Index

Symbols

--allow-naked-names pybel-compile command line option --bel pybel-serialize command line option --connection pybel command line option pybel-neo command line option --debug pybel-manage-examples command line option --disallow-nested pybel-compile command line option --disallow-unqualified-translocations pybel-compile command line option --edgelist pybel-serialize command line option --graphml pybel-serialize command line option --gsea pybel-serialize command line option --host pybel-machine command line option pybel-upload command line option --limit pybel-manage-edges-ls command line option --local pybel-machine command line option --namespace-id pybel-manage-namespaces-ls command line option --network-id pybel-manage-networks-drop command line option --no-citation-clearing pybel-compile command line option --no-identifier-validation pybel-compile command line option --nodelink pybel-serialize command line option --offset pybel-manage-edges-ls command line option --password pybel-neo command line option pybel-upload command line option

--pprint pybel-parse command line option --required-annotations pybel-compile command line option --sif pybel-serialize command line option --skip-tqdm pybel-compile command line option --tsv pybel-serialize command line option --upgrade-urls pybel-compile command line option --url pybel-manage-namespaces-ls command line option --user pybel-upload command line option --verbose pybel-compile command line option --version pybel command line option --yes pybel-manage-drop command line option pybel-manage-networks-drop command line option -c pybel command line option -i pybel-manage-namespaces-ls command line option -n pybel-manage-networks-drop command line option -r pybel-compile command line option -u pybel-manage-namespaces-ls command line option -v pybel-compile command line option pybel-manage-examples command line option -y pybel-manage-networks-drop command line option

_

__add__() (pybel.BELGraph method) __and__() (pybel.BELGraph method)

__iadd__() (pybel.BELGraph method) __iand__() (pybel.BELGraph method)

A

Abundance (class in pybel.dsl) ABUNDANCE (in module pybel.constants) abundance_labels (in module pybel.language) abundance_list (pybel.parser.parse_bel.BELParser attribute) abundance_sbo_mapping (in module pybel.language) activity (pybel.parser.parse_bel.BELParser attribute) activity_labels (in module pybel.language) activity_mapping (in module pybel.language) add_activates() (pybel.BELGraph method) add_annotation_value() (in module pybel.struct.mutation.metadata) add_association() (pybel.BELGraph method) add_binds() (pybel.BELGraph method) add_causes_no_change() (pybel.BELGraph method) add_correlation() (pybel.BELGraph method) add_decreases() (pybel.BELGraph method) add_dephosphorylates() (pybel.BELGraph method) add_directly_decreases() (pybel.BELGraph method) add_directly_dephosphorylates() (pybel.BELGraph method) add_directly_increases() (pybel.BELGraph method) add_directly_phosphorylates() (pybel.BELGraph method) add_directly_regulates() (pybel.BELGraph method) add_equivalence() (pybel.BELGraph method) add_has_product() (pybel.BELGraph method) add_has_reactant() (pybel.BELGraph method) add_has_variant() (pybel.BELGraph method) add_increases() (pybel.BELGraph method) add_inhibits() (pybel.BELGraph method) add_is_a() (pybel.BELGraph method) add_negative_correlation() (pybel.BELGraph method) add_no_correlation() (pybel.BELGraph method) add_node_from_data() (pybel.BELGraph method) add_orthology() (pybel.BELGraph method) add_part_of() (pybel.BELGraph method) add_phosphorylates() (pybel.BELGraph method) add_positive_correlation() (pybel.BELGraph method) add_qualified_edge() (pybel.BELGraph method) add_reaction() (pybel.BELGraph method) add_regulates() (pybel.BELGraph method) add_transcription() (pybel.BELGraph method) add_transitivity() (pybel.BELGraph method)

add_translation() (pybel.BELGraph method) add_unqualified_edge() (pybel.BELGraph method) AGENTS pybel-machine command line option ANALOGOUS_TO (in module pybel.constants) and_edge_predicates() (in module pybel.struct.filters) annotation() (pybel.struct.graph.InduceDispatch method) annotation_curie (pybel.BELGraph property) annotation_list (pybel.BELGraph property) annotation_miriam (pybel.BELGraph property) annotation_pattern (pybel.BELGraph property) annotation_to_local (pybel.parser.parse_metadata.MetadataParser attribute) annotation_to_pattern (pybel.parser.parse_metadata.MetadataParser attribute) annotation_to_term (pybel.parser.parse_metadata.MetadataParser attribute) annotation_url (pybel.BELGraph property) annotation_url_dict (pybel.parser.parse_metadata.MetadataParser attribute) AnnotationIdentifierWarning ANNOTATIONS (in module pybel.constants) annotations() (pybel.struct.graph.CountDispatch method) AnnotationWarning append() (pybel.Pipeline method) append_annotation() (pybel.struct.query.Seeding method) append_induction() (pybel.struct.query.Seeding method) append_neighbors() (pybel.struct.query.Seeding method) append_network() (pybel.struct.query.Query method) append_pipeline() (pybel.struct.query.Query method) append_sample() (pybel.struct.query.Seeding method) append_seeding_annotation() (pybel.struct.query.Query method) append_seeding_induction() (pybel.struct.query.Query method) append_seeding_neighbors() (pybel.struct.query.Query method) append_seeding_sample() (pybel.struct.query.Query method) article_type (pybel.manager.models.Citation attribute) as_bel() (pybel.manager.models.Network method) (pybel.manager.models.Node method) ASSOCIATION (in module pybel.constants) Author (class in pybel.manager.models) author (pybel.manager.models.Namespace attribute) authors (pybel.BELGraph property) (pybel.manager.models.Network attribute) authors() (pybel.struct.graph.CountDispatch method)

B

Base (class in pybel.manager.models) base (pybel.manager.BaseManager attribute) BaseAbundance (class in pybel.dsl) BaseEntity (class in pybel.dsl) BaseManager (class in pybel.manager) bel (pybel.manager.models.Edge attribute) (pybel.manager.models.Node attribute) bel_contains() (pybel.manager.models.Node class method) BELGraph (class in pybel) belns_encodings (in module pybel.constants) BELParser (class in pybel.parser.parse_bel) BELParserWarning BELSyntaxError bind() (pybel.manager.BaseManager method) BINDS (in module pybel.constants) biological_process (pybel.parser.parse_bel.BELParser attribute)

