kgx
latest
Installation
Installation for users
Installing from PyPI
Installing from GitHub
Installation for developers
Setting up a development environment
Setting up a testing environment
Reference
KGX Command Line Interface
KGX CLI
kgx
graph-summary
merge
neo4j-download
neo4j-upload
transform
validate
CLI Utils
kgx.cli.cli_utils
Graph
kgx.graph.base_graph.BaseGraph
kgx.graph.nx_graph.NxGraph
Transformer
Inspecting the Knowledge Data Flow
Provenance of Nodes and Edges
InfoRes Identifier Rewriting
kgx.transformer
Source
kgx.source.source
kgx.source.graph_source
kgx.source.tsv_source
kgx.source.json_source
kgx.source.jsonl_source
kgx.source.trapi_source
kgx.source.obograph_source
kgx.source.sssom_source
kgx.source.neo_source
kgx.source.rdf_source
kgx.source.owl_source
kgx.source.sparql_source
Sink
__init__
method
write_nodes
method
write_edges
method
finalize
method
kgx.sink.sink
kgx.sink.graph_sink
kgx.sink.tsv_sink
kgx.sink.json_sink
kgx.sink.jsonl_sink
kgx.sink.trapi_sink
kgx.sink.neo_sink
kgx.sink.rdf_sink
Validator
Streaming Data Processing Mode
Biolink Model Versioning
kgx.validator
Graph Operations
Clique Merge
kgx.graph_operations.clique_merge
Graph Merge
kgx.graph_operations.graph_merge
Summarize Graph
Streaming Data Processing Mode
kgx.graph_operations.summarize_graph
Remap Node Identifier
kgx.graph_operations.remap_node_identifier
Remap Node Property
kgx.graph_operations.remap_node_property
Remap Edge Property
kgx.graph_operations.remap_edge_property
Fold Predicate
kgx.graph_operations.fold_predicate
Unfold Node Property
kgx.graph_operations.unfold_node_property
Remove Singleton Nodes
kgx.graph_operations.remove_singleton_nodes
Utilities
KGX Utils
kgx.utils.kgx_utils
Graph Utils
kgx.utils.graph_utils
RDF Utils
kgx.utils.rdf_utils
Prefix Manager
kgx.prefix_manager
CURIE Lookup Service
kgx.curie_lookup_service
KGX Format
Examples
Using KGX as a module
Using KGX CLI
graph-summary
validate
neo4j-download
neo4j-upload
transform
merge
kgx
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Index
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T
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U
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V
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W
Symbols
--biolink-release <biolink_release>
kgx-validate command line option
--destination <destination>
kgx-merge command line option
--edge-facet-properties <edge_facet_properties>
kgx-graph-summary command line option
--edge-filters <edge_filters>
kgx-neo4j-download command line option
kgx-neo4j-upload command line option
kgx-transform command line option
--error-log <error_log>
kgx-graph-summary command line option
--graph-name <graph_name>
kgx-graph-summary command line option
--infores-catalog <infores_catalog>
kgx-transform command line option
--input-compression <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 <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 <knowledge_sources>
kgx-transform command line option
--merge-config <merge_config>
kgx-merge command line option
--node-facet-properties <node_facet_properties>
kgx-graph-summary command line option
--node-filters <node_filters>
kgx-neo4j-download command line option
kgx-neo4j-upload command line option
kgx-transform command line option
--output <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 <output_compression>
kgx-neo4j-download command line option
kgx-transform command line option
--output-format <output_format>
kgx-neo4j-download command line option
kgx-transform command line option
--password <password>
kgx-neo4j-download command line option
kgx-neo4j-upload command line option
--processes <processes>
kgx-merge command line option
kgx-transform command line option
--report-format <report_format>
kgx-graph-summary command line option
--report-type <report_type>
kgx-graph-summary command line option
--source <source>
kgx-merge command line option
kgx-transform command line option
--stream
kgx-graph-summary command line option
kgx-neo4j-download command line option
kgx-neo4j-upload command line option
kgx-transform command line option
kgx-validate command line option
--transform-config <transform_config>
kgx-transform command line option
--uri <uri>
kgx-neo4j-download command line option
kgx-neo4j-upload command line option
--username <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-graph-summary command line option
kgx-neo4j-download command line option
kgx-neo4j-upload command line option
kgx-validate command line option
-u
kgx-neo4j-download command line option
kgx-neo4j-upload command line option
_
__call__() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method)
(kgx.graph_operations.summarize_graph.GraphSummary method)
(kgx.validator.Validator method)
__init__() (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)
(kgx.prefix_manager.PrefixManager method)
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)
(kgx.source.sparql_source.SparqlSource 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)
(kgx.source.sparql_source.SparqlSource 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)
(kgx.source.sparql_source.SparqlSource 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)
analyse_node() (kgx.graph_operations.meta_knowledge_graph.MetaKnowledgeGraph method)
(kgx.graph_operations.summarize_graph.GraphSummary 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)
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.sparql_source.SparqlSource 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.sparql_source.SparqlSource 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_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.sparql_source.SparqlSource 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)
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_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)
(kgx.source.sparql_source.SparqlSource 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)
ErrorType (class in kgx.validator)
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.rdf_sink.RdfSink method)
(kgx.sink.sink.Sink method)
(kgx.sink.trapi_sink.TrapiSink 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)
