Remove incorrect ice nucleation and antifreeze synonyms

[dragon-ai-agent]

Shadow ticket of geneontology/go-ontology#31127

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@dragon-ai-agent please analyze the synonyms on these terms, they seem incorrect, remove them if so

id: GO:0042309
name: homoiothermy
namespace: biological_process
def: "Any homoeostatic process in which an organism maintains its internal body temperature at a relatively constant value. This is achieved by using metabolic processes to counteract fluctuations in the temperature of the environment." [ISBN:0192801023]
synonym: "antifreeze activity" RELATED []
synonym: "ice nucleation activity" RELATED []
synonym: "ice nucleation inhibitor activity" RELATED []
is_a: GO:0001659 ! temperature homeostasis

id: GO:0050826
name: response to freezing
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a freezing stimulus, temperatures below 0 degrees Celsius." [GOC:jl]
synonym: "antifreeze activity" RELATED []
synonym: "ice nucleation inhibitor activity" RELATED []
is_a: GO:0009409 ! response to cold

id: GO:0071497
name: cellular response to freezing
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a freezing stimulus, temperatures below 0 degrees Celsius." [GOC:mah]
synonym: "antifreeze activity" RELATED [GOC:mah]
synonym: "ice nucleation inhibitor activity" RELATED [GOC:mah]
is_a: GO:0050826 ! response to freezing
is_a: GO:0070417 ! cellular response to cold

Related:

• #29149
• #1437

[cmungall]

@dragon-ai-agent please analyze and implement

[dragon-ai-agent]

🤖 Working on it...

Follow along: View workflow run

— @dragon-ai-agent

[dragon-ai-agent]

Analysis Complete ✅

I've analyzed the synonyms on the three GO terms and confirmed they are incorrect:

Findings

Term	Incorrect Synonyms Removed
GO:0042309 (homoiothermy)	"antifreeze activity", "ice nucleation activity", "ice nucleation inhibitor activity"
GO:0050826 (response to freezing)	"antifreeze activity", "ice nucleation inhibitor activity"
GO:0071497 (cellular response to freezing)	"antifreeze activity", "ice nucleation inhibitor activity"

Rationale

These synonyms were incorrectly placed on biological process terms:

1. "antifreeze activity" is GO:0016172 - a molecular function that inhibits ice crystal growth
2. "ice nucleation activity" is GO:0019833 - a molecular function that catalyzes ice crystal formation
3. "ice nucleation inhibitor activity" (GO:0016173) is obsolete

Homoiothermy is about maintaining body temperature through metabolic processes - completely unrelated to ice-binding activities.

While organisms may express proteins with antifreeze activity as part of their response to freezing, the molecular function is not a synonym for the biological process.

PR Created

🔗 PR #15: #15

Removed 7 incorrect synonym lines total from go-edit.obo.

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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

[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...

Follow along: View workflow run

— @dragon-ai-agent

[dragon-ai-agent]

Analysis Complete

I've re-analyzed the synonyms and confirmed they are incorrect. Here's the breakdown:

Findings

Term	Incorrect Synonyms Removed
GO:0042309 (homoiothermy)	"antifreeze activity", "ice nucleation activity", "ice nucleation inhibitor activity"
GO:0050826 (response to freezing)	"antifreeze activity", "ice nucleation inhibitor activity"
GO:0071497 (cellular response to freezing)	"antifreeze activity", "ice nucleation inhibitor activity"

Rationale

These synonyms were incorrectly placed on biological process terms:

1. "antifreeze activity" is GO:0016172 - a molecular function that inhibits ice crystal growth
2. "ice nucleation activity" is GO:0019833 - a molecular function that catalyzes ice crystal formation
3. "ice nucleation inhibitor activity" (GO:0016173) is obsolete

Homoiothermy is about maintaining body temperature through metabolic processes - completely unrelated to ice-binding activities. While organisms may express proteins with antifreeze activity as part of their response to freezing, the molecular function is not a synonym for the biological process.

PR Created

PR #23: #23

Removed 7 incorrect synonym lines total. All validation tests passed.

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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