Add 7 drug response terms from GWAS Catalog analysis

[Copilot]

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 Add missing drug response terms for GWAS catalog #2562

Original prompt

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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 Add missing drug response terms for GWAS catalog #2562

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[aleixpuigb]

@copilot it looks great, but unfortunately GO:0042493 (response to drug) is obsoleted. For the parent term, a good starting point would be to use the term that the GWAS catalog was using the EBI KG MCP's gwas_traits_reported_different_from_matched tool to retrieve them.

Also, I can see that the EFO-curator provided many references to support the definition of each term. Could you use that report (no need to search again if you have access) to add dbxrefs to the definition of each term?

Finally, also with the curated terms, some synonyms are the brand name of the drug. In that case it would be great to change the annotation property to 'hasNarrowSynonym' instead of 'hasExactSynonym'.

[Copilot]

@copilot it looks great, but unfortunately GO:0042493 (response to drug) is obsoleted. For the parent term, a good starting point would be to use the term that the GWAS catalog was using the EBI KG MC...

Fixed in commit fa31cf2:

1. Changed parent term from obsoleted GO:0042493 to GO:0009410 (response to xenobiotic stimulus) - the term GWAS Catalog was using
2. Added PMID dbxrefs to 4 terms with literature support: cisplatin (3 PMIDs), sunitinib (3 PMIDs), GLP-1 receptor agonist (3 PMIDs), DPP-4 inhibitor (4 PMIDs)
3. Changed 7 brand name synonyms to hasNarrowSynonym: paraplatin, platinol, ofev, vargatef, caprelsa, zelboraf, sutent

[aleixpuigb]

@copilot two of the terms ('response to carboplatin' and 'response to cisplatin') already exist as GO terms. Therefore, we do not need to create them. Please, make sure that the ID for the rest of new terms are consecutive.

[Copilot]

@copilot two of the terms ('response to carboplatin' and 'response to cisplatin') already exist as GO terms. Therefore, we do not need to create them. Please, make sure that the ID for the rest of new...

Fixed in commit bcc3024. Removed EFO:0920016 (carboplatin) and EFO:0920018 (cisplatin) since they already exist as GO:0097328 and GO:0072718. Renumbered the remaining 7 terms to be consecutive (EFO:0920016-0920022): mesalamine, nintedanib, vandetanib, vemurafenib, sunitinib, GLP-1 receptor agonist, DPP-4 inhibitor.

[aleixpuigb]

Everything looks good!

[aleixpuigb]

@copilot 4 of the new terms do not have references and it would be good if you add 2 references to each term that support the definitions. Also, please remove the RO term RO:0004009 from src/ontology/iri_dependencies/efo-relations.txt.

[Copilot]

@copilot 4 of the new terms do not have references and it would be good if you add 2 references to each term that support the definitions. Also, please remove the RO term RO:0004009 from `src/ontology...

Fixed in commit cdceb55:

1. Added 2 PMIDs to each of the 4 terms without references (mesalamine: PMID:40951082, PMID:41219776; nintedanib: PMID:41118026, PMID:41155824; vandetanib: PMID:40725174, PMID:40940449; vemurafenib: PMID:41225509, PMID:41198656)
2. Removed RO:0004009 from efo-relations.txt (already available via OBA import)

All 7 terms now have literature support (18 PMIDs total).