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verified publisher icon EBISPOT

Add 7 drug response terms from GWAS Catalog analysis

Open Copilot opened this issue 3 months ago • 6 comments

GWAS Catalog contains associations where reported traits mention specific drugs (e.g., "response to mesalamine") but are mapped to generic parent terms like "response to xenobiotic stimulus". This adds precise drug response terms to enable accurate trait annotation.

Changes

New Terms (7)

  • 5 individual drugs: mesalamine, nintedanib, vandetanib, vemurafenib, sunitinib
  • 2 drug classes: GLP-1 receptor agonist, DPP-4 inhibitor
  • IDs: EFO:0920016-0920022
  • Parent: GO:0009410 (response to xenobiotic stimulus)
  • Relationship: has_primary_input (RO:0004009) → ChEBI entity

Terms Not Created (already exist in GO)

  • GO:0097328 (response to carboplatin) - existing GO term
  • GO:0072718 (response to cisplatin) - existing GO term

ChEBI Imports

  • Added 5 new: nintedanib, vandetanib, vemurafenib, GLP-1 receptor agonist, DPP-4 inhibitor
  • Verified 2 existing: mesalamine, sunitinib

Metadata

  • Literature support: ALL 7 terms include PMID dbxrefs (18 PMIDs total)
  • Synonyms: Chemical names and abbreviations use hasExactSynonym; brand names use hasNarrowSynonym

Source Identified via EBI Knowledge Graph query filtering GWAS associations under GO:0009410 where reported trait was more specific than mapped trait (93 associations analyzed).

Each term includes mechanism-based definition, clinical context, appropriately typed synonyms, and literature references.

  • Fixes EBISPOT/efo#2562
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>

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

  • Fixes EBISPOT/efo#2562

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Copilot avatar Nov 20 '25 11:11 Copilot