npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.7.10 → 2.8.0 - Mend

@cyanheads/pubmed-mcp-server 2.7.10 → 2.8.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (25) hide show

package/AGENTS.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Agent Protocol
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.7.10
+**Version:** 2.8.0
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.21`
 **Engines:** Bun ≥1.3.2, Node ≥24.0.0

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Agent Protocol
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.7.10
+**Version:** 2.8.0
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.21`
 **Engines:** Bun ≥1.3.2, Node ≥24.0.0

package/README.md CHANGED Viewed

@@ -9,7 +9,7 @@
-[![Version](https://img.shields.io/badge/Version-2.7.10-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-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) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.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/)
+[![Version](https://img.shields.io/badge/Version-2.8.0-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-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) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.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/)
 </div>
@@ -39,7 +39,7 @@
 | `pubmed_europepmc_search` | Search Europe PMC for preprints, patents, Agricola, and EPMC-only OA records that don't surface in PubMed. Cursor-based pagination. |
 | `pubmed_fetch_articles` | Fetch full article metadata by PMIDs — abstract, authors, journal, MeSH terms, grants |
 | `pubmed_fetch_fulltext` | Fetch full-text articles via a chain: NCBI PMC EFetch → Europe PMC `fullTextXML` → Unpaywall. Accepts PMIDs, PMCIDs, or DOIs. |
-| `pubmed_format_citations` | Generate formatted citations in APA 7th, MLA 9th, BibTeX, or RIS |
+| `pubmed_format_citations` | Generate formatted citations in APA 7th, MLA 9th, BibTeX, RIS, or Vancouver (ICMJE/NLM) |
 | `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 |
@@ -78,7 +78,7 @@ Fetch full article metadata by PubMed IDs.
 Fetch full-text articles via a three-stage chain: NCBI PMC EFetch → Europe PMC `fullTextXML` → Unpaywall.
-- Accepts exactly one of `pmcids` (direct PMC IDs), `pmids` (PubMed IDs, auto-resolved), or `dois` (covers preprints and EPMC-only OA records that lack PMID/PMCID)
+- Accepts exactly one of `pmcids` (direct PMC IDs), `pmids` (PubMed IDs, auto-resolved), or `dois` (auto-resolved to PMC via the ID Converter; preprints and EPMC-only OA fall through to Europe PMC / Unpaywall)
 - NCBI PMC and Europe PMC both return structured JATS; output records origin via `viaSource: "pmc" | "europepmc" | "unpaywall"`
 - Europe PMC layer (enabled by default; disable with `EUROPEPMC_ENABLED=false`) recovers PMC-counterpart records that NCBI PMC EFetch missed, and resolves DOI input to PMC counterparts when one exists. EPMC's `fullTextXML` is PMC-keyed, so preprints (PPR), patents (PAT), and Agricola (AGR) are reachable via `pubmed_europepmc_search` for metadata but have no full text via this chain.
 - Unpaywall layer (enabled by setting `UNPAYWALL_EMAIL`) resolves DOIs to legal OA copies; extracts HTML landing pages to Markdown via Defuddle or PDFs to text via unpdf
@@ -106,7 +106,7 @@ Search Europe PMC (EBI/EMBL-EBI), a broader open-access biomedical corpus than P
 Generate formatted citations for articles.
-- Four citation styles: APA 7th, MLA 9th, BibTeX, RIS
+- Five citation styles: APA 7th, MLA 9th, BibTeX, RIS, Vancouver (ICMJE/NLM)
 - Request multiple styles per article in a single call
 - Hand-rolled formatters — zero external dependencies, fully Workers-compatible
 - Up to 50 articles per request
@@ -187,7 +187,7 @@ PubMed-specific:
 - 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
+- Hand-rolled citation formatters (APA, MLA, BibTeX, RIS, Vancouver) — zero deps, Workers-compatible
 Agent-friendly output:

package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts CHANGED Viewed

@@ -104,5 +104,7 @@ export declare const fetchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDef
     readonly code: JsonRpcErrorCode.SerializationError;
     readonly when: "NCBI EFetch returned a payload missing the PubmedArticleSet wrapper.";
     readonly recovery: "Retry once; if it persists, NCBI returned malformed data — try fewer PMIDs at once.";
-}], undefined>;
+}], {
+    readonly notice: z.ZodOptional<z.ZodString>;
+}>;
 //# sourceMappingURL=fetch-articles.tool.d.ts.map

package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/fetch-articles.tool.js CHANGED Viewed

