@inflexa-ai/harness 0.35.7 → 0.36.0

package/dist/workflows/target-assessment/lib/evidence-conflict-detector.js

@@ -1,100 +0,0 @@
-/**
- * Deterministic structural conflict detector.
- *
- * Each rule is a pure function over the dossier body. A row is emitted
- * when the body internally contradicts itself in a way that should be
- * impossible post-pipeline-fix. The post-fix pipeline should produce an
- * empty array for any well-formed body; the rules exist to catch
- * regressions and to surface upstream pipeline bugs.
- */
-import { HIGH_EXPRESSION_TPM_THRESHOLD } from "./expression-constants.js";
-function checkFaersCoverage(body) {
-    const faers = body?.safety_profile?.faers;
-    const cp = body?.safety_profile?.class_precedent;
-    if (faers?.coverage !== "queried_no_data")
-        return null;
-    if (cp?.coverage !== "available")
-        return null;
-    let total = 0;
-    for (const o of cp.data?.per_organ ?? []) {
-        for (const ae of o.top_aes ?? [])
-            total += ae.report_count ?? 0;
-    }
-    if (total === 0)
-        return null;
-    return {
-        evidence_item_id: "structural:faers_coverage",
-        predicate: "safety_profile.faers.coverage=queried_no_data",
-        contradicting_predicates: [`safety_profile.class_precedent has ${total} FAERS-derived reports across per_organ.top_aes`],
-        surfaced_in_section: "safety_profile.faers",
-        evidence: [],
-    };
-}
-function checkFatalSignal(body) {
-    const signal = body?.derived?.risk_summary?.any_fatal_signal;
-    if (signal !== "unknown")
-        return null;
-    const bullets = body?.liability_summary?.liability_bullets ?? [];
-    const fatal = bullets.find((b) => b?.category === "fatal_post_market");
-    if (!fatal)
-        return null;
-    return {
-        evidence_item_id: "structural:fatal_signal",
-        predicate: "derived.risk_summary.any_fatal_signal=unknown",
-        contradicting_predicates: ["liability_summary.liability_bullets contains a fatal_post_market entry"],
-        surfaced_in_section: "derived.risk_summary",
-        evidence: [],
-    };
-}
-function checkTrialCount(body) {
-    const trials = body?.clinical_development?.trials;
-    const outcomes = body?.clinical_development?.outcomes;
-    if (trials?.coverage !== "queried_no_data")
-        return null;
-    const outcomeRows = outcomes?.coverage === "available" ? (outcomes.data?.rows ?? []) : [];
-    if (outcomeRows.length === 0)
-        return null;
-    return {
-        evidence_item_id: "structural:trial_count",
-        predicate: "clinical_development.trials.coverage=queried_no_data",
-        contradicting_predicates: [`clinical_development.outcomes.data.rows has ${outcomeRows.length} row(s)`],
-        surfaced_in_section: "clinical_development.outcomes",
-        evidence: [],
-    };
-}
-function checkHighExpressionCount(body) {
-    const reported = body?.derived?.liability_summary?.expression_breadth?.high_expression_tissue_count;
-    if (typeof reported !== "number")
-        return null;
-    const set = new Set();
-    const consensusRows = body?.reference_biology?.normal_tissue_expression?.data?.rows ?? [];
-    for (const r of consensusRows) {
-        if ((r.value ?? 0) >= HIGH_EXPRESSION_TPM_THRESHOLD && r.tissue) {
-            set.add(`${r.tissue}::human`);
-        }
-    }
-    const cells = body?.reference_biology?.preclinical?.expression_heatmap?.data?.cells ?? [];
-    for (const c of cells) {
-        if (c.rank === "high" && c.tissue)
-            set.add(`${c.tissue}::${c.species ?? "unknown"}`);
-    }
-    if (set.size === reported)
-        return null;
-    return {
-        evidence_item_id: "structural:high_expression_count",
-        predicate: `derived.liability_summary.expression_breadth.high_expression_tissue_count=${reported}`,
-        contradicting_predicates: [`body-recomputed count is ${set.size}`],
-        surfaced_in_section: "derived.liability_summary.expression_breadth",
-        evidence: [],
-    };
-}
-export function detectStructuralEvidenceConflicts(bodyInput) {
-    const body = bodyInput;
-    const out = [];
-    for (const fn of [checkFaersCoverage, checkFatalSignal, checkTrialCount, checkHighExpressionCount]) {
-        const row = fn(body);
-        if (row)
-            out.push(row);
-    }
-    return out;
-}

