Term merge: GO:0061502 early endosome to recycling endosome transport

[dragon-ai-agent]

Shadow ticket of geneontology/go-ontology#31240

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• Term to be merged: Provide GO ID and term label

GO:0061502 early endosome to recycling endosome transport
The directed movement of substances, in membrane-bounded vesicles, from the early sorting endosomes to the recycling endosomes.

5 EXP annotations

• Which term do you propose this term merge into? Provide GO ID and term label

GO:0032456 endocytic recycling
The directed movement of membrane-bounded vesicles from endosomes back to the plasma membrane, a trafficking pathway that promotes the recycling of internalized transmembrane proteins

• Reason for merge

GO:0032456 endocytic recycling represents the pathway.

GO:0061502 describes the same pathway by vesicle type

• Reference(s)
  PMID:nnnnnn

• Any other information

[cmungall]

@dragon-ai-agent please analyze and implement

[dragon-ai-agent]

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[dragon-ai-agent]

Analysis of Term Merge Request: GO:0061502 → GO:0032456

Summary of Terms

Source (to be obsoleted): GO:0061502 "early endosome to recycling endosome transport"

• Definition: "The directed movement of substances, in membrane-bounded vesicles, from the early sorting endosomes to the recycling endosomes."
• Logical definition:
  • intersection_of: GO:0016192 ! vesicle-mediated transport
  • intersection_of: has_target_end_location GO:0055037 ! recycling endosome
  • intersection_of: has_target_start_location GO:0005769 ! early endosome
  • intersection_of: occurs_in GO:0005737 ! cytoplasm
• 5 EXP annotations (PMIDs: 20026645, 24270184, 11208135)

Target (merge into): GO:0032456 "endocytic recycling"

• Definition: "The directed movement of membrane-bounded vesicles from endosomes back to the plasma membrane, a trafficking pathway that promotes the recycling of internalized transmembrane proteins."
• Logical definition:
  • is_a: GO:0016197 ! endosomal transport
  • intersection_of: has_target_end_location GO:0005886 ! plasma membrane
  • intersection_of: has_target_start_location GO:0005768 ! endosome
• Children: GO:0032457 (fast endocytic recycling), GO:0032458 (slow endocytic recycling)

Terms Affected by This Merge

Regulatory terms that would also need to be obsoleted/merged:

1. GO:1902954 - regulation of early endosome to recycling endosome transport
2. GO:1902955 - positive regulation of early endosome to recycling endosome transport

These would need to merge with:

1. GO:2001135 - regulation of endocytic recycling
2. GO:2001137 - positive regulation of endocytic recycling

Analysis

⚠️ Concerns About This Merge

The two terms describe different biological processes with different endpoints:

Aspect	GO:0061502	GO:0032456
Start location	Early endosome	Endosome (general)
End location	Recycling endosome	Plasma membrane
Scope	Specific intracellular step	Complete recycling pathway

The key issue is that GO:0061502 describes transport TO the recycling endosome, while GO:0032456 describes transport FROM endosomes back TO the plasma membrane. These are sequential steps in the recycling pathway, not the same process.

Potential Information Loss

1. Mechanistic specificity - The 5 experimental annotations specifically support the early endosome → recycling endosome step, not the complete pathway to plasma membrane
2. Distinct biological concept - The recycling endosome is a distinct compartment; transport to it vs from it represents different machinery

Recommendation

🔴 I recommend AGAINST this merge because the terms describe distinct biological processes with different target locations.

Alternative suggestions:

1. Add a relationship instead: GO:0061502 part_of GO:0032456 - this would capture that early endosome to recycling endosome transport is part of the overall endocytic recycling pathway
2. Keep both terms with improved definitions clarifying their scope

However, if the curators determine that for annotation purposes these should be merged, I am prepared to implement the obsoletion. Please advise on how you would like to proceed.

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• Agent harness: claude-code
• Triggered by: @cmungall
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[cmungall]

@dragon-ai-agent please do this again. I closed the first PR as it was accidentally using old agent instructions

[dragon-ai-agent]

🤖 Working on it...

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— @dragon-ai-agent

[dragon-ai-agent]

Term Merge Implementation Complete

I've implemented the requested term merge for issue geneontology/go-ontology#31240.

Terms Obsoleted

Obsoleted Term	Replacement
GO:0061502 "early endosome to recycling endosome transport"	GO:0032456 "endocytic recycling"
GO:1902954 "regulation of early endosome to recycling endosome transport"	GO:2001135 "regulation of endocytic recycling"
GO:1902955 "positive regulation of early endosome to recycling endosome transport"	GO:2001137 "positive regulation of endocytic recycling"

Biological Rationale

Based on literature review, early endosome to recycling endosome transport represents a specific step within the broader endocytic recycling pathway:

• The endocytic recycling pathway operates through two routes: fast recycling (direct from early endosomes to plasma membrane) and slow recycling (through recycling endosomes)
• Transport TO the recycling endosome is an integral component of the slow recycling pathway
• The molecular machinery regulating both processes overlaps substantially (Rab11, effector proteins)

Supporting literature:

• PMID:19696797 - Comprehensive review on pathways and mechanisms of endocytic recycling
• PMID:10811830 - Landmark study showing endosomes as mosaics of distinct membrane domains
• PMID:32842549 - Recent review on the endosomal recycling pathway

Pull Request

PR #30 contains the changes: #30

All automated validations pass (make travis_build - 20/20 SPARQL QC checks pass).

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🤖 Generated by @dragon-ai-agent

• Model: claude-opus-4-5-20251101
• Agent harness: claude-code
• Triggered by: @cmungall
• Run: View workflow run