Index

A

add_all_edges() (in module kgx.operations.graph_merge) add_all_nodes() (in module kgx.operations.graph_merge) add_edge() (kgx.transformers.rdf_graph_mixin.RdfGraphMixin method) (kgx.transformers.rdf_transformer.ObanRdfTransformer method) (kgx.transformers.rdf_transformer.RdfOwlTransformer method) (kgx.transformers.rdf_transformer.RdfTransformer method) (kgx.transformers.sparql_transformer.MonarchSparqlTransformer method) (kgx.transformers.sparql_transformer.RedSparqlTransformer method) (kgx.transformers.sparql_transformer.SparqlTransformer method) add_edge_attribute() (kgx.transformers.rdf_graph_mixin.RdfGraphMixin method) (kgx.transformers.rdf_transformer.ObanRdfTransformer method) (kgx.transformers.rdf_transformer.RdfOwlTransformer method) (kgx.transformers.rdf_transformer.RdfTransformer method) (kgx.transformers.sparql_transformer.MonarchSparqlTransformer method) (kgx.transformers.sparql_transformer.RedSparqlTransformer method) (kgx.transformers.sparql_transformer.SparqlTransformer method) add_node() (kgx.transformers.rdf_graph_mixin.RdfGraphMixin method) (kgx.transformers.rdf_transformer.ObanRdfTransformer method) (kgx.transformers.rdf_transformer.RdfOwlTransformer method) (kgx.transformers.rdf_transformer.RdfTransformer method) (kgx.transformers.sparql_transformer.MonarchSparqlTransformer method) (kgx.transformers.sparql_transformer.RedSparqlTransformer method) (kgx.transformers.sparql_transformer.SparqlTransformer method)

add_node_attribute() (kgx.transformers.rdf_graph_mixin.RdfGraphMixin method) (kgx.transformers.rdf_transformer.ObanRdfTransformer method) (kgx.transformers.rdf_transformer.RdfOwlTransformer method) (kgx.transformers.rdf_transformer.RdfTransformer method) (kgx.transformers.sparql_transformer.MonarchSparqlTransformer method) (kgx.transformers.sparql_transformer.RedSparqlTransformer method) (kgx.transformers.sparql_transformer.SparqlTransformer method) apply_edge_filters() (in module kgx.utils.kgx_utils) apply_filters() (in module kgx.cli.cli_utils) (in module kgx.utils.kgx_utils) apply_node_filters() (in module kgx.utils.kgx_utils) apply_operations() (in module kgx.cli.cli_utils)

B

build_cliques() (in module kgx.operations.clique_merge)

C

camelcase_to_sentencecase() (in module kgx.utils.kgx_utils) categorize() (kgx.transformers.sparql_transformer.RedSparqlTransformer method) check_all_categories() (in module kgx.operations.clique_merge) check_categories() (in module kgx.operations.clique_merge) check_edge_filter() (kgx.transformers.json_transformer.JsonTransformer method) (kgx.transformers.json_transformer.ObographJsonTransformer method) (kgx.transformers.pandas_transformer.PandasTransformer method) check_node_filter() (kgx.transformers.json_transformer.JsonTransformer method) (kgx.transformers.json_transformer.ObographJsonTransformer method) (kgx.transformers.pandas_transformer.PandasTransformer method)

clique_merge() (in module kgx.operations.clique_merge) consolidate_edges() (in module kgx.operations.clique_merge) contract() (in module kgx.utils.kgx_utils) count() (kgx.transformers.neo_transformer.NeoTransformer method) create_constraint_query() (kgx.transformers.neo_transformer.NeoTransformer static method) create_constraints() (kgx.transformers.neo_transformer.NeoTransformer method) curie_lookup() (in module kgx.utils.graph_utils) current_time_in_millis() (in module kgx.utils.kgx_utils)

D

dereify() (kgx.transformers.rdf_transformer.ObanRdfTransformer method) (kgx.transformers.rdf_transformer.RdfOwlTransformer method) (kgx.transformers.rdf_transformer.RdfTransformer method)

