@cyanheads/pubmed-mcp-server 2.2.6 → 2.3.0

package/CLAUDE.md

@@ -1,7 +1,7 @@
 # Agent Protocol
 
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.2.6
+**Version:** 2.3.0
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
 
 > **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
@@ -185,7 +185,7 @@ src/
       parsing/                          # XML parsers (article, esummary, PMC)
       formatting/                       # Citation formatter (APA, MLA, BibTeX, RIS)
   mcp-server/
-    tools/definitions/                  # 7 tool definitions (*.tool.ts)
+    tools/definitions/                  # 9 tool definitions (*.tool.ts)
     resources/definitions/              # database-info.resource.ts
     prompts/definitions/                # research-plan.prompt.ts
 ```

package/README.md

@@ -1,13 +1,13 @@
 <div align="center">
   <h1>@cyanheads/pubmed-mcp-server</h1>
   <p><b>MCP server for the NCBI E-utilities API. Search PubMed, fetch article metadata and full text, generate citations, explore MeSH terms, and discover related research. STDIO or Streamable HTTP.</b>
-  <div>7 Tools • 1 Resource • 1 Prompt</div>
+  <div>9 Tools • 1 Resource • 1 Prompt</div>
   </p>
 </div>
 
 <div align="center">
 
-[![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![Version](https://img.shields.io/badge/Version-2.2.6-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.27.1-green.svg?style=flat-square)](https://modelcontextprotocol.io/) 
+[![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![Version](https://img.shields.io/badge/Version-2.3.0-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.27.1-green.svg?style=flat-square)](https://modelcontextprotocol.io/) 
 
 [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
 
@@ -23,7 +23,7 @@
 
 ## Tools
 
-Seven tools for working with PubMed and NCBI data:
+Nine tools for working with PubMed and NCBI data:
 
 | Tool | Description |
 |:---|:---|
@@ -34,6 +34,8 @@ Seven tools for working with PubMed and NCBI data:
 | `pubmed_find_related` | Find similar articles, citing articles, or references for a given PMID |
 | `pubmed_spell_check` | Spell-check biomedical queries using NCBI's ESpell service |
 | `pubmed_lookup_mesh` | Search and explore MeSH vocabulary — tree numbers, scope notes, entry terms |
+| `pubmed_lookup_citation` | Resolve partial bibliographic references to PubMed IDs via ECitMatch |
+| `pubmed_convert_ids` | Convert between DOI, PMID, and PMCID using the PMC ID Converter API |
 
 ### `pubmed_search_articles`
 
@@ -114,6 +116,28 @@ Search and explore the MeSH (Medical Subject Headings) vocabulary.
 - Detailed records with tree numbers, scope notes, and entry terms by default
 - Useful for building precise PubMed queries with controlled vocabulary
 
+---
+
+### `pubmed_lookup_citation`
+
+Resolve partial bibliographic references to PubMed IDs via NCBI ECitMatch.
+
+- Match citations by journal, year, volume, first page, and/or author name
+- More fields = better match accuracy; at least one field required
+- Batch up to 25 citations per request
+- Deterministic matching — more reliable than free-text search for known references
+
+---
+
+### `pubmed_convert_ids`
+
+Convert between article identifiers (DOI, PMID, PMCID) using the PMC ID Converter API.
+
+- Batch up to 50 IDs per request
+- Accepts DOIs, PMIDs, or PMCIDs (all IDs must be the same type)
+- Only resolves articles indexed in PubMed Central
+- Returns all available identifier mappings for each input ID
+
 ## Resource and prompt
 
 | Type | Name | Description |
@@ -134,7 +158,7 @@ Built on [`@cyanheads/mcp-ts-core`](https://github.com/cyanheads/mcp-ts-core):
 
 PubMed-specific:
 
-- Complete NCBI E-utilities integration (ESearch, EFetch, ESummary, ELink, ESpell, EInfo)
+- Complete NCBI E-utilities integration (ESearch, EFetch, ESummary, ELink, ESpell, EInfo, ECitMatch) plus PMC ID Converter
 - Sequential request queue with configurable delay for NCBI rate limit compliance
 - NCBI-specific XML parser with `isArray` hints for PubMed's inconsistent XML structure
 - Hand-rolled citation formatters (APA, MLA, BibTeX, RIS) — zero deps, Workers-compatible
