heor-agent-mcp 0.2.0 → 0.7.0

package/dist/tools/populationAdjustedComparison.js.map

@@ -0,0 +1 @@
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package/dist/tools/screenAbstracts.d.ts

@@ -0,0 +1,99 @@
+import type { ToolResult } from "../providers/types.js";
+export declare function handleScreenAbstracts(rawParams: unknown): Promise<ToolResult>;
+export declare const screenAbstractsToolSchema: {
+    name: string;
+    description: string;
+    inputSchema: {
+        type: string;
+        properties: {
+            results: {
+                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[];
+                };
+            };
+            criteria: {
+                type: string;
+                description: string;
+                properties: {
+                    population: {
+                        type: string;
+                        description: string;
+                    };
+                    intervention: {
+                        type: string;
+                        description: string;
+                    };
+                    comparator: {
+                        type: string;
+                        description: string;
+                    };
+                    outcomes: {
+                        type: string;
+                        items: {
+                            type: string;
+                        };
+                        description: string;
+                    };
+                };
+                required: string[];
+            };
+            exclude_study_types: {
+                type: string;
+                items: {
+                    type: string;
+                };
+                description: string;
+            };
+            min_year: {
+                type: string;
+                description: string;
+            };
+            include_threshold: {
+                type: string;
+                description: string;
+            };
+            output_format: {
+                type: string;
+                enum: string[];
+            };
+            project: {
+                type: string;
+                description: string;
+            };
+        };
+        required: string[];
+    };
+};
+//# sourceMappingURL=screenAbstracts.d.ts.map

package/dist/tools/screenAbstracts.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"screenAbstracts.d.ts","sourceRoot":"","sources":["../../src/tools/screenAbstracts.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,UAAU,EAAoB,MAAM,uBAAuB,CAAC;AA6O1E,wBAAsB,qBAAqB,CACzC,SAAS,EAAE,OAAO,GACjB,OAAO,CAAC,UAAU,CAAC,CAoOrB;AAED,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAsErC,CAAC"}

package/dist/tools/screenAbstracts.js

@@ -0,0 +1,442 @@
+import { z } from "zod";
+import { createAuditRecord, addAssumption, addWarning, setMethodology, } from "../audit/builder.js";
+import { auditToMarkdown } from "../formatters/markdown.js";
+/**
+ * Abstract Screening Tool
+ *
+ * Applies PICO-based inclusion/exclusion criteria to literature search
+ * results. Scores each abstract by relevance, classifies study design,
+ * and returns a ranked shortlist with reasons for inclusion/exclusion.
+ *
+ * Follows Cochrane Handbook Chapter 4 screening methodology.
+ */
+const PICOCriteriaSchema = z.object({
+    population: z.string().min(1).describe("Target population (e.g., 'adults with type 2 diabetes')"),
+    intervention: z.string().min(1).describe("Intervention of interest (e.g., 'semaglutide')"),
+    comparator: z.string().optional().describe("Comparator (e.g., 'placebo', 'sitagliptin')"),
+    outcomes: z.array(z.string()).optional().describe("Outcomes of interest (e.g., ['HbA1c', 'weight', 'cardiovascular events'])"),
+});
+const ScreenAbstractsSchema = z.object({
+    results: z.array(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(),
+    })).min(1, "At least 1 result required"),
+    criteria: PICOCriteriaSchema,
+    exclude_study_types: z
+        .array(z.string())
+        .optional()
+        .describe("Study types to exclude (e.g., ['case_report', 'editorial', 'letter', 'commentary'])"),
+    min_year: z.number().optional().describe("Exclude studies before this year"),
+    include_threshold: z
+        .number()
+        .min(0)
+        .max(1)
+        .default(0.3)
+        .describe("Relevance score threshold for inclusion (0-1, default 0.3)"),
+    output_format: z.enum(["text", "json"]).optional(),
+    project: z.string().optional(),
+});
+// Study design hierarchy (higher = stronger evidence)
