npm - heor-agent-mcp - Versions diffs - 0.9.4 → 0.9.5 - Mend

heor-agent-mcp 0.9.4 → 0.9.5

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Files changed (14) hide show

package/README.md +29 -4
package/dist/providers/types.d.ts +1 -0
package/dist/providers/types.d.ts.map +1 -1
package/dist/server.js +5 -0
package/dist/server.js.map +1 -1
package/dist/tools/htaDossierPrep.d.ts +3 -0
package/dist/tools/htaDossierPrep.d.ts.map +1 -1
package/dist/tools/htaDossierPrep.js +23 -14
package/dist/tools/htaDossierPrep.js.map +1 -1
package/dist/tools/riskOfBias.d.ts +73 -0
package/dist/tools/riskOfBias.d.ts.map +1 -0
package/dist/tools/riskOfBias.js +570 -0
package/dist/tools/riskOfBias.js.map +1 -0
package/package.json +2 -2

package/README.md CHANGED Viewed

@@ -6,7 +6,7 @@
 **AI-powered Health Economics and Outcomes Research (HEOR) agent as a Model Context Protocol server.**
-Automates literature review across 41 data sources, state-of-the-art cost-effectiveness modelling, HTA dossier preparation for NICE / EMA / FDA / IQWiG / HAS / EU JCA, and a persistent project knowledge base — all callable as MCP tools from Claude.ai, Claude Code, and any MCP-compatible host.
+Automates literature review across 41 data sources, risk of bias assessment (RoB 2 / ROBINS-I / AMSTAR-2), state-of-the-art cost-effectiveness modelling, HTA dossier preparation for NICE / EMA / FDA / IQWiG / HAS / EU JCA, and a persistent project knowledge base — all callable as MCP tools from Claude.ai, Claude Code, and any MCP-compatible host.
 Built for pharmaceutical, biotech, CRO, and medical affairs teams who need rigorous, auditable HEOR workflows without building infrastructure from scratch.
@@ -50,8 +50,10 @@ Add to your MCP configuration:
 | Tool | Purpose |
 |------|---------|
 | `literature_search` | Search 41 data sources with a full PRISMA-style audit trail |
+| `screen_abstracts` | PICO-based relevance scoring and study design classification |
+| `risk_of_bias` | Cochrane RoB 2 / ROBINS-I / AMSTAR-2 with GRADE RoB domain summary |
 | `cost_effectiveness_model` | Markov / PartSA / decision-tree CEA with PSA, OWSA, CEAC, EVPI |
-| `hta_dossier_prep` | Draft submissions for NICE, EMA, FDA, IQWiG, HAS, and EU JCA |
+| `hta_dossier_prep` | Draft submissions for NICE, EMA, FDA, IQWiG, HAS, and EU JCA — GRADE table uses structured RoB when `rob_results` passed |
 | `project_create` | Initialize a persistent project workspace |
 | `knowledge_search` | Full-text search across a project's raw/ and wiki/ trees |
 | `knowledge_read` | Read any file from a project's knowledge base |
@@ -113,6 +115,29 @@ Drafts submission-ready sections for six HTA frameworks with gap analysis:
 Accepts piped output from `literature_search` and `cost_effectiveness_model`.
+### `risk_of_bias`
+Assesses risk of bias using the appropriate Cochrane instrument, auto-detected from `study_type`:
+| Study type | Instrument |
+|-----------|-----------|
+| RCT | RoB 2 (5 domains: randomization, deviations, missing data, measurement, reporting) |
+| Observational | ROBINS-I (7 domains: confounding, selection, classification, deviations, missing data, measurement, reporting) |
+| Systematic review | AMSTAR-2 (16 items, critical vs non-critical) |
+Returns a `rob_results` object you can pass directly to `hta_dossier_prep` — this replaces the heuristic RoB estimate in the GRADE table with structured domain judgments.
+**Example call:**
+```json
+{
+  "studies": [{ "id": "pmid_1", "study_type": "RCT", "title": "...", "abstract": "..." }],
+  "output_format": "json"
+}
+```
+**Pipeline:**
+> `literature_search` → `screen_abstracts` → `risk_of_bias` → `hta_dossier_prep`
 ### Knowledge base tools
 Projects live at `~/.heor-agent/projects/{project-id}/` with:
@@ -164,9 +189,9 @@ Copy-paste prompts to try in Claude Code, Claude Desktop, or the [web UI](https:
 ### End-to-end HTA workflow
 **Full dossier preparation**
-> Create a project for semaglutide in obesity targeting NICE and ICER. Search literature for evidence, screen the results for adults with obesity comparing semaglutide to placebo for weight loss outcomes, then draft a NICE STA dossier using the screened results.
+> Create a project for semaglutide in obesity targeting NICE and ICER. Search literature for evidence, screen the results for adults with obesity comparing semaglutide to placebo for weight loss outcomes, assess risk of bias on the screened studies, then draft a NICE STA dossier using the screened results and rob_results.
-This single prompt exercises: `project_create` → `literature_search` → `screen_abstracts` → `hta_dossier_prep` (with auto-GRADE).
+This single prompt exercises: `project_create` → `literature_search` → `screen_abstracts` → `risk_of_bias` → `hta_dossier_prep` (GRADE RoB from structured assessment).
 ---

package/dist/providers/types.d.ts CHANGED Viewed

@@ -95,6 +95,7 @@ export interface DossierParams {
     output_format?: OutputFormat;
     picos?: PicoDefinition[];
     project?: string;
+    rob_results?: any;
 }
 export interface ToolResult {
     content: string | object;

package/dist/providers/types.d.ts.map CHANGED Viewed

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package/dist/server.js CHANGED Viewed