@@ -287,7 +311,7 @@ All configuration is validated at startup via Zod schemas in `src/config/server-
 
 | Directory | Purpose |
 |:---|:---|
-| `src/mcp-server/tools` | Tool definitions (`*.tool.ts`). Seven PubMed tools. |
+| `src/mcp-server/tools` | Tool definitions (`*.tool.ts`). Nine PubMed tools. |
 | `src/mcp-server/resources` | Resource definitions. Database info resource. |
 | `src/mcp-server/prompts` | Prompt definitions. Research plan prompt. |
 | `src/services/ncbi` | NCBI E-utilities service layer — API client, queue, parser, formatter. |

package/dist/index.js

@@ -6,10 +6,12 @@
 import { createApp } from '@cyanheads/mcp-ts-core';
 import { researchPlanPrompt } from './mcp-server/prompts/definitions/research-plan.prompt.js';
 import { databaseInfoResource } from './mcp-server/resources/definitions/database-info.resource.js';
+import { convertIdsTool } from './mcp-server/tools/definitions/convert-ids.tool.js';
 import { fetchArticlesTool } from './mcp-server/tools/definitions/fetch-articles.tool.js';
 import { fetchFulltextTool } from './mcp-server/tools/definitions/fetch-fulltext.tool.js';
 import { findRelatedTool } from './mcp-server/tools/definitions/find-related.tool.js';
 import { formatCitationsTool } from './mcp-server/tools/definitions/format-citations.tool.js';
+import { lookupCitationTool } from './mcp-server/tools/definitions/lookup-citation.tool.js';
 import { lookupMeshTool } from './mcp-server/tools/definitions/lookup-mesh.tool.js';
 import { searchArticlesTool } from './mcp-server/tools/definitions/search-articles.tool.js';
 import { spellCheckTool } from './mcp-server/tools/definitions/spell-check.tool.js';
@@ -23,6 +25,8 @@ await createApp({
         findRelatedTool,
         spellCheckTool,
         lookupMeshTool,
+        lookupCitationTool,
+        convertIdsTool,
     ],
     resources: [databaseInfoResource],
     prompts: [researchPlanPrompt],

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;GAGG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,kBAAkB,EAAE,MAAM,0DAA0D,CAAC;AAC9F,OAAO,EAAE,oBAAoB,EAAE,MAAM,8DAA8D,CAAC;AACpG,OAAO,EAAE,cAAc,EAAE,MAAM,oDAAoD,CAAC;AACpF,OAAO,EAAE,iBAAiB,EAAE,MAAM,uDAAuD,CAAC;AAC1F,OAAO,EAAE,iBAAiB,EAAE,MAAM,uDAAuD,CAAC;AAC1F,OAAO,EAAE,eAAe,EAAE,MAAM,qDAAqD,CAAC;AACtF,OAAO,EAAE,mBAAmB,EAAE,MAAM,yDAAyD,CAAC;AAC9F,OAAO,EAAE,kBAAkB,EAAE,MAAM,wDAAwD,CAAC;AAC5F,OAAO,EAAE,cAAc,EAAE,MAAM,oDAAoD,CAAC;AACpF,OAAO,EAAE,kBAAkB,EAAE,MAAM,wDAAwD,CAAC;AAC5F,OAAO,EAAE,cAAc,EAAE,MAAM,oDAAoD,CAAC;AACpF,OAAO,EAAE,eAAe,EAAE,MAAM,iCAAiC,CAAC;AAElE,MAAM,SAAS,CAAC;IACd,KAAK,EAAE;QACL,kBAAkB;QAClB,iBAAiB;QACjB,iBAAiB;QACjB,mBAAmB;QACnB,eAAe;QACf,cAAc;QACd,cAAc;QACd,kBAAkB;QAClB,cAAc;KACf;IACD,SAAS,EAAE,CAAC,oBAAoB,CAAC;IACjC,OAAO,EAAE,CAAC,kBAAkB,CAAC;IAC7B,KAAK;QACH,eAAe,EAAE,CAAC;IACpB,CAAC;CACF,CAAC,CAAC"}

package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts

@@ -0,0 +1,25 @@
+/**
+ * @fileoverview Article ID conversion tool. Converts between DOI, PMID, and PMCID
+ * using the NCBI PMC ID Converter API for deterministic, batch-friendly resolution.
+ * @module src/mcp-server/tools/definitions/convert-ids.tool
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+export declare const convertIdsTool: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    ids: z.ZodArray<z.ZodString>;
+    idtype: z.ZodEnum<{
+        pmcid: "pmcid";
+        pmid: "pmid";
+        doi: "doi";
+    }>;
+}, z.core.$strip>, z.ZodObject<{
+    records: z.ZodArray<z.ZodObject<{
+        requestedId: z.ZodString;
+        pmid: z.ZodOptional<z.ZodString>;
+        pmcid: z.ZodOptional<z.ZodString>;
+        doi: z.ZodOptional<z.ZodString>;
+        errmsg: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>>;
+    totalConverted: z.ZodNumber;
+    totalSubmitted: z.ZodNumber;
+}, z.core.$strip>>;
+//# sourceMappingURL=convert-ids.tool.d.ts.map

package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/definitions/convert-ids.tool.js

@@ -0,0 +1,75 @@
+/**
+ * @fileoverview Article ID conversion tool. Converts between DOI, PMID, and PMCID
+ * using the NCBI PMC ID Converter API for deterministic, batch-friendly resolution.
