feat: add NCATS GARD rare-disease registry as a biolink:Disease source

[SkyeAv]

Adds GARD — the NCATS Genetic and Rare Diseases rare-disease registry — as a biolink:Disease source in the existing disease (diseasephenotype) pipeline. GARD is a flat CSV of rare-disease terms (CURIE, preferred label, pipe-separated synonyms); it carries no cross-references, so it contributes identifiers and labels/synonyms only — no concord — and every term is typed biolink:Disease.

Ingest

• New handler: src/datahandlers/gard.py downloads the Salesforce ContentVersion CSV (pull_gard) and parses it to per-prefix labels/synonyms files (pull_gard_labels_and_synonyms). The DisplayName is emitted as a label and as an exact synonym; each pipe-separated Synonyms value becomes its own OIO:hasExactSynonym row (matching the Orphanet/DOID convention). The URL column is read for reference only and is not ingested — the CURIE resolves via the Biolink prefix map.
• Download: get_gard / get_gard_labels_and_synonyms rules in src/snakefiles/datacollect.snakefile; disease_gard_ids (an awk transform of the labels file, mirroring DOID/Orphanet) in src/snakefiles/diseasephenotype.snakefile. The download URL is configured as gard_download_url in config.yaml (a query-string Salesforce link with no stable filename, fetched directly rather than via pull_via_urllib); pin or repoint it there for a reproducible build.
• Wiring: GARD added to disease_ids and disease_labelsandsynonyms; GARD joins the existing Disease.txt (no new compendium file), so the util.py aggregators and report_tables.py need no change.

Design (load-bearing)

• extra_prefixes=[GARD]: GARD is not in the Biolink Model's disease id_prefixes (verified against the pinned biolink_version), so write_compendium would silently drop every GARD CURIE; the disease build passes extra_prefixes=[GARD] at the write_compendium call site in build_compendium (the documented escape hatch). Filing GARD with the Biolink team is the long-term fix — the same situation GTDB is in (PR feat: add GTDB as a biolink:OrganismTaxon source in the taxon pipeline #978). Two network-marked tests in tests/datahandlers/test_gard.py lock this in: one asserts GARD is absent from disease id_prefixes (and flips to prompt dropping the line once registered), the other asserts NodeFactory.create_node(..., extra_prefixes=[GARD]) for biolink:Disease does not raise (mirroring test_all_override_target_types_are_writable). The committed source-impact report's section-4 samples are flagged "NOT emitted — prefix not registered", which is exactly this precondition made visible.
• No concords: GARD provides no xrefs to other disease vocabularies, so there is no GARD concord file. A GARD term no other source already maps joins the build as a single-identifier clique (a new clique); the impact report confirms this (see below).
• Parse safety net: the handler logs a parsed/skipped/empty-name summary at the end of the parse so a future NCATS format change (e.g. a header or ID-column rename) can't silently zero the output. A scan of the published CSV found no DisplayName/Synonyms value with an embedded tab or newline and no row with an empty DisplayName.

Impact report

Generated (synthetic mode) and committed at docs/sources/GARD/impact-report.md (+ impact-report/ detail CSVs). The baseline disease intermediates were assembled from the 2025dec11 published build snapshot; that snapshot's concords predate the MP-in-disease addition, so MP's concord was rebuilt locally from UberGraph for the baseline (the report's Babel commit header pins the exact tree). GARD's own intermediates were built locally. Results: 16,214 identifiers / 16,214 new single-identifier cliques (a 6.72% increase, 241,269 → 257,483 total cliques), 0 merges, 0 modified cliques, 0 xrefs — the addition is purely additive; GARD disturbs no existing clique.

Docs

• docs/sources/GARD/README.md (new) + an entry in the docs/sources/ index + the committed impact-report.md.
• Also adds [tool.ruff.format] exclude = ["*.md"] to pyproject.toml: origin/main lacks this CI fix and ruff 0.16.0 began formatting Python code fences inside Markdown (overlapping rumdl), which would fail this PR's "Check Python formatting with ruff" job. It is a prerequisite for this PR's CI and is documented inline.

