pybel.io
pybel.load
pybel.dump
The PyBEL parser has several modes that can be enabled and disabled. They are described below.
By default, this is set to False. The parser does not allow identifiers that are not qualified with namespaces (naked names), like in p(YFG). A proper namespace, like p(HGNC:YFG) must be used. By setting this to True, the parser becomes permissive to naked names. In general, this is bad practice and this feature will be removed in the future.
By default, this is set to False. The parser does not allow nested statements is disabled. See overview. By setting this to True the parser will accept nested statements one level deep.
By default, this is set to True. While the BEL specification clearly states how the language should be used as a state machine, many BEL documents do not conform to the strict SET/UNSET rules. To guard against annotations accidentally carried from one set of statements to the next, the parser has two modes. By default, in citation clearing mode, when a SET CITATION command is reached, it will clear all other annotations (except the STATEMENT_GROUP, which has higher priority). This behavior can be disabled by setting this to False to re-enable strict parsing.
pybel.from_bel_script
pybel.from_bel_script_url
pybel.to_bel_script
pybel.io.hetionet
pybel.from_hetionet_json
pybel.from_hetionet_file
pybel.from_hetionet_gz
pybel.get_hetionet
All transport pairs are reflective and data-preserving.
pybel.io.gpickle
pybel.from_bytes
pybel.to_bytes
pybel.from_bytes_gz
pybel.to_bytes_gz
pybel.from_pickle
pybel.to_pickle
pybel.from_pickle_gz
pybel.to_pickle_gz
pybel.io.nodelink
pybel.from_nodelink
pybel.to_nodelink
pybel.from_nodelink_jsons
pybel.to_nodelink_jsons
pybel.from_nodelink_file
pybel.to_nodelink_file
pybel.from_nodelink_gz
pybel.to_nodelink_gz
pybel.io.sbel
pybel.from_sbel
pybel.to_sbel
pybel.from_sbel_file
pybel.to_sbel_file
pybel.from_sbel_gz
pybel.to_sbel_gz
pybel.io.cx
pybel.from_cx
pybel.to_cx
pybel.from_cx_jsons
pybel.to_cx_jsons
pybel.from_cx_file
pybel.to_cx_file
pybel.from_cx_gz
pybel.to_cx_gz
pybel.io.jgif
pybel.from_jgif
pybel.to_jgif
pybel.from_jgif_jsons
pybel.to_jgif_jsons
pybel.from_jgif_file
pybel.to_jgif_file
pybel.from_jgif_gz
pybel.to_jgif_gz
pybel.post_jgif
pybel.from_cbn_jgif
pybel.from_cbn_jgif_file
pybel.io.graphdati
pybel.to_graphdati
pybel.from_graphdati
pybel.to_graphdati_file
pybel.from_graphdati_file
pybel.to_graphdati_gz
pybel.from_graphdati_gz
pybel.to_graphdati_jsons
pybel.from_graphdati_jsons
pybel.to_graphdati_jsonl
pybel.to_graphdati_jsonl_gz
pybel.io.indra
pybel.from_indra_statements
pybel.from_indra_statements_json
pybel.from_indra_statements_json_file
pybel.to_indra_statements
pybel.to_indra_statements_json
pybel.to_indra_statements_json_file
pybel.from_biopax
pybel.io.jupyter
pybel.to_jupyter
pybel.io.pynpa
pybel.to_npa_directory
pybel.to_npa_dfs
pybel.io.hipathia
pybel.to_hipathia
pybel.to_hipathia_dfs
pybel.from_hipathia_paths
pybel.from_hipathia_dfs
pybel.io.spia
pybel.to_spia_dfs
pybel.to_spia_excel
pybel.to_spia_tsvs
pybel.io.pykeen
pybel.io.pykeen.get_triples_from_bel
pybel.io.pykeen.get_triples_from_bel_nodelink
pybel.io.pykeen.get_triples_from_bel_pickle
pybel.io.pykeen.get_triples_from_bel_commons
pybel.io.triples
pybel.to_triples
pybel.to_triples_file
pybel.to_edgelist
pybel.io.bel_commons_client
pybel.from_bel_commons
pybel.to_bel_commons
pybel.io.aws
pybel.to_s3
pybel.from_s3
pybel.io.biodati_client
pybel.to_biodati
pybel.from_biodati
pybel.io.fraunhofer_orientdb
pybel.from_fraunhofer_orientdb
pybel.io.emmaa
pybel.from_emmaa
pybel.manager.database_io
pybel.from_database
pybel.to_database
pybel.io.neo4j
pybel.to_neo4j
pybel.io.umbrella_nodelink
pybel.to_umbrella_nodelink
pybel.to_umbrella_nodelink_file
pybel.to_umbrella_nodelink_gz
pybel.io.graphml
pybel.to_graphml
pybel.io.extras
pybel.to_csv
pybel.to_sif
pybel.to_gsea