+ * @module src/mcp-server/tools/definitions/convert-ids.tool
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
+export const convertIdsTool = tool('pubmed_convert_ids', {
+    description: `Convert between article identifiers (DOI, PMID, PMCID). Accepts up to 50 IDs of a single type per request. Uses the NCBI PMC ID Converter API — only resolves articles indexed in PubMed Central. For articles not in PMC, use pubmed_search_articles instead.`,
+    annotations: { readOnlyHint: true, openWorldHint: true },
+    input: z.object({
+        ids: z
+            .array(z.string().min(1))
+            .min(1)
+            .max(50)
+            .describe('Article identifiers to convert. All IDs must be the same type. ' +
+            'DOIs: "10.1093/nar/gks1195", PMIDs: "23193287", PMCIDs: "PMC3531190".'),
+        idtype: z
+            .enum(['pmcid', 'pmid', 'doi'])
+            .describe('The type of IDs being submitted. Required so the API can unambiguously resolve them.'),
+    }),
+    output: z.object({
+        records: z
+            .array(z.object({
+            requestedId: z.string().describe('The ID that was submitted'),
+            pmid: z.string().optional().describe('PubMed ID'),
+            pmcid: z.string().optional().describe('PubMed Central ID'),
+            doi: z.string().optional().describe('Digital Object Identifier'),
+            errmsg: z.string().optional().describe('Error message if conversion failed'),
+        }))
+            .describe('Conversion results, one per input ID'),
+        totalConverted: z.number().describe('Number of IDs successfully converted'),
+        totalSubmitted: z.number().describe('Number of IDs submitted'),
+    }),
+    async handler(input, ctx) {
+        ctx.log.info('Executing pubmed_convert_ids', {
+            count: input.ids.length,
+            idtype: input.idtype,
+        });
+        const raw = await getNcbiService().idConvert(input.ids, input.idtype);
+        // NCBI returns pmid as a number in JSON — coerce all ID fields to strings
+        const records = raw.map((r) => ({
+            requestedId: String(r['requested-id']),
+            ...(r.pmid !== undefined && { pmid: String(r.pmid) }),
+            ...(r.pmcid !== undefined && { pmcid: String(r.pmcid) }),
+            ...(r.doi !== undefined && { doi: String(r.doi) }),
+            ...(r.errmsg !== undefined && { errmsg: String(r.errmsg) }),
+        }));
+        const totalConverted = records.filter((r) => !r.errmsg).length;
+        ctx.log.info('pubmed_convert_ids completed', {
+            totalConverted,
+            totalSubmitted: input.ids.length,
+        });
+        return { records, totalConverted, totalSubmitted: input.ids.length };
+    },
+    format: (result) => {
+        const lines = [
+            `## ID Conversion Results`,
+            `**Converted:** ${result.totalConverted}/${result.totalSubmitted}`,
+            '',
+            '| Requested ID | PMID | PMCID | DOI |',
+            '|:---|:---|:---|:---|',
+        ];
+        for (const r of result.records) {
+            if (r.errmsg) {
+                lines.push(`| ${r.requestedId} | - | - | Error: ${r.errmsg} |`);
+            }
+            else {
+                lines.push(`| ${r.requestedId} | ${r.pmid ?? '-'} | ${r.pmcid ?? '-'} | ${r.doi ?? '-'} |`);
+            }
+        }
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+//# sourceMappingURL=convert-ids.tool.js.map

package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map

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package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts

@@ -0,0 +1,25 @@
+/**
+ * @fileoverview Citation lookup tool. Resolves partial bibliographic references
+ * to PubMed IDs using NCBI's ECitMatch service.
+ * @module src/mcp-server/tools/definitions/lookup-citation.tool
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+export declare const lookupCitationTool: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    citations: z.ZodArray<z.ZodObject<{
+        journal: z.ZodOptional<z.ZodString>;
+        year: z.ZodOptional<z.ZodString>;
+        volume: z.ZodOptional<z.ZodString>;
+        firstPage: z.ZodOptional<z.ZodString>;
+        authorName: z.ZodOptional<z.ZodString>;
+        key: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>>;
+}, z.core.$strip>, z.ZodObject<{
+    results: z.ZodArray<z.ZodObject<{
+        key: z.ZodString;
+        pmid: z.ZodOptional<z.ZodString>;
+        matched: z.ZodBoolean;
+    }, z.core.$strip>>;
+    totalMatched: z.ZodNumber;
+    totalSubmitted: z.ZodNumber;
+}, z.core.$strip>>;
+//# sourceMappingURL=lookup-citation.tool.d.ts.map

package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/definitions/lookup-citation.tool.js

@@ -0,0 +1,89 @@
+/**
+ * @fileoverview Citation lookup tool. Resolves partial bibliographic references
+ * to PubMed IDs using NCBI's ECitMatch service.