@@ -121,6 +121,14 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
             .optional()
             .describe('PMIDs that returned no article data'),
     }),
+    // Recovery guidance when no articles are returned — agent-facing context, surfaced via
+    // ctx.enrich.notice() to both structuredContent and content[]; absent on success.
+    enrichment: {
+        notice: z
+            .string()
+            .optional()
+            .describe('Optional guidance when no articles were returned — points to discovery tools. Absent on successful fetches.'),
+    },
     async handler(input, ctx) {
         ctx.log.info('Executing pubmed_fetch', { pmidCount: input.pmids.length });
         const xmlData = await getNcbiService().eFetch({ db: 'pubmed', id: input.pmids.join(','), retmode: 'xml' }, { retmode: 'xml', usePost: input.pmids.length >= 100, signal: ctx.signal });
@@ -150,6 +158,9 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
             requested: input.pmids.length,
             returned: articles.length,
         });
+        if (articles.length === 0) {
+            ctx.enrich.notice('No articles were returned. These PMIDs may be invalid, unpublished, or withdrawn. Try pubmed_search_articles to discover valid PMIDs.');
+        }
         return {
             articles,
             totalReturned: articles.length,
@@ -161,9 +172,6 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
         if (result.unavailablePmids?.length) {
             lines.push(`**Unavailable PMIDs:** ${result.unavailablePmids.join(', ')}`);
         }
-        if (result.totalReturned === 0) {
-            lines.push(`\n> No articles were returned. These PMIDs may be invalid, unpublished, or withdrawn. Try \`pubmed_search_articles\` to discover valid PMIDs.`);
-        }
         for (const a of result.articles) {
             lines.push(`\n### ${a.title ?? a.pmid ?? 'Unknown'}`);
             if (a.authors?.length) {

package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts CHANGED Viewed

@@ -6,9 +6,9 @@
  *   - `pmcids` — fetch directly by PMC ID. Articles not in PMC fall through to
  *     EPMC by PMC ID, then to Unpaywall when the DOI is available.
  *   - `pmids` — resolve PMID → PMCID via PMC ID Converter, then run the chain.
- *   - `dois` — skip PMC EFetch (no PMCID); resolve via EPMC search-by-DOI →
- *     fullTextXML, then Unpaywall. Covers EPMC-only OA and preprints with no
- *     PubMed presence.
+ *   - `dois` — resolve DOI → PMCID via the PMC ID Converter (mirroring `pmids`),
+ *     then run the chain. DOIs with no PMC counterpart fall through to EPMC
+ *     search-by-DOI → fullTextXML, then Unpaywall (EPMC-only OA, preprints).
  *
  * Output uses a discriminated union on `source` (`pmc` | `unpaywall`) with an
  * extra `viaSource` discriminator that records which layer produced the
@@ -18,6 +18,17 @@
  * @module src/mcp-server/tools/definitions/fetch-fulltext.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
+/**
+ * Compose the tool description for the fallback tiers enabled in this
+ * deployment. PMC EFetch is always present; Europe PMC (`EUROPEPMC_ENABLED`)
+ * and Unpaywall (`UNPAYWALL_EMAIL`) are optional, so the advertised chain must
+ * match what the server can actually deliver — otherwise the model requests
+ * recoveries that silently can't happen.
+ */
+export declare function buildFulltextDescription(tiers: {
+    europePmc: boolean;
+    unpaywall: boolean;
+}): string;
 export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     pmcids: z.ZodOptional<z.ZodArray<z.ZodString>>;
     pmids: z.ZodOptional<z.ZodArray<z.ZodString>>;

package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AAoR~~/D,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~cAgd5B~~,CAAC"}
1	+ {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAqR/D;;;;;;GAMG;AACH,wBAAgB,wBAAwB,CAAC,KAAK,EAAE;IAC9C,SAAS,EAAE,OAAO,CAAC;IACnB,SAAS,EAAE,OAAO,CAAC;CACpB,GAAG,MAAM,CA+BT;AAID,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA4f5B,CAAC"}