@@ -21,6 +21,7 @@ import { handleBudgetImpactModel, budgetImpactModelToolSchema, } from "./tools/b
 import { handlePopulationAdjustedComparison, populationAdjustedComparisonToolSchema, } from "./tools/populationAdjustedComparison.js";
 import { handleSurvivalFitting, survivalFittingToolSchema, } from "./tools/survivalFitting.js";
 import { handleScreenAbstracts, screenAbstractsToolSchema, } from "./tools/screenAbstracts.js";
+import { handleRiskOfBias, riskOfBiasToolSchema } from "./tools/riskOfBias.js";
 import { handleValidateLinks, validateLinksToolSchema, } from "./tools/validateLinks.js";
 import { randomUUID } from "node:crypto";
 import { trackToolCall, trackSession, shutdownAnalytics } from "./analytics.js";
@@ -147,6 +148,7 @@ function createMcpServer() {
             populationAdjustedComparisonToolSchema,
             survivalFittingToolSchema,
             screenAbstractsToolSchema,
+            riskOfBiasToolSchema,
             validateLinksToolSchema,
         ],
     }));
@@ -195,6 +197,9 @@ function createMcpServer() {
                 case "screen_abstracts":
                     result = await handleScreenAbstracts(args);
                     break;
+                case "risk_of_bias":
+                    result = await handleRiskOfBias(args);
+                    break;
                 case "validate_links":
                     result = await handleValidateLinks(args);
                     break;

package/dist/server.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/tools/htaDossierPrep.d.ts CHANGED Viewed

@@ -75,6 +75,9 @@ export declare const htaDossierPrepToolSchema: {
                 type: string;
                 description: string;
             };
+            rob_results: {
+                description: string;
+            };
         };
         required: string[];
     };

package/dist/tools/htaDossierPrep.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"htaDossierPrep.d.ts","sourceRoot":"","sources":["../../src/tools/htaDossierPrep.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAEV,UAAU,EAGX,MAAM,uBAAuB,CAAC;~~AA0jB~~/B,wBAAsB,oBAAoB,CACxC,SAAS,EAAE,OAAO,GACjB,OAAO,CAAC,UAAU,CAAC,~~CAiHrB~~;AAED,eAAO,MAAM,wBAAwB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAqFpC~~,CAAC"}
1	+ {"version":3,"file":"htaDossierPrep.d.ts","sourceRoot":"","sources":["../../src/tools/htaDossierPrep.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAEV,UAAU,EAGX,MAAM,uBAAuB,CAAC;AAolB/B,wBAAsB,oBAAoB,CACxC,SAAS,EAAE,OAAO,GACjB,OAAO,CAAC,UAAU,CAAC,CAkHrB;AAED,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAyFpC,CAAC"}