+const STUDY_DESIGN_SCORES = {
+    systematic_review: 5,
+    meta_analysis: 5,
+    meta: 5,
+    rct: 4,
+    randomized: 4,
+    randomised: 4,
+    controlled_trial: 4,
+    cohort: 3,
+    observational: 3,
+    prospective: 3,
+    retrospective: 2,
+    case_control: 2,
+    cross_sectional: 2,
+    case_series: 1,
+    case_report: 1,
+    editorial: 0,
+    letter: 0,
+    commentary: 0,
+    opinion: 0,
+    narrative_review: 1,
+    review: 2,
+    guideline: 3,
+    hta_report: 4,
+    clinical_trial: 4,
+};
+const EXCLUDE_TYPES = new Set([
+    "editorial", "letter", "commentary", "opinion", "erratum", "corrigendum",
+    "news", "interview", "book_review",
+]);
+function classifyStudyDesign(studyType, title, abstract) {
+    const combined = `${studyType} ${title} ${abstract}`.toLowerCase();
+    if (combined.includes("systematic review") || combined.includes("meta-analysis") || combined.includes("meta analysis"))
+        return "Systematic Review / Meta-Analysis";
+    if (combined.includes("randomized") || combined.includes("randomised") || combined.includes("rct") || combined.includes("phase iii") || combined.includes("phase 3"))
+        return "RCT";
+    if (combined.includes("phase ii") || combined.includes("phase 2") || combined.includes("phase i") || combined.includes("phase 1"))
+        return "Clinical Trial (Phase I/II)";
+    if (combined.includes("clinical trial") || combined.includes("controlled trial"))
+        return "Clinical Trial";
+    if (combined.includes("cohort") || combined.includes("prospective") || combined.includes("longitudinal"))
+        return "Cohort Study";
+    if (combined.includes("retrospective") || combined.includes("database") || combined.includes("claims") || combined.includes("real-world") || combined.includes("registry"))
+        return "Retrospective / RWE";
+    if (combined.includes("case-control") || combined.includes("case control"))
+        return "Case-Control";
+    if (combined.includes("cross-sectional") || combined.includes("survey"))
+        return "Cross-Sectional";
+    if (combined.includes("cost-effectiveness") || combined.includes("cost effectiveness") || combined.includes("economic") || combined.includes("budget impact") || combined.includes("icer") || combined.includes("qaly"))
+        return "Health Economic Study";
+    if (combined.includes("guideline") || combined.includes("recommendation") || combined.includes("consensus"))
+        return "Guideline / Consensus";
+    if (combined.includes("hta") || combined.includes("appraisal") || combined.includes("reimbursement") || combined.includes("technology assessment"))
+        return "HTA Report";
+    if (combined.includes("review") || combined.includes("overview"))
+        return "Narrative Review";
+    if (combined.includes("editorial") || combined.includes("commentary") || combined.includes("letter") || combined.includes("opinion"))
+        return "Editorial / Commentary";
+    if (combined.includes("case report") || combined.includes("case series"))
+        return "Case Report / Series";
+    return "Other";
+}
+function getDesignScore(designClass) {
+    if (designClass.includes("Systematic") || designClass.includes("Meta"))
+        return 5;
+    if (designClass.includes("RCT"))
+        return 4;
+    if (designClass.includes("Clinical Trial"))
+        return 4;
+    if (designClass.includes("HTA"))
+        return 4;
+    if (designClass.includes("Cohort"))
+        return 3;
+    if (designClass.includes("Guideline"))
+        return 3;
+    if (designClass.includes("Health Economic"))
+        return 3;
+    if (designClass.includes("Retrospective"))
+        return 2;
+    if (designClass.includes("Case-Control"))
+        return 2;
+    if (designClass.includes("Cross-Sectional"))
+        return 2;
+    if (designClass.includes("Narrative"))
+        return 1;
+    if (designClass.includes("Editorial"))
+        return 0;
+    if (designClass.includes("Case Report"))
+        return 1;
+    return 1;
+}
+function computeRelevanceScore(result, criteria) {
+    const text = `${result.title} ${result.abstract}`.toLowerCase();
+    const reasons = [];
+    let score = 0;
+    const maxScore = 4; // P + I + C + O
+    // Population match
+    const popTerms = criteria.population.toLowerCase().split(/\s+/).filter((t) => t.length > 3);
+    const popMatches = popTerms.filter((t) => text.includes(t));
+    const popMatch = popMatches.length / Math.max(1, popTerms.length) >= 0.3;
+    if (popMatch) {
+        score += 1;
