PyBEL
v0.14.6
Getting Started
Overview
Installation
Data Structure
Data Model
Example Networks
Summary
Operations
Filters
Transformations
Grouping
Pipeline
Conversion
Input and Output
Database
Manager
Models
Topic Guide
Cookbook
Command Line Interface
Reference
Constants
Parsers
Internal DSL
Logging Messages
Project
References
Roadmap
Current Issues
Technology
PyBEL
Docs
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Index
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Index
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X
Symbols
--allow-naked-names
pybel-compile command line option
--bel <bel>
pybel-serialize command line option
--connection <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 <edgelist>
pybel-serialize command line option
--graphml <graphml>
pybel-serialize command line option
--gsea <gsea>
pybel-serialize command line option
--host <host>
pybel-machine command line option
pybel-post command line option
--limit <limit>
pybel-manage-edges-ls command line option
--local
pybel-machine command line option
--namespace-id <namespace_id>
pybel-manage-namespaces-ls command line option
--network-id <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 <nodelink>
pybel-serialize command line option
--offset <offset>
pybel-manage-edges-ls command line option
--password <password>
pybel-neo command line option
--required-annotations <required_annotations>
pybel-compile command line option
--sif <sif>
pybel-serialize command line option
--skip-tqdm
pybel-compile command line option
--tsv <tsv>
pybel-serialize command line option
--upgrade-urls
pybel-compile command line option
--url <url>
pybel-manage-namespaces-ls 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 (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)
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_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_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_list() (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)
AnnotationWarning
append() (pybel.Pipeline method)
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.manager.models.Network attribute)
authors() (pybel.BELGraph property)
B
Base (class in pybel.manager.models)
base (pybel.manager.BaseManager attribute)
BaseManager (class in pybel.manager)
bel (pybel.manager.models.Edge attribute)
(pybel.manager.models.Node attribute)
bel_contains() (pybel.manager.models.Node class method)
BEL_DEFAULT_NAMESPACE (in module pybel.constants)
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)
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_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_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)
check_function_semantics() (pybel.parser.parse_bel.BELParser method)
Citation (class in pybel.manager.models)
CITATION (in module pybel.constants)
CITATION_AUTHORS (in module pybel.constants)
CITATION_DATE (in module pybel.constants)
CITATION_DB (in module pybel.constants)
CITATION_DB_NAME (in module pybel.constants)
CITATION_FIRST_AUTHOR (in module pybel.constants)
CITATION_IDENTIFIER (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_TYPES (in module pybel.constants)
CITATION_VOLUME (in module pybel.constants)
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_nodes() (in module pybel.struct.mutation)
collapse_pair() (in module pybel.struct.mutation)
collapse_to_genes() (in module pybel.struct.mutation)
compartment_mapping (in module pybel.language)
COMPLEX (in module pybel.constants)
complex_singleton (pybel.parser.parse_bel.BELParser attribute)
COMPOSITE (in module pybel.constants)
composite_abundance (pybel.parser.parse_bel.BELParser attribute)
concatenate_node_predicates() (in module pybel.struct.filters)
CONCEPT (in module pybel.constants)
ConceptParser (class in pybel.parser.parse_concept)
contact (pybel.manager.models.Namespace attribute)
(pybel.manager.models.Network attribute)
contact() (pybel.BELGraph property)
ControlParser (class in pybel.parser.parse_control)
copyright (pybel.manager.models.Network attribute)
copyright() (pybel.BELGraph property)
CORRELATION (in module pybel.constants)
CORRELATIVE_RELATIONS (in module pybel.constants)
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)
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)
DEFAULT_SERVICE_URL (in module pybel.constants)
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.manager.models.Namespace attribute)
(pybel.manager.models.Network attribute)
description() (pybel.BELGraph property)
description_contains() (pybel.manager.models.Network class method)
DIRECT_CAUSAL_RELATIONS (in module pybel.constants)
DIRECTLY_DECREASES (in module pybel.constants)
DIRECTLY_INCREASES (in module pybel.constants)
DIRTY (in module pybel.constants)
disclaimer (pybel.manager.models.Network attribute)
disclaimer() (pybel.BELGraph property)
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)