package/dist/tools/htaDossierPrep.js CHANGED Viewed

@@ -23,6 +23,7 @@ const DossierSchema = z.object({
         .optional(),
     output_format: z.enum(["text", "json", "docx"]).optional(),
     project: z.string().optional(),
+    rob_results: z.any().optional(),
 });
 import { createAuditRecord, addAssumption, addWarning, setMethodology, } from "../audit/builder.js";
 import { auditToMarkdown } from "../formatters/markdown.js";
@@ -98,15 +99,7 @@ const METHODOLOGY_BY_BODY = {
     jca: "EUHTA Regulation (EU) 2021/2282 — Joint Clinical Assessment",
     gvd: "Global Value Dossier — cross-market foundational evidence document (ISPOR GVD best practices)",
 };
-/**
- * Auto-generate GRADE evidence quality assessment from literature results.
- *
- * GRADE domains: Risk of bias, Inconsistency, Indirectness, Imprecision, Publication bias
- * Ratings: High, Moderate, Low, Very Low
- *
- * Uses study type counts and basic heuristics from the evidence set.
- */
-function generateGradeTable(evidence, outcomes) {
+function generateGradeTable(evidence, outcomes, robResults) {
     if (evidence.length === 0)
         return "";
     // Count study types
@@ -126,8 +119,12 @@ function generateGradeTable(evidence, outcomes) {
         const relevant = evidence.filter((r) => r.title?.toLowerCase().includes(outcome.toLowerCase()) ||
             r.abstract?.toLowerCase().includes(outcome.toLowerCase()));
         const nRelevant = relevant.length;
-        // Risk of bias
-        const rob = hasRCTs || hasMAs ? "Low" : "High";
+        // Risk of bias — use structured assessment when available, else heuristic
+        const rob = robResults
+            ? robResults.summary.rob_judgment
+            : hasRCTs || hasMAs
+                ? "Low"
+                : "High";
         // Inconsistency: if multiple studies, assume some inconsistency possible
         const inconsistency = nRelevant > 3 ? "Low" : nRelevant > 1 ? "Moderate" : "Serious";
         // Indirectness: assume moderate unless direct evidence exists
@@ -148,7 +145,13 @@ function generateGradeTable(evidence, outcomes) {
             downgrades++;
         if (pub_bias === "Suspected")
             downgrades++;
-        const baseLevel = hasRCTs ? 4 : 2; // High=4, Low=2
+        const baseLevel = robResults
+            ? robResults.overall_certainty_start === "High"
+                ? 4
+                : 2
+            : hasRCTs
+                ? 4
+                : 2; // High=4, Low=2
         const finalLevel = Math.max(1, baseLevel - downgrades);
         const certainty = finalLevel >= 4
             ? "High"
@@ -204,7 +207,10 @@ function generateGradeTable(evidence, outcomes) {
         lines.push(`| ${outcome} | **${a.certainty}** ${certIcon} | ${a.rob} | ${a.inconsistency} | ${a.indirectness} | ${a.imprecision} | ${a.pub_bias} | ${a.rationale} |`);
     }
     lines.push(``);
-    lines.push(`> **Note:** This is an automated GRADE assessment based on study counts and types. A definitive GRADE evaluation requires clinical expert judgment on each domain. See [GRADE Handbook](https://gdt.gradepro.org/app/handbook/handbook.html).`);
+    const robSource = robResults
+        ? "structured Risk of Bias assessment (RoB 2/ROBINS-I/AMSTAR-2)"
+        : "study counts and types (heuristic — run `risk_of_bias` tool for structured assessment)";
+    lines.push(`> **Note:** RoB domain sourced from ${robSource}. All other domains are automated estimates. A definitive GRADE evaluation requires clinical expert judgment. See [GRADE Handbook](https://gdt.gradepro.org/app/handbook/handbook.html).`);
     lines.push(``);
     return lines.join("\n");
 }
@@ -456,7 +462,7 @@ export async function handleHtaDossierPrep(rawParams) {
     // Auto-generate GRADE table when evidence is provided as LiteratureResult[]
     if (Array.isArray(params.evidence_summary) &&
         params.evidence_summary.length > 0) {
-        const gradeTable = generateGradeTable(params.evidence_summary, []);
+        const gradeTable = generateGradeTable(params.evidence_summary, [], params.rob_results);
         if (gradeTable) {
             lines.push(gradeTable);
             audit = addAssumption(audit, "GRADE evidence quality assessment auto-generated from literature search results");
@@ -562,6 +568,9 @@ export const htaDossierPrepToolSchema = {
                 type: "string",
                 description: "Project ID for knowledge base persistence. When set, dossier draft is saved to ~/.heor-agent/projects/{project}/raw/dossiers/",
             },
+            rob_results: {
+                description: "Output from the risk_of_bias tool. When provided, the GRADE Risk of Bias domain uses the structured judgment (rob_judgment, downgrade, rationale) instead of a heuristic estimate.",
+            },
         },
         required: ["hta_body", "submission_type", "drug_name", "indication"],
     },

package/dist/tools/htaDossierPrep.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/tools/riskOfBias.d.ts ADDED Viewed

@@ -0,0 +1,73 @@
+import type { ToolResult } from "../providers/types.js";
+export declare function handleRiskOfBias(rawParams: unknown): Promise<ToolResult>;
+export declare const riskOfBiasToolSchema: {
+    name: string;
+    description: string;
+    annotations: {
+        title: string;
+        readOnlyHint: boolean;
+        destructiveHint: boolean;
+        idempotentHint: boolean;
+        openWorldHint: boolean;
+    };
+    inputSchema: {
+        type: string;
+        properties: {
+            studies: {
+                type: string;
+                description: string;
+                items: {
+                    type: string;
+                    properties: {
+                        id: {
+                            type: string;
+                        };
+                        source: {
+                            type: string;
+                        };
+                        title: {
+                            type: string;
+                        };
+                        authors: {
+                            type: string;
+                            items: {
+                                type: string;
+                            };
+                        };
+                        date: {
+                            type: string;
+                        };
+                        study_type: {
+                            type: string;
+                        };
+                        abstract: {
+                            type: string;
+                        };
+                        url: {
+                            type: string;
+                        };
+                    };
+                    required: string[];
+                };
+            };
+            instrument: {
+                type: string;
+                enum: string[];
+                description: string;
+            };
+            outcomes: {
+                type: string;
+                items: {
+                    type: string;
+                };
+                description: string;
+            };
+            output_format: {
+                type: string;
+                enum: string[];
+            };
+        };
+        required: string[];
+    };
+};
+//# sourceMappingURL=riskOfBias.d.ts.map