package/dist/workflows/target-assessment/lib/expression-constants.d.ts

@@ -1,21 +0,0 @@
-/**
- * TPM threshold for "high expression" classification, aligned with the
- * Human Protein Atlas tissue-expression categorisation. Tissues with
- * TPM >= this threshold count toward
- * liability_summary.expression_breadth.high_expression_tissue_count
- * and inform organ-rollup signal scoring.
- */
-export declare const HIGH_EXPRESSION_TPM_THRESHOLD = 50;
-/**
- * Off-tissue floor for CNS regions. Brain subregions (hypothalamus excepted)
- * carry biologically meaningful CALCR/peptide-GPCR expression at single-digit
- * nTPM; the default 100 floor produced organ_claim_without_probe_pass audit
- * failures for CNS bullets that the recommendation makes.
- */
-export declare const CNS_REGION_TPM_FLOOR = 5;
-/**
- * Off-tissue floor for musculoskeletal tissues. Skeletal muscle and bone
- * surfaces routinely show 20-80 nTPM for GPCRs whose ligands affect
- * mineral and muscle metabolism.
- */
-export declare const MUSCULOSKELETAL_TPM_FLOOR = 20;

package/dist/workflows/target-assessment/lib/expression-constants.js

@@ -1,21 +0,0 @@
-/**
- * TPM threshold for "high expression" classification, aligned with the
- * Human Protein Atlas tissue-expression categorisation. Tissues with
- * TPM >= this threshold count toward
- * liability_summary.expression_breadth.high_expression_tissue_count
- * and inform organ-rollup signal scoring.
- */
-export const HIGH_EXPRESSION_TPM_THRESHOLD = 50;
-/**
- * Off-tissue floor for CNS regions. Brain subregions (hypothalamus excepted)
- * carry biologically meaningful CALCR/peptide-GPCR expression at single-digit
- * nTPM; the default 100 floor produced organ_claim_without_probe_pass audit
- * failures for CNS bullets that the recommendation makes.
- */
-export const CNS_REGION_TPM_FLOOR = 5;
-/**
- * Off-tissue floor for musculoskeletal tissues. Skeletal muscle and bone
- * surfaces routinely show 20-80 nTPM for GPCRs whose ligands affect
- * mineral and muscle metabolism.
- */
-export const MUSCULOSKELETAL_TPM_FLOOR = 20;

package/dist/workflows/target-assessment/lib/family-complex-supplement.d.ts

@@ -1,20 +0,0 @@
-/**
- * Build the obligate-cofactor supplement rows shown in
- * OffTargetPanel.excluded_rows from the IUPHAR family-complexes collector
- * bundle.
- *
- * pchembl is set to 0 because IUPHAR exposes complex structure, not
- * ligand affinity for the complex; the row is marked selectivity_unknown
- * with an explicit reason so downstream readers see the obligate-cofactor
- * surface rather than a developable potency claim. The per-row LLM
- * clinical_consequence annotator populates `clinical_consequence` once
- * the per-row annotation step runs.
- */
-import type { ExcludedOffTargetRowSchema } from "@inflexa-ai/harness/contracts/target-dossier.js";
-import type { z } from "zod";
-import type { FamilyComplexesBundle } from "../schemas.js";
-type ExcludedOffTargetRow = z.infer<typeof ExcludedOffTargetRowSchema>;
-export declare function buildFamilyComplexSupplement(bundle: FamilyComplexesBundle): (Omit<ExcludedOffTargetRow, "evidence"> & {
-    evidence: [];
-})[];
-export {};