dumps() (pybel.Pipeline 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)
encoding (pybel.manager.models.NamespaceEntry attribute)
enrich_protein_and_rna_origins() (in module pybel.struct.mutation)
enrich_proteins_with_rnas() (in module pybel.struct.mutation)
enrich_rnas_with_genes() (in module pybel.struct.mutation)
ensure_node() (pybel.parser.parse_bel.BELParser method)
Entity (class in pybel.language)
EQUIVALENT_TO (in module pybel.constants)
Evidence (class in pybel.manager.models)
EVIDENCE (in module pybel.constants)
expand_all_node_neighborhoods() (in module pybel.struct.mutation)
expand_by_edge_filter() (in module pybel.struct.mutation)
expand_downstream_causal() (in module pybel.struct.mutation)
expand_node_neighborhood() (in module pybel.struct.mutation)
expand_node_predecessors() (in module pybel.struct.mutation)
expand_node_successors() (in module pybel.struct.mutation)
expand_nodes_neighborhoods() (in module pybel.struct.mutation)
expand_upstream_causal() (in module pybel.struct.mutation)
extend() (pybel.Pipeline method)
F
filter_edges() (in module pybel.struct.filters)
filter_nodes() (in module pybel.struct.filters)
first_id (pybel.manager.models.Citation attribute)
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_script() (in module pybel)
from_bel_script_url() (in module pybel)
from_biopax() (in module pybel)
from_bytes() (in module pybel)
from_cbn_jgif() (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_functions() (pybel.Pipeline static method)
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)
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_web() (in module pybel)
FUNCTION (in module pybel.constants)
function_inclusion_filter_builder() (in module pybel.struct.filters)
fusion (pybel.parser.parse_bel.BELParser attribute)
G
GENE (in module pybel.constants)
gene (pybel.parser.parse_bel.BELParser attribute)
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_cache_connection() (in module pybel.constants)
get_citation() (pybel.parser.parse_control.ControlParser method)
get_downstream_causal_subgraph() (in module pybel.struct.mutation)
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)
get_graphs_by_ids() (pybel.manager.NetworkManager method)
get_hetionet() (in module pybel)
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)
get_multi_causal_upstream() (in module pybel.struct.mutation)
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)
get_pubmed_identifiers() (in module pybel.struct.summary)
get_random_node() (in module pybel.struct.mutation)
get_random_path() (in module pybel.struct.mutation)
get_random_subgraph() (in module pybel.struct.mutation)
get_subgraph_by_all_shortest_paths() (in module pybel.struct.mutation)
get_subgraph_by_annotation_value() (in module pybel.struct.mutation)
get_subgraph_by_annotations() (in module pybel.struct.mutation)
get_subgraph_by_authors() (in module pybel.struct.mutation)
get_subgraph_by_edge_filter() (in module pybel.struct.mutation)
get_subgraph_by_induction() (in module pybel.struct.mutation)
get_subgraph_by_neighborhood() (in module pybel.struct.mutation)
get_subgraph_by_pubmed() (in module pybel.struct.mutation)
get_subgraph_by_second_neighbors() (in module pybel.struct.mutation)
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_top_hubs() (in module pybel.struct.summary)
get_top_pathologies() (in module pybel.struct.summary)
get_transformation() (in module pybel.struct.pipeline.decorators)
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)
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)
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_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_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_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_enumerated_namespace_name() (pybel.parser.parse_concept.ConceptParser method)
has_fragment() (in module pybel.struct.filters)
has_fusion (pybel.manager.models.Node attribute)
has_gene_modification() (in module pybel.struct.filters)
has_hgvs() (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_concept.ConceptParser method)
(pybel.parser.parse_metadata.MetadataParser method)
has_namespace_name() (pybel.parser.parse_concept.ConceptParser method)
has_pathology_causal() (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_regex_namespace_name() (pybel.parser.parse_concept.ConceptParser method)
HAS_VARIANT (in module pybel.constants)
has_variant() (in module pybel.struct.filters)
HASH (in module pybel.constants)
HGVS (in module pybel.constants)
I
id_in() (pybel.manager.models.Network class method)
IDENTIFIER (in module pybel.constants)
identifier (pybel.manager.models.NamespaceEntry attribute)
identifier() (pybel.language.Entity property)
IllegalAnnotationValueWarning
in_place_transformation() (in module pybel.struct.pipeline.decorators)
InconsistentDefinitionError
INCREASES (in module pybel.constants)
INDIRECT_CAUSAL_RELATIONS (in module pybel.constants)