package/dist/tools/riskOfBias.d.ts.map ADDED Viewed

	@@ -0,0 +1 @@
1	+ {"version":3,"file":"riskOfBias.d.ts","sourceRoot":"","sources":["../../src/tools/riskOfBias.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,UAAU,EAAoB,MAAM,uBAAuB,CAAC;AAmhB1E,wBAAsB,gBAAgB,CACpC,SAAS,EAAE,OAAO,GACjB,OAAO,CAAC,UAAU,CAAC,CA+NrB;AAED,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CA0DhC,CAAC"}

package/dist/tools/riskOfBias.js ADDED Viewed

@@ -0,0 +1,570 @@
+import { z } from "zod";
+import { createAuditRecord, addAssumption, addWarning, setMethodology, } from "../audit/builder.js";
+import { auditToMarkdown } from "../formatters/markdown.js";
+const StudyInputSchema = z.object({
+    id: z.string(),
+    source: z.string(),
+    title: z.string(),
+    authors: z.array(z.string()),
+    date: z.string(),
+    study_type: z.string(),
+    abstract: z.string(),
+    url: z.string(),
+});
+const RiskOfBiasSchema = z.object({
+    studies: z.array(StudyInputSchema).min(1, "At least 1 study required"),
+    instrument: z
+        .enum(["auto", "rob2", "robins_i", "amstar2"])
+        .default("auto")
+        .describe("Assessment instrument. auto detects from study_type."),
+    outcomes: z
+        .array(z.string())
+        .optional()
+        .describe("Outcomes of interest for domain-level context"),
+    output_format: z.enum(["text", "json"]).optional(),
+});
+function detectInstrument(studyType, title, abstract) {
+    const text = `${studyType} ${title} ${abstract}`.toLowerCase();
+    if (text.includes("systematic review") ||
+        text.includes("meta-analysis") ||
+        text.includes("meta analysis") ||
+        /\b(sr|ma)\b/.test(text))
+        return "amstar2";
+    if (text.includes("randomized") ||
+        text.includes("randomised") ||
+        text.includes("rct") ||
+        text.includes("phase iii") ||
+        text.includes("phase 3") ||
+        // Phase II only counts if there is also a randomization signal
+        ((text.includes("phase ii") || text.includes("phase 2")) &&
+            (text.includes("randomized") || text.includes("randomised"))) ||
+        text.includes("clinical trial") ||
+        text.includes("controlled trial"))
+        return "rob2";
+    if (text.includes("cohort") ||
+        text.includes("observational") ||
+        text.includes("case-control") ||
+        text.includes("cross-sectional") ||
+        text.includes("registry") ||
+        text.includes("retrospective") ||
+        text.includes("real-world") ||
+        text.includes("claims"))
+        return "robins_i";
+    return "rob2"; // default
+}
+function inferDomain(text, positiveSignals, negativeSignals, lowLabel, highLabel) {
+    const lower = text.toLowerCase();
+    const posHits = positiveSignals.filter((s) => lower.includes(s));
+    const negHits = negativeSignals.filter((s) => lower.includes(s));
+    if (negHits.length > 0) {
+        return {
+            judgment: highLabel,
+            rationale: `Concern signals: ${negHits.join(", ")}`,
+        };
+    }
+    if (posHits.length >= 2) {
+        return {
+            judgment: lowLabel,
+            rationale: `Quality signals: ${posHits.join(", ")}`,
+        };
+    }
+    if (posHits.length === 1) {
+        return {
+            judgment: `Probably ${lowLabel}`,
+            rationale: `Partial signal: ${posHits[0]}`,
+        };
+    }
+    return {
+        judgment: "Unclear",
+        rationale: "No relevant methodological details reported in abstract",
+        uncertainty_note: "Full-text review required for this domain",
+    };
+}
+// ── RoB 2 (RCTs) ─────────────────────────────────────────────────────────────
+function assessRob2(study) {
+    const text = `${study.title} ${study.abstract}`;
+    const domains = {
+        "D1: Randomization": inferDomain(text, [
+            "randomized",
+            "randomised",
+            "allocation concealment",
+            "stratified",
+            "computer-generated",
+            "central randomization",
+            "sealed envelope",
+        ], [
+            "open-label",
+            "no allocation concealment",
+            "quasi-randomized",
+            "non-randomized",
+        ], "Low", "High"),
+        "D2: Deviations": inferDomain(text, [
+            "intention-to-treat",
+            "itt analysis",
+            "full analysis set",
+            "double-blind",
+            "blinded",
+            "masked",
+            "double blind",
+        ], ["open-label", "per-protocol only", "unblinded", "protocol deviation"], "Low", "High"),
+        "D3: Missing data": inferDomain(text, [
+            "complete follow-up",
+            "no missing data",
+            "multiple imputation",
+            "locf",
+            "full analysis set",
+            "low dropout",
+            "itt population",
+        ], [
+            "high dropout",
+            "substantial missing",
+            "lost to follow-up >20%",
+            "withdrew",
+        ], "Low", "High"),
+        "D4: Measurement": inferDomain(text, [
+            "blinded assessment",
+            "central adjudication",
+            "adjudicated",
+            "objective outcome",
+            "independent committee",
+            "blinded evaluator",
+        ], [
+            "self-reported",
+            "unblinded assessment",
+            "investigator-assessed without blinding",
+        ], "Low", "High"),
+        "D5: Reporting": inferDomain(text, [
+            "pre-registered",
+            "nct",
+            "clinicaltrials.gov",
+            "isrctn",
+            "protocol pre-specified",
+            "primary endpoint pre-specified",
+            "registered trial",
+        ], ["post-hoc", "unregistered", "exploratory analysis as primary"], "Low", "High"),
+    };
+    const judgments = Object.values(domains).map((d) => d.judgment);
+    const hasHigh = judgments.some((j) => j === "High" || j === "Critical");
+    const hasProbHigh = judgments.some((j) => j.includes("Probably High"));
+    const hasUnclear = judgments.some((j) => j === "Unclear");
+    let overall;
+    if (!hasHigh && !hasProbHigh && !hasUnclear)
+        overall = "Low";
