DrugBank (indra.sources.drugbank)

This module provides an API and processor for DrugBank content. It builds on the XML-formatted data schema of DrugBank and expects the XML file to be available locally. The full DrugBank download can be obtained at: https://www.drugbank.ca/releases/latest. Once the XML file is decompressed, it can be processed using the process_xml function.

DrugBank API (indra.sources.drugbank.api)

indra.sources.drugbank.api.process_xml(fname)[source]

Return a processor by extracting Statement from DrugBank XML.

Parameters:fname (str) – The path to a DrugBank XML file to process.
Returns:A DrugbankProcessor instance which contains a list of INDRA Statements in its statements attribute that were extracted from the given XML file.
Return type:DrugbankProcessor

DrugBank Processor (indra.sources.drugbank.processor)

class indra.sources.drugbank.processor.DrugbankProcessor(xml_tree: xml.etree.ElementTree.ElementTree)[source]

Processor to extract INDRA Statements from DrugBank content.

The processor assumes that an ElementTree is available which it then traverses to find drug-target information.

Parameters:xml_tree (xml.etree.ElementTree.ElementTree) – An XML ElementTree representing DrugBank XML content.
statements

A list of INDRA Statements that were extracted from DrugBank content.

Type:list of indra.statements.Statement