E

elect_leader() (in module kgx.operations.clique_merge) expand() (in module kgx.utils.kgx_utils) export() (kgx.transformers.json_transformer.JsonTransformer method) (kgx.transformers.json_transformer.ObographJsonTransformer method) export_edges() (kgx.transformers.json_transformer.JsonTransformer method) (kgx.transformers.json_transformer.ObographJsonTransformer method) (kgx.transformers.pandas_transformer.PandasTransformer method) (kgx.transformers.rdf_transformer.ObanRdfTransformer method) (kgx.transformers.rdf_transformer.RdfOwlTransformer method) (kgx.transformers.rdf_transformer.RdfTransformer method) export_neo4j_edges() (kgx.transformers.json_transformer.JsonTransformer method) (kgx.transformers.json_transformer.ObographJsonTransformer method) (kgx.transformers.pandas_transformer.PandasTransformer method)

export_neo4j_nodes() (kgx.transformers.json_transformer.JsonTransformer method) (kgx.transformers.json_transformer.ObographJsonTransformer method) (kgx.transformers.pandas_transformer.PandasTransformer method) export_nodes() (kgx.transformers.json_transformer.JsonTransformer method) (kgx.transformers.json_transformer.ObographJsonTransformer method) (kgx.transformers.pandas_transformer.PandasTransformer method) (kgx.transformers.rdf_transformer.ObanRdfTransformer method) (kgx.transformers.rdf_transformer.RdfOwlTransformer method) (kgx.transformers.rdf_transformer.RdfTransformer method)

F

fold_predicate() (in module kgx.utils.graph_utils)

format_biolink_category() (in module kgx.utils.kgx_utils)

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.operations.summarize_graph) generate_unwind_edge_query() (kgx.transformers.neo_transformer.NeoTransformer static method) generate_unwind_node_query() (kgx.transformers.neo_transformer.NeoTransformer static method) generate_uuid() (in module kgx.utils.kgx_utils) get_all_edge_properties() (kgx.transformers.json_transformer.JsonTransformer static method) (kgx.transformers.json_transformer.ObographJsonTransformer static method) (kgx.transformers.pandas_transformer.PandasTransformer static method) get_all_node_properties() (kgx.transformers.json_transformer.JsonTransformer static method) (kgx.transformers.json_transformer.ObographJsonTransformer static method) (kgx.transformers.pandas_transformer.PandasTransformer 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.transformers.rdf_graph_mixin.RdfGraphMixin method) (kgx.transformers.rdf_transformer.ObanRdfTransformer method) (kgx.transformers.rdf_transformer.RdfOwlTransformer method) (kgx.transformers.rdf_transformer.RdfTransformer method) (kgx.transformers.sparql_transformer.MonarchSparqlTransformer method) (kgx.transformers.sparql_transformer.RedSparqlTransformer method) (kgx.transformers.sparql_transformer.SparqlTransformer method)

get_biolink_property_types() (in module kgx.utils.kgx_utils) get_cache() (in module kgx.utils.kgx_utils) get_category() (kgx.transformers.json_transformer.ObographJsonTransformer method) get_category_from_equivalence() (in module kgx.operations.clique_merge) get_category_via_superclass() (in module kgx.utils.graph_utils) get_clique_category() (in module kgx.operations.clique_merge) get_curie_lookup_service() (in module kgx.utils.kgx_utils) get_edge_filter() (kgx.transformers.neo_transformer.NeoTransformer method) get_edges() (kgx.transformers.neo_transformer.NeoTransformer method) get_facet_counts() (in module kgx.operations.summarize_graph) get_file_types() (in module kgx.cli.cli_utils) get_leader_by_annotation() (in module kgx.operations.clique_merge) get_leader_by_prefix_priority() (in module kgx.operations.clique_merge) get_leader_by_sort() (in module kgx.operations.clique_merge) get_node_filter() (kgx.transformers.neo_transformer.NeoTransformer method) get_nodes() (kgx.transformers.neo_transformer.NeoTransformer method) get_pages() (kgx.transformers.neo_transformer.NeoTransformer method) get_parents() (in module kgx.utils.graph_utils) get_prefix_prioritization_map() (in module kgx.utils.kgx_utils) get_toolkit() (in module kgx.utils.kgx_utils) get_transformer() (in module kgx.cli.cli_utils) get_type_for_property() (in module kgx.utils.kgx_utils) graph_summary() (in module kgx.cli.cli_utils)

I

infer_category() (in module kgx.utils.rdf_utils) is_empty() (kgx.transformers.json_transformer.JsonTransformer method) (kgx.transformers.json_transformer.ObographJsonTransformer method) (kgx.transformers.logicterm_transformer.LogicTermTransformer method) (kgx.transformers.neo_transformer.NeoTransformer method) (kgx.transformers.pandas_transformer.PandasTransformer method) (kgx.transformers.rdf_transformer.ObanRdfTransformer method) (kgx.transformers.rdf_transformer.RdfOwlTransformer method) (kgx.transformers.rdf_transformer.RdfTransformer method) (kgx.transformers.sparql_transformer.MonarchSparqlTransformer method) (kgx.transformers.sparql_transformer.RedSparqlTransformer method) (kgx.transformers.sparql_transformer.SparqlTransformer method) (kgx.transformers.transformer.Transformer method)

is_null() (kgx.transformers.json_transformer.JsonTransformer static method) (kgx.transformers.json_transformer.ObographJsonTransformer static method) (kgx.transformers.pandas_transformer.PandasTransformer static method)