BiologicalProcess (class in pybel.dsl) BIOMARKER_FOR (in module pybel.constants) BIOPROCESS (in module pybel.constants) blob (pybel.manager.models.Network attribute) build_annotation_dict_all_filter() (in module pybel.struct.filters) build_annotation_dict_any_filter() (in module pybel.struct.filters) build_author_inclusion_filter() (in module pybel.struct.filters) build_downstream_edge_predicate() (in module pybel.struct.filters) build_node_data_search() (in module pybel.struct.filters) build_node_graph_data_search() (in module pybel.struct.filters) build_node_key_search() (in module pybel.struct.filters) build_node_name_search() (in module pybel.struct.filters) build_pmid_exclusion_filter() (in module pybel.struct.filters) build_pmid_inclusion_filter() (in module pybel.struct.filters) build_relation_predicate() (in module pybel.struct.filters) build_upstream_edge_predicate() (in module pybel.struct.filters)

C

calculate_error_by_annotation() (in module pybel.struct.summary) calculate_incorrect_name_dict() (in module pybel.struct.summary) CAUSAL_APOLAR_RELATIONS (in module pybel.constants) CAUSAL_DECREASE_RELATIONS (in module pybel.constants) CAUSAL_INCREASE_RELATIONS (in module pybel.constants) CAUSAL_POLAR_RELATIONS (in module pybel.constants) CAUSAL_RELATIONS (in module pybel.constants) CAUSES_NO_CHANGE (in module pybel.constants) CentralDogma (class in pybel.dsl) check_function_semantics() (pybel.parser.parse_bel.BELParser method) child() (pybel.BELGraph method) Citation (class in pybel.manager.models) CITATION (in module pybel.constants) CITATION_ARTICLE_TYPE (in module pybel.constants) CITATION_AUTHORS (in module pybel.constants) CITATION_DATE (in module pybel.constants) citation_dict() (in module pybel.language) CITATION_FIRST_AUTHOR (in module pybel.constants) citation_is_set (pybel.parser.parse_control.ControlParser property) CITATION_ISSUE (in module pybel.constants) CITATION_JOURNAL (in module pybel.constants) CITATION_LAST_AUTHOR (in module pybel.constants) CITATION_PAGES (in module pybel.constants) CITATION_VOLUME (in module pybel.constants) CitationDict (class in pybel.language) citations() (pybel.struct.graph.CountDispatch method) (pybel.struct.graph.SummarizeDispatch method) CitationTooLongException CitationTooShortException clear() (pybel.parser.parse_bel.BELParser method) (pybel.parser.parse_control.ControlParser method) clear_citation() (pybel.parser.parse_control.ControlParser method) collapse_all_variants() (in module pybel.struct.mutation.collapse) collapse_nodes() (in module pybel.struct.mutation.collapse) collapse_pair() (in module pybel.struct.mutation.collapse) collapse_to_genes() (in module pybel.struct.mutation.collapse)

compartment_mapping (in module pybel.language) COMPLEX (in module pybel.constants) complex_singleton (pybel.parser.parse_bel.BELParser attribute) ComplexAbundance (class in pybel.dsl) COMPOSITE (in module pybel.constants) composite_abundance (pybel.parser.parse_bel.BELParser attribute) CompositeAbundance (class in pybel.dsl) concatenate_node_predicates() (in module pybel.struct.filters) CONCEPT (in module pybel.constants) ConceptParser (class in pybel.parser.parse_concept) contact (pybel.BELGraph property) (pybel.manager.models.Namespace attribute) (pybel.manager.models.Network attribute) ControlParser (class in pybel.parser.parse_control) copyright (pybel.BELGraph property) (pybel.manager.models.Network attribute) CORRELATION (in module pybel.constants) CORRELATIVE_RELATIONS (in module pybel.constants) count (pybel.BELGraph property) count_annotations() (in module pybel.struct.summary) count_edges() (pybel.manager.QueryManager method) count_error_types() (in module pybel.struct.summary) count_functions() (in module pybel.struct.summary) count_naked_names() (in module pybel.struct.summary) count_names_by_namespace() (in module pybel.struct.summary) count_namespaces() (in module pybel.struct.summary) count_networks() (pybel.manager.NetworkManager method) count_nodes() (pybel.manager.QueryManager method) count_passed_edge_filter() (in module pybel.struct.filters) count_passed_node_filter() (in module pybel.struct.filters) count_pathologies() (in module pybel.struct.summary) count_relations() (in module pybel.struct.summary) count_variants() (in module pybel.struct.summary) CountDispatch (class in pybel.struct.graph) create_all() (pybel.manager.BaseManager method) created (pybel.manager.models.Namespace attribute) curie (pybel.language.Entity property)

D

data (pybel.manager.models.Edge attribute) (pybel.manager.models.Node attribute) data_missing_key_builder() (in module pybel.struct.filters) date (pybel.manager.models.Citation attribute) db (pybel.manager.models.Citation attribute) db_id (pybel.manager.models.Citation attribute) DECREASES (in module pybel.constants) default_namespace (pybel.parser.parse_metadata.MetadataParser attribute) defined_annotation_keywords (pybel.BELGraph property) defined_namespace_keywords (pybel.BELGraph property) degradation (pybel.parser.parse_bel.BELParser attribute) DeprecationMappingError DESCRIPTION (in module pybel.constants) description (pybel.BELGraph property) (pybel.manager.models.Namespace attribute) (pybel.manager.models.Network attribute) description_contains() (pybel.manager.models.Network class method) dict() (pybel.struct.graph.SummarizeDispatch method) DIRECT_CAUSAL_RELATIONS (in module pybel.constants)

DIRECTLY_DECREASES (in module pybel.constants) DIRECTLY_INCREASES (in module pybel.constants) DIRECTLY_REGULATES (in module pybel.constants) DIRTY (in module pybel.constants) disclaimer (pybel.BELGraph property) (pybel.manager.models.Network attribute) DOCUMENT_KEYS (in module pybel.constants) document_metadata (pybel.parser.parse_metadata.MetadataParser attribute) domain (pybel.manager.models.Namespace attribute) drop_all() (pybel.manager.BaseManager method) drop_network() (pybel.manager.NetworkManager method) drop_network_by_id() (pybel.manager.NetworkManager method) drop_networks() (pybel.manager.NetworkManager method) dump() (in module pybel) (pybel.Pipeline method) (pybel.struct.query.Query method) (pybel.struct.query.Seeding method) dumps() (pybel.Pipeline method) (pybel.struct.query.Query method) (pybel.struct.query.Seeding method)

