Index

Symbols

--connection <connection> bio2bel-actions command line option bio2bel-bel-write command line option bio2bel-belns-write command line option bio2bel-drop command line option bio2bel-populate command line option bio2bel-sheet command line option bio2bel-summarize command line option bio2bel-web command line option --directory <directory> bio2bel-bel-write command line option bio2bel-belns-write command line option bio2bel-er command line option --file <file> bio2bel-sheet command line option --force bio2bel-bel-write command line option bio2bel-belns-write command line option bio2bel-populate command line option --host <host> bio2bel-web command line option --index bio2bel-sheet command line option --port <port> bio2bel-web command line option --reset bio2bel-populate command line option --skip <skip> bio2bel-bel-write command line option bio2bel-belns-write command line option bio2bel-cache-clear command line option bio2bel-drop command line option bio2bel-populate command line option bio2bel-sheet command line option bio2bel-summarize command line option

--tablefmt <tablefmt> bio2bel-sheet command line option -c bio2bel-actions command line option bio2bel-bel-write command line option bio2bel-belns-write command line option bio2bel-drop command line option bio2bel-populate command line option bio2bel-sheet command line option bio2bel-summarize command line option bio2bel-web command line option -d bio2bel-bel-write command line option bio2bel-belns-write command line option bio2bel-er command line option -f bio2bel-belns-write command line option bio2bel-sheet command line option -s bio2bel-bel-write command line option bio2bel-belns-write command line option bio2bel-cache-clear command line option bio2bel-drop command line option bio2bel-populate command line option bio2bel-sheet command line option bio2bel-summarize command line option

A

AbstractManager (class in bio2bel) AbstractTemporaryCacheClassMixin (class in bio2bel.testing)

AbstractTemporaryCacheMethodMixin (class in bio2bel.testing) Action (class in bio2bel.models) add_namespace_to_graph() (bio2bel.manager.namespace_manager.BELNamespaceManagerMixin method)

B

BELManagerMixin (class in bio2bel.manager.bel_manager) BELNamespaceManagerMixin (class in bio2bel.manager.namespace_manager) bio2bel module bio2bel-actions command line option --connection <connection> -c bio2bel-bel-write command line option --connection <connection> --directory <directory> --force --skip <skip> -c -d -s bio2bel-belns-write command line option --connection <connection> --directory <directory> --force --skip <skip> -c -d -f -s bio2bel-cache-clear command line option --skip <skip> -s bio2bel-drop command line option --connection <connection> --skip <skip> -c -s Drop all? bio2bel-er command line option --directory <directory> -d bio2bel-install command line option NAME bio2bel-populate command line option --connection <connection> --force --reset --skip <skip> -c -s

bio2bel-sheet command line option --connection <connection> --file <file> --index --skip <skip> --tablefmt <tablefmt> -c -f -s bio2bel-summarize command line option --connection <connection> --skip <skip> -c -s bio2bel-web command line option --connection <connection> --host <host> --port <port> -c bio2bel.downloading module bio2bel.io.automate module bio2bel.io.pykeen module bio2bel.models module bio2bel.sources.pid module bio2bel.sources.tfregulons module bio2bel.testing module bio2bel.utils module

C

clear_cache() (in module bio2bel.utils) connection() (bio2bel.AbstractManager property) count() (bio2bel.models.Action class method)

count_relations() (bio2bel.manager.bel_manager.BELManagerMixin method) create_all() (bio2bel.AbstractManager method) (in module bio2bel.models) created (bio2bel.models.Action attribute)

D

Drop all? bio2bel-drop command line option

drop_all() (bio2bel.AbstractManager method) drop_bel_namespace() (bio2bel.manager.namespace_manager.BELNamespaceManagerMixin method)

E

enrich_graph() (in module bio2bel.sources.tfregulons) ensure_bio2bel_installation() (in module bio2bel.io.automate) ensure_graph() (in module bio2bel.io.automate)

ensure_path() (in module bio2bel.utils) ensure_triples() (in module bio2bel.io.pykeen) ensure_tsv() (in module bio2bel.io.automate) entrez_id (bio2bel.sources.pid.Protein attribute)

F

flask_admin_models (bio2bel.manager.flask_manager.FlaskMixin attribute)

FlaskMixin (class in bio2bel.manager.flask_manager)