J

JsonTransformer (class in kgx.transformers.json_transformer)

K

kgx.cli.cli_utils module kgx.operations.clique_merge module kgx.operations.graph_merge module kgx.operations.summarize_graph module kgx.transformers.json_transformer module kgx.transformers.logicterm_transformer module kgx.transformers.neo_transformer module kgx.transformers.pandas_transformer module

kgx.transformers.rdf_graph_mixin module kgx.transformers.rdf_transformer module kgx.transformers.sparql_transformer module kgx.transformers.transformer module kgx.utils.graph_utils module kgx.utils.kgx_utils module kgx.utils.rdf_utils module

L

load() (kgx.transformers.json_transformer.JsonTransformer method) (kgx.transformers.json_transformer.ObographJsonTransformer method) (kgx.transformers.neo_transformer.NeoTransformer method) load_edge() (kgx.transformers.json_transformer.JsonTransformer method) (kgx.transformers.json_transformer.ObographJsonTransformer method) (kgx.transformers.neo_transformer.NeoTransformer method) (kgx.transformers.pandas_transformer.PandasTransformer method) load_edges() (kgx.transformers.json_transformer.JsonTransformer method) (kgx.transformers.json_transformer.ObographJsonTransformer method) (kgx.transformers.neo_transformer.NeoTransformer method) (kgx.transformers.pandas_transformer.PandasTransformer method) load_graph() (kgx.transformers.rdf_graph_mixin.RdfGraphMixin method) (kgx.transformers.rdf_transformer.ObanRdfTransformer method) (kgx.transformers.rdf_transformer.RdfOwlTransformer method) (kgx.transformers.rdf_transformer.RdfTransformer method) (kgx.transformers.sparql_transformer.MonarchSparqlTransformer method) (kgx.transformers.sparql_transformer.RedSparqlTransformer method) (kgx.transformers.sparql_transformer.SparqlTransformer method)

load_node() (kgx.transformers.json_transformer.JsonTransformer method) (kgx.transformers.json_transformer.ObographJsonTransformer method) (kgx.transformers.neo_transformer.NeoTransformer method) (kgx.transformers.pandas_transformer.PandasTransformer method) load_nodes() (kgx.transformers.json_transformer.JsonTransformer method) (kgx.transformers.json_transformer.ObographJsonTransformer method) (kgx.transformers.neo_transformer.NeoTransformer method) (kgx.transformers.pandas_transformer.PandasTransformer method) (kgx.transformers.sparql_transformer.RedSparqlTransformer method) LogicTermTransformer (class in kgx.transformers.logicterm_transformer)

M

merge() (in module kgx.cli.cli_utils) merge_all_graphs() (in module kgx.operations.graph_merge) merge_edge() (in module kgx.operations.graph_merge) merge_graphs() (in module kgx.operations.graph_merge) merge_node() (in module kgx.operations.graph_merge) module kgx.cli.cli_utils kgx.operations.clique_merge kgx.operations.graph_merge kgx.operations.summarize_graph kgx.transformers.json_transformer kgx.transformers.logicterm_transformer kgx.transformers.neo_transformer kgx.transformers.pandas_transformer kgx.transformers.rdf_graph_mixin kgx.transformers.rdf_transformer kgx.transformers.sparql_transformer kgx.transformers.transformer kgx.utils.graph_utils kgx.utils.kgx_utils kgx.utils.rdf_utils

MonarchSparqlTransformer (class in kgx.transformers.sparql_transformer)

N

neo4j_download() (in module kgx.cli.cli_utils) neo4j_report() (kgx.transformers.neo_transformer.NeoTransformer method)

neo4j_upload() (in module kgx.cli.cli_utils) NeoTransformer (class in kgx.transformers.neo_transformer)

O

ObanRdfTransformer (class in kgx.transformers.rdf_transformer)

ObographJsonTransformer (class in kgx.transformers.json_transformer)