+ * @module src/mcp-server/tools/definitions/lookup-citation.tool
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
+export const lookupCitationTool = tool('pubmed_lookup_citation', {
+    description: `Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID. Uses NCBI ECitMatch for deterministic matching — more reliable than searching by citation fields.`,
+    annotations: { readOnlyHint: true, openWorldHint: true },
+    input: z.object({
+        citations: z
+            .array(z.object({
+            journal: z
+                .string()
+                .optional()
+                .describe('Journal title or ISO abbreviation (e.g., "proc natl acad sci u s a")'),
+            year: z.string().optional().describe('Publication year (e.g., "1991")'),
+            volume: z.string().optional().describe('Volume number'),
+            firstPage: z.string().optional().describe('First page number'),
+            authorName: z
+                .string()
+                .optional()
+                .describe('Author name, typically "lastname initials" (e.g., "mann bj")'),
+            key: z
+                .string()
+                .optional()
+                .describe('Arbitrary label to track this citation in results. Auto-assigned if omitted.'),
+        }))
+            .min(1)
+            .max(25)
+            .describe('Citations to look up. More fields = better match accuracy.'),
+    }),
+    output: z.object({
+        results: z
+            .array(z.object({
+            key: z.string().describe('Citation tracking key'),
+            pmid: z.string().optional().describe('Matched PubMed ID'),
+            matched: z.boolean().describe('Whether a PMID was found'),
+        }))
+            .describe('Match results, one per input citation'),
+        totalMatched: z.number().describe('Number of citations with PMID matches'),
+        totalSubmitted: z.number().describe('Number of citations submitted'),
+    }),
+    async handler(input, ctx) {
+        ctx.log.info('Executing pubmed_lookup_citation', { count: input.citations.length });
+        for (const c of input.citations) {
+            if (!c.journal && !c.year && !c.volume && !c.firstPage && !c.authorName) {
+                throw new Error('Each citation must include at least one bibliographic field (journal, year, volume, firstPage, or authorName).');
+            }
+        }
+        const citations = input.citations.map((c, i) => ({
+            journal: c.journal,
+            year: c.year,
+            volume: c.volume,
+            firstPage: c.firstPage,
+            authorName: c.authorName,
+            key: c.key ?? String(i + 1),
+        }));
+        const results = await getNcbiService().eCitMatch(citations);
+        const mapped = results.map((r) => ({
+            key: r.key,
+            matched: r.matched,
+            ...(r.pmid && { pmid: r.pmid }),
+        }));
+        const totalMatched = mapped.filter((r) => r.matched).length;
+        ctx.log.info('pubmed_lookup_citation completed', {
+            totalMatched,
+            totalSubmitted: citations.length,
+        });
+        return { results: mapped, totalMatched, totalSubmitted: citations.length };
+    },
+    format: (result) => {
+        const lines = [
+            `## Citation Lookup Results`,
+            `**Matched:** ${result.totalMatched}/${result.totalSubmitted}`,
+            '',
+            '| Key | PMID | Status |',
+            '|:---|:---|:---|',
+        ];
+        for (const r of result.results) {
+            const pmid = r.pmid ?? '-';
+            const status = r.matched ? 'Matched' : 'No match';
+            lines.push(`| ${r.key} | ${pmid} | ${status} |`);
+        }
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+//# sourceMappingURL=lookup-citation.tool.js.map

package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map

@@ -0,0 +1 @@
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package/dist/services/ncbi/api-client.d.ts

@@ -20,6 +20,13 @@ export declare class NcbiApiClient {
     private readonly config;
     constructor(config: NcbiApiClientConfig);
     makeRequest(endpoint: string, params: NcbiRequestParams, options?: NcbiRequestOptions): Promise<string>;
+    /**
+     * Make a GET request to a non-eutils NCBI endpoint (e.g., PMC ID Converter).
+     * Uses plain fetch (not fetchWithTimeout) so we can capture response bodies on
+     * error status codes — fetchWithTimeout throws before the body can be read.
+     * Injects tool and email params but not api_key (eutils-specific).
