BEL (indra.sources.bel
)
BEL API (indra.sources.bel.api
)
High level API functions for the PyBEL processor.
- indra.sources.bel.api.process_bel_stmt(bel, squeeze=False)[source]
Process a single BEL statement and return the PybelProcessor or a single statement if
squeeze
is True.- Parameters
- Returns
statements – A list of INDRA statments derived from the BEL statement. If squeeze is true and there was only one statement, the unpacked INDRA statement will be returned.
- Return type
Union[Statement, PybelProcessor]
Examples
>>> from indra.sources.bel import process_bel_stmt >>> bel_s = 'kin(p(FPLX:MEK)) -> kin(p(FPLX:ERK))' >>> process_bel_stmt(bel_s, squeeze=True) Activation(MEK(kinase), ERK(), kinase)
- indra.sources.bel.api.process_belscript(file_name, **kwargs)[source]
Return a PybelProcessor by processing a BEL script file.
Key word arguments are passed directly to pybel.from_path, for further information, see pybel.readthedocs.io/en/latest/io.html#pybel.from_path Some keyword arguments we use here differ from the defaults of PyBEL, namely we set citation_clearing to False and no_identifier_validation to True.
- Parameters
file_name (str) – The path to a BEL script file.
- Returns
bp – A PybelProcessor object which contains INDRA Statements in bp.statements.
- Return type
- indra.sources.bel.api.process_cbn_jgif_file(file_name)[source]
Return a PybelProcessor by processing a CBN JGIF JSON file.
- Parameters
file_name (str) – The path to a CBN JGIF JSON file.
- Returns
bp – A PybelProcessor object which contains INDRA Statements in bp.statements.
- Return type
- indra.sources.bel.api.process_json_file(file_name)[source]
Return a PybelProcessor by processing a Node-Link JSON file.
For more information on this format, see: http://pybel.readthedocs.io/en/latest/io.html#node-link-json
- Parameters
file_name (str) – The path to a Node-Link JSON file.
- Returns
bp – A PybelProcessor object which contains INDRA Statements in bp.statements.
- Return type
- indra.sources.bel.api.process_large_corpus()[source]
Return PybelProcessor with statements from Selventa Large Corpus.
- Returns
bp – A PybelProcessor object which contains INDRA Statements in its statements attribute.
- Return type
- indra.sources.bel.api.process_pybel_graph(graph)[source]
Return a PybelProcessor by processing a PyBEL graph.
- Parameters
graph (pybel.struct.BELGraph) – A PyBEL graph to process
- Returns
bp – A PybelProcessor object which contains INDRA Statements in bp.statements.
- Return type
- indra.sources.bel.api.process_pybel_neighborhood(entity_names, network_type='graph_jsongz_url', network_file=None, **kwargs)[source]
Return PybelProcessor around neighborhood of given genes in a network.
This function processes the given network file and filters the returned Statements to ones that contain genes in the given list.
- Parameters
entity_names (list[str]) – A list of entity names (e.g., gene names) which will be used as the basis of filtering the result. If any of the Agents of an extracted INDRA Statement has a name appearing in this list, the Statement is retained in the result.
network_type (Optional[str]) – The type of network that network_file is. The options are: belscript, json, cbn_jgif, graph_pickle, and graph_jsongz_url. Default: graph_jsongz_url
network_file (Optional[str]) – Path to the network file/URL to process. If not given, by default, the Selventa Large Corpus is used via a URL pointing to a gzipped PyBEL Graph JSON file.
- Returns
bp – A PybelProcessor object which contains INDRA Statements in bp.statements.
- Return type
- indra.sources.bel.api.process_pybel_network(network_type, network_file, **kwargs)[source]
Return PybelProcessor by processing a given network file.
- Parameters
- Returns
bp – A PybelProcessor object which contains INDRA Statements in bp.statements.
- Return type
PyBEL Processor (indra.sources.bel.processor
)
Processor for PyBEL.
- class indra.sources.bel.processor.PybelProcessor(graph)[source]
Extract INDRA Statements from a PyBEL Graph.
Currently does not handle non-causal relationships (positiveCorrelation, (negativeCorrelation, hasVariant, etc.)
- Parameters
graph (pybel.BELGraph) – PyBEL graph containing the BEL content.