package/dist/workflows/target-assessment/lib/family-complex-supplement.js

@@ -1,36 +0,0 @@
-/**
- * Build the obligate-cofactor supplement rows shown in
- * OffTargetPanel.excluded_rows from the IUPHAR family-complexes collector
- * bundle.
- *
- * pchembl is set to 0 because IUPHAR exposes complex structure, not
- * ligand affinity for the complex; the row is marked selectivity_unknown
- * with an explicit reason so downstream readers see the obligate-cofactor
- * surface rather than a developable potency claim. The per-row LLM
- * clinical_consequence annotator populates `clinical_consequence` once
- * the per-row annotation step runs.
- */
-export function buildFamilyComplexSupplement(bundle) {
-    return bundle.complexes.map((c) => {
-        const accDesc = c.accessoryNames.length > 0 ? c.accessoryNames.join("+") : "an accessory protein";
-        return {
-            off_target_id: null,
-            off_target_name: c.complexName,
-            target_class: "GPCR receptor-accessory complex",
-            pchembl: 0,
-            is_safety_panel_target: false,
-            organ_system: null,
-            clinical_consequence: null,
-            selectivity: {
-                selectivity_unknown: true,
-                reason: "obligate cofactor (same primary protein, different accessory)",
-            },
-            selectivity_window_below_threshold: false,
-            relationship: "obligate_cofactor",
-            reason: `${c.complexName} is ${bundle.primaryTargetGene} heterodimerised with ${accDesc}; ` +
-                `selectivity is not pharmacologically attainable. Surfaced as an intrinsic-pharmacology ` +
-                `liability rather than a developable off-target.`,
-            evidence: [],
-        };
-    });
-}

package/dist/workflows/target-assessment/lib/fda-label-safety.d.ts

@@ -1,72 +0,0 @@
-/**
- * The typed form of an FDA Structured Product Label's safety prose, and the
- * per-organ projection over it.
- *
- * A label arrives as prose in a handful of named sections. Ingesting it once
- * into this shape is what lets the same warning reach two places without being
- * fetched twice: the synthesis markdown renders the sections, and the dossier's
- * per-organ regulatory signals are segmented out of them. Everything a reader
- * needs to find a signal again — the application number and the label section —
- * rides on the signal, so it satisfies the claim-evidence locator requirement.
- */
-import type { OrganSystem } from "../../../contracts/organ-system.js";
-import type { EvidenceItem } from "../../../contracts/target-dossier.js";
-/** The label sections whose prose carries a safety finding. */
-export declare const LABEL_SAFETY_SECTIONS: readonly ["boxed_warning", "warnings_and_precautions", "warnings", "contraindications"];
-export type LabelSafetySection = (typeof LABEL_SAFETY_SECTIONS)[number];
-/** One block of prose, keyed to the label section it was published under. */
-export interface LabelSafetyText {
-    readonly section: LabelSafetySection;
-    readonly text: string;
-}
-/**
- * One label's identity plus its safety prose.
- *
- * `application_number` is required rather than nullable because it is half of
- * what makes a signal resolvable; a producer holding a label without one has
- * nothing to cite and does not construct this shape.
- */
-export interface FdaLabelSafety {
-    readonly application_number: string;
-    readonly drug_name: string;
-    readonly effective_time?: string;
-    readonly source_url?: string;
-    readonly sections: readonly LabelSafetyText[];
-}
-/** A warning fragment attributed to one canonical organ, with its locator. */
-export interface RegulatoryOrganSignal {
-    readonly organ: OrganSystem;
-    readonly drug_name: string;
-    readonly application_number: string;
-    /** The label section the prose was published under. */
-    readonly source_section: LabelSafetySection;
-    /** What a reader opens to find the excerpt: a numbered marker when the prose carried one. */
-    readonly label_section: string;
-    readonly excerpt: string;
-    readonly evidence: EvidenceItem;
-}
-export interface OrganSignalProjection {
-    readonly signals: readonly RegulatoryOrganSignal[];
-    /** Fragments whose organ did not resolve and were therefore not emitted. */
-    readonly dropped_count: number;
-}
-/** What the section reports as having emptied it when nothing resolved. */
-export declare const ORGAN_RESOLUTION_FILTER = "label warning fragments with no resolvable organ";
-interface WarningFragment {
-    readonly marker: string | null;
-    readonly text: string;
-}
-/**
- * Split one section's prose into the fragments an organ can be attributed to:
- * numbered label-section markers first, then bullets inside each marked block.
- */
-export declare function splitWarningProse(text: string): WarningFragment[];
-/**
- * Project a set of ingested labels onto per-organ regulatory signals.
- *
- * A fragment that resolves to no canonical organ is dropped and counted rather
- * than filed under a neighbouring organ. A fragment the highlights section
- * repeats from the full section is emitted once.
- */
-export declare function segmentLabelSafety(labels: readonly FdaLabelSafety[]): OrganSignalProjection;
-export {};