E

Edge (class in pybel.manager.models) edge_has_activity() (in module pybel.struct.filters) edge_has_annotation() (in module pybel.struct.filters) edge_has_degradation() (in module pybel.struct.filters) edge_has_translocation() (in module pybel.struct.filters) edge_predicate() (in module pybel.struct.filters) edge_to_bel() (pybel.BELGraph static method) edges() (pybel.struct.graph.SummarizeDispatch method) encoding (pybel.manager.models.NamespaceEntry attribute) enrich_pmc_citations() (in module pybel.manager) enrich_protein_and_rna_origins() (in module pybel.struct.mutation.inference) enrich_proteins_with_rnas() (in module pybel.struct.mutation.inference) enrich_pubmed_citations() (in module pybel.manager) enrich_rnas_with_genes() (in module pybel.struct.mutation.inference) ensure_node() (pybel.parser.parse_bel.BELParser method) ensure_resources() (pybel.parser.parse_metadata.MetadataParser method) Entity (class in pybel.dsl) (class in pybel.language)

EnumeratedFusionRange (class in pybel.dsl) EQUIVALENT_TO (in module pybel.constants) error_types() (pybel.struct.graph.CountDispatch method) Evidence (class in pybel.manager.models) EVIDENCE (in module pybel.constants) expand (pybel.BELGraph property) expand_all_node_neighborhoods() (in module pybel.struct.mutation.expansion) expand_by_edge_filter() (in module pybel.struct.mutation.utils) expand_downstream_causal() (in module pybel.struct.mutation.expansion) expand_internal() (in module pybel.struct.mutation.expansion) expand_node_neighborhood() (in module pybel.struct.mutation.expansion) expand_node_predecessors() (in module pybel.struct.mutation.expansion) expand_node_successors() (in module pybel.struct.mutation.expansion) expand_nodes_neighborhoods() (in module pybel.struct.mutation.expansion) expand_upstream_causal() (in module pybel.struct.mutation.expansion) ExpandDispatch (class in pybel.struct.graph) extend() (pybel.Pipeline method)

F

false_edge_predicate() (in module pybel.struct.filters) false_node_predicate() (in module pybel.struct.filters) filter_edges() (in module pybel.struct.filters) filter_nodes() (in module pybel.struct.filters) first_id (pybel.manager.models.Citation attribute) Fragment (class in pybel.dsl) FRAGMENT (in module pybel.constants) FRAGMENT_DESCRIPTION (in module pybel.constants) FRAGMENT_MISSING (in module pybel.constants) FRAGMENT_START (in module pybel.constants) FRAGMENT_STOP (in module pybel.constants) from_bel_commons() (in module pybel) from_bel_script() (in module pybel) from_bel_script_url() (in module pybel) from_biodati() (in module pybel) from_biopax() (in module pybel) from_bytes() (in module pybel) from_bytes_gz() (in module pybel) from_cbn_jgif() (in module pybel) from_cbn_jgif_file() (in module pybel) from_cx() (in module pybel) from_cx_file() (in module pybel) from_cx_gz() (in module pybel) from_cx_jsons() (in module pybel) from_database() (in module pybel) from_emmaa() (in module pybel) from_fraunhofer_orientdb() (in module pybel) from_functions() (pybel.Pipeline static method) from_graphdati() (in module pybel) from_graphdati_file() (in module pybel) from_graphdati_gz() (in module pybel) from_graphdati_jsons() (in module pybel)

from_hetionet_file() (in module pybel) from_hetionet_gz() (in module pybel) from_hetionet_json() (in module pybel) from_hipathia_dfs() (in module pybel) from_hipathia_paths() (in module pybel) from_indra_statements() (in module pybel) from_indra_statements_json() (in module pybel) from_indra_statements_json_file() (in module pybel) from_jgif() (in module pybel) from_jgif_file() (in module pybel) from_jgif_gz() (in module pybel) from_jgif_jsons() (in module pybel) from_json() (pybel.Pipeline static method) (pybel.struct.query.Query static method) (pybel.struct.query.Seeding static method) from_nodelink() (in module pybel) from_nodelink_file() (in module pybel) from_nodelink_gz() (in module pybel) from_nodelink_jsons() (in module pybel) from_pickle() (in module pybel) from_pickle_gz() (in module pybel) from_s3() (in module pybel) from_sbel() (in module pybel) from_sbel_file() (in module pybel) from_sbel_gz() (in module pybel) FUNCTION (in module pybel.constants) function_exclusion_filter_builder() (in module pybel.struct.filters) function_inclusion_filter_builder() (in module pybel.struct.filters) functions() (pybel.struct.graph.CountDispatch method) fusion (pybel.parser.parse_bel.BELParser attribute) FusionBase (class in pybel.dsl) FusionRangeBase (class in pybel.dsl)

G

Gene (class in pybel.dsl) GENE (in module pybel.constants) gene (pybel.parser.parse_bel.BELParser attribute) GeneFusion (class in pybel.dsl) GeneModification (class in pybel.dsl) general_abundance (pybel.parser.parse_bel.BELParser attribute) get_annotation_values() (in module pybel.struct.summary) get_annotation_values_by_annotation() (in module pybel.struct.summary) get_annotations() (in module pybel.struct.summary) (pybel.parser.parse_bel.BELParser method) (pybel.parser.parse_control.ControlParser method) get_annotations_json() (pybel.manager.models.Edge method) get_authors() (pybel.BELGraph method) get_cache_connection() (in module pybel.constants) get_causal_subgraph() (in module pybel.struct.mutation.induction) get_citation() (pybel.parser.parse_control.ControlParser method) get_downstream_causal_subgraph() (in module pybel.struct.mutation.induction) get_edge_annotations() (pybel.BELGraph method) get_edge_citation() (pybel.BELGraph method) get_edge_evidence() (pybel.BELGraph method) get_edges_with_annotation() (pybel.manager.QueryManager method) get_edges_with_citation() (pybel.manager.QueryManager method) get_edges_with_citations() (pybel.manager.QueryManager method) get_equivalent_nodes() (pybel.BELGraph method) get_functions() (in module pybel.struct.summary) get_graph_by_id() (pybel.manager.NetworkManager method) get_graph_by_ids() (pybel.manager.NetworkManager method) get_graph_by_most_recent() (pybel.manager.NetworkManager method) get_graph_by_name_version() (pybel.manager.NetworkManager method) get_graph_with_random_edges() (in module pybel.struct.mutation.induction) get_graphs_by_ids() (pybel.manager.NetworkManager method) get_hetionet() (in module pybel) get_largest_component() (in module pybel.struct.mutation.induction) get_metaedge_to_key() (in module pybel.struct.summary) get_missing_required_annotations() (pybel.parser.parse_control.ControlParser method) get_most_recent_network_by_name() (pybel.manager.NetworkManager method) get_multi_causal_downstream() (in module pybel.struct.mutation.induction_expansion) get_multi_causal_upstream() (in module pybel.struct.mutation.induction_expansion) get_naked_names() (in module pybel.struct.summary) get_names() (in module pybel.struct.summary) get_names_by_namespace() (in module pybel.struct.summary) get_namespaces() (in module pybel.struct.summary) get_network_by_id() (pybel.manager.NetworkManager method) get_network_by_name_version() (pybel.manager.NetworkManager method) get_network_versions() (pybel.manager.NetworkManager method) get_networks_by_ids() (pybel.manager.NetworkManager method) get_networks_by_name() (pybel.manager.NetworkManager method)