package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js CHANGED Viewed

@@ -6,9 +6,9 @@
  *   - `pmcids` — fetch directly by PMC ID. Articles not in PMC fall through to
  *     EPMC by PMC ID, then to Unpaywall when the DOI is available.
  *   - `pmids` — resolve PMID → PMCID via PMC ID Converter, then run the chain.
- *   - `dois` — skip PMC EFetch (no PMCID); resolve via EPMC search-by-DOI →
- *     fullTextXML, then Unpaywall. Covers EPMC-only OA and preprints with no
- *     PubMed presence.
+ *   - `dois` — resolve DOI → PMCID via the PMC ID Converter (mirroring `pmids`),
+ *     then run the chain. DOIs with no PMC counterpart fall through to EPMC
+ *     search-by-DOI → fullTextXML, then Unpaywall (EPMC-only OA, preprints).
  *
  * Output uses a discriminated union on `source` (`pmc` | `unpaywall`) with an
  * extra `viaSource` discriminator that records which layer produced the
@@ -19,6 +19,7 @@
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { htmlExtractor, pdfParser } from '@cyanheads/mcp-ts-core/utils';
+import { getServerConfig } from '../../../config/server-config.js';
 import { EUROPEPMC_SERVICE_ERRORS, NCBI_SERVICE_ERRORS, UNPAYWALL_SERVICE_ERRORS, } from '../../../services/error-contracts.js';
 import { getEuropePmcService, } from '../../../services/europe-pmc/europe-pmc-service.js';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
@@ -221,8 +222,47 @@ const UnavailableSchema = z
 })
     .describe('One identifier that could not be returned, with the full chain it traversed');
 // ─── Tool Definition ─────────────────────────────────────────────────────────
+/**
+ * Compose the tool description for the fallback tiers enabled in this
+ * deployment. PMC EFetch is always present; Europe PMC (`EUROPEPMC_ENABLED`)
+ * and Unpaywall (`UNPAYWALL_EMAIL`) are optional, so the advertised chain must
+ * match what the server can actually deliver — otherwise the model requests
+ * recoveries that silently can't happen.
+ */
+export function buildFulltextDescription(tiers) {
+    const base = 'Fetch full-text articles from PubMed Central with structured sections and references.';
+    const epmcClause = 'Europe PMC `fullTextXML` (structured JATS for records with a PMC counterpart)';
+    const unpaywallClause = 'Unpaywall — publisher-hosted or institutional open-access copies as HTML-as-Markdown or PDF-as-text';
+    let fallback;
+    if (tiers.europePmc && tiers.unpaywall) {
+        fallback = `When PMC misses, transparently falls back to ${epmcClause}, then to ${unpaywallClause}.`;
+    }
+    else if (tiers.europePmc) {
+        fallback = `When PMC misses, transparently falls back to ${epmcClause}.`;
+    }
+    else if (tiers.unpaywall) {
+        fallback = `When PMC misses, falls back to ${unpaywallClause}.`;
+    }
+    else {
+        fallback =
+            'Full text is sourced from PubMed Central only; articles not in PMC return no full text in this configuration.';
+    }
+    const doiTail = tiers.europePmc && tiers.unpaywall
+        ? '; preprints and EPMC-only OA fall through to the Europe PMC and Unpaywall layers'
+        : tiers.europePmc
+            ? '; preprints with a PMC counterpart recover via Europe PMC'
+            : tiers.unpaywall
+                ? '; DOIs with no PMC copy recover via Unpaywall open access'
+                : '';
+    const input = `Provide exactly one of \`pmcids\` (PMC IDs directly), \`pmids\` (PubMed IDs, auto-resolved), or \`dois\` (DOIs, auto-resolved to PMC via the ID Converter${doiTail}).`;
+    return `${base} ${fallback} ${input}`;
+}
+const serverConfig = getServerConfig();
 export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
-    description: 'Fetch full-text articles from PubMed Central with structured sections and references. When PMC misses, transparently falls back to Europe PMC `fullTextXML` (structured JATS for records with a PMC counterpart), then to Unpaywall — publisher-hosted or institutional open-access copies as HTML-as-Markdown or PDF-as-text. Provide exactly one of `pmcids` (PMC IDs directly), `pmids` (PubMed IDs, auto-resolved), or `dois` (preprints and EPMC-only OA records that lack PMID/PMCID).',
+    description: buildFulltextDescription({
+        europePmc: serverConfig.europepmcEnabled,
+        unpaywall: Boolean(serverConfig.unpaywallEmail),
+    }),
     annotations: { readOnlyHint: true, openWorldHint: true },
     _meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL]),
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/fetch-fulltext.tool.ts',
@@ -252,7 +292,7 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
             .min(1)
             .max(10)
             .optional()
-            .describe('DOIs to resolve (e.g. ["10.21203/rs.3.rs-9010375/v1"]). Provide exactly one of `pmcids`, `pmids`, or `dois`. Covers preprints and EPMC-only OA records that lack PMID/PMCID. Chain: Europe PMC search-by-DOI → fullTextXML → Unpaywall.'),