package/dist/workflows/target-assessment/lib/fda-label-safety.js

@@ -1,166 +0,0 @@
-/**
- * The typed form of an FDA Structured Product Label's safety prose, and the
- * per-organ projection over it.
- *
- * A label arrives as prose in a handful of named sections. Ingesting it once
- * into this shape is what lets the same warning reach two places without being
- * fetched twice: the synthesis markdown renders the sections, and the dossier's
- * per-organ regulatory signals are segmented out of them. Everything a reader
- * needs to find a signal again — the application number and the label section —
- * rides on the signal, so it satisfies the claim-evidence locator requirement.
- */
-import { classifyOrgan } from "./meddra-organ-map.js";
-/** The label sections whose prose carries a safety finding. */
-export const LABEL_SAFETY_SECTIONS = ["boxed_warning", "warnings_and_precautions", "warnings", "contraindications"];
-/** What the section reports as having emptied it when nothing resolved. */
-export const ORGAN_RESOLUTION_FILTER = "label warning fragments with no resolvable organ";
-/**
- * Numbered label-section markers ("5.1 Hepatotoxicity"). Split as a lookahead
- * so the marker stays with the prose it heads. The trailing uppercase-or-paren
- * requirement is what keeps a dose ("2.5 mg") from reading as a marker.
- */
-const SECTION_MARKER_SPLIT = /(?=\b\d{1,2}\.\d{1,2}\s+[A-Z(])/;
-const SECTION_MARKER_HEAD = /^(\d{1,2}\.\d{1,2})\s+/;
-/**
- * Bullet boundaries. Single newlines are NOT boundaries — labels wrap prose
- * mid-sentence, and splitting on the wrap would sever a finding from the organ
- * named in its own heading.
- */
-const FRAGMENT_SPLIT = /[•·▪‣]+|\r?\n\s*\r?\n+|\r?\n[ \t]*[-*]\s+/;
-/** Below this a fragment is a stray heading remnant, not a finding. */
-const MIN_FRAGMENT_CHARS = 16;
-/** Excerpt budget per signal — enough to read the finding, bounded for storage. */
-const MAX_EXCERPT_CHARS = 400;
-function clipExcerpt(text) {
-    if (text.length <= MAX_EXCERPT_CHARS)
-        return text;
-    return `${text.slice(0, MAX_EXCERPT_CHARS - 1).trimEnd()}…`;
-}
-/**
- * Split one section's prose into the fragments an organ can be attributed to:
- * numbered label-section markers first, then bullets inside each marked block.
- */
-export function splitWarningProse(text) {
-    const fragments = [];
-    for (const block of text.split(SECTION_MARKER_SPLIT)) {
-        const head = SECTION_MARKER_HEAD.exec(block);
-        const marker = head?.[1] ?? null;
-        const body = head ? block.slice(head[0].length) : block;
-        for (const piece of body.split(FRAGMENT_SPLIT)) {
-            const collapsed = piece.replace(/\s+/g, " ").trim();
-            if (collapsed.length < MIN_FRAGMENT_CHARS)
-                continue;
-            fragments.push({ marker, text: collapsed });
-        }
-    }
-    return fragments;
-}
-/**
- * Resolve a fragment onto the canonical organ vocabulary at its own boundary.
- * The heading — the prose up to its first colon — is tried first, because a
- * label states the organ there and then discusses it; scanning the whole
- * fragment first would let an incidental mention outrank the heading.
- */
-function resolveFragmentOrgan(fragment) {
-    const colon = fragment.indexOf(":");
-    const heading = colon > 0 ? fragment.slice(0, colon) : "";
-    return (heading ? classifyOrgan(heading) : null) ?? classifyOrgan(fragment);
-}
-function buildEvidence(label, labelSection, excerpt, organ) {
-    return {
-        source: "openfda:label",
-        predicate: "label_warning",
-        excerpt,
-        regulatory_reference: {
-            document: `FDA prescribing information — ${label.drug_name}`,
-            section: labelSection,
-            doc_id: label.application_number,