get_nodes() (in module pybel.struct.filters) get_nodes_by_function() (in module pybel.struct.filters) get_nodes_by_namespace() (in module pybel.struct.filters) get_nodes_in_all_shortest_paths() (in module pybel.struct.mutation.induction) get_pmc_identifiers() (in module pybel.struct.summary) get_pubmed_identifiers() (in module pybel.struct.summary) get_random_node() (in module pybel.struct.mutation.induction) get_random_path() (in module pybel.struct.mutation.induction) get_random_subgraph() (in module pybel.struct.mutation.induction) get_subgraph() (in module pybel.struct.query) get_subgraph_by_all_shortest_paths() (in module pybel.struct.mutation.induction) get_subgraph_by_annotation_value() (in module pybel.struct.mutation.induction) get_subgraph_by_annotations() (in module pybel.struct.mutation.induction) get_subgraph_by_authors() (in module pybel.struct.mutation.induction) get_subgraph_by_edge_filter() (in module pybel.struct.mutation.induction) get_subgraph_by_induction() (in module pybel.struct.mutation.induction) get_subgraph_by_neighborhood() (in module pybel.struct.mutation.induction) get_subgraph_by_node_filter() (in module pybel.struct.mutation.induction) get_subgraph_by_pubmed() (in module pybel.struct.mutation.induction) get_subgraph_by_second_neighbors() (in module pybel.struct.mutation.induction_expansion) get_subgraphs_by_annotation() (in module pybel.struct.grouping) get_subgraphs_by_citation() (in module pybel.struct.grouping) get_syntax_errors() (in module pybel.struct.summary) get_term_to_encodings() (pybel.manager.models.Namespace method) get_tf_pairs() (in module pybel.struct.getters) get_top_hubs() (in module pybel.struct.summary) get_top_pathologies() (in module pybel.struct.summary) get_transformation() (in module pybel.struct.pipeline.decorators) get_triples_from_bel() (in module pybel.io.pykeen) get_triples_from_bel_commons() (in module pybel.io.pykeen) get_triples_from_bel_nodelink() (in module pybel.io.pykeen) get_triples_from_bel_pickle() (in module pybel.io.pykeen) get_ungrounded_nodes() (in module pybel.struct.summary) get_unused_annotations() (in module pybel.struct.summary) get_unused_list_annotation_values() (in module pybel.struct.summary) get_unused_namespaces() (in module pybel.struct.summary) get_upstream_causal_subgraph() (in module pybel.struct.mutation.induction) GMOD (in module pybel.constants) gmod (pybel.parser.parse_bel.BELParser attribute) gmod_mappings (in module pybel.language) gmod_namespace (in module pybel.language) GMOD_ORDER (in module pybel.constants) GRAPH_METADATA (in module pybel.constants) ground() (pybel.BELGraph method) GSUB_POSITION (in module pybel.constants) GSUB_REFERENCE (in module pybel.constants) GSUB_VARIANT (in module pybel.constants)

H

handle_annotation_key() (pybel.parser.parse_control.ControlParser method) handle_annotation_list() (pybel.parser.parse_metadata.MetadataParser method) handle_annotation_pattern() (pybel.parser.parse_metadata.MetadataParser method) handle_annotations_url() (pybel.parser.parse_metadata.MetadataParser method) handle_document() (pybel.parser.parse_metadata.MetadataParser method) handle_has_components() (pybel.parser.parse_bel.BELParser method) handle_has_members() (pybel.parser.parse_bel.BELParser method) handle_identifier_fqualified() (pybel.parser.parse_concept.ConceptParser method) handle_identifier_qualified() (pybel.parser.parse_concept.ConceptParser method) handle_inverse_unqualified_relation() (pybel.parser.parse_bel.BELParser method) handle_namespace_default() (pybel.parser.parse_concept.ConceptParser method) handle_namespace_invalid() (pybel.parser.parse_concept.ConceptParser method) handle_namespace_lenient() (pybel.parser.parse_concept.ConceptParser static method) handle_namespace_pattern() (pybel.parser.parse_metadata.MetadataParser method) handle_namespace_url() (pybel.parser.parse_metadata.MetadataParser method) handle_nested_relation() (pybel.parser.parse_bel.BELParser method) handle_set_citation() (pybel.parser.parse_control.ControlParser method) handle_set_command() (pybel.parser.parse_control.ControlParser method) handle_set_command_list() (pybel.parser.parse_control.ControlParser method) handle_set_evidence() (pybel.parser.parse_control.ControlParser method) handle_set_statement_group() (pybel.parser.parse_control.ControlParser method) handle_term() (pybel.parser.parse_bel.BELParser method) handle_translocation_illegal() (pybel.parser.parse_bel.BELParser method) handle_unqualified_relation() (pybel.parser.parse_bel.BELParser method) handle_unset_all() (pybel.parser.parse_control.ControlParser method) handle_unset_citation() (pybel.parser.parse_control.ControlParser method) handle_unset_command() (pybel.parser.parse_control.ControlParser method) handle_unset_evidence() (pybel.parser.parse_control.ControlParser method) handle_unset_list() (pybel.parser.parse_control.ControlParser method) handle_unset_statement_group() (pybel.parser.parse_control.ControlParser method) has_activity() (in module pybel.struct.filters) has_annotation() (pybel.parser.parse_control.ControlParser method) (pybel.parser.parse_metadata.MetadataParser method) has_authors() (in module pybel.struct.filters) has_causal_edges() (in module pybel.struct.filters) has_causal_in_edges() (in module pybel.struct.filters) has_causal_out_edges() (in module pybel.struct.filters)