+     */
+    makeExternalRequest(url: string, params: NcbiRequestParams): Promise<string>;
     private buildParams;
     private shouldPost;
     private getRequest;

package/dist/services/ncbi/api-client.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAKH,OAAO,EAAwB,KAAK,kBAAkB,EAAE,KAAK,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAKnG,MAAM,WAAW,mBAAmB;IAClC,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,MAAM,CAAC;IAClB,cAAc,EAAE,MAAM,CAAC;CACxB;AAED;;;;GAIG;AACH,qBAAa,aAAa;IACZ,OAAO,CAAC,QAAQ,CAAC,MAAM;gBAAN,MAAM,EAAE,mBAAmB;IAElD,WAAW,CACf,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,OAAO,CAAC,MAAM,CAAC;IAqClB;;;;;OAKG;IACG,mBAAmB,CAAC,GAAG,EAAE,MAAM,EAAE,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,MAAM,CAAC;IA0ClF,OAAO,CAAC,WAAW;IAiBnB,OAAO,CAAC,UAAU;IAMlB,OAAO,CAAC,UAAU;IAOlB,OAAO,CAAC,WAAW;CASpB"}

package/dist/services/ncbi/api-client.js

@@ -22,7 +22,8 @@ export class NcbiApiClient {
     async makeRequest(endpoint, params, options) {
         const finalParams = this.buildParams(params);
         const usePost = this.shouldPost(finalParams, options);
-        const url = `${NCBI_EUTILS_BASE_URL}/${endpoint}.fcgi`;
+        const suffix = endpoint.includes('.') ? '' : '.fcgi';
+        const url = `${NCBI_EUTILS_BASE_URL}/${endpoint}${suffix}`;
         try {
             logger.debug(`NCBI HTTP request: ${usePost ? 'POST' : 'GET'} ${url}`, {
                 endpoint,
@@ -31,7 +32,13 @@ export class NcbiApiClient {
                 ? await this.postRequest(url, finalParams)
                 : await this.getRequest(url, finalParams);
             if (!response.ok) {
-                throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `NCBI API returned HTTP ${response.status}.`, { endpoint, status: response.status });
+                const code = response.status >= 400 && response.status < 500
+                    ? JsonRpcErrorCode.InvalidRequest
+                    : JsonRpcErrorCode.ServiceUnavailable;
+                throw new McpError(code, `NCBI API returned HTTP ${response.status}.`, {
+                    endpoint,
+                    status: response.status,
+                });
             }
             return await response.text();
         }
@@ -44,6 +51,46 @@ export class NcbiApiClient {
             });
         }
     }
+    /**
+     * Make a GET request to a non-eutils NCBI endpoint (e.g., PMC ID Converter).
+     * Uses plain fetch (not fetchWithTimeout) so we can capture response bodies on
+     * error status codes — fetchWithTimeout throws before the body can be read.
+     * Injects tool and email params but not api_key (eutils-specific).
+     */
+    async makeExternalRequest(url, params) {
+        const finalParams = {
+            tool: this.config.toolIdentifier,
+            ...(this.config.adminEmail && { email: this.config.adminEmail }),
+        };
+        for (const [key, value] of Object.entries(params)) {
+            if (value != null)
+                finalParams[key] = String(value);
+        }
+        const qs = new URLSearchParams(finalParams).toString();
+        const fullUrl = qs ? `${url}?${qs}` : url;
+        try {
+            logger.debug(`NCBI external request: GET ${fullUrl}`, { url });
+            const response = await fetch(fullUrl, {
+                signal: AbortSignal.timeout(this.config.timeoutMs),
+            });
+            const body = await response.text();
+            if (!response.ok) {
+                const code = response.status >= 400 && response.status < 500
+                    ? JsonRpcErrorCode.InvalidRequest
+                    : JsonRpcErrorCode.ServiceUnavailable;
+                throw new McpError(code, `NCBI API returned HTTP ${response.status}: ${body.substring(0, 300)}`, { url, status: response.status, body: body.substring(0, 500) });
+            }
+            return body;
+        }
+        catch (error) {
+            if (error instanceof McpError)
+                throw error;
+            const msg = error instanceof Error ? error.message : String(error);
+            throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `NCBI request failed: ${msg}`, {
+                url,
+            });
+        }
+    }
     buildParams(params) {
         const raw = {
             tool: this.config.toolIdentifier,

package/dist/services/ncbi/api-client.js.map

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package/dist/services/ncbi/ncbi-service.d.ts

@@ -7,7 +7,7 @@
 import { NcbiApiClient } from './api-client.js';
 import { NcbiRequestQueue } from './request-queue.js';
 import { NcbiResponseHandler } from './response-handler.js';
-import type { ESearchResult, ESpellResult, ESummaryResult, NcbiRequestOptions, NcbiRequestParams, XmlPubmedArticleSet } from './types.js';
+import { type ECitMatchCitation, type ECitMatchResult, type ESearchResult, type ESpellResult, type ESummaryResult, type IdConvertRecord, type NcbiRequestOptions, type NcbiRequestParams, type XmlPubmedArticleSet } from './types.js';
 /**
  * Facade over NCBI's E-utility suite. Each public method corresponds to a
  * single E-utility endpoint.