-            ...(label.source_url ? { doc_url: label.source_url } : {}),
-        },
-        metadata: {
-            organ,
-            drug_name: label.drug_name,
-            ...(label.effective_time ? { effective_time: label.effective_time } : {}),
-        },
-    };
-}
-/**
- * A short fragment can be a substring of a longer unrelated one, so containment
- * only settles a repeat once the contained text is long enough to be prose
- * rather than a phrase.
- */
-const MIN_CONTAINMENT_CHARS = 60;
-function isRepeatOf(seen, candidate) {
-    if (seen === candidate)
-        return true;
-    if (seen.includes(candidate))
-        return candidate.length >= MIN_CONTAINMENT_CHARS;
-    if (candidate.includes(seen))
-        return seen.length >= MIN_CONTAINMENT_CHARS;
-    return false;
-}
-/**
- * Order a label's sections for segmentation: published section order, then
- * longest prose first within a section. openFDA returns the highlights summary
- * and the full section under the same key, so reading the longer one first is
- * what makes the shorter repeat recognisable as a repeat rather than the other
- * way round.
- */
-function segmentationOrder(sections) {
-    const firstSeenAt = new Map();
-    for (const [index, s] of sections.entries()) {
-        if (!firstSeenAt.has(s.section))
-            firstSeenAt.set(s.section, index);
-    }
-    return [...sections].sort((a, b) => firstSeenAt.get(a.section) - firstSeenAt.get(b.section) || b.text.length - a.text.length);
-}
-/**
- * Project a set of ingested labels onto per-organ regulatory signals.
- *
- * A fragment that resolves to no canonical organ is dropped and counted rather
- * than filed under a neighbouring organ. A fragment the highlights section
- * repeats from the full section is emitted once.
- */
-export function segmentLabelSafety(labels) {
-    const signals = [];
-    let droppedCount = 0;
-    for (const label of labels) {
-        const seenMarkers = new Set();
-        const seenText = [];
-        for (const section of segmentationOrder(label.sections)) {
-            // A numbered marker settles a repeat only across blocks: one block
-            // legitimately carries several fragments under its own `5.1`, while
-            // a second block reprising `5.1` is the highlights summary of it.
-            const blockMarkers = new Set();
-            for (const fragment of splitWarningProse(section.text)) {
-                const normalized = fragment.text.toLowerCase();
-                const markerKey = fragment.marker ? `${section.section}:${fragment.marker}` : null;
-                const repeated = (markerKey !== null && seenMarkers.has(markerKey)) || seenText.some((seen) => isRepeatOf(seen, normalized));
-                if (repeated)
-                    continue;
-                if (markerKey !== null)
-                    blockMarkers.add(markerKey);
-                seenText.push(normalized);
-                const organ = resolveFragmentOrgan(fragment.text);
-                if (organ === null) {
-                    droppedCount += 1;
-                    continue;
-                }
-                const labelSection = fragment.marker ?? section.section;
-                const excerpt = clipExcerpt(fragment.text);
-                signals.push({
-                    organ,
-                    drug_name: label.drug_name,
-                    application_number: label.application_number,
-                    source_section: section.section,
-                    label_section: labelSection,
-                    excerpt,
-                    evidence: buildEvidence(label, labelSection, excerpt, organ),
-                });
-            }
-            for (const marker of blockMarkers)
-                seenMarkers.add(marker);
-        }
-    }
-    return { signals, dropped_count: droppedCount };
-}