has_edge_citation() (pybel.BELGraph method) has_edge_evidence() (pybel.BELGraph method) has_edge_modifier() (in module pybel.struct.filters) has_enumerated_annotation() (pybel.parser.parse_control.ControlParser method) (pybel.parser.parse_metadata.MetadataParser method) has_enumerated_namespace() (pybel.parser.parse_concept.ConceptParser method) (pybel.parser.parse_metadata.MetadataParser method) has_fragment() (in module pybel.struct.filters) has_gene_modification() (in module pybel.struct.filters) has_hgvs() (in module pybel.struct.filters) has_in_edges() (in module pybel.struct.filters) has_local_annotation() (pybel.parser.parse_control.ControlParser method) (pybel.parser.parse_metadata.MetadataParser method) has_member (pybel.parser.parse_bel.BELParser attribute) has_name_in() (pybel.manager.models.Author class method) has_name_version() (pybel.manager.NetworkManager method) has_namespace() (pybel.parser.parse_metadata.MetadataParser method) has_out_edges() (in module pybel.struct.filters) has_pathology_causal() (in module pybel.struct.filters) has_pmc() (in module pybel.struct.filters) has_polarity() (in module pybel.struct.filters) HAS_PRODUCT (in module pybel.constants) has_protein_modification() (in module pybel.struct.filters) has_provenance() (in module pybel.struct.filters) has_pubmed() (in module pybel.struct.filters) HAS_REACTANT (in module pybel.constants) has_regex_annotation() (pybel.parser.parse_control.ControlParser method) (pybel.parser.parse_metadata.MetadataParser method) has_regex_namespace() (pybel.parser.parse_concept.ConceptParser method) (pybel.parser.parse_metadata.MetadataParser method) HAS_VARIANT (in module pybel.constants) has_variant() (in module pybel.struct.filters) HASH (in module pybel.constants) Hgvs (class in pybel.dsl) HGVS (in module pybel.constants) HgvsReference (class in pybel.dsl) HgvsUnspecified (class in pybel.dsl)

I

id_in() (pybel.manager.models.Network class method) IDENTIFIER (in module pybel.constants) identifier (pybel.language.Entity property) (pybel.manager.models.NamespaceEntry attribute) IllegalAnnotationValueWarning in_place_transformation() (in module pybel.struct.pipeline.decorators) InconsistentDefinitionError INCREASES (in module pybel.constants) INDIRECT_CAUSAL_RELATIONS (in module pybel.constants) induce (pybel.BELGraph property) InduceDispatch (class in pybel.struct.graph) infer_child_relations() (in module pybel.struct.mutation.inference) insert_into_graph() (pybel.manager.models.Edge method) internal() (pybel.struct.graph.ExpandDispatch method) intersection() (pybel.Pipeline static method) InvalidCitationLengthException InvalidCitationType InvalidEntity InvalidFunctionSemantic InvalidMetadataException InvalidPubMedIdentifierWarning INVERSE_DOCUMENT_KEYS (in module pybel.constants)

invert_edge_predicate() (in module pybel.struct.filters) invert_node_predicate() (in module pybel.struct.filters) IS_A (in module pybel.constants) is_associative_relation() (in module pybel.struct.filters) is_causal_central() (in module pybel.struct.filters) is_causal_relation() (in module pybel.struct.filters) is_causal_sink() (in module pybel.struct.filters) is_causal_source() (in module pybel.struct.filters) is_degraded() (in module pybel.struct.filters) is_direct_causal_relation() (in module pybel.struct.filters) is_enriched (pybel.manager.models.Citation property) is_isolated_list_abundance() (in module pybel.struct.filters) is_pubmed (pybel.manager.models.Citation property) is_translocated() (in module pybel.struct.filters) issue (pybel.manager.models.Citation attribute) iter_annotation_value_pairs() (in module pybel.struct.summary) iter_annotation_values() (in module pybel.struct.summary) iter_equivalent_nodes() (pybel.BELGraph method) iter_sample_metaedges() (in module pybel.struct.summary) iterate_entities() (in module pybel.struct.summary) iterate_node_entities() (in module pybel.struct.summary) iterate_pmc_identifiers() (in module pybel.struct.summary) iterate_pubmed_identifiers() (in module pybel.struct.summary)

J

journal (pybel.manager.models.Citation attribute)

K

keyword (pybel.manager.models.Namespace attribute)

KIND (in module pybel.constants)

L

LABEL (in module pybel.constants) last_id (pybel.manager.models.Citation attribute) left_full_join() (in module pybel.struct) left_outer_join() (in module pybel.struct) license (pybel.BELGraph property) (pybel.manager.models.Namespace attribute) licenses (pybel.manager.models.Network attribute) LINE (in module pybel.constants) list() (pybel.struct.graph.SummarizeDispatch method) list_networks() (pybel.manager.NetworkManager method)

list_recent_networks() (pybel.manager.NetworkManager method) ListAbundance (class in pybel.dsl) load() (in module pybel) (pybel.Pipeline static method) (pybel.struct.query.Query static method) (pybel.struct.query.Seeding static method) loads() (pybel.Pipeline static method) (pybel.struct.query.Query static method) (pybel.struct.query.Seeding static method) location (pybel.parser.parse_bel.BELParser attribute)

