Biofactoid (indra.sources.biofactoid)

This module implements an interface to Biofactoid (https://biofactoid.org/) which contains interactions curated from publications by authors. Documents are retrieved from the web and processed into INDRA Statements.

Biofactoid API (indra.sources.biofactoid.api)

indra.sources.biofactoid.api.process_from_web(url=None)

Process BioFactoid documents from the web.

Parameters

url (Optional[str]) – The URL for the web service endpoint which contains all the document data.

Returns

A processor which contains extracted INDRA Statements in its statements attribute.

Return type

BioFactoidProcessor

indra.sources.biofactoid.api.process_json(biofactoid_json)

Process BioFactoid JSON.

Parameters

biofactoid_json (json) – The BioFactoid JSON object to process.

Returns

A processor which contains extracted INDRA Statements in its statements attribute.

Return type

BioFactoidProcessor

Biofactoid Processor (indra.sources.biofactoid.processor)

class indra.sources.biofactoid.processor.BioFactoidProcessor(biofactoid_json)

Processor which extracts INDRA Statements from BioFactoid JSON.

Parameters

biofactoid_json (json) – BioFactoid JSON to process.

statements

A list of INDRA Statements extracted from the BioFactoid JSON.

Type

list[indra.statements.Statement]