+    else if (hasHigh)
+        overall = "High";
+    else
+        overall = "Some concerns";
+    return { domains, overall, instrument: "rob2" };
+}
+// ── ROBINS-I (observational) ──────────────────────────────────────────────────
+function assessRobinsI(study) {
+    const text = `${study.title} ${study.abstract}`;
+    const domains = {
+        "D1: Confounding": inferDomain(text, [
+            "adjusted for",
+            "propensity score",
+            "multivariable",
+            "multivariate",
+            "controlled for",
+            "adjusted analysis",
+            "regression adjustment",
+        ], ["unadjusted", "no adjustment for confounding", "crude analysis only"], "Low", "Serious"),
+        "D2: Selection": inferDomain(text, [
+            "consecutive patients",
+            "population-based",
+            "all eligible",
+            "prospective enrollment",
+            "inception cohort",
+        ], [
+            "selection bias",
+            "convenience sample",
+            "volunteer bias",
+            "selected population",
+        ], "Low", "Serious"),
+        "D3: Classification": inferDomain(text, [
+            "clearly defined",
+            "objective criteria",
+            "validated definition",
+            "icd codes",
+            "standardized criteria",
+        ], ["misclassification", "unclear definition", "subjective classification"], "Low", "Serious"),
+        "D4: Deviations": inferDomain(text, ["adherence monitored", "compliance assessed", "as-treated analysis"], ["substantial crossover", "contamination", "protocol deviation"], "Low", "Moderate"),
+        "D5: Missing data": inferDomain(text, [
+            "complete data",
+            "no missing",
+            "multiple imputation",
+            "complete case analysis justified",
+        ], [
+            "substantial missing data",
+            "high proportion missing",
+            "incomplete follow-up",
+            "high attrition",
+        ], "Low", "Serious"),
+        "D6: Measurement": inferDomain(text, [
+            "validated instrument",
+            "objective measure",
+            "medical records",
+            "electronic health records",
+            "blinded outcome assessment",
+        ], ["self-reported", "recall bias", "subjective measure", "unvalidated"], "Low", "Serious"),
+        "D7: Reporting": inferDomain(text, [
+            "registered",
+            "protocol available",
+            "pre-specified analysis",
+            "prospero",
+        ], ["post-hoc", "unplanned exploratory", "outcome switching suspected"], "Low", "Serious"),
+    };
+    const judgments = Object.values(domains).map((d) => d.judgment);
+    const hasCritical = judgments.some((j) => j === "Critical");
+    const hasSerious = judgments.some((j) => j === "Serious");
+    const hasModerate = judgments.some((j) => j === "Moderate");
+    let overall;
+    if (hasCritical)
+        overall = "Critical";
+    else if (hasSerious)
+        overall = "Serious";
+    else if (hasModerate)
+        overall = "Moderate";
+    else
+        overall = "Low";
+    return { domains, overall, instrument: "robins_i" };
+}
+// ── AMSTAR-2 (systematic reviews) ─────────────────────────────────────────────
+function assessAmstar2(study) {
+    const text = `${study.title} ${study.abstract}`;
+    const domains = {
+        "Item 1: PICO pre-specified": inferDomain(text, ["protocol", "prospero", "pre-specified", "registered", "pico"], ["no protocol", "unregistered review"], "Yes", "No"),
+        "Item 2: Comprehensive search": inferDomain(text, [
+            "multiple databases",
+            "pubmed",
+            "medline",
+            "embase",
+            "cochrane",
+            "grey literature",
+            "hand search",
+            "systematic search",
+        ], ["single database", "limited search"], "Yes", "No"),
+        "Item 7: RoB in primary studies": inferDomain(text, [
+            "risk of bias",
+            "quality assessment",
+            "rob",
+            "cochrane tool",
+            "newcastle-ottawa",
+            "study quality",
+        ], ["no quality assessment", "quality not assessed"], "Yes", "No"),
+        "Item 11: Meta-analysis methods": inferDomain(text, [
+            "heterogeneity",
+            "i²",
+            "i2",
+            "random effects",
+            "fixed effects",
+            "pooled",
+            "forest plot",
+        ], ["inappropriate pooling", "ignored heterogeneity"], "Yes", "No"),
+        "Item 13: Publication bias": inferDomain(text, [
+            "funnel plot",
+            "egger",
+            "begg",
+            "publication bias",
+            "small study effects",
+        ], ["publication bias not assessed", "no funnel plot"], "Yes", "No"),
+        "Item 16: Funding/COI": inferDomain(text, ["funding", "conflict of interest", "coi", "sponsor", "no conflict"], ["funding not reported", "coi not disclosed"], "Yes", "No"),
+    };
+    const judgments = Object.values(domains).map((d) => d.judgment);
+    const yesCount = judgments.reduce((sum, j) => {
+        if (j === "Yes")
+            return sum + 1;
+        if (j === "Probably Yes")
+            return sum + 0.5;
+        return sum;
+    }, 0);
+    const total = judgments.length;
+    let overall;
+    if (yesCount === total)
+        overall = "High";
+    else if (yesCount >= total * 0.7)
+        overall = "Moderate";
+    else if (yesCount >= total * 0.4)
+        overall = "Low";
+    else
+        overall = "Critically Low";
+    return { domains, overall, instrument: "amstar2" };
+}
+// ── Overall badge ─────────────────────────────────────────────────────────────
+function overallBadge(overall, instrument) {
+    if (instrument === "rob2") {
+        if (overall === "Low")
+            return "✅ Low";
+        if (overall === "Some concerns")
+            return "⚠️ Some concerns";
+        return "❌ High";
+    }
+    if (instrument === "robins_i") {
+        if (overall === "Low")
+            return "✅ Low";
+        if (overall === "Moderate")
+            return "🟡 Moderate";
