Hide practically-redundant edges from the entity tree browser (with "Show redundant" toggle)

[Copilot]

The tree browser renders a child directly under a high-level ancestor even when it is already reachable via a more specific term, producing huge flat lists (e.g. ~1,974 direct children under GO:anatomical structure development). The redundant edges are OWL-valid (adenohypophysis development is_a anatomical structure development is not entailment-redundant), so the fix belongs at the display layer, not in the data.

Where the fix lives

• Applied in frontend/src/pages/ontologies/entities/extractEntityHierarchy.ts, which already operates on the in-memory entity subgraph loaded for the tree.
• Not in rdf2json / HierarchicalParentsAnnotator: that would silently strip edges from the documented hierarchicalParents / hierarchicalAncestors API responses and from every other consumer of HIERARCHICAL_PARENT (HierarchyMetricsAnnotator, V1TermRepository, McpClass, …), and would require a full re-ingest to reconfigure.

"Show redundant" toggle

A new "Show redundant" checkbox is added in EntityTree.tsx alongside the existing tree-view checkboxes (Show counts / Show obsolete terms / Show all siblings). Unticked by default → new (reduced) behaviour. Tick to restore the pre-fix behaviour where every hierarchical edge is shown.

State lives in the Redux ontologies slice as displayRedundant (default false); showRedundant / hideRedundant actions wire the checkbox to the slice; the flag is plumbed through createTreeFromEntities → extractEntityHierarchy, where the reduction pass is skipped entirely when showRedundant === true. The tree refetches when the toggle changes, and the setting resets along with the other tree settings on ontology / entity changes.

Algorithm

Transitive reduction on the child→parent multimap, run after the existing cycle breaker (skipped entirely when "Show redundant" is ticked):

• For each child c with ≥ 2 parents, compute each parent's strict ancestor closure by walking childToParentRelations upward (memoised across children).
• Mark parent pᵢ redundant iff some other parent pⱼ reaches pᵢ, and pᵢ does not also reach pⱼ — the asymmetry guard keeps both endpoints of a hierarchical cycle.
• Delete the redundant (c → pᵢ) relation in place; parentToChildRelations and root detection downstream automatically reflect the trim.

Behaviour on the canonical example

c is_a   a
c part_of b
b is_a   a

With "Show redundant" unticked (default), parents of c go from {a, b} → {b}. c still appears under a in the tree, just transitively via b. With "Show redundant" ticked, both edges remain (pre-fix behaviour).

Edge cases handled

• Independent siblings (no ancestor relation) — both kept.
• Chains of length > 2 — only the most specific parent retained.
• Mutual a ↔ b cycles — both kept.
• Single-parent nodes — untouched (early exit).

[jamesamcl]

@copilot Can you put this under a toggle "Show redundant" with the other checkboxes. Unticked by default (the new behaviour). But you can tick it to go back to the old behaviour.

[Copilot]

@copilot Can you put this under a toggle "Show redundant" with the other checkboxes. Unticked by default (the new behaviour). But you can tick it to go back to the old behaviour.

Added a "Show redundant" checkbox alongside the existing tree-view toggles, unticked by default (new reduced behaviour); ticking it restores the previous behaviour. The flag is held in the Redux slice as displayRedundant, plumbed through createTreeFromEntities → extractEntityHierarchy, and the tree refetches when toggled. In 1274dcc.