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CTD Python

Pyhton interface to access data from The Comparative Toxicogenomics Database (CTD)

install

pip3 install ctd-python

import the package in order to pull the data

from ctd import get_data

The package offers the following resources as DataFrames

  • GeneInteractionTypes
  • ChemicalPathwaysEnriched
  • GeneDisease
  • GenePathways
  • DiseasePathways
  • ChemocalPhenoTypeInteractions
  • Chemicals
  • Genes
  • ChemicalGeneInteractions
  • Chemicals
  • Diseases

Get the Gene Information for TNF

gene_df = get_data('Genes')
tnf_df = gene_df[gene_df['GeneSymbol'] == 'TNF']

Get Chemical Interactions for TNF

chem_gene_df = get_data('ChemicalGeneInteractions')
tnf_chem_df = chem_gene_df[chem_gene_df['GeneSymbol'] == 'TNF']

Get Disease Hierarchy for Parkinson Disease

child_diseases = get_disease_hierarchy('MESH:D010300')