+        if (overall === "Serious")
+            return "⚠️ Serious";
+        return "❌ Critical";
+    }
+    // amstar2
+    if (overall === "High")
+        return "✅ High";
+    if (overall === "Moderate")
+        return "🟡 Moderate";
+    if (overall === "Low")
+        return "⚠️ Low";
+    return "❌ Critically Low";
+}
+// ── GRADE RoB summary ─────────────────────────────────────────────────────────
+function buildGradeSummary(assessments) {
+    const rctCount = assessments.filter((a) => a.instrument === "rob2").length;
+    const obsCount = assessments.filter((a) => a.instrument === "robins_i").length;
+    // amstar2-only → inherit from the reviews' included studies (unknown here) → conservative Low
+    const overall_certainty_start = rctCount > 0 ? "High" : "Low";
+    const rob2Overalls = assessments
+        .filter((a) => a.instrument === "rob2")
+        .map((a) => a.overall);
+    const robinsOveralls = assessments
+        .filter((a) => a.instrument === "robins_i")
+        .map((a) => a.overall);
+    const hasHighRob = rob2Overalls.some((o) => o === "High");
+    const hasSomeConcerns = rob2Overalls.some((o) => o === "Some concerns");
+    const hasSeriousRobins = robinsOveralls.some((o) => o === "Serious" || o === "Critical");
+    let rob_judgment;
+    let downgrade;
+    let rationale;
+    if (hasHighRob || hasSeriousRobins) {
+        rob_judgment = "High";
+        downgrade = true;
+        rationale = "One or more studies rated High/Serious risk of bias";
+    }
+    else if (hasSomeConcerns) {
+        rob_judgment = "Some concerns";
+        downgrade = false;
+        rationale = "Some studies have concerns but no serious flaws detected";
+    }
+    else {
+        rob_judgment = "Probably Low";
+        downgrade = false;
+        rationale =
+            "Majority of evidence from studies with low or probably low risk of bias";
+    }
+    return { rob_judgment, downgrade, rationale, overall_certainty_start };
+}
+// ── Main handler ──────────────────────────────────────────────────────────────
+export async function handleRiskOfBias(rawParams) {
+    const params = RiskOfBiasSchema.parse(rawParams);
+    const outputFormat = params.output_format ?? "text";
+    let audit = createAuditRecord("risk_of_bias", {
+        n_studies: params.studies.length,
+        instrument: params.instrument,
+    }, outputFormat);
+    audit = setMethodology(audit, "Cochrane RoB 2 (RCTs), ROBINS-I (observational), AMSTAR-2 (systematic reviews). Domain judgments inferred from abstract text; domains without reporting signals marked Unclear.");
+    audit = addAssumption(audit, "Abstract-based inference: allocation concealment, blinding, and registration details are often not reported in abstracts — expect Unclear in some domains. Full-text review recommended for high-stakes assessments.");
+    // Assess each study
+    const studyAssessments = [];
+    for (const study of params.studies) {
+        const chosen = params.instrument === "auto"
+            ? detectInstrument(study.study_type, study.title, study.abstract)
+            : params.instrument;
+        const assumed = params.instrument === "auto";
+        let result;
+        if (chosen === "rob2")
+            result = assessRob2(study);
+        else if (chosen === "robins_i")
+            result = assessRobinsI(study);
+        else
+            result = assessAmstar2(study);
+        studyAssessments.push({
+            id: study.id,
+            title: study.title,
+            url: study.url,
+            date: study.date,
+            instrument: chosen,
+            instrument_assumed: assumed,
+            domains: result.domains,
+            overall: result.overall,
+        });
+    }
+    const gradeSummary = buildGradeSummary(studyAssessments);
+    // rob_results structured object — passed to hta_dossier_prep
+    const rob_results = {
+        studies: studyAssessments.map((s) => ({
+            id: s.id,
+            title: s.title,
+            url: s.url,
+            date: s.date,
+            instrument: s.instrument,
+            instrument_assumed: s.instrument_assumed,
+            domains: s.domains,
+            overall: s.overall,
+        })),
+        summary: {
+            n_assessed: studyAssessments.length,
+            rob2_count: studyAssessments.filter((s) => s.instrument === "rob2")
+                .length,
+            robins_i_count: studyAssessments.filter((s) => s.instrument === "robins_i").length,
+            amstar2_count: studyAssessments.filter((s) => s.instrument === "amstar2")
+                .length,
+            rob_judgment: gradeSummary.rob_judgment,
+            downgrade: gradeSummary.downgrade,
+            rationale: gradeSummary.rationale,
+        },
+        overall_certainty_start: gradeSummary.overall_certainty_start,
+    };
+    if (outputFormat === "json") {
+        return { content: rob_results, audit };
+    }
+    // ── Markdown output ───────────────────────────────────────────────────────
+    const rob2Studies = studyAssessments.filter((s) => s.instrument === "rob2");
+    const robinsStudies = studyAssessments.filter((s) => s.instrument === "robins_i");
+    const amstarStudies = studyAssessments.filter((s) => s.instrument === "amstar2");
+    const instrumentSummary = [
+        rob2Studies.length > 0 ? `RoB 2 (RCT): ${rob2Studies.length}` : null,
+        robinsStudies.length > 0
+            ? `ROBINS-I (observational): ${robinsStudies.length}`
+            : null,
+        amstarStudies.length > 0
+            ? `AMSTAR-2 (SR/MA): ${amstarStudies.length}`
+            : null,
+    ]
+        .filter(Boolean)
+        .join(" | ");
+    const lines = [
+        `## Risk of Bias Assessment`,
+        ``,
+        `**Studies assessed:** ${studyAssessments.length} (${instrumentSummary})`,
+        ``,
+    ];
+    // RoB 2 table
+    if (rob2Studies.length > 0) {
+        lines.push(`### RoB 2 — Randomized Controlled Trials`);
+        const domainKeys = Object.keys(rob2Studies[0].domains);
+        lines.push(`| Study | ${domainKeys.join(" | ")} | Overall |`);
+        lines.push(`|---|${domainKeys.map(() => "---").join("|")}|---|`);