@@ -26,6 +26,21 @@ export declare class NcbiService {
     eLink<T = Record<string, unknown>>(params: NcbiRequestParams): Promise<T>;
     eSpell(params: NcbiRequestParams): Promise<ESpellResult>;
     eInfo(params: NcbiRequestParams): Promise<unknown>;
+    /**
+     * Look up PMIDs from partial citation strings via NCBI ECitMatch.
+     * Each citation can include journal, year, volume, first page, and author name.
+     */
+    eCitMatch(citations: ECitMatchCitation[]): Promise<ECitMatchResult[]>;
+    /**
+     * Convert between article identifiers (DOI, PMID, PMCID) using the PMC ID Converter API.
+     * Accepts up to 200 IDs in a single request. Only works for articles in PMC.
+     */
+    idConvert(ids: string[], idtype?: string): Promise<IdConvertRecord[]>;
+    /**
+     * Retry wrapper for transient NCBI errors (ServiceUnavailable, Timeout).
+     * Non-transient errors (validation, serialization) fail immediately.
+     */
+    private withRetry;
     /**
      * Enqueues a request with retry logic that covers both HTTP-level failures
      * (network errors, timeouts) and XML-level errors (NCBI returning 200 OK

package/dist/services/ncbi/ncbi-service.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,EACL,KAAK,iBAAiB,EACtB,KAAK,eAAe,EAEpB,KAAK,aAAa,EAElB,KAAK,YAAY,EAEjB,KAAK,cAAc,EACnB,KAAK,eAAe,EAGpB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;AAEpB;;;GAGG;AACH,qBAAa,WAAW;IAEpB,OAAO,CAAC,QAAQ,CAAC,SAAS;IAC1B,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,eAAe;IAChC,OAAO,CAAC,QAAQ,CAAC,UAAU;gBAHV,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB,EACpC,UAAU,EAAE,MAAM;IAG/B,OAAO,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,aAAa,CAAC;IAmB1D,QAAQ,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,cAAc,CAAC;IAQlE,MAAM,CAAC,CAAC,GAAG;QAAE,gBAAgB,CAAC,EAAE,mBAAmB,CAAA;KAAE,EACnD,MAAM,EAAE,iBAAiB,EACzB,OAAO,GAAE,kBAAuC,GAC/C,OAAO,CAAC,CAAC,CAAC;IAMb,KAAK,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAAE,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,CAAC,CAAC;IAInE,MAAM,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,YAAY,CAAC;IAsB9D,KAAK,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,OAAO,CAAC;IAIlD;;;OAGG;IACG,SAAS,CAAC,SAAS,EAAE,iBAAiB,EAAE,GAAG,OAAO,CAAC,eAAe,EAAE,CAAC;IA6B3E;;;OAGG;IACG,SAAS,CAAC,GAAG,EAAE,MAAM,EAAE,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,eAAe,EAAE,CAAC;IA+B3E;;;OAGG;YACW,SAAS;IAuCvB;;;;;OAKG;IACH,OAAO,CAAC,cAAc;CAevB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CAgBtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}

package/dist/services/ncbi/ncbi-service.js

@@ -10,6 +10,7 @@ import { getServerConfig } from '../../config/server-config.js';
 import { NcbiApiClient } from './api-client.js';
 import { NcbiRequestQueue } from './request-queue.js';
 import { NcbiResponseHandler } from './response-handler.js';
+import { NCBI_PMC_IDCONV_URL, } from './types.js';
 /**
  * Facade over NCBI's E-utility suite. Each public method corresponds to a
  * single E-utility endpoint.
@@ -77,6 +78,79 @@ export class NcbiService {
     eInfo(params) {
         return this.performRequest('einfo', params, { retmode: 'xml' });
     }
+    /**
+     * Look up PMIDs from partial citation strings via NCBI ECitMatch.
+     * Each citation can include journal, year, volume, first page, and author name.