M

make() (pybel.exceptions.MissingMetadataException static method) MalformedMetadataException MalformedTranslocationWarning Manager (class in pybel.manager) manager (pybel.parser.parse_metadata.MetadataParser attribute) md5 (pybel.manager.models.Edge attribute) MEMBERS (in module pybel.constants) METADATA_AUTHORS (in module pybel.constants) METADATA_CONTACT (in module pybel.constants) METADATA_COPYRIGHT (in module pybel.constants) METADATA_DESCRIPTION (in module pybel.constants) METADATA_DISCLAIMER (in module pybel.constants) METADATA_INSERT_KEYS (in module pybel.constants) METADATA_LICENSES (in module pybel.constants) METADATA_NAME (in module pybel.constants) METADATA_PROJECT (in module pybel.constants) METADATA_VERSION (in module pybel.constants) MetadataException MetadataParser (class in pybel.parser.parse_metadata) MetaValueError MicroRna (class in pybel.dsl) miriam_id (pybel.manager.models.Namespace attribute) MIRNA (in module pybel.constants) mirna (pybel.parser.parse_bel.BELParser attribute) MissingAnnotationKeyWarning MissingAnnotationRegexWarning MissingAnnotationWarning MissingCitationException MissingDefaultNameWarning MissingFusionRange (class in pybel.dsl) MissingMetadataException MissingNamespaceNameWarning MissingNamespaceRegexWarning MissingPipelineFunctionError MissingSupportWarning MissingUniverseError modifications() (pybel.struct.graph.CountDispatch method) module pybel.constants pybel.dsl pybel.examples pybel.examples.braf_example pybel.examples.egf_example pybel.examples.sialic_acid_example pybel.examples.statin_example pybel.examples.tloc_example pybel.exceptions pybel.io pybel.io.aws pybel.io.bel_commons_client pybel.io.biodati_client pybel.io.cx pybel.io.emmaa pybel.io.extras pybel.io.fraunhofer_orientdb pybel.io.gpickle pybel.io.graphdati pybel.io.graphml pybel.io.hetionet pybel.io.hipathia pybel.io.indra pybel.io.jgif pybel.io.jupyter pybel.io.neo4j pybel.io.nodelink pybel.io.pykeen pybel.io.pynpa pybel.io.sbel pybel.io.spia pybel.io.triples pybel.io.umbrella_nodelink pybel.language pybel.manager.database_io pybel.manager.models pybel.parser.modifiers pybel.parser.modifiers.fragment pybel.parser.modifiers.fusion pybel.parser.modifiers.gene_modification pybel.parser.modifiers.gene_substitution pybel.parser.modifiers.location pybel.parser.modifiers.protein_modification pybel.parser.modifiers.protein_substitution pybel.parser.modifiers.truncation pybel.parser.modifiers.variant pybel.struct pybel.struct.filters pybel.struct.getters pybel.struct.grouping pybel.struct.mutation.collapse pybel.struct.mutation.deletion pybel.struct.mutation.expansion pybel.struct.mutation.induction pybel.struct.mutation.induction_expansion pybel.struct.mutation.inference pybel.struct.mutation.metadata pybel.struct.mutation.utils pybel.struct.pipeline.decorators pybel.struct.pipeline.exc pybel.struct.query pybel.struct.summary

molecular_activity (pybel.parser.parse_bel.BELParser attribute)

N

NakedNameWarning NAME (in module pybel.constants) name (pybel.BELGraph property) (pybel.language.Entity property) (pybel.manager.models.Namespace attribute) (pybel.manager.models.NamespaceEntry attribute) (pybel.manager.models.Network attribute) name_contains() (pybel.manager.models.Author class method) (pybel.manager.models.NamespaceEntry class method) (pybel.manager.models.Network class method) Namespace (class in pybel.manager.models) NAMESPACE (in module pybel.constants) namespace (pybel.language.Entity property) NAMESPACE_DOMAIN_TYPES (in module pybel.constants) namespace_inclusion_builder() (in module pybel.struct.filters) namespace_pattern (pybel.BELGraph property) namespace_to_pattern (pybel.parser.parse_metadata.MetadataParser attribute) namespace_to_term_to_encoding (pybel.parser.parse_metadata.MetadataParser attribute) namespace_url (pybel.BELGraph property) namespace_url_dict (pybel.parser.parse_metadata.MetadataParser attribute) NamespaceEntry (class in pybel.manager.models) NamespaceIdentifierWarning namespaces() (pybel.struct.graph.CountDispatch method) (pybel.struct.graph.SummarizeDispatch method)

NameWarning NEGATIVE_CORRELATION (in module pybel.constants) neighborhood() (pybel.struct.graph.ExpandDispatch method) (pybel.struct.graph.InduceDispatch method) NestedRelationWarning Network (class in pybel.manager.models) NetworkManager (class in pybel.manager) no_causal_edges() (in module pybel.struct.filters) no_causal_in_edges() (in module pybel.struct.filters) no_causal_out_edges() (in module pybel.struct.filters) NO_CORRELATION (in module pybel.constants) no_in_edges() (in module pybel.struct.filters) no_out_edges() (in module pybel.struct.filters) Node (class in pybel.manager.models) node_has_namespace() (pybel.BELGraph method) node_is_grounded() (in module pybel.struct.summary) node_predicate() (in module pybel.struct.filters) node_to_bel() (pybel.BELGraph static method) NodeDegreeIterError nodes() (pybel.struct.graph.SummarizeDispatch method) none_of() (in module pybel.struct.filters) not_causal_relation() (in module pybel.struct.filters) number_of_authors() (pybel.BELGraph method) number_of_citations() (pybel.BELGraph method) number_of_warnings() (pybel.BELGraph method)

O

obo (pybel.language.Entity property)

one_of() (in module pybel.struct.filters) ORTHOLOGOUS (in module pybel.constants)