+        for (const s of rob2Studies) {
+            const titleLink = `[${s.title.slice(0, 55)}${s.title.length > 55 ? "..." : ""}](${s.url})`;
+            const domainCells = domainKeys
+                .map((k) => s.domains[k].judgment)
+                .join(" | ");
+            lines.push(`| ${titleLink} | ${domainCells} | ${overallBadge(s.overall, "rob2")} |`);
+        }
+        lines.push(``);
+        // Uncertainty notes
+        const uncertainStudies = rob2Studies.filter((s) => Object.values(s.domains).some((d) => d.uncertainty_note));
+        if (uncertainStudies.length > 0) {
+            lines.push(`**Unclear domains** (abstract lacked methodological detail — full-text review recommended):`);
+            for (const s of uncertainStudies) {
+                const unclearDomains = Object.entries(s.domains)
+                    .filter(([, d]) => d.uncertainty_note)
+                    .map(([k]) => k);
+                lines.push(`- ${s.title.slice(0, 60)}: ${unclearDomains.join(", ")}`);
+            }
+            lines.push(``);
+        }
+    }
+    // ROBINS-I table
+    if (robinsStudies.length > 0) {
+        lines.push(`### ROBINS-I — Observational Studies`);
+        const domainKeys = Object.keys(robinsStudies[0].domains);
+        lines.push(`| Study | ${domainKeys.join(" | ")} | Overall |`);
+        lines.push(`|---|${domainKeys.map(() => "---").join("|")}|---|`);
+        for (const s of robinsStudies) {
+            const titleLink = `[${s.title.slice(0, 55)}${s.title.length > 55 ? "..." : ""}](${s.url})`;
+            const domainCells = domainKeys
+                .map((k) => s.domains[k].judgment)
+                .join(" | ");
+            lines.push(`| ${titleLink} | ${domainCells} | ${overallBadge(s.overall, "robins_i")} |`);
+        }
+        lines.push(``);
+    }
+    // AMSTAR-2 table
+    if (amstarStudies.length > 0) {
+        lines.push(`### AMSTAR-2 — Systematic Reviews / Meta-Analyses`);
+        const domainKeys = Object.keys(amstarStudies[0].domains);
+        lines.push(`| Review | ${domainKeys.join(" | ")} | Confidence |`);
+        lines.push(`|---|${domainKeys.map(() => "---").join("|")}|---|`);
+        for (const s of amstarStudies) {
+            const titleLink = `[${s.title.slice(0, 55)}${s.title.length > 55 ? "..." : ""}](${s.url})`;
+            const domainCells = domainKeys
+                .map((k) => s.domains[k].judgment)
+                .join(" | ");
+            lines.push(`| ${titleLink} | ${domainCells} | ${overallBadge(s.overall, "amstar2")} |`);
+        }
+        lines.push(``);
+    }
+    // GRADE RoB summary
+    lines.push(`### GRADE Risk of Bias Domain`);
+    lines.push(`| Aspect | Assessment |`);
+    lines.push(`|---|---|`);
+    lines.push(`| RoB judgment | **${gradeSummary.rob_judgment}** |`);
+    lines.push(`| Downgrade GRADE certainty? | ${gradeSummary.downgrade ? "**Yes (−1)** " : "No"} |`);
+    lines.push(`| Rationale | ${gradeSummary.rationale} |`);
+    lines.push(`| Evidence base starts at | ${gradeSummary.overall_certainty_start} (before other GRADE domains) |`);
+    lines.push(``);
+    if (gradeSummary.downgrade) {
+        audit = addWarning(audit, "RoB domain triggers GRADE downgrade — overall certainty reduced by 1 level");
+    }
+    lines.push(`> **Pass \`rob_results\` to \`hta_dossier_prep\`** to use this assessment in the GRADE table instead of the heuristic fallback.`);
+    lines.push(``);
+    lines.push(auditToMarkdown(audit));
+    return { content: lines.join("\n"), audit };
+}
+export const riskOfBiasToolSchema = {
+    name: "risk_of_bias",
+    description: "Assess risk of bias for a set of studies using the appropriate Cochrane instrument: RoB 2 (RCTs), ROBINS-I (observational studies), or AMSTAR-2 (systematic reviews/meta-analyses). Instrument is auto-detected from study_type or can be specified. Judgments are inferred from abstract text — domains without sufficient reporting are marked Unclear. Returns a per-study table and a rob_results object to pass to hta_dossier_prep for evidence-based GRADE assessment.",
+    annotations: {
+        title: "Risk of Bias Assessment",
+        readOnlyHint: true,
+        destructiveHint: false,
+        idempotentHint: true,
+        openWorldHint: false,
+    },
+    inputSchema: {
+        type: "object",
+        properties: {
+            studies: {
+                type: "array",
+                description: "Array of study objects from screen_abstracts or literature_search (output_format='json')",
+                items: {
+                    type: "object",
+                    properties: {
+                        id: { type: "string" },
+                        source: { type: "string" },
+                        title: { type: "string" },
+                        authors: { type: "array", items: { type: "string" } },
+                        date: { type: "string" },
+                        study_type: { type: "string" },
+                        abstract: { type: "string" },
+                        url: { type: "string" },
+                    },
+                    required: [
+                        "id",
+                        "source",
+                        "title",
+                        "authors",
+                        "date",
+                        "study_type",
+                        "abstract",
+                        "url",
+                    ],
+                },
+            },
+            instrument: {
+                type: "string",
+                enum: ["auto", "rob2", "robins_i", "amstar2"],
+                description: "Assessment instrument. auto (default) detects from study_type. rob2 for RCTs, robins_i for observational, amstar2 for systematic reviews.",
+            },
+            outcomes: {
+                type: "array",
+                items: { type: "string" },
+                description: "Outcomes of interest for contextual domain assessment (optional)",
+            },
+            output_format: { type: "string", enum: ["text", "json"] },
+        },
+        required: ["studies"],
+    },
+};
+//# sourceMappingURL=riskOfBias.js.map