package/dist/workflows/target-assessment/lib/heterodimer-filter.d.ts

@@ -1,30 +0,0 @@
-/**
- * Detect receptor-accessory heterodimer entries that share the assessment
- * target's gene product. These are NOT off-targets in the pharmacological
- * sense: the primary protein is the same, only the obligate accessory
- * cofactor differs. Selectivity windows between such partner complexes are
- * not pharmacologically attainable and should not be reported as off-target
- * liabilities.
- *
- * The accessory list is supplied by the IUPHAR family-complexes collector
- * at runtime — there is no hardcoded RAMP/MRAP/RGS pattern. For a CALCR
- * assessment the collector returns ["RAMP1","RAMP2","RAMP3"], so the
- * regex matches "CALCR/RAMP1", "CALCR/RAMP2", "CALCR/RAMP3" only.
- */
-export interface HeterodimerFilterInput {
-    assessmentGeneSymbol: string;
-    accessoryProteinNames: string[];
-}
-/**
- * Build a predicate that returns true when an off-target name describes a
- * heterodimer of the assessment target's primary protein with one of the
- * supplied accessory gene symbols. Returns a constant-false predicate when
- * the inputs cannot produce a meaningful match (missing gene symbol or
- * empty accessory list).
- *
- * Matched substrings:
- *   "<primary>/<accessory>"  (e.g., "CALCR/RAMP3")
- *   "<primary> + <accessory>"
- *   "<primary>-<accessory>"  (some sources use a hyphen)
- */
-export declare function makeHeterodimerOfAssessmentFilter(input: HeterodimerFilterInput): (offTargetName: string) => boolean;

package/dist/workflows/target-assessment/lib/heterodimer-filter.js

@@ -1,44 +0,0 @@
-/**
- * Detect receptor-accessory heterodimer entries that share the assessment
- * target's gene product. These are NOT off-targets in the pharmacological
- * sense: the primary protein is the same, only the obligate accessory
- * cofactor differs. Selectivity windows between such partner complexes are
- * not pharmacologically attainable and should not be reported as off-target
- * liabilities.
- *
- * The accessory list is supplied by the IUPHAR family-complexes collector
- * at runtime — there is no hardcoded RAMP/MRAP/RGS pattern. For a CALCR
- * assessment the collector returns ["RAMP1","RAMP2","RAMP3"], so the
- * regex matches "CALCR/RAMP1", "CALCR/RAMP2", "CALCR/RAMP3" only.
- */
-const ACC_ESCAPE_RE = /[.*+?^${}()|[\]\\]/g;
-function escapeForRegex(token) {
-    return token.replace(ACC_ESCAPE_RE, "\\$&");
-}
-/**
- * Build a predicate that returns true when an off-target name describes a
- * heterodimer of the assessment target's primary protein with one of the
- * supplied accessory gene symbols. Returns a constant-false predicate when
- * the inputs cannot produce a meaningful match (missing gene symbol or
- * empty accessory list).
- *
- * Matched substrings:
- *   "<primary>/<accessory>"  (e.g., "CALCR/RAMP3")
- *   "<primary> + <accessory>"
- *   "<primary>-<accessory>"  (some sources use a hyphen)
- */
-export function makeHeterodimerOfAssessmentFilter(input) {
-    const target = input.assessmentGeneSymbol.trim().toUpperCase();
-    const accessories = input.accessoryProteinNames.map((n) => n.trim()).filter((n) => n.length > 0);
-    if (!target || accessories.length === 0) {
-        return () => false;
-    }
-    const alternation = accessories.map(escapeForRegex).join("|");
-    const re = new RegExp(`\\b([A-Z][A-Z0-9]{1,9})\\s*[\\/+\\-]\\s*(${alternation})\\b`, "i");
-    return (offTargetName) => {
-        const m = re.exec(offTargetName);
-        if (!m)
-            return false;
-        return m[1].toUpperCase() === target;
-    };
-}