P

pages (pybel.manager.models.Citation attribute) parent (pybel.BELGraph attribute) (pybel.struct.graph.ExpandDispatch property) parse() (pybel.parser.parse_bel.BELParser method) parse_lines() (in module pybel.io.line_utils) parse_result_to_dsl() (in module pybel.tokens) part_has_modifier() (in module pybel.struct.filters) PART_OF (in module pybel.constants) PARTNER_3P (in module pybel.constants) PARTNER_5P (in module pybel.constants) PATH pybel-compile command line option path pybel-insert command line option pybel-neo command line option pybel-serialize command line option pybel-summarize command line option pybel-upload command line option pybel-warnings command line option path (pybel.BELGraph property) pathologies() (pybel.struct.graph.CountDispatch method) Pathology (class in pybel.dsl) PATHOLOGY (in module pybel.constants) pathology (pybel.parser.parse_bel.BELParser attribute) paths() (pybel.struct.graph.InduceDispatch method) pattern (pybel.manager.models.Namespace attribute) periphery() (pybel.struct.graph.ExpandDispatch method) Pipeline (class in pybel) PipelineNameError PlaceholderAminoAcidWarning plot (pybel.BELGraph property) PlotDispatch (class in pybel.struct.graph) PMOD (in module pybel.constants) pmod (pybel.parser.parse_bel.BELParser attribute) PMOD_CODE (in module pybel.constants) pmod_legacy_labels (in module pybel.language) pmod_mappings (in module pybel.language) pmod_namespace (in module pybel.language) PMOD_ORDER (in module pybel.constants) PMOD_POSITION (in module pybel.constants) POLAR_RELATIONS (in module pybel.constants) Population (class in pybel.dsl) POPULATION (in module pybel.constants) POSITIVE_CORRELATION (in module pybel.constants) post_jgif() (in module pybel) PRODUCTS (in module pybel.constants) PROGONSTIC_BIOMARKER_FOR (in module pybel.constants) Protein (class in pybel.dsl) PROTEIN (in module pybel.constants) protein (pybel.parser.parse_bel.BELParser attribute) ProteinFusion (class in pybel.dsl) ProteinModification (class in pybel.dsl) ProteinSubstitution (class in pybel.dsl) prune_protein_rna_origins() (in module pybel.struct.mutation.deletion) PSUB_POSITION (in module pybel.constants) PSUB_REFERENCE (in module pybel.constants) PSUB_VARIANT (in module pybel.constants) pybel command line option --connection --version -c pybel-compile command line option --allow-naked-names --disallow-nested --disallow-unqualified-translocations --no-citation-clearing --no-identifier-validation --required-annotations --skip-tqdm --upgrade-urls --verbose -r -v PATH pybel-insert command line option path pybel-machine command line option --host --local AGENTS pybel-manage-drop command line option --yes pybel-manage-edges-ls command line option --limit --offset pybel-manage-examples command line option --debug -v pybel-manage-namespaces-drop command line option URL pybel-manage-namespaces-insert command line option URL pybel-manage-namespaces-ls command line option --namespace-id --url -i -u pybel-manage-networks-drop command line option --network-id --yes -n -y pybel-neo command line option --connection --password path pybel-parse command line option --pprint TEXT pybel-serialize command line option --bel --edgelist --graphml --gsea --nodelink --sif --tsv path pybel-summarize command line option path pybel-upload command line option --host --password --user path pybel-warnings command line option path pybel.constants module pybel.dsl module pybel.examples module

pybel.examples.braf_example module pybel.examples.braf_example_graph (in module pybel.examples.braf_example) pybel.examples.egf_example module pybel.examples.egf_graph (in module pybel.examples.egf_example) pybel.examples.ras_tloc_graph (in module pybel.examples.tloc_example) pybel.examples.sialic_acid_example module pybel.examples.sialic_acid_graph (in module pybel.examples.sialic_acid_example) pybel.examples.statin_example module pybel.examples.statin_graph (in module pybel.examples.statin_example) pybel.examples.tloc_example module pybel.exceptions module pybel.io module pybel.io.aws module pybel.io.bel_commons_client module pybel.io.biodati_client module pybel.io.cx module pybel.io.emmaa module pybel.io.extras module pybel.io.fraunhofer_orientdb module pybel.io.gpickle module pybel.io.graphdati module pybel.io.graphml module pybel.io.hetionet module pybel.io.hipathia module pybel.io.indra module pybel.io.jgif module pybel.io.jupyter module pybel.io.neo4j module pybel.io.nodelink module pybel.io.pykeen module pybel.io.pynpa module pybel.io.sbel module pybel.io.spia module pybel.io.triples module pybel.io.umbrella_nodelink module pybel.language module pybel.manager.database_io module pybel.manager.models module pybel.parser.modifiers module pybel.parser.modifiers.fragment module pybel.parser.modifiers.fusion module pybel.parser.modifiers.gene_modification module pybel.parser.modifiers.gene_substitution module pybel.parser.modifiers.location module pybel.parser.modifiers.protein_modification module pybel.parser.modifiers.protein_substitution module pybel.parser.modifiers.truncation module pybel.parser.modifiers.variant module pybel.struct module pybel.struct.filters module pybel.struct.getters module pybel.struct.grouping module pybel.struct.mutation.collapse module pybel.struct.mutation.deletion module pybel.struct.mutation.expansion module pybel.struct.mutation.induction module pybel.struct.mutation.induction_expansion module pybel.struct.mutation.inference module pybel.struct.mutation.metadata module pybel.struct.mutation.utils module pybel.struct.pipeline.decorators module pybel.struct.pipeline.exc module pybel.struct.query module pybel.struct.summary module PYBEL_EDGE_ALL_KEYS (in module pybel.constants) PYBEL_EDGE_DATA_KEYS (in module pybel.constants) PYBEL_EDGE_METADATA_KEYS (in module pybel.constants) PYBEL_NODE_DATA_KEYS (in module pybel.constants) PYBEL_NODE_FUNCTIONS (in module pybel.constants) PYBEL_VARIANT_KINDS (in module pybel.constants) pybel_version (pybel.BELGraph property) PyBELWarning

Q

Query (class in pybel.struct.query) query_citations() (pybel.manager.QueryManager method) query_edges() (pybel.manager.QueryManager method) query_edges_by_pubmed_identifiers() (pybel.manager.QueryManager method) query_induction() (pybel.manager.QueryManager method)

query_neighbors() (pybel.manager.QueryManager method) query_nodes() (pybel.manager.QueryManager method) query_singleton_edges_from_network() (pybel.manager.NetworkManager method) query_url (pybel.manager.models.Namespace attribute) QueryManager (class in pybel.manager) QueryMissingNetworksError

R

raise_for_invalid_annotation_value() (pybel.parser.parse_control.ControlParser method) raise_for_missing_citation() (pybel.parser.parse_control.ControlParser method) raise_for_missing_name() (pybel.parser.parse_concept.ConceptParser method) raise_for_missing_namespace() (pybel.parser.parse_concept.ConceptParser method) raise_for_redefined_annotation() (pybel.parser.parse_metadata.MetadataParser method) raise_for_redefined_namespace() (pybel.parser.parse_metadata.MetadataParser method) raise_for_undefined_annotation() (pybel.parser.parse_control.ControlParser method) raise_for_version() (pybel.parser.parse_metadata.MetadataParser method) random() (pybel.struct.graph.InduceDispatch method) RANGE_3P (in module pybel.constants) RANGE_5P (in module pybel.constants) rate_limit (pybel.parser.parse_bel.BELParser attribute) RATE_LIMITING_STEP_OF (in module pybel.constants) REACTANTS (in module pybel.constants) reactants (pybel.parser.parse_bel.BELParser attribute) Reaction (class in pybel.dsl) REACTION (in module pybel.constants) RedefinedAnnotationError RedefinedNamespaceError REGULATES (in module pybel.constants) RELATION (in module pybel.constants)

