NosoGraph v2.3.0 — Disease-General Core & Computational Comparison (Legacy prototype)

NosoGraph v2.3.0 — Disease-General Core & Computational Comparison

NosoGraph v2.3.0 expands the public alpha into a more disease-general, validated, evidence-traceable computational research platform.

Maturity: Public Alpha — research use only; not production clinical software.

Highlights

Disease-general core

• Centralized disease identifier resolution and explicit disease selection where semantically required.
• Removal of inappropriate SLE/RA platform defaults in P1 scope.
• Multi-disease CLI/API behavior with preserved legacy compatibility.

Strict curated validation

• Batch validation: nosograph disease validate-batch --tier L2 --strict
• 88/88 current L2 modules pass strict validation (recomputed at release).
• CI reference-tier gate on pull requests; weekly full L2 run in slow-test workflow.

NosoGraph Compare (experimental initial slice)

• Multidimensional comparison across phenotype, gene, mechanism, treatment, and evidence_coverage.
• Explicit missingness semantics: NOT_RECORDED ≠ KNOWN_ABSENT.
• Engine + API (POST /api/v1/nosograph/compare) + dashboard panel — not a finished standalone Compare product.

Evidence & provenance

• Claim, evidence, and provenance APIs connected with end-to-end traceability.
• Golden trace verified from condition → claim → evidence → provenance → source snapshot.
• Polished Evidence Explorer UX remains incomplete.

Biomedical source synchronization

• Nine-stage sync lifecycle with Open Targets vertical slice.
• nosograph biomed sync open_targets --dry-run CLI.
• Hosted dry-run workflow proven on GitHub Actions (publish skipped in dry-run mode).

CLI

• Canonical: nosograph
• Legacy alias: med-research (same implementation)
• Python import: med_research
• PyPI package: med-research (unchanged)

Validation

Check	Result
Offline unit suite	2351 passed
L2 strict	88/88
Compare tests	19/19
Provenance API	3/3
Hosted CI (required)	lint, security, test 3.12, integration — PASS

Current corpus

Tier	Count	Notes
Registry modules	10,407	Mostly scaffolds
L2 strict-validated	88	Pipeline-ready
Reference	6	Deep reference set
CI-validated	8	Original eight diseases
L3	2	In sampled status report

Registry size ≠ curation depth. Scaffold modules are starting points, not validated clinical models.

Experimental / partial capabilities

• NosoGraph Compare (initial slice)
• Source sync (Open Targets only)
• Evidence/provenance APIs (backend complete; UX partial)
• Optional LLM enrichment

Not implemented

• Polished Evidence Explorer
• Full Compare standalone workflow
• Public hosted demo
• FHIR / OMOP / Phenopackets export
• PyPI package rename to nosograph

Compatibility

• v2.2.0 tag and release unchanged.
• Breaking package rename deferred to a future major release.

Research scope

Outputs are computational prioritization hypotheses for research use only — not medical advice.