package/dist/workflows/target-assessment/lib/hpo-organ-map.d.ts

@@ -1,34 +0,0 @@
-/**
- * Human Phenotype Ontology terms onto the canonical organ vocabulary.
- *
- * HPO organises every phenotypic abnormality under organ-system roots, and a
- * phenotype association carries its full ancestor closure. Resolution is
- * therefore membership of an ancestor id in this table — equality on
- * identifiers, not matching on prose, so a renamed term keeps resolving and an
- * incidental word in a label never decides an organ.
- *
- * The table is ordered most specific first, because a term sits under several
- * roots at once: a liver phenotype's closure also contains the digestive-system
- * root, and reading the broad root first would file every hepatic finding under
- * `gi`. Roots with no canonical organ to land in (ear, head and neck, growth,
- * prenatal) are absent — a phenotype is reported under the organ it affects or
- * not at all.
- *
- * A root broader than any single token is absent for that same reason, even
- * where a token's name is close to it: the endocrine-system root spans every
- * endocrine organ while the only endocrine token names the thyroid, so an
- * adrenal phenotype resolves through no root and is dropped. The neoplasm root
- * says a phenotype is malignant, not where it sits, so a neoplasm resolves
- * through the organ root it also carries — a lung neoplasm is respiratory, and
- * a neoplasm with no organ root at all resolves to nothing.
- *
- * The values are the canonical tokens, so this module declares no organ
- * enumeration of its own.
- */
-import type { OrganSystem } from "../../../contracts/organ-system.js";
-/**
- * Resolve an HPO term onto a canonical organ from its own id plus its ancestor
- * closure. Returns null when nothing in the ancestry denotes a canonical organ
- * system — the caller drops the phenotype and counts it.
- */
-export declare function resolveHpoOrgan(termId: string, ancestorIds: readonly string[]): OrganSystem | null;