relations() (pybel.struct.graph.CountDispatch method) remove_annotation_value() (in module pybel.struct.mutation.metadata) remove_associations() (in module pybel.struct.mutation.deletion) remove_biological_processes() (in module pybel.struct.mutation.deletion) remove_extra_citation_metadata() (in module pybel.struct.mutation.metadata) remove_filtered_edges() (in module pybel.struct.mutation.deletion) remove_filtered_nodes() (in module pybel.struct.mutation.deletion) remove_isolated_list_abundances() (in module pybel.struct.mutation.deletion) remove_isolated_nodes() (in module pybel.struct.mutation.utils) remove_isolated_nodes_op() (in module pybel.struct.mutation.utils) remove_non_causal_edges() (in module pybel.struct.mutation.deletion) remove_pathologies() (in module pybel.struct.mutation.deletion) REQUIRED_METADATA (in module pybel.constants) rev_abundance_labels (in module pybel.constants) Rna (class in pybel.dsl) RNA (in module pybel.constants) rna (pybel.parser.parse_bel.BELParser attribute) RnaFusion (class in pybel.dsl) run() (pybel.Pipeline method) (pybel.struct.query.Query method) (pybel.struct.query.Seeding method)

S

search_edges_with_bel() (pybel.manager.QueryManager method) search_edges_with_evidence() (pybel.manager.QueryManager method) Seeding (class in pybel.struct.query) SOURCE_MODIFIER (in module pybel.constants) source_modifier (pybel.manager.models.Edge attribute) species (pybel.manager.models.Namespace attribute) statistics() (pybel.struct.graph.SummarizeDispatch method) store_bel() (pybel.manager.models.Network method) str() (pybel.struct.graph.SummarizeDispatch method)

strip_annotations() (in module pybel.struct.mutation.metadata) SUBPROCESS_OF (in module pybel.constants) subprocess_of (pybel.parser.parse_bel.BELParser attribute) summarize (pybel.BELGraph property) summarize_node_filter() (in module pybel.struct.filters) SummarizeDispatch (class in pybel.struct.graph) summary() (pybel.struct.graph.PlotDispatch method) summary_dict() (pybel.BELGraph method) summary_str() (pybel.BELGraph method) surviors_are_inconsistent() (in module pybel.struct.mutation.collapse)

T

TARGET_MODIFIER (in module pybel.constants) target_modifier (pybel.manager.models.Edge attribute) TEXT pybel-parse command line option text (pybel.manager.models.Evidence attribute) title (pybel.manager.models.Citation attribute) to_bel_commons() (in module pybel) to_bel_script() (in module pybel) to_biodati() (in module pybel) to_bytes() (in module pybel) to_bytes_gz() (in module pybel) to_csv() (in module pybel) to_cx() (in module pybel) to_cx_file() (in module pybel) to_cx_gz() (in module pybel) to_cx_jsons() (in module pybel) to_database() (in module pybel) to_edgelist() (in module pybel) to_graphdati() (in module pybel) to_graphdati_file() (in module pybel) to_graphdati_gz() (in module pybel) to_graphdati_jsonl() (in module pybel) to_graphdati_jsonl_gz() (in module pybel) to_graphdati_jsons() (in module pybel) to_graphml() (in module pybel) to_gsea() (in module pybel) to_hipathia() (in module pybel) to_hipathia_dfs() (in module pybel) to_indra_statements() (in module pybel) to_indra_statements_json() (in module pybel) to_indra_statements_json_file() (in module pybel) to_jgif() (in module pybel) to_jgif_file() (in module pybel) to_jgif_gz() (in module pybel) to_jgif_jsons() (in module pybel) to_json() (pybel.manager.models.Citation method) (pybel.manager.models.Edge method) (pybel.manager.models.Evidence method) (pybel.manager.models.Namespace method) (pybel.manager.models.NamespaceEntry method) (pybel.manager.models.Network method) (pybel.manager.models.Node method) (pybel.Pipeline method) (pybel.struct.query.Query method) (pybel.struct.query.Seeding method)

to_jupyter() (in module pybel) to_neo4j() (in module pybel) to_nodelink() (in module pybel) to_nodelink_file() (in module pybel) to_nodelink_gz() (in module pybel) to_nodelink_jsons() (in module pybel) to_npa_dfs() (in module pybel) to_npa_directory() (in module pybel) to_pickle() (in module pybel) to_pickle_gz() (in module pybel) to_s3() (in module pybel) to_sbel() (in module pybel) to_sbel_file() (in module pybel) to_sbel_gz() (in module pybel) to_sif() (in module pybel) to_spia_dfs() (in module pybel) to_spia_excel() (in module pybel) to_spia_tsvs() (in module pybel) to_triples() (in module pybel) to_triples_file() (in module pybel) to_umbrella_nodelink() (in module pybel) to_umbrella_nodelink_file() (in module pybel) to_umbrella_nodelink_gz() (in module pybel) Transcribable (class in pybel.dsl) transcribed (pybel.parser.parse_bel.BELParser attribute) TRANSCRIBED_TO (in module pybel.constants) transformation() (in module pybel.struct.pipeline.decorators) transitivities (pybel.BELGraph attribute) translated (pybel.parser.parse_bel.BELParser attribute) TRANSLATED_TO (in module pybel.constants) translocation (pybel.parser.parse_bel.BELParser attribute) true_edge_predicate() (in module pybel.struct.filters) true_node_predicate() (in module pybel.struct.filters) TRUNCATION_POSITION (in module pybel.constants) TWO_WAY_RELATIONS (in module pybel.constants) type (pybel.manager.models.Node attribute)

U

uncachable_namespaces (pybel.parser.parse_metadata.MetadataParser attribute) UndefinedAnnotationWarning UndefinedNamespaceWarning uni_in_place_transformation() (in module pybel.struct.pipeline.decorators) uni_transformation() (in module pybel.struct.pipeline.decorators) union() (in module pybel.struct) (pybel.Pipeline static method)

UNQUALIFIED_EDGES (in module pybel.constants) uploaded (pybel.manager.models.Namespace attribute) URL pybel-manage-namespaces-drop command line option pybel-manage-namespaces-insert command line option url (pybel.manager.models.Namespace attribute)

V

validate_unset_command() (pybel.parser.parse_control.ControlParser method) Variant (class in pybel.dsl) VARIANTS (in module pybel.constants) variants() (pybel.struct.graph.CountDispatch method)

version (pybel.BELGraph property) (pybel.manager.models.Namespace attribute) (pybel.manager.models.Network attribute) VersionFormatWarning volume (pybel.manager.models.Citation attribute)

W

warnings (pybel.BELGraph property)

X

XREFS (in module pybel.constants)