Testing

• uv run pytest tests/datahandlers/test_gard.py -m unit --no-cov -q → 2 passed, 2 deselected
• uv run pytest tests/datahandlers/test_gard.py --network --no-cov -q → 4 passed
• uv run pytest -m unit --no-cov -q → 404 passed, 107 deselected
• uv run ruff check . / ruff format --check . / snakefmt --check . / rumdl check . (committed files) → all clean
• uv run snakemake -c 1 -n get_gard get_gard_labels_and_synonyms disease_gard_ids → 3 jobs resolve in the correct chain
• uv run source-impact-report --source GARD --mode synthetic --intermediate-root /tmp/impact/intermediate → report written (16,214 new cliques, 0 merges)

Deferred

• Biolink registration: registering GARD in the Biolink Model's disease id_prefixes is the long-term fix for the extra_prefixes=[GARD] escape hatch (and removes the report's "NOT emitted" flag).

Questions for the reviewer

• extra_prefixes vs. Biolink-first. This PR ships the extra_prefixes=[GARD] escape hatch so the ~16k rare-disease terms actually surface in Disease.txt now (rather than being silently dropped), with Biolink registration tracked as the long-term fix — is that the preferred path, or should GARD wait on upstream Biolink registration before being kept?

[SkyeAv]

Update: no-URL exclusion + source-impact report

Per the GARD URL field: a row with no URL has no public rarediseases.info.nih.gov page and is a candidate/provisional term — not a real rare disease — so it is now excluded from the ingest. This drops ~9,949 of ~16,214 rows, keeping 6,265 real rare-disease terms.

• The filter is the single if not (row.get("URL") or "").strip(): continue line in src/datahandlers/gard.py; because disease_gard_ids derives ids from the labels file via awk, the exclusion cascades into the ids file and the compendium automatically. The parse logs a kept/skipped/no-URL/empty-name summary so a future NCATS format change can't silently zero the output.
• A source-impact report (synthetic mode) is now generated and committed at docs/sources/GARD/impact-report.md (+ impact-report/ detail CSVs). Baseline disease intermediates came from the 2025dec11 published snapshot (MP's concord, absent from that snapshot, was rebuilt locally from UberGraph). Result: 6,265 new single-identifier cliques (241,269 → 247,534), 0 merges / 0 modified / 0 xrefs — purely additive, no existing clique disturbed.
• The report's section-4 samples are flagged "NOT emitted — prefix not registered in Biolink Model for biolink:Disease"; that flag is why the build passes extra_prefixes=[GARD] (see the PR body's Design section). Registering GARD upstream removes both the flag and the need for the escape hatch.

[SkyeAv]

Reverted: the URL-field filter was a false positive

A missing GARD URL does not mean a row isn't a real rare disease — a term may simply lack a GARD page. Per maintainer feedback: GARD:0001049 "Cerebral arteriopathy ... type 1" (CADASIL) has a URL, while GARD:0024558 "Cerebral arteriopathy with subcortical infarcts and leukoencephalopathy" (also CADASIL) does not — same disease family, so excluding the no-URL one would drop a real rare disease.

• The if not (row.get("URL") or "").strip(): continue filter in src/datahandlers/gard.py is removed; all 16,214 GARD terms are ingested (no URL gating). The URL column is back to "reference only, not ingested" (the CURIE resolves via the Biolink prefix map).
• The source-impact report is regenerated: 16,214 new cliques (241,269 → 257,483, +6.72%), 0 merges / 0 modified / 0 xrefs — still purely additive.
• Tests updated: the verbatim fixture (one row with a URL+synonyms, one without either) now asserts both are kept.

[SkyeAv]

@gaurav this branch successfully rebuilt the Disease Compendia at /projects/babel/runs/goetzs/NIH-GARD-1.18 on HT1 with the GARD ontology. Do you want me to put anything from that here or is a path to the sucessful output enough to merge this?