PyBEL
v0.14.9
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 Domain Specific Language
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 (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_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)
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)
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)
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)
BiologicalProcess (class in pybel.dsl)
BIOMARKER_FOR (in module pybel.constants)
BIOPROCESS (in module pybel.constants)
blob (pybel.manager.models.Network attribute)
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)
CentralDogma (class in pybel.dsl)
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)
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)
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_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)
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_to_bel() (pybel.BELGraph static method)
encoding (pybel.manager.models.NamespaceEntry attribute)
ensure_node() (pybel.parser.parse_bel.BELParser method)
Entity (class in pybel.dsl)
(class in pybel.language)
EnumeratedFusionRange (class in pybel.dsl)
EQUIVALENT_TO (in module pybel.constants)
Evidence (class in pybel.manager.models)
EVIDENCE (in module pybel.constants)
extend() (pybel.Pipeline method)
F
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_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_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)
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)
FUNCTION (in module pybel.constants)
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_citation() (pybel.parser.parse_control.ControlParser method)
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_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_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_pubmed_identifiers() (in module pybel.struct.summary)
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)
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_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_annotation() (pybel.parser.parse_control.ControlParser method)
(pybel.parser.parse_metadata.MetadataParser method)
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_fusion (pybel.manager.models.Node attribute)
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_PRODUCT (in module pybel.constants)
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)
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.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)
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)
IS_A (in module pybel.constants)
is_enriched() (pybel.manager.models.Citation property)
is_pubmed() (pybel.manager.models.Citation property)
is_subject (pybel.manager.models.Property attribute)
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
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)
ListAbundance (class in pybel.dsl)
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
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
Modification (class in pybel.manager.models)
modifier (pybel.manager.models.Property attribute)
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.bel_commons_client
pybel.io.biodati_client
pybel.io.cx
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.pynpa
pybel.io.spia
pybel.io.tsv
pybel.io.umbrella_nodelink
pybel.language
pybel.manager.database_io
pybel.manager.models
pybel.parser.exc
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.grouping
pybel.struct.mutation
pybel.struct.pipeline.decorators
pybel.struct.pipeline.exc
pybel.struct.summary
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_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_has_namespace() (pybel.BELGraph method)
node_to_bel() (pybel.BELGraph static method)
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_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 (class in pybel.dsl)
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 (class in pybel.dsl)
POPULATION (in module pybel.constants)
position (pybel.manager.models.Modification attribute)
POSITIVE_CORRELATION (in module pybel.constants)
post_jgif() (in module pybel)
PRODUCTS (in module pybel.constants)
PROGONSTIC_BIOMARKER_FOR (in module pybel.constants)
Property (class in pybel.manager.models)
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)
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.bel_commons_client
module
pybel.io.biodati_client
module
pybel.io.cx
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.pynpa
module
pybel.io.spia
module
pybel.io.tsv
module
pybel.io.umbrella_nodelink
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_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 (class in pybel.dsl)
REACTION (in module pybel.constants)
RedefinedAnnotationError
RedefinedNamespaceError
REGULATES (in module pybel.constants)
RELATION (in module pybel.constants)
relative_key (pybel.manager.models.Property attribute)
REQUIRED_METADATA (in module pybel.constants)
residue (pybel.manager.models.Modification attribute)
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)
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)
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)
T
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_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.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_jupyter() (in module pybel.io.jupyter)
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_spia_dfs() (in module pybel)
to_spia_excel() (in module pybel)
to_spia_tsvs() (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)
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)
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)
Variant (class in pybel.dsl)
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: v0.14.9
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