+        reasons.push(`Population match: ${popMatches.join(", ")}`);
+    }
+    // Intervention match
+    const intTerms = criteria.intervention.toLowerCase().split(/[\s,]+/).filter((t) => t.length > 2);
+    const intMatches = intTerms.filter((t) => text.includes(t));
+    const intMatch = intMatches.length > 0;
+    if (intMatch) {
+        score += 1;
+        reasons.push(`Intervention match: ${intMatches.join(", ")}`);
+    }
+    // Comparator match
+    let compMatch = false;
+    if (criteria.comparator) {
+        const compTerms = criteria.comparator.toLowerCase().split(/[\s,]+/).filter((t) => t.length > 2);
+        const compMatches = compTerms.filter((t) => text.includes(t));
+        compMatch = compMatches.length > 0;
+        if (compMatch) {
+            score += 1;
+            reasons.push(`Comparator match: ${compMatches.join(", ")}`);
+        }
+    }
+    else {
+        score += 0.5; // No comparator specified — partial credit
+        compMatch = true;
+    }
+    // Outcomes match
+    let outMatch = false;
+    if (criteria.outcomes && criteria.outcomes.length > 0) {
+        const outMatches = criteria.outcomes.filter((o) => text.includes(o.toLowerCase()));
+        outMatch = outMatches.length > 0;
+        if (outMatch) {
+            score += 1;
+            reasons.push(`Outcome match: ${outMatches.join(", ")}`);
+        }
+    }
+    else {
+        score += 0.5;
+        outMatch = true;
+    }
+    // Bonus for study design quality
+    const designClass = classifyStudyDesign(result.study_type, result.title, result.abstract);
+    const designScore = getDesignScore(designClass);
+    score += designScore * 0.1; // Small bonus, max 0.5
+    const normalizedScore = Math.min(1, score / maxScore);
+    return {
+        score: Math.round(normalizedScore * 100) / 100,
+        match: {
+            population: popMatch,
+            intervention: intMatch,
+            comparator: compMatch,
+            outcomes: outMatch,
+        },
+        reasons,
+    };
+}
+export async function handleScreenAbstracts(rawParams) {
+    const params = ScreenAbstractsSchema.parse(rawParams);
+    const outputFormat = params.output_format ?? "text";
+    const threshold = params.include_threshold;
+    let audit = createAuditRecord("screen_abstracts", { n_input: params.results.length, criteria: params.criteria }, outputFormat);
+    audit = setMethodology(audit, "PICO-based abstract screening with relevance scoring. Study design classification per Cochrane Handbook Ch. 4.");
+    audit = addAssumption(audit, `Inclusion threshold: ${threshold} (scores below this are excluded)`);
+    audit = addAssumption(audit, `PICO: P=${params.criteria.population}, I=${params.criteria.intervention}, C=${params.criteria.comparator ?? "any"}, O=${params.criteria.outcomes?.join(", ") ?? "any"}`);
+    const excludeTypes = new Set((params.exclude_study_types ?? []).map((t) => t.toLowerCase()));
+    for (const t of EXCLUDE_TYPES)
+        excludeTypes.add(t);
+    const screeningResults = [];
+    for (const result of params.results) {
+        const designClass = classifyStudyDesign(result.study_type, result.title, result.abstract);
+        // Year filter
+        if (params.min_year) {
+            const year = parseInt(result.date?.slice(0, 4) ?? "0", 10);
+            if (year > 0 && year < params.min_year) {
+                screeningResults.push({
+                    id: result.id,
+                    title: result.title,
+                    source: result.source,
+                    authors: result.authors,
+                    date: result.date,
+                    url: result.url,
+                    study_type: result.study_type,
+                    study_design_class: designClass,
+                    relevance_score: 0,
+                    decision: "exclude",
+                    reasons: [`Published ${year}, before minimum year ${params.min_year}`],
+                    pico_match: { population: false, intervention: false, comparator: false, outcomes: false },
+                });
+                continue;
+            }
+        }
+        // Excluded study types
+        const typeKey = result.study_type?.toLowerCase().replace(/[\s-]/g, "_") ?? "";
+        if (excludeTypes.has(typeKey) || designClass === "Editorial / Commentary") {
+            screeningResults.push({
+                id: result.id,
+                title: result.title,
+                source: result.source,
+                authors: result.authors,
