source.jsonl_source.JsonlSource method) (kgx.source.neo_source.NeoSource method) (kgx.source.obograph_source.ObographSource method) (kgx.source.owl_source.OwlSource method) (kgx.source.rdf_source.RdfSource method) (kgx.source.source.Source method) (kgx.source.sssom_source.SssomSource method) (kgx.source.trapi_source.TrapiSource method) (kgx.source.tsv_source.TsvSource method) validate_node_properties() (kgx.validator.Validator method) validate_node_property_types() (kgx.validator.Validator method) validate_node_property_values() (kgx.validator.Validator method) validate_nodes() (kgx.validator.Validator method) Validator (class in kgx.validator)

W

write_edge() (kgx.sink.graph_sink.GraphSink method) (kgx.sink.json_sink.JsonSink method) (kgx.sink.jsonl_sink.JsonlSink method) (kgx.sink.neo_sink.NeoSink method) (kgx.sink.parquet_sink.ParquetSink method) (kgx.sink.rdf_sink.RdfSink method) (kgx.sink.sink.Sink method) (kgx.sink.tsv_sink.TsvSink method) write_node() (kgx.sink.graph_sink.GraphSink method) (kgx.sink.json_sink.JsonSink method) (kgx.sink.jsonl_sink.JsonlSink method) (kgx.sink.neo_sink.NeoSink method) (kgx.sink.parquet_sink.ParquetSink method) (kgx.sink.rdf_sink.RdfSink method) (kgx.sink.sink.Sink method) (kgx.sink.tsv_sink.TsvSink method)

write_report() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method) (kgx.graph_operations.summarize_graph.GraphSummary method) (kgx.transformer.Transformer method) (kgx.validator.Validator method)