+     */
+    async eCitMatch(citations) {
+        const bdata = citations
+            .map((c) => `${c.journal ?? ''}|${c.year ?? ''}|${c.volume ?? ''}|${c.firstPage ?? ''}|${c.authorName ?? ''}|${c.key}|`)
+            .join('\r');
+        const text = await this.performRequest('ecitmatch.cgi', { db: 'pubmed', retmode: 'xml', bdata }, { retmode: 'text' });
+        return text
+            .split(/[\r\n]+/)
+            .filter((line) => line.trim().length > 0)
+            .map((line) => {
+            const parts = line.split('|');
+            const key = parts[5]?.trim() ?? '';
+            const pmidField = parts[6]?.trim() ?? '';
+            const pmid = pmidField && !pmidField.startsWith('NOT_FOUND') && !pmidField.startsWith('AMBIGUOUS')
+                ? pmidField
+                : null;
+            return { key, matched: pmid !== null, pmid };
+        });
+    }
+    /**
+     * Convert between article identifiers (DOI, PMID, PMCID) using the PMC ID Converter API.
+     * Accepts up to 200 IDs in a single request. Only works for articles in PMC.
+     */
+    async idConvert(ids, idtype) {
+        const params = {
+            ids: ids.join(','),
+            format: 'json',
+            ...(idtype && { idtype }),
+        };
+        const text = await this.queue.enqueue(() => this.withRetry(() => this.apiClient.makeExternalRequest(NCBI_PMC_IDCONV_URL, params), 'idconv'), 'idconv', params);
+        let parsed;
+        try {
+            parsed = JSON.parse(text);
+        }
+        catch {
+            throw new McpError(JsonRpcErrorCode.SerializationError, 'Failed to parse ID Converter JSON response.', { responseSnippet: text.substring(0, 200) });
+        }
+        return parsed.records ?? [];
+    }
+    /**
+     * Retry wrapper for transient NCBI errors (ServiceUnavailable, Timeout).
+     * Non-transient errors (validation, serialization) fail immediately.
+     */
+    async withRetry(execute, label) {
+        for (let attempt = 0; attempt <= this.maxRetries; attempt++) {
+            try {
+                return await execute();
+            }
+            catch (error) {
+                if (error instanceof McpError) {
+                    if (error.code !== JsonRpcErrorCode.ServiceUnavailable &&
+                        error.code !== JsonRpcErrorCode.Timeout) {
+                        throw error;
+                    }
+                }
+                if (attempt < this.maxRetries) {
+                    const retryDelay = 1000 * 2 ** attempt; // 1s, 2s, 4s
+                    logger.warning(`NCBI request to ${label} failed. Retrying (${attempt + 1}/${this.maxRetries}) in ${retryDelay}ms.`, { endpoint: label, attempt: attempt + 1, retryDelay });
+                    await new Promise((r) => setTimeout(r, retryDelay));
+                    continue;
+                }
+                const attempts = this.maxRetries + 1;
+                const msg = error instanceof Error ? error.message : String(error);
+                throw new McpError(error instanceof McpError ? error.code : JsonRpcErrorCode.ServiceUnavailable, `${msg} (failed after ${attempts} attempts)`, { endpoint: label, attempts });
+            }
+        }
+        throw new McpError(JsonRpcErrorCode.InternalError, 'Request failed after all retries.', {
+            endpoint: label,
+        });
+    }
     /**
      * Enqueues a request with retry logic that covers both HTTP-level failures
      * (network errors, timeouts) and XML-level errors (NCBI returning 200 OK
@@ -84,38 +158,10 @@ export class NcbiService {
      * surfaced as C++ exception traces).
      */
     performRequest(endpoint, params, options) {
-        return this.queue.enqueue(async () => {
-            for (let attempt = 0; attempt <= this.maxRetries; attempt++) {
-                try {
-                    const text = await this.apiClient.makeRequest(endpoint, params, options);
-                    return this.responseHandler.parseAndHandleResponse(text, endpoint, options);
-                }
-                catch (error) {
-                    // Only retry transient errors (ServiceUnavailable, Timeout).
-                    // Validation, serialization, and other errors fail immediately.
-                    if (error instanceof McpError) {
-                        if (error.code !== JsonRpcErrorCode.ServiceUnavailable &&
-                            error.code !== JsonRpcErrorCode.Timeout) {
-                            throw error;
-                        }
-                    }
-                    if (attempt < this.maxRetries) {
-                        const retryDelay = 1000 * 2 ** attempt; // 1s, 2s, 4s
-                        logger.warning(`NCBI request to ${endpoint} failed. Retrying (${attempt + 1}/${this.maxRetries}) in ${retryDelay}ms.`, { endpoint, attempt: attempt + 1, retryDelay });
-                        await new Promise((r) => setTimeout(r, retryDelay));
-                        continue;
-                    }
-                    // Final attempt exhausted — surface retry context so the caller
-                    // knows this wasn't a single failed request.