package/dist/workflows/target-assessment/lib/hpo-organ-map.js

@@ -1,63 +0,0 @@
-/**
- * Human Phenotype Ontology terms onto the canonical organ vocabulary.
- *
- * HPO organises every phenotypic abnormality under organ-system roots, and a
- * phenotype association carries its full ancestor closure. Resolution is
- * therefore membership of an ancestor id in this table — equality on
- * identifiers, not matching on prose, so a renamed term keeps resolving and an
- * incidental word in a label never decides an organ.
- *
- * The table is ordered most specific first, because a term sits under several
- * roots at once: a liver phenotype's closure also contains the digestive-system
- * root, and reading the broad root first would file every hepatic finding under
- * `gi`. Roots with no canonical organ to land in (ear, head and neck, growth,
- * prenatal) are absent — a phenotype is reported under the organ it affects or
- * not at all.
- *
- * A root broader than any single token is absent for that same reason, even
- * where a token's name is close to it: the endocrine-system root spans every
- * endocrine organ while the only endocrine token names the thyroid, so an
- * adrenal phenotype resolves through no root and is dropped. The neoplasm root
- * says a phenotype is malignant, not where it sits, so a neoplasm resolves
- * through the organ root it also carries — a lung neoplasm is respiratory, and
- * a neoplasm with no organ root at all resolves to nothing.
- *
- * The values are the canonical tokens, so this module declares no organ
- * enumeration of its own.
- */
-/** HPO ancestor id → canonical organ, most specific ancestor first. */
-const HPO_ORGAN_ANCESTORS = [
-    ["HP:0001392", "hepatic"], // Abnormality of the liver
-    ["HP:0001733", "pancreas"], // Abnormality of the pancreas
-    ["HP:0000820", "endocrine_thyroid"], // Abnormality of the thyroid gland
-    ["HP:0000079", "renal"], // Abnormality of the urinary system
-    ["HP:0000078", "reproductive"], // Abnormality of the genital system
-    ["HP:0002597", "vascular"], // Abnormality of the vasculature
-    ["HP:0001627", "cardiac"], // Abnormal heart morphology
-    ["HP:0001626", "cardiac"], // Abnormality of the cardiovascular system
-    ["HP:0000759", "pns"], // Abnormal peripheral nervous system morphology
-    ["HP:0012639", "cns"], // Abnormal nervous system morphology
-    ["HP:0000707", "cns"], // Abnormality of the nervous system
-    ["HP:0002715", "immune"], // Abnormality of the immune system
-    ["HP:0001871", "hematologic"], // Abnormality of blood and blood-forming tissues
-    ["HP:0001939", "metabolic"], // Abnormality of metabolism/homeostasis
-    ["HP:0002086", "respiratory"], // Abnormality of the respiratory system
-    ["HP:0025031", "gi"], // Abnormality of the digestive system
-    ["HP:0000478", "ocular"], // Abnormality of the eye
-    ["HP:0001574", "dermatologic"], // Abnormality of the integument
-    ["HP:0003011", "musculoskeletal"], // Abnormality of the musculature
-    ["HP:0000924", "musculoskeletal"], // Abnormality of the skeletal system
-];
-/**
- * Resolve an HPO term onto a canonical organ from its own id plus its ancestor
- * closure. Returns null when nothing in the ancestry denotes a canonical organ
- * system — the caller drops the phenotype and counts it.
- */
-export function resolveHpoOrgan(termId, ancestorIds) {
-    const ancestry = new Set([termId, ...ancestorIds]);
-    for (const [id, organ] of HPO_ORGAN_ANCESTORS) {
-        if (ancestry.has(id))
-            return organ;
-    }
-    return null;
-}

package/dist/workflows/target-assessment/lib/impc-organ-map.d.ts

@@ -1,19 +0,0 @@
-/**
- * The IMPC top-level-phenotype vocabulary onto the canonical organ vocabulary.
- *
- * Buckets with no organ system to land in (hearing, growth, mortality,
- * craniofacial) are absent: a phenotype is reported under the organ it affects
- * or not at all, never under an approximate neighbour. The map's values are the
- * canonical tokens, so it declares no enumeration of its own.
- *
- * The endocrine bucket is absent for the same reason: IMPC's
- * "endocrine/exocrine gland phenotype" spans every endocrine organ and the
- * exocrine glands besides, while the only endocrine token names the thyroid.
- * A knockout in that bucket names no canonical organ, so it is dropped and
- * counted rather than read as a thyroid finding.
- */
-import type { OrganSystem } from "../../../contracts/organ-system.js";
-/** Resolve one IMPC bucket, or null when it denotes no canonical organ. */
-export declare function resolveImpcOrgan(bucket: string): OrganSystem | null;
-/** Resolve a set of IMPC buckets, dropping those with no canonical organ. */
-export declare function toOrganSystems(impcOrganSystems: readonly string[]): OrganSystem[];