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parse_interactions.py — extracts drug-drug interactions and SNP data.
Tables populated:
drug_interactions — directed DDI edges (both A→B and B→A preserved; descriptions differ)
drug_snp_data — SNP pharmacogenomic effects + SNP adverse reactions (merged with snp_type)
"""
from config import NP
from utils import t, clean
def extract(drug_el, primary_id, state):
return {
"drug_interactions": _drug_interactions(drug_el, primary_id),
"drug_snp_data": _snp_data(drug_el, primary_id),
}
# ── drug_interactions ─────────────────────────────────────────────────────────
def _drug_interactions(drug_el, primary_id):
rows = []
ddi_el = drug_el.find(f"{NP}drug-interactions")
if ddi_el is None:
return rows
for ddi in ddi_el.findall(f"{NP}drug-interaction"):
other_id = t(ddi, "drugbank-id")
if other_id:
rows.append({
"drugbank_id": primary_id,
"interacting_drugbank_id": other_id,
"description": t(ddi, "description"),
})
return rows
# ── drug_snp_data (effects + adverse reactions merged) ────────────────────────
def _snp_data(drug_el, primary_id):
rows = []
# SNP effects
snp_eff = drug_el.find(f"{NP}snp-effects")
if snp_eff is not None:
for eff in snp_eff.findall(f"{NP}effect"):
rows.append({
"drugbank_id": primary_id,
"snp_type": "effect",
"protein_name": t(eff, "protein-name"),
"gene_symbol": t(eff, "gene-symbol"),
"uniprot_id": t(eff, "uniprot-id"),
"rs_id": t(eff, "rs-id"),
"allele": t(eff, "allele"),
"defining_change": t(eff, "defining-change"),
"adverse_reaction": None,
"description": t(eff, "description"),
"pubmed_id": t(eff, "pubmed-id"),
})
# SNP adverse drug reactions
snp_adr = drug_el.find(f"{NP}snp-adverse-drug-reactions")
if snp_adr is not None:
for rxn in snp_adr.findall(f"{NP}reaction"):
rows.append({
"drugbank_id": primary_id,
"snp_type": "adverse_reaction",
"protein_name": t(rxn, "protein-name"),
"gene_symbol": t(rxn, "gene-symbol"),
"uniprot_id": t(rxn, "uniprot-id"),
"rs_id": t(rxn, "rs-id"),
"allele": t(rxn, "allele"),
"defining_change": None,
"adverse_reaction": t(rxn, "adverse-reaction"),
"description": t(rxn, "description"),
"pubmed_id": t(rxn, "pubmed-id"),
})
return rows
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