(kgx.source.sparql_source.SparqlSource 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_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_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_error_messages() (kgx.validator.Validator method)
get_facet_counts() (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.sparql_source.SparqlSource 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_toolkit() (in module kgx.utils.kgx_utils)
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)
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 <edge_facet_properties>
--error-log <error_log>
--graph-name <graph_name>
--input-compression <input_compression>
--input-format <input_format>
--node-facet-properties <node_facet_properties>
--output <output>
--report-format <report_format>
--report-type <report_type>
--stream
-c
-f
-i
-l
-n
-o
-r
-s
INPUTS
kgx-merge command line option
--destination <destination>
--merge-config <merge_config>
--processes <processes>
--source <source>
-p
kgx-neo4j-download command line option
--edge-filters <edge_filters>
--node-filters <node_filters>
--output <output>
--output-compression <output_compression>
--output-format <output_format>
--password <password>
--stream
--uri <uri>
--username <username>
-d
-e
-f
-l
-n
-o
-p
-s
-u
kgx-neo4j-upload command line option
--edge-filters <edge_filters>
--input-compression <input_compression>
--input-format <input_format>
--node-filters <node_filters>
--password <password>
--stream
--uri <uri>
--username <username>
-c
-e
-i
-l
-n
-p
-s
-u
INPUTS
kgx-transform command line option
--edge-filters <edge_filters>
--infores-catalog <infores_catalog>
--input-compression <input_compression>
--input-format <input_format>
--knowledge-sources <knowledge_sources>
--node-filters <node_filters>
--output <output>
--output-compression <output_compression>
--output-format <output_format>
--processes <processes>
--source <source>
--stream
--transform-config <transform_config>
-c
-d
-e
-f
-i
-k
-n
-o
-p
INPUTS
kgx-validate command line option
--biolink-release <biolink_release>
--input-compression <input_compression>
--input-format <input_format>
--output <output>
--stream
-b
-c
-i
-o
-s
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.rdf_sink (module)
kgx.sink.sink (module)
kgx.sink.trapi_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.sparql_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)
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)
MessageLevel (class in kgx.validator)
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)
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
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.sparql_source.SparqlSource 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)
(kgx.source.sparql_source.SparqlSource 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_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)
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)
report() (kgx.validator.Validator static method)
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_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.sparql_source.SparqlSource 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.sparql_source.SparqlSource method)
(kgx.source.sssom_source.SssomSource method)
(kgx.source.trapi_source.TrapiSource method)
(kgx.source.tsv_source.TsvSource method)
set_edge_properties() (kgx.sink.trapi_sink.TrapiSink method)
(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.sparql_source.SparqlSource 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.sparql_source.SparqlSource 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.sparql_source.SparqlSource method)
(kgx.source.sssom_source.SssomSource method)
(kgx.source.trapi_source.TrapiSource method)
(kgx.source.tsv_source.TsvSource method)
set_node_properties() (kgx.sink.trapi_sink.TrapiSink method)
(kgx.sink.tsv_sink.TsvSink method)
set_node_property_predicates() (kgx.source.owl_source.OwlSource method)
(kgx.source.rdf_source.RdfSource method)
(kgx.source.sparql_source.SparqlSource 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.sparql_source.SparqlSource 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)
(kgx.source.sparql_source.SparqlSource 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.sparql_source.SparqlSource 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.sparql_source.SparqlSource 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.rdf_sink.RdfSink method)
(kgx.sink.sink.Sink method)
(kgx.sink.trapi_sink.TrapiSink 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)
SparqlSource (class in kgx.source.sparql_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)
TrapiSink (class in kgx.sink.trapi_sink)
TrapiSource (class in kgx.source.trapi_source)
triple() (kgx.source.owl_source.OwlSource method)
(kgx.source.rdf_source.RdfSource method)
(kgx.source.sparql_source.SparqlSource 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)
(kgx.source.sparql_source.SparqlSource 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)
(kgx.source.sparql_source.SparqlSource 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 static method)
validate_edge() (in module kgx.utils.kgx_utils)
validate_edge_predicate() (kgx.validator.Validator static method)
validate_edge_properties() (kgx.validator.Validator static method)
validate_edge_property_types() (kgx.validator.Validator static method)
validate_edge_property_values() (kgx.validator.Validator static method)
validate_edges() (kgx.validator.Validator method)
validate_node() (in module kgx.utils.kgx_utils)
validate_node_properties() (kgx.validator.Validator static method)
validate_node_property_types() (kgx.validator.Validator static method)
validate_node_property_values() (kgx.validator.Validator static method)
validate_nodes() (kgx.validator.Validator method)
ValidationError (class in kgx.validator)
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.rdf_sink.RdfSink method)
(kgx.sink.sink.Sink method)
(kgx.sink.trapi_sink.TrapiSink 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.rdf_sink.RdfSink method)
(kgx.sink.sink.Sink method)
(kgx.sink.trapi_sink.TrapiSink method)
(kgx.sink.tsv_sink.TsvSink method)
write_report() (kgx.validator.Validator method)
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