P

PandasTransformer (class in kgx.transformers.pandas_transformer) parse() (kgx.transformers.json_transformer.JsonTransformer method) (kgx.transformers.json_transformer.ObographJsonTransformer method) (kgx.transformers.pandas_transformer.PandasTransformer method) (kgx.transformers.rdf_transformer.ObanRdfTransformer method) (kgx.transformers.rdf_transformer.RdfOwlTransformer method) (kgx.transformers.rdf_transformer.RdfTransformer method)

parse_meta() (kgx.transformers.json_transformer.ObographJsonTransformer method) parse_source() (in module kgx.cli.cli_utils) parse_source_input() (in module kgx.cli.cli_utils) prepare_data_dict() (in module kgx.utils.kgx_utils) process_predicate() (in module kgx.utils.rdf_utils)

Q

query() (kgx.transformers.sparql_transformer.MonarchSparqlTransformer method) (kgx.transformers.sparql_transformer.RedSparqlTransformer method) (kgx.transformers.sparql_transformer.SparqlTransformer method)

R

RdfGraphMixin (class in kgx.transformers.rdf_graph_mixin) RdfOwlTransformer (class in kgx.transformers.rdf_transformer) RdfTransformer (class in kgx.transformers.rdf_transformer) RedSparqlTransformer (class in kgx.transformers.sparql_transformer) reify() (kgx.transformers.rdf_transformer.ObanRdfTransformer method) (kgx.transformers.rdf_transformer.RdfOwlTransformer method) (kgx.transformers.rdf_transformer.RdfTransformer method) remap_edge_property() (in module kgx.utils.graph_utils) remap_node_identifier() (in module kgx.utils.graph_utils) remap_node_property() (in module kgx.utils.graph_utils) remove_singleton_nodes() (in module kgx.utils.graph_utils)

report() (kgx.transformers.json_transformer.JsonTransformer method) (kgx.transformers.json_transformer.ObographJsonTransformer method) (kgx.transformers.logicterm_transformer.LogicTermTransformer method) (kgx.transformers.neo_transformer.NeoTransformer method) (kgx.transformers.pandas_transformer.PandasTransformer method) (kgx.transformers.rdf_transformer.ObanRdfTransformer method) (kgx.transformers.rdf_transformer.RdfOwlTransformer method) (kgx.transformers.rdf_transformer.RdfTransformer method) (kgx.transformers.sparql_transformer.MonarchSparqlTransformer method) (kgx.transformers.sparql_transformer.RedSparqlTransformer method) (kgx.transformers.sparql_transformer.SparqlTransformer method) (kgx.transformers.transformer.Transformer method)

S

sanitize_category() (kgx.transformers.neo_transformer.NeoTransformer static method) save() (kgx.transformers.json_transformer.JsonTransformer method) (kgx.transformers.json_transformer.ObographJsonTransformer method) (kgx.transformers.logicterm_transformer.LogicTermTransformer method) (kgx.transformers.neo_transformer.NeoTransformer method) (kgx.transformers.pandas_transformer.PandasTransformer method) (kgx.transformers.rdf_transformer.ObanRdfTransformer method) (kgx.transformers.rdf_transformer.RdfOwlTransformer method) (kgx.transformers.rdf_transformer.RdfTransformer method) save_edge() (kgx.transformers.neo_transformer.NeoTransformer method) save_node() (kgx.transformers.neo_transformer.NeoTransformer method) sentencecase_to_camelcase() (in module kgx.utils.kgx_utils) sentencecase_to_snakecase() (in module kgx.utils.kgx_utils) set_edge_filter() (kgx.transformers.json_transformer.JsonTransformer method) (kgx.transformers.json_transformer.ObographJsonTransformer method) (kgx.transformers.logicterm_transformer.LogicTermTransformer method) (kgx.transformers.neo_transformer.NeoTransformer method) (kgx.transformers.pandas_transformer.PandasTransformer method) (kgx.transformers.rdf_transformer.ObanRdfTransformer method) (kgx.transformers.rdf_transformer.RdfOwlTransformer method) (kgx.transformers.rdf_transformer.RdfTransformer method) (kgx.transformers.sparql_transformer.MonarchSparqlTransformer method) (kgx.transformers.sparql_transformer.RedSparqlTransformer method) (kgx.transformers.sparql_transformer.SparqlTransformer method) (kgx.transformers.transformer.Transformer method)