G

get_bel() (in module bio2bel.sources.tfregulons) get_bio2bel_modules() (in module bio2bel.utils) get_cli() (bio2bel.AbstractManager class method) (bio2bel.manager.bel_manager.BELManagerMixin class method) (bio2bel.manager.flask_manager.FlaskMixin class method) (bio2bel.manager.namespace_manager.BELNamespaceManagerMixin class method) get_connection() (in module bio2bel.utils)

get_data_dir() (in module bio2bel.utils) get_df() (in module bio2bel.sources.tfregulons) get_flask_admin_app() (bio2bel.manager.flask_manager.FlaskMixin method) get_graph_from_cx() (in module bio2bel.sources.pid) get_hgnc_ids() (in module bio2bel.sources.tfregulons) get_namespace_hash() (bio2bel.manager.namespace_manager.BELNamespaceManagerMixin method) get_url_filename() (in module bio2bel.utils)

H

has_names (bio2bel.manager.namespace_manager.BELNamespaceManagerMixin attribute)

hgnc_id (bio2bel.sources.pid.Protein attribute) hgnc_symbol (bio2bel.sources.pid.Protein attribute)

I

identifier (bio2bel.sources.pid.Pathway attribute)

is_populated() (bio2bel.AbstractManager method) iterate_graphs() (in module bio2bel.sources.pid)

L

ls() (bio2bel.models.Action class method)

M

make_df_getter() (in module bio2bel.downloading) make_downloader() (in module bio2bel.downloading) make_drop() (bio2bel.models.Action static method) make_json_getter() (in module bio2bel.downloading) make_populate() (bio2bel.models.Action static method) make_populate_failed() (bio2bel.models.Action static method) make_temporary_cache_class_mixin() (in module bio2bel.testing) make_zipped_df_getter() (in module bio2bel.downloading) Manager (class in bio2bel.sources.pid) MockConnectionMixin (class in bio2bel.testing)

module bio2bel bio2bel.downloading bio2bel.io.automate bio2bel.io.pykeen bio2bel.models bio2bel.sources.pid bio2bel.sources.tfregulons bio2bel.testing bio2bel.utils

N

NAME bio2bel-install command line option

name (bio2bel.sources.pid.Pathway attribute) namespace_model (bio2bel.sources.pid.Manager attribute)

P

Pathway (class in bio2bel.sources.pid) pathway_model (bio2bel.sources.pid.Manager attribute) populate() (bio2bel.AbstractManager method) (bio2bel.sources.pid.Manager method) (bio2bel.testing.AbstractTemporaryCacheClassMixin class method) (bio2bel.testing.AbstractTemporaryCacheMethodMixin method)

prefix_directory_join() (in module bio2bel.utils) Protein (class in bio2bel.sources.pid) protein_model (bio2bel.sources.pid.Manager attribute)

R

resource (bio2bel.models.Action attribute)

S

setUp() (bio2bel.testing.AbstractTemporaryCacheMethodMixin method) (bio2bel.testing.MockConnectionMixin method) (bio2bel.testing.TemporaryConnectionMethodMixin method) setUpClass() (bio2bel.testing.AbstractTemporaryCacheClassMixin class method) (bio2bel.testing.TemporaryConnectionMixin class method)

store_drop() (bio2bel.models.Action class method) store_populate() (bio2bel.models.Action class method) store_populate_failed() (bio2bel.models.Action class method) summarize() (bio2bel.AbstractManager method)

T

tearDown() (bio2bel.testing.AbstractTemporaryCacheMethodMixin method) (bio2bel.testing.TemporaryConnectionMethodMixin method) tearDownClass() (bio2bel.testing.AbstractTemporaryCacheClassMixin class method) (bio2bel.testing.TemporaryConnectionMixin class method)

TemporaryConnectionMethodMixin (class in bio2bel.testing) TemporaryConnectionMixin (class in bio2bel.testing) to_bel() (bio2bel.manager.bel_manager.BELManagerMixin method) to_indra_statements() (bio2bel.manager.bel_manager.BELManagerMixin method) to_pybel() (bio2bel.sources.pid.Protein method)

U

upload_bel_namespace() (bio2bel.manager.namespace_manager.BELNamespaceManagerMixin method)

W

write_bel_annotation() (bio2bel.manager.namespace_manager.BELNamespaceManagerMixin method) write_bel_namespace() (bio2bel.manager.namespace_manager.BELNamespaceManagerMixin method)

write_bel_namespace_mappings() (bio2bel.manager.namespace_manager.BELNamespaceManagerMixin method) write_directory() (bio2bel.manager.namespace_manager.BELNamespaceManagerMixin method)