Activate the MONDO close-match guard in disease glom (with build-vs-build clique-diff tool)

[gaurav]

Summary

Fixes a latent bug in how the disease/phenotype build reads the MONDO_close concord, which
left glom's close-match guard a silent no-op, and adds a reusable build-vs-build clique-diff
tool plus the before/after impact analysis that this change requires.

This is the dedicated follow-up promised in #790, where the same code was touched only enough to
stop the build crashing (validating the real 3-column MONDO_close format while preserving
the dormant x[1] behaviour). Activating the guard changes disease clique merging broadly and is
orthogonal to adding MP, so it lives here with its own evidence.

Note

Based on add-mpo (#790), not main — it builds on that PR's compute_cliques_for_impact_report
refactor. Merge #790 first; this PR will retarget to main automatically.

The bug

compute_cliques_for_impact_report() read MONDO_close (a 3-column subject predicate object
concord) with close_mondos[x[0]].add(x[1]) — keying the MONDO subject to column 2, the
predicate (oio:closeMatch) instead of column 3, the close-match object. No clique ever
contains the literal string oio:closeMatch, so glom's close= guard (if cd in newset) never
matched. The guard has therefore never fired, on main and before it; close (but not exact)
matches were free to collapse into exact cliques.

The fix is one line of intent: key on x[2], matching the (stuff[0], stuff[2]) parsing every
other concord in that function already uses.

Impact (why this needs SME review)

Measured on a full local disease build (Biolink 4.4.3), same intermediate ids/concords,
differing only in x[1] vs x[2]. glom is deterministic — two x[1] builds were clique-identical
— so every difference is signal, not run-to-run noise.

• 1,219 identifiers, all MEDDRA, are dropped from Disease.txt. They were present only because
  the dormant guard let them merge into a MONDO disease clique; correctly kept out, they have no
  independent disease typing in this pipeline and leave the compendium entirely.
• 1,191 of 365,465 Disease cliques lose ≥1 member; net Disease clique count +20, PhenotypicFeature +13.
• PhenotypicFeature.txt is essentially unaffected (the close pairs are MONDO-subject).

Dropping 1,219 MEDDRA codes is correct if they are genuinely distinct concepts (the guard's
premise), but a coverage loss if anything relies on that MEDDRA → MONDO normalization. Per the
project rule against dropping valid identifiers without good reason, this is an SME call — the
evidence is in docs/pipelines/diseasephenotype/mondo-close-match-guard/ (README.md,
clique-diff.csv, dropped-members.csv, summary.json).

New tool: babel-clique-diff

A reusable build-vs-build clique diff (tools/clique_diff) that compares the finished compendia of
two builds and reports split/merged/lost cliques and, crucially, dropped CURIEs.

It is deliberately distinct from source-impact-report: that answers "what does adding source
X do?" by re-glomming intermediates with vs. without one source; this answers "how did the cliques
change between build A and build B?" given the same inputs but different code/config/data.
Because it works on finished compendia rather than glom state, it can also compare a local build
against a published stars.renci.org build with no re-glom — useful for validating any glom-logic
change (close-match, unique_prefixes, overuse filtering) or as a release regression check.

Test plan

• uv run ruff check / ruff format --check — clean.
• uv run rumdl check . — clean.
• uv run pytest -m unit -q — green (243 passed), including new tests/tools/test_clique_diff_tool.py.

Out of scope

• The MP source-impact report on Add MP (Mammalian Phenotype Ontology) as a disease/phenotype source #790 reflects x[1] (the production behaviour of that PR) and is
  not regenerated here.
• Deciding whether to keep the guard active — that is the SME question this PR's evidence exists to inform.

🤖 Generated with Claude Code

[gaurav]

Heads up: the babel-clique-diff tool commit from this PR has been extracted into its own standalone PR off main (#885) so it can land independently of the MONDO close-match-guard change here. Once #885 merges, please rebase this PR to drop its now-duplicated babel-clique-diff commit. The new "MP kept disjoint from HP" PR (#886) depends on #885.