-                    const attempts = this.maxRetries + 1;
-                    const msg = error instanceof Error ? error.message : String(error);
-                    throw new McpError(error instanceof McpError ? error.code : JsonRpcErrorCode.ServiceUnavailable, `${msg} (failed after ${attempts} attempts)`, { endpoint, attempts });
-                }
-            }
-            throw new McpError(JsonRpcErrorCode.InternalError, 'Request failed after all retries.', {
-                endpoint,
-            });
-        }, endpoint, params);
+        return this.queue.enqueue(() => this.withRetry(async () => {
+            const text = await this.apiClient.makeRequest(endpoint, params, options);
+            return this.responseHandler.parseAndHandleResponse(text, endpoint, options);
+        }, endpoint), endpoint, params);
     }
 }
 // ─── Init / Accessor ────────────────────────────────────────────────────────

package/dist/services/ncbi/ncbi-service.js.map

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package/dist/services/ncbi/types.d.ts

@@ -5,6 +5,8 @@
  */
 /** Base URL for all NCBI E-utility endpoints. */
 export declare const NCBI_EUTILS_BASE_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils";
+/** Base URL for the PMC ID Converter API (separate from E-utilities). */
+export declare const NCBI_PMC_IDCONV_URL = "https://pmc.ncbi.nlm.nih.gov/tools/idconv/api/v1/articles/";
 /**
  * Common NCBI E-utility request parameters.
  * Specific endpoints extend this with their own fields via the index signature.
@@ -593,4 +595,50 @@ export interface ParsedPmcReference {
     id?: string;
     label?: string;
 }
+/** Single citation for ECitMatch lookup. */
+export interface ECitMatchCitation {
+    /** Author name (e.g., "mann bj") */
+    authorName?: string | undefined;
+    /** First page number */
+    firstPage?: string | undefined;
+    /** Journal title or ISO abbreviation */
+    journal?: string | undefined;
+    /** Arbitrary key for tracking this citation in results */
+    key: string;
+    /** Volume number */
+    volume?: string | undefined;
+    /** Publication year */
+    year?: string | undefined;
+}
+/** Single result from ECitMatch lookup. */
+export interface ECitMatchResult {
+    /** The tracking key from the input citation */
+    key: string;
+    /** Whether a PMID was found */
+    matched: boolean;
+    /** Matched PubMed ID, or null if no match */
+    pmid: string | null;
+}
+/** Single record from the PMC ID Converter API response. */
+export interface IdConvertRecord {
+    /** Digital Object Identifier */
+    doi?: string;
+    /** Error message if conversion failed for this ID */
+    errmsg?: string;
+    /** PubMed Central ID (e.g., "PMC1234567") */
+    pmcid?: string;
+    /** PubMed ID (numeric string) */
+    pmid?: string;
+    /** The ID that was originally requested */
+    'requested-id': string;
+    /** Record-level status: present only on error records */
+    status?: string;
+}
+/** JSON response from the PMC ID Converter API. */
+export interface IdConvertResponse {
+    records: IdConvertRecord[];
+    request: Record<string, unknown>;
+    'response-date': string;
+    status: string;
+}
 //# sourceMappingURL=types.d.ts.map

package/dist/services/ncbi/types.d.ts.map

@@ -1 +1 @@
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package/dist/services/ncbi/types.js

@@ -6,4 +6,6 @@
 // ─── NCBI API Constants & Request Types ─────────────────────────────────────
 /** Base URL for all NCBI E-utility endpoints. */
 export const NCBI_EUTILS_BASE_URL = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils';
+/** Base URL for the PMC ID Converter API (separate from E-utilities). */
+export const NCBI_PMC_IDCONV_URL = 'https://pmc.ncbi.nlm.nih.gov/tools/idconv/api/v1/articles/';
 //# sourceMappingURL=types.js.map

package/dist/services/ncbi/types.js.map

@@ -1 +1 @@
-{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../src/services/ncbi/types.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,+EAA+E;AAE/E,iDAAiD;AACjD,MAAM,CAAC,MAAM,oBAAoB,GAAG,+CAA+C,CAAC"}
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../src/services/ncbi/types.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,+EAA+E;AAE/E,iDAAiD;AACjD,MAAM,CAAC,MAAM,oBAAoB,GAAG,+CAA+C,CAAC;AAEpF,yEAAyE;AACzE,MAAM,CAAC,MAAM,mBAAmB,GAAG,4DAA4D,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.2.6",
+  "version": "2.3.0",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata, generate citations, explore MeSH terms, and discover related research.",
   "type": "module",

package/server.json

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.2.6",
+  "version": "2.3.0",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.2.6",
+      "version": "2.3.0",
       "packageArguments": [
         {
           "type": "positional",
@@ -60,7 +60,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.2.6",
+      "version": "2.3.0",
       "packageArguments": [
         {
           "type": "positional",