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+ 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package/package.json CHANGED Viewed

@@ -1,13 +1,13 @@
 {
   "name": "heor-agent-mcp",
-  "version": "0.9.4",
+  "version": "0.9.5",
   "mcpName": "io.github.neptun2000/heor-agent",
   "license": "MIT",
   "author": "mnaumov",
   "engines": {
     "node": ">=20.0.0"
   },
-  "description": "AI-powered Health Economics and Outcomes Research (HEOR) MCP server — 14 tools across literature search (41 data sources incl. PubMed/ClinicalTrials.gov/Cochrane/NICE/CADTH/ICER), cost-effectiveness modeling (Markov/PartSA/PSA/EVPPI), budget impact analysis, abstract screening, survival curve fitting (NICE DSU TSD 14), indirect comparisons (Bucher/NMA/MAIC/STC), and HTA dossier prep (NICE/EMA/FDA/IQWiG/HAS/EU JCA) with auto-GRADE",
+  "description": "AI-powered Health Economics and Outcomes Research (HEOR) MCP server — 15 tools across literature search (41 data sources incl. PubMed/ClinicalTrials.gov/Cochrane/NICE/CADTH/ICER), risk of bias (RoB 2/ROBINS-I/AMSTAR-2), cost-effectiveness modeling (Markov/PartSA/PSA/EVPPI), budget impact analysis, abstract screening, survival curve fitting (NICE DSU TSD 14), indirect comparisons (Bucher/NMA/MAIC/STC), and HTA dossier prep (NICE/EMA/FDA/IQWiG/HAS/EU JCA) with auto-GRADE",
   "type": "module",
   "main": "dist/server.js",
   "bin": {