infer_child_relations() (in module pybel.struct.mutation)
insert_into_graph() (pybel.manager.models.Edge 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_abundance() (in module pybel.struct.filters)
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_gene() (in module pybel.struct.filters)
is_isolated_list_abundance() (in module pybel.struct.filters)
is_pathology() (in module pybel.struct.filters)
is_protein() (in module pybel.struct.filters)
is_pubmed() (pybel.manager.models.Citation property)
is_subject (pybel.manager.models.Property attribute)
is_translocated() (in module pybel.struct.filters)
is_variant (pybel.manager.models.Node attribute)
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)
iterate_pubmed_identifiers() (in module pybel.struct.summary)
J
journal (pybel.manager.models.Citation attribute)
K
keep_edge_permissive() (in module pybel.struct.filters)
keep_node_permissive() (in module pybel.struct.filters)
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.manager.models.Namespace attribute)
license() (pybel.BELGraph property)
licenses (pybel.manager.models.Network attribute)
LINE (in module pybel.constants)
list_networks() (pybel.manager.NetworkManager method)
list_recent_networks() (pybel.manager.NetworkManager method)
load() (in module pybel)
(pybel.Pipeline static method)
loads() (pybel.Pipeline static method)
location (pybel.parser.parse_bel.BELParser attribute)
M
make() (pybel.parser.exc.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
miriam_id (pybel.manager.models.Namespace attribute)
MIRNA (in module pybel.constants)
mirna (pybel.parser.parse_bel.BELParser attribute)
MissingAnnotationKeyWarning
MissingAnnotationRegexWarning
MissingAnnotationWarning
MissingCitationException
MissingDefaultNameWarning
MissingMetadataException
MissingNamespaceNameWarning
MissingNamespaceRegexWarning
MissingPipelineFunctionError
MissingSupportWarning
MissingUniverseError
Modification (class in pybel.manager.models)
modifier (pybel.manager.models.Property attribute)
molecular_activity (pybel.parser.parse_bel.BELParser attribute)
N
NakedNameWarning
NAME (in module pybel.constants)
name (pybel.manager.models.Namespace attribute)
(pybel.manager.models.NamespaceEntry attribute)
(pybel.manager.models.Network attribute)
name() (pybel.BELGraph property)
(pybel.language.Entity property)
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
NameWarning
NEGATIVE_CORRELATION (in module pybel.constants)
NestedRelationWarning
Network (class in pybel.manager.models)
NetworkManager (class in pybel.manager)
NO_CORRELATION (in module pybel.constants)
Node (class in pybel.manager.models)
node_exclusion_predicate_builder() (in module pybel.struct.filters)
node_has_namespace() (pybel.BELGraph method)
node_inclusion_predicate_builder() (in module pybel.struct.filters)
node_predicate() (in module pybel.struct.filters)
node_to_bel() (pybel.BELGraph static method)
not_causal_relation() (in module pybel.struct.filters)
not_pathology() (in module pybel.struct.filters)
number_of_authors() (pybel.BELGraph method)
number_of_citations() (pybel.BELGraph method)
number_of_warnings() (pybel.BELGraph method)
O
OBJECT (in module pybel.constants)
obo() (pybel.language.Entity property)
ORTHOLOGOUS (in module pybel.constants)
P
pages (pybel.manager.models.Citation attribute)
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-post command line option
pybel-serialize command line option
pybel-summarize command line option
pybel-warnings command line option
path() (pybel.BELGraph property)
PATHOLOGY (in module pybel.constants)
pathology (pybel.parser.parse_bel.BELParser attribute)
pattern (pybel.manager.models.Namespace attribute)
Pipeline (class in pybel)
PipelineNameError
PlaceholderAminoAcidWarning
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 (in module pybel.constants)
position (pybel.manager.models.Modification attribute)
POSITIVE_CORRELATION (in module pybel.constants)
post_graphdati() (in module pybel)
post_jgif() (in module pybel)
PRODUCTS (in module pybel.constants)
PROGONSTIC_BIOMARKER_FOR (in module pybel.constants)
Property (class in pybel.manager.models)
PROTEIN (in module pybel.constants)
protein (pybel.parser.parse_bel.BELParser attribute)
prune_protein_rna_origins() (in module pybel.struct.mutation)
PSUB_POSITION (in module pybel.constants)
PSUB_REFERENCE (in module pybel.constants)
PSUB_VARIANT (in module pybel.constants)
pybel command line option
--connection <connection>
--version
-c
pybel-compile command line option
--allow-naked-names
--disallow-nested
--disallow-unqualified-translocations
--no-citation-clearing
--no-identifier-validation
--required-annotations <required_annotations>
--skip-tqdm
--upgrade-urls
--verbose
-r
-v
PATH
pybel-insert command line option
path
pybel-machine command line option
--host <host>
--local
AGENTS
pybel-manage-drop command line option
--yes
pybel-manage-edges-ls command line option
