DrugBank_parse

Get information on drugs, targets and indications in DrugBank from downloaded XML file. Inspired by https://github.com/Deshan-Zhou/deal_DrugBank.

Folder Description

• v1: An early version with fast parsing speed but obscure code.
• v2: Improved legibility, but slower file processing.
• vR: R version, much slower than the python version (about 25 times) and takes up very little memory (about 20M) during runtime.
• dev: Development version, using the lxml library to rewrite the parsing logic. Not finished yet.

File Description

• DrugBank_parse.py: This script implements a class to parse the xml file downloaded from DrugBank to obtain DrugID, DrugName, DrugInChI, TargetID, GeneName, Indications and their mapping relationship.
• DrugBank_TDI.R: This script is used to obtain the final target_drug_indication form of DrugBank.
• test-database.xml: A small test xml file containing the first drug of the xml file provided by the drugbank database.

You can get the xml file on https://go.drugbank.com/releases/latest. The current code has tested on release v5.1.12.

Detailed introductions can be found in the comments at the beginning of these scripts.

dev log

The dev script currantly extract the following info:

• All Drugs: list[dict]
  • DrugBankID: list[string] - The primary DrugBank identifier for the drug.
  • DrugName: list[string] - The name of the drug.
  • Description: list[string] - A description of the drug.
  • DrugReferences: list[dict]
    • PMID: string - PubMed ID of the reference.
    • Citation: string - Citation text.
  • Indication: list[string] - The indication or medical use of the drug.
  • DrugInteractions: list[dict]
    • InteractionDrugBankID: string - DrugBank ID of the interacting drug.
    • InteractionDrugName: string - Name of the interacting drug.
    • InteractionDescription: string - Description of the drug interaction.
  • CalculatedProperties: list[dict]
    • CalculatedPropertyKind: string - The kind of calculated property (e.g., logP, molecular weight).
    • CalculatedPropertyValue: string - The value of the calculated property.
    • CalculatedPropertySource: string - The source of the calculated property.
  • DrugExIdentifiers: list[dict]
    • Resource: string - The resource name of the external identifier (e.g., UniProt, GenBank).
    • Identifier: string - The external identifier value.
  • SNP: list[dict]
    • ProteinName: string - Name of the protein affected by the SNP.
    • GeneSymbol: string - Gene symbol associated with the SNP.
    • UniProtID: string - UniProt ID associated with the SNP.
    • RsID: string - Reference SNP ID.
    • DefiningChange: string - The defining change of the SNP.
    • Description: string - Description of the SNP effect.
    • PMID: string - PubMed ID associated with the SNP effect.
  • Targets: list[dict]
    • ID: string - The DrugBank ID of the target.
    • Name: string - Name of the target.
    • Organism: string - Organism in which the target is found.
    • Actions: list[string] - List of actions of the drug on the target (e.g., inhibitor, agonist).
    • References: list[dict]
      • PMID: string - PubMed ID of the reference.
      • Citation: string - Citation text.
    • Function: string - General function of the target protein.
    • FunctionDetails: string - Specific function of the target protein.
    • Chr: string - Chromosome location.
    • Locus: string - Locus of the gene.
    • Identifiers: list[dict]
      • Resource: string - The resource name of the external identifier.
      • Identifier: string - The external identifier value.
    • AminoAcidSequence: string - Amino acid sequence of the target protein.
    • GeneSequence: string - Gene sequence associated with the target.
    • Pfams: list[dict]
      • Identifier: string - Pfam identifier.
      • Name: string - Pfam name.
    • GO: list[dict]
      • Category: string - GO category (component, function, process).
      • Description: string - GO description.