Gap Detection in Scientific Ontologies

One-paragraph result. A pr4xis adjunction automatically detected that the molecular biology ontology had collapsed two functionally distinct roles of voltage-gated potassium channels (Kv) into a single entity. Categorical math surfaced the gap; a ContextDef resolution disambiguated the two roles; the gap closed. 85.2% of molecular entities collapse in the Molecular ⊣ Bioelectric round-trip — every collapse is a missing distinction the math detected automatically. Reproduce in 5 seconds:

cargo test -p pr4xis-domains test_full_chain_collapse_measurement -- --nocapture

This page is the casual-reader summary of a categorical methodology that is described in full as a draft research paper — see Adjunction Information Loss in Scientific Ontologies for the methods, the per-entity tables, the literature verification, and the testable predictions.

What gets verified

• Three biomedical adjunctions between Molecular ↔ Bioelectric, Pharmacology ↔ Molecular, Biology ↔ Bioelectric. Code at crates/domains/src/natural/biomedical/adjunctions.rs.
• Per-adjunction collapse percentages computed live by the gap-analysis runner. The output of test_full_chain_collapse_measurement is the source of truth.
• The Kv channel discovery — voltage-gated potassium channels serve two functionally distinct roles (constitutive homeostasis vs therapeutic target). The molecular ontology had collapsed them; the adjunction surfaced the gap; a ContextDef::resolve distinguishes (Kv, Constitutive) from (Kv, Therapeutic). Verified by cargo test -p pr4xis-domains test_kv_gap_is_resolved_by_context.

Why this matters in one sentence

The discovery was made by mathematics, not by domain experts — the categorical adjunction surfaced the conflation as a forced consequence of the round-trip, and the methodology generalizes to any pair of ontologies connected by an adjunction.

Read more

• Paper 02 — Adjunction Information Loss — the academic version: methods, results, discussion, references, with inline footnote verification next to every numerical claim.
• Concepts — what adjunctions are and why they detect gaps, in plain English.
• Foundations — academic lineage including the categorical machinery this result builds on.
• #60 — once the source-of-truth pipeline lands, the percentages on this page will pull from a deployed JSON instead of being hand-typed.

• Document date: 2026-04-14