Functional Innovation KO Atlas

Reusable Object

This product captures clade-level functional innovation and acquisition-depth patterns. It is intended as a reusable substrate for projects asking where gene function is conserved, exchanged, recently gained, or ecologically anchored.

Review Brief

What changed: this candidate product is now explicitly part of the review queue because it has broad potential but no declared downstream consumers.

Why review matters: functional innovation outputs could become a reusable Atlas layer, but only if reviewers trust the exported tables, resolution choices, and diagnostics.

Evidence to inspect:

• gene_function_ecological_agora for multi-resolution innovation outputs.
• pangenome_pathway_ecology and pangenome_pathway_geography for possible downstream consumers.
• KO extraction diagnostics and synthesis figures listed as artifacts.
• Functional Innovation KO Atlas Reuse Test for the consumer decision.

Questions for reviewers:

• Are stable table artifacts available, or only diagnostics and figures?
• Which resolution should be canonical: KO, UniRef, Pfam architecture, clade, or acquisition depth?
• What downstream analysis would prove the product is worth promoting?
• Are phenotype and environment checks strong enough to prevent overinterpreting annotation patterns?

Why It Is High Value

The analysis combines UniRef, KO, Pfam architecture, environmental anchoring, and phenotype checks. That makes it valuable as a map of where function varies across the tree and which claims are robust to resolution changes.

High-Value Joins

• Join KO-level prevalence to pangenome openness and clade rank.
• Join acquisition-depth calls to environment or phenotype metadata.
• Join functional innovation classes to candidate genes or pathway gaps.

Caveats

This is a candidate derived product until stable exported tables and downstream consumers are promoted into the Atlas.