+                date: result.date,
+                url: result.url,
+                study_type: result.study_type,
+                study_design_class: designClass,
+                relevance_score: 0,
+                decision: "exclude",
+                reasons: [`Study type excluded: ${designClass}`],
+                pico_match: { population: false, intervention: false, comparator: false, outcomes: false },
+            });
+            continue;
+        }
+        // PICO relevance scoring
+        const { score, match, reasons } = computeRelevanceScore(result, params.criteria);
+        let decision;
+        if (score >= threshold + 0.2) {
+            decision = "include";
+        }
+        else if (score >= threshold) {
+            decision = "uncertain";
+        }
+        else {
+            decision = "exclude";
+            reasons.push(`Relevance score ${score.toFixed(2)} below threshold ${threshold}`);
+        }
+        screeningResults.push({
+            id: result.id,
+            title: result.title,
+            source: result.source,
+            authors: result.authors,
+            date: result.date,
+            url: result.url,
+            study_type: result.study_type,
+            study_design_class: designClass,
+            relevance_score: score,
+            decision,
+            reasons,
+            pico_match: match,
+        });
+    }
+    // Sort: include first, then uncertain, then exclude. Within each: by relevance score descending
+    const order = { include: 0, uncertain: 1, exclude: 2 };
+    screeningResults.sort((a, b) => order[a.decision] - order[b.decision] ||
+        b.relevance_score - a.relevance_score);
+    const included = screeningResults.filter((r) => r.decision === "include");
+    const uncertain = screeningResults.filter((r) => r.decision === "uncertain");
+    const excluded = screeningResults.filter((r) => r.decision === "exclude");
+    audit = addAssumption(audit, `Screening result: ${included.length} included, ${uncertain.length} uncertain, ${excluded.length} excluded (from ${params.results.length} input)`);
+    if (included.length === 0 && uncertain.length === 0) {
+        audit = addWarning(audit, "No studies met inclusion criteria — consider broadening PICO or lowering threshold");
+    }
+    if (outputFormat === "json") {
+        return {
+            content: {
+                summary: {
+                    total_input: params.results.length,
+                    included: included.length,
+                    uncertain: uncertain.length,
+                    excluded: excluded.length,
+                },
+                criteria: params.criteria,
+                results: screeningResults,
+            },
+            audit,
+        };
+    }
+    // Text output — PRISMA-style flow + ranked table
+    const picoStr = [
+        `**P:** ${params.criteria.population}`,
+        `**I:** ${params.criteria.intervention}`,
+        params.criteria.comparator ? `**C:** ${params.criteria.comparator}` : null,
+        params.criteria.outcomes ? `**O:** ${params.criteria.outcomes.join(", ")}` : null,
+    ]
+        .filter(Boolean)
+        .join(" | ");
+    const lines = [
+        `## Abstract Screening Report`,
+        ``,
+        `### PICO Criteria`,
+        picoStr,
+        ``,
+        `### PRISMA Screening Flow`,
+        `- **Records identified:** ${params.results.length}`,
+        `- **Records excluded (study type/date):** ${excluded.filter((r) => r.relevance_score === 0).length}`,
+        `- **Records screened by PICO:** ${params.results.length - excluded.filter((r) => r.relevance_score === 0).length}`,
+        `- **Included:** ${included.length}`,
+        `- **Uncertain (manual review recommended):** ${uncertain.length}`,
+        `- **Excluded (low relevance):** ${excluded.filter((r) => r.relevance_score > 0).length}`,
+        ``,
+    ];
+    if (included.length > 0) {
+        lines.push(`### Included Studies (${included.length})`);
+        lines.push(`| # | Study | Design | Score | P | I | C | O | Source |`);
+        lines.push(`|---|-------|--------|-------|---|---|---|---|--------|`);
+        included.forEach((r, i) => {
+            const p = r.pico_match.population ? "+" : "-";
+            const int = r.pico_match.intervention ? "+" : "-";
+            const c = r.pico_match.comparator ? "+" : "-";
+            const o = r.pico_match.outcomes ? "+" : "-";
+            const titleLink = `[${r.title.slice(0, 60)}${r.title.length > 60 ? "..." : ""}](${r.url})`;