set_node_filter() (kgx.transformers.json_transformer.JsonTransformer method) (kgx.transformers.json_transformer.ObographJsonTransformer method) (kgx.transformers.logicterm_transformer.LogicTermTransformer method) (kgx.transformers.neo_transformer.NeoTransformer method) (kgx.transformers.pandas_transformer.PandasTransformer method) (kgx.transformers.rdf_transformer.ObanRdfTransformer method) (kgx.transformers.rdf_transformer.RdfOwlTransformer method) (kgx.transformers.rdf_transformer.RdfTransformer method) (kgx.transformers.sparql_transformer.MonarchSparqlTransformer method) (kgx.transformers.sparql_transformer.RedSparqlTransformer method) (kgx.transformers.sparql_transformer.SparqlTransformer method) (kgx.transformers.transformer.Transformer method) set_predicate_mapping() (kgx.transformers.rdf_transformer.ObanRdfTransformer method) (kgx.transformers.rdf_transformer.RdfOwlTransformer method) (kgx.transformers.rdf_transformer.RdfTransformer method) set_property_types() (kgx.transformers.rdf_transformer.ObanRdfTransformer method) (kgx.transformers.rdf_transformer.RdfOwlTransformer method) (kgx.transformers.rdf_transformer.RdfTransformer method) snakecase_to_sentencecase() (in module kgx.utils.kgx_utils) sort_categories() (in module kgx.operations.clique_merge) SparqlTransformer (class in kgx.transformers.sparql_transformer) summarize_edges() (in module kgx.operations.summarize_graph) summarize_graph() (in module kgx.operations.summarize_graph) summarize_nodes() (in module kgx.operations.summarize_graph)

T

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

triple() (kgx.transformers.rdf_transformer.ObanRdfTransformer method) (kgx.transformers.rdf_transformer.RdfOwlTransformer method) (kgx.transformers.rdf_transformer.RdfTransformer method)

U

unfold_node_property() (in module kgx.utils.graph_utils) update_edge() (kgx.transformers.rdf_graph_mixin.RdfGraphMixin method) (kgx.transformers.rdf_transformer.ObanRdfTransformer method) (kgx.transformers.rdf_transformer.RdfOwlTransformer method) (kgx.transformers.rdf_transformer.RdfTransformer method) (kgx.transformers.sparql_transformer.MonarchSparqlTransformer method) (kgx.transformers.sparql_transformer.RedSparqlTransformer method) (kgx.transformers.sparql_transformer.SparqlTransformer method) update_node() (kgx.transformers.rdf_graph_mixin.RdfGraphMixin method) (kgx.transformers.rdf_transformer.ObanRdfTransformer method) (kgx.transformers.rdf_transformer.RdfOwlTransformer method) (kgx.transformers.rdf_transformer.RdfTransformer method) (kgx.transformers.sparql_transformer.MonarchSparqlTransformer method) (kgx.transformers.sparql_transformer.RedSparqlTransformer method) (kgx.transformers.sparql_transformer.SparqlTransformer method)

update_node_categories() (in module kgx.operations.clique_merge) uriref() (kgx.transformers.rdf_transformer.ObanRdfTransformer method) (kgx.transformers.rdf_transformer.RdfOwlTransformer method) (kgx.transformers.rdf_transformer.RdfTransformer method)

V

validate() (in module kgx.cli.cli_utils) validate_edge() (kgx.transformers.json_transformer.JsonTransformer static method) (kgx.transformers.json_transformer.ObographJsonTransformer static method) (kgx.transformers.logicterm_transformer.LogicTermTransformer static method) (kgx.transformers.neo_transformer.NeoTransformer static method) (kgx.transformers.pandas_transformer.PandasTransformer static method) (kgx.transformers.rdf_transformer.ObanRdfTransformer static method) (kgx.transformers.rdf_transformer.RdfOwlTransformer static method) (kgx.transformers.rdf_transformer.RdfTransformer static method) (kgx.transformers.sparql_transformer.MonarchSparqlTransformer static method) (kgx.transformers.sparql_transformer.RedSparqlTransformer static method) (kgx.transformers.sparql_transformer.SparqlTransformer static method) (kgx.transformers.transformer.Transformer static method)

validate_node() (kgx.transformers.json_transformer.JsonTransformer static method) (kgx.transformers.json_transformer.ObographJsonTransformer static method) (kgx.transformers.logicterm_transformer.LogicTermTransformer static method) (kgx.transformers.neo_transformer.NeoTransformer static method) (kgx.transformers.pandas_transformer.PandasTransformer static method) (kgx.transformers.rdf_transformer.ObanRdfTransformer static method) (kgx.transformers.rdf_transformer.RdfOwlTransformer static method) (kgx.transformers.rdf_transformer.RdfTransformer static method) (kgx.transformers.sparql_transformer.MonarchSparqlTransformer static method) (kgx.transformers.sparql_transformer.RedSparqlTransformer static method) (kgx.transformers.sparql_transformer.SparqlTransformer static method) (kgx.transformers.transformer.Transformer static method)