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')