+            lines.push(`| ${i + 1} | ${titleLink} | ${r.study_design_class} | ${r.relevance_score.toFixed(2)} | ${p} | ${int} | ${c} | ${o} | ${r.source} |`);
+        });
+        lines.push(``);
+    }
+    if (uncertain.length > 0) {
+        lines.push(`### Uncertain — Manual Review Recommended (${uncertain.length})`);
+        lines.push(`| # | Study | Design | Score | Reason |`);
+        lines.push(`|---|-------|--------|-------|--------|`);
+        uncertain.forEach((r, i) => {
+            const titleLink = `[${r.title.slice(0, 60)}${r.title.length > 60 ? "..." : ""}](${r.url})`;
+            lines.push(`| ${i + 1} | ${titleLink} | ${r.study_design_class} | ${r.relevance_score.toFixed(2)} | ${r.reasons.join("; ")} |`);
+        });
+        lines.push(``);
+    }
+    if (excluded.length > 0) {
+        lines.push(`### Excluded (${excluded.length})`);
+        lines.push(`<details><summary>Click to expand excluded studies</summary>\n`);
+        lines.push(`| Study | Reason |`);
+        lines.push(`|-------|--------|`);
+        excluded.forEach((r) => {
+            lines.push(`| ${r.title.slice(0, 70)} | ${r.reasons[0] ?? "Low relevance"} |`);
+        });
+        lines.push(`\n</details>\n`);
+    }
+    lines.push(`---`);
+    lines.push(`> **Note:** This is automated screening based on keyword matching against PICO criteria. It supplements but does not replace manual screening by a qualified reviewer. Per Cochrane Handbook, at least two independent reviewers should screen abstracts for systematic reviews.`);
+    lines.push(``);
+    lines.push(auditToMarkdown(audit));
+    return { content: lines.join("\n"), audit };
+}
+export const screenAbstractsToolSchema = {
+    name: "screen_abstracts",
+    description: "Screen literature search results using PICO criteria. Scores each abstract by relevance to the research question, classifies study design, and returns a ranked shortlist with inclusion/exclusion decisions and reasons. Pass the results array from a prior literature_search call (use output_format='json'). Follows Cochrane Handbook Chapter 4 screening methodology.",
+    inputSchema: {
+        type: "object",
+        properties: {
+            results: {
+                type: "array",
+                description: "Array of LiteratureResult objects from a prior literature_search call (use 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"],
+                },
+            },
+            criteria: {
+                type: "object",
+                description: "PICO inclusion criteria",
+                properties: {
+                    population: {
+                        type: "string",
+                        description: "Target population (e.g., 'adults with type 2 diabetes')",
+                    },
+                    intervention: {
+                        type: "string",
+                        description: "Intervention of interest (e.g., 'semaglutide')",
+                    },
+                    comparator: {
+                        type: "string",
+                        description: "Comparator (e.g., 'placebo', 'sitagliptin'). Optional.",
+                    },
+                    outcomes: {
+                        type: "array",
+                        items: { type: "string" },
+                        description: "Outcomes of interest (e.g., ['HbA1c', 'weight loss', 'MACE']). Optional.",
+                    },
+                },
+                required: ["population", "intervention"],
+            },
+            exclude_study_types: {
+                type: "array",
+                items: { type: "string" },
+                description: "Additional study types to exclude (e.g., ['case_report', 'narrative_review']). Editorials/commentaries are always excluded.",
+            },
+            min_year: {
+                type: "number",
+                description: "Exclude studies published before this year",
+            },
+            include_threshold: {
+                type: "number",
+                description: "Relevance score threshold for inclusion (0-1, default 0.3). Lower = more inclusive.",
+            },
+            output_format: { type: "string", enum: ["text", "json"] },
+            project: { type: "string", description: "Project ID for persistence" },
+        },
+        required: ["results", "criteria"],
+    },
+};
+//# sourceMappingURL=screenAbstracts.js.map

package/dist/tools/screenAbstracts.js.map

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