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verified publisher icon EBISPOT

Add 10 drug response terms for GWAS catalog phenotypes

Open Copilot opened this issue 3 months ago • 0 comments

GWAS catalog contains 93 associations under "response to xenobiotic stimulus" where reported traits specify drugs (e.g., "Response to carboplatin in ovarian cancer") but map only to generic GO:0009410. This adds specific EFO terms to enable precise phenotype annotation.

Changes

ChEBI imports

  • Added penicillin (CHEBI:17334) and amphetamine (CHEBI:2679) to chebi_terms.txt
  • Regenerated ChEBI import with 8 drug entities

New EFO terms (EFO_0920016-0920025)

Added 10 "response to [drug]" terms:

  • Chemotherapy: carboplatin, cisplatin
  • Anti-inflammatory: mesalamine
  • Antibiotics: penicillin
  • CNS: amphetamine, zonisamide
  • Drug classes: anticoagulant, antioxidant
  • Supplements: zinc
  • Biologics: sarilumab

Each term includes:

  • Parent: GO:0009410 (response to xenobiotic stimulus)
  • Logical axiom: has_primary_input (RO:0004009) to drug entity
  • Definition with ≥2 embedded PMIDs
  • Typed synonyms (exact/related/narrow/broad)

Coverage

Addresses 20+ specific GWAS associations previously annotated only to GO:0009410, including:

  • Penicillin allergy (PheCode 960.2)
  • Mesalamine-induced diarrhea in IBD (3 associations)
  • Anticoagulant adverse effects (PheCode 964.1)
  • Antioxidant/zinc response in macular degeneration
  • Zonisamide response in Parkinson's motor symptoms

Note

tocilizumab identified in GWAS data but not added—exists in DRON which EFO doesn't currently import.

Original prompt

This section details on the original issue you should resolve

<issue_title>Add missing drug response terms for GWAS catalog</issue_title> <issue_description>Using the EBI KG MCP's gwas_traits_reported_different_from_matched tool, find GWAS associations under "response to xenobiotic stimulus" where the reported trait is a more specific drug than the mapped trait, and if the response terms for the drugs don't exist in EFO create new terms using the OLS MCP to find drugs in ChEBI (relation: has_primary_input (RO:0004009)).</issue_description>

<agent_instructions>Make sure to look carefully all terms that start with 'response to ...', and include all drugs and drug classes.</agent_instructions>

Comments on the Issue (you are @copilot in this section)

  • Fixes EBISPOT/efo#2562

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Copilot avatar Nov 21 '25 15:11 Copilot