--limit <limit>
--offset <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 <namespace_id>
--url <url>
-i
-u
pybel-manage-networks-drop command line option
--network-id <network_id>
--yes
-n
-y
pybel-neo command line option
--connection <connection>
--password <password>
path
pybel-post command line option
--host <host>
path
pybel-serialize command line option
--bel <bel>
--edgelist <edgelist>
--graphml <graphml>
--gsea <gsea>
--nodelink <nodelink>
--sif <sif>
--tsv <tsv>
path
pybel-summarize command line option
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.cx (module)
pybel.io.extras (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.neo4j (module)
pybel.io.nodelink (module)
pybel.io.pynpa (module)
pybel.io.umbrella_nodelink (module)
pybel.io.web (module)
pybel.language (module)
pybel.manager.database_io (module)
pybel.manager.models (module)
pybel.parser.exc (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.grouping (module)
pybel.struct.mutation (module)
pybel.struct.pipeline.decorators (module)
pybel.struct.pipeline.exc (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_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)
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_default() (pybel.parser.parse_concept.ConceptParser 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)
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 (in module pybel.constants)
RedefinedAnnotationError
RedefinedNamespaceError
REGULATES (in module pybel.constants)
RELATION (in module pybel.constants)
relative_key (pybel.manager.models.Property attribute)
remove_annotation_value() (in module pybel.struct.mutation)
remove_associations() (in module pybel.struct.mutation)
remove_biological_processes() (in module pybel.struct.mutation)
remove_citation_metadata() (in module pybel.struct.mutation)
remove_filtered_edges() (in module pybel.struct.mutation)
remove_filtered_nodes() (in module pybel.struct.mutation)
remove_isolated_list_abundances() (in module pybel.struct.mutation)
remove_isolated_nodes() (in module pybel.struct.mutation)
remove_isolated_nodes_op() (in module pybel.struct.mutation)
remove_non_causal_edges() (in module pybel.struct.mutation)
remove_pathologies() (in module pybel.struct.mutation)
REQUIRED_METADATA (in module pybel.constants)
residue (pybel.manager.models.Modification attribute)
rev_abundance_labels (in module pybel.constants)
RNA (in module pybel.constants)
rna (pybel.parser.parse_bel.BELParser attribute)
run() (pybel.Pipeline method)
S
search_edges_with_bel() (pybel.manager.QueryManager method)
search_edges_with_evidence() (pybel.manager.QueryManager method)
side() (pybel.manager.models.Property property)
species (pybel.manager.models.Namespace attribute)
store_bel() (pybel.manager.models.Network method)
strip_annotations() (in module pybel.struct.mutation)
SUBJECT (in module pybel.constants)
SUBPROCESS_OF (in module pybel.constants)
subprocess_of (pybel.parser.parse_bel.BELParser attribute)
summarize() (pybel.BELGraph method)
summary_dict() (pybel.BELGraph method)
summary_str() (pybel.BELGraph method)
surviors_are_inconsistent() (in module pybel.struct.mutation)
T
text (pybel.manager.models.Evidence attribute)
title (pybel.manager.models.Citation attribute)
to_bel_script() (in module pybel)
to_bytes() (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_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.Modification method)
(pybel.manager.models.Namespace method)
(pybel.manager.models.NamespaceEntry method)
(pybel.manager.models.Network method)
(pybel.manager.models.Node method)
(pybel.manager.models.Property method)
(pybel.Pipeline method)
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_sif() (in module pybel)
to_tsv() (in module pybel)
to_umbrella_nodelink() (in module pybel)
to_umbrella_nodelink_file() (in module pybel)
to_umbrella_nodelink_gz() (in module pybel)
to_web() (in module pybel)
transcribed (pybel.parser.parse_bel.BELParser attribute)
TRANSCRIBED_TO (in module pybel.constants)
transformation() (in module pybel.struct.pipeline.decorators)
translated (pybel.parser.parse_bel.BELParser attribute)
TRANSLATED_TO (in module pybel.constants)
translocation (pybel.parser.parse_bel.BELParser attribute)
TRUNCATION_POSITION (in module pybel.constants)
TWO_WAY_RELATIONS (in module pybel.constants)
type (pybel.manager.models.Modification attribute)
(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)
VARIANTS (in module pybel.constants)
variantString (pybel.manager.models.Modification attribute)
version (pybel.manager.models.Namespace attribute)
(pybel.manager.models.Network attribute)
version() (pybel.BELGraph property)
VersionFormatWarning
volume (pybel.manager.models.Citation attribute)
W
warnings() (pybel.BELGraph property)
X
XREFS (in module pybel.constants)
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v: v0.14.6
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