OncoRef 1.25.0: categorical protein decisions

OncoRef 1.25.0 provides a categorical decision for every assessed protein: CTA, Unsafe, or one of eight named Other categories. Missing required normal evidence or unresolved normal-screen holds remain Unassessed.

698 CTA / 600 Other / 18,031 Unsafe / 534 Unassessed across 19,863 representative proteins. The 698 CTAs cover 741 gene loci. All 522 prior CTAs remain included; Unsafe membership is unchanged.

Other category	Proteins
Low	254
Normal	171
Weak	92
Tumor-supported	66
Diffuse	8
Inducible	5
Reproductive	2
Disposable	2

Reproductive admission now uses the full mapped bulk panel, reliable reproductive IHC, supported reproductive-cell RNA, or supported developmental RNA. Indirect signals in generic/immune cells require complete outside-cluster coverage, all outside values below 5 nTPM, and no published normal-induction conflict. IFNA2/14 remain Other:Inducible. Safety, cancer, coverage and concentration gates remain independent.

from oncoref import cta_selection
cta_selection.results()[["label", "classification", "reasons"]]
cta_selection.results(category="Other", subtype="Low")

The old category="Neither" query is a deprecated alias for Other. candidates() returns CTA only. Native dog/mouse nominations remain Unassessed. Existing legacy CTA and exact-protein/k-mer background APIs retain their separate versioned policies.

Full report and funnel · Rules and API · Every category and change · Clinical SAE review · Reviewed PR #652

Assets include the 35-slide PDF and editable deck, one-page logic PDF, clinical SAE PDF, and categorical CSV tables. Complete/cached replays are byte-identical. Exact-head CI passed Python 3.10–3.14, Windows, lint and minimal-install checks; installed-wheel, source-archive, receipt and strict documentation checks passed.

These are research screening assignments, not clinical safety or clearance of every epitope. Raw values without adequate read/cell support remain explicit (Other:Weak); the 66 Tumor-supported proteins require rare-normal-context review. Human decisions do not transfer through orthology.

Publication note: the GitHub trusted-publisher exchange failed with invalid-publisher (run). The tested wheel and source archive were then uploaded successfully using the repository's existing PyPI credentials. Trusted-publisher configuration remains tracked in #371.