ACSN Database (indra.sources.acsn)

This module implements an API and processor for the ACSN resource which is available at https://acsn.curie.fr/ACSN2/ACSN2.html.

ACSN API (indra.sources.acsn.api)

indra.sources.acsn.api.process_df(relations_df, correspondence_dict)[source]

Process ACSN data from input data structures.

Parameters

  • relations_df (DataFrame) – An ACSN tab-separated data frame which consists of binary relationships between proteins with PMIDs.

  • correspondence_dict (Mapping) – A dictionary with correspondences between ACSN entities and their HGNC symbols.

Return type

AcsnProcessor

Returns

A processor with a list of INDRA statements that were extracted in its statements attribute.

indra.sources.acsn.api.process_files(relations_path, correspondence_path)[source]

Process ACSN data from input files.

Parameters

  • relations_path (str) – Path to the ACSN binary relations file.

  • correspondence_path (str) – Path to the ACSN correspondence GMT file.

Return type

AcsnProcessor

Returns

A processor with a list of INDRA statements that were extracted in its statements attribute.

indra.sources.acsn.api.process_from_web()[source]

Process ACSN data directly from the web.

Return type

AcsnProcessor

Returns

A processor with a list of INDRA statements that were extracted in its statements attribute.

ACSN Processor (indra.sources.acsn.processor)

class indra.sources.acsn.processor.AcsnProcessor(relations_df, correspondence_dict)[source]

Processes Atlas of cancer signalling network (ACSN) relationships into INDRA statements

relations_df

A tab-separated data frame which consists of binary relationship between proteins with PMIDs.

Type

pandas.DataFrame

correspondence_dict

A dictionary with correspondences between ACSN entities and their HGNC symbols.

Type

dict

extract_statements()[source]

Return INDRA Statements Extracted from ACSN relations.

get_agent(acsn_agent)[source]

Return an INDRA Agent corresponding to an ACSN agent.

Parameters

acsn_agent (str) – Agent extracted from the relations statement data frame

Return type

Optional[Agent]

Returns

Returns INDRA agent with HGNC or FamPlex ID in db_refs. If there are no groundings available, we return None.

indra.sources.acsn.processor.get_stmt_type(stmt_type)[source]

Return INDRA statement type from ACSN relation.

Parameters

stmt_type (str) – An ACSN relationship type

Return type

Optional[Statement]

Returns

INDRA equivalent of the ACSN relation type or None if a mappings is not available.