+            .describe('DOIs to resolve (e.g. ["10.21203/rs.3.rs-9010375/v1"]). Provide exactly one of `pmcids`, `pmids`, or `dois`. Resolved to a PMCID via the PMC ID Converter and returned as structured JATS when the article is in PMC; DOIs with no PMC counterpart (preprints, EPMC-only OA) fall through to Europe PMC, then Unpaywall, when those layers are enabled.'),
         includeReferences: z
             .boolean()
             .default(false)
@@ -294,9 +334,10 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
         // for, so we can skip them when building `unavailable[]`.
         const chainByInput = new Map();
         const recoveredIds = new Set();
-        // PMCIDs the converter resolved from a pmid → PMID, for back-mapping after
-        // the PMC and EPMC stages.
-        const pmcidToPmid = new Map();
+        // Back-map from a converter-resolved prefixed PMCID to the input id that
+        // seeded it — a PMID for `pmids` input, a DOI for `dois` input — so the PMC
+        // and EPMC stages attribute recoveries and misses to the original input id.
+        const pmcidToInputId = new Map();
         // DOI hints captured during pmids→pmcid routing so PMC-misses on the pmids
         // branch can still reach Unpaywall without re-fetching from PubMed metadata.
         const pmidContext = new Map();
@@ -319,7 +360,7 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
                 if (r.pmcid) {
                     const normalized = normalizePmcId(String(r.pmcid));
                     pmcIds.push(normalized);
-                    pmcidToPmid.set(withPmcPrefix(normalized), pmid);
+                    pmcidToInputId.set(withPmcPrefix(normalized), pmid);
                     pmidContext.set(pmid, { pmid, ...(r.doi && { doi: r.doi }) });
                 }
                 else {
@@ -348,17 +389,52 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
             pmcIds = input.pmcids.map(normalizePmcId);
         }
         else if (input.dois) {
-            for (const doi of input.dois) {
-                chainByInput.set(doi, [
-                    { tier: 'pmc', outcome: 'not-attempted', detail: 'DOI input bypasses PMC EFetch' },
-                ]);
+            // Mirror the `pmids` branch: resolve DOI → PMCID via the PMC ID Converter
+            // so PMC-indexed DOIs reach PMC EFetch instead of going straight to the
+            // EPMC/Unpaywall fallback (which misses articles whose only OA copy is the
+            // PMC JATS). DOIs the converter can't place in PMC seed `doiCandidates`.
+            const requestedDois = new Set(input.dois);
+            for (const doi of input.dois)
+                chainByInput.set(doi, []);
+            const records = await getNcbiService().idConvert(input.dois, 'doi', ctx.signal ? { signal: ctx.signal } : undefined);
+            const seen = new Set();
+            for (const r of records) {
+                // The converter echoes the submitted id verbatim in `requested-id`;
+                // match on it, not `r.doi` (DOIs aren't case-stable across the API).
+                const doi = String(r['requested-id']);
+                if (!requestedDois.has(doi))
+                    continue;
+                seen.add(doi);
+                if (r.pmcid) {
+                    const normalized = normalizePmcId(String(r.pmcid));
+                    pmcIds.push(normalized);
+                    pmcidToInputId.set(withPmcPrefix(normalized), doi);
+                }
+                else {
+                    chainByInput.get(doi)?.push({
+                        tier: 'pmc',
+                        outcome: 'not-attempted',
+                        detail: 'DOI has no PMC counterpart',
+                    });
+                    doiCandidates.push({ doi });
+                }
+            }
+            for (const requested of input.dois) {
+                if (!seen.has(requested)) {
+                    chainByInput.get(requested)?.push({
+                        tier: 'pmc',
+                        outcome: 'not-attempted',
+                        detail: 'ID Converter returned no record for this DOI',
+                    });
+                    doiCandidates.push({ doi: requested });
+                }
             }
-            doiCandidates = input.dois.map((doi) => ({ doi }));
         }
         // Route PMC-missed prefixed PMCIDs into the fallback buckets so EPMC and
-        // (for pmids) Unpaywall still get a chance. For pmids input we look up the
-        // captured DOI hint via `pmidContext` to avoid an extra PubMed eFetch when
-        // available; the converter often returns the DOI alongside a PMCID match.
+        // (for pmids/dois) Unpaywall still get a chance. For pmids input we look up
+        // the captured DOI hint via `pmidContext` to avoid an extra PubMed eFetch
+        // when available; the converter often returns the DOI alongside a PMCID
+        // match. For dois input the original DOI is the fallback key directly.
         const routePmcMissesToFallback = (missingPrefixed) => {
             if (missingPrefixed.length === 0)
                 return;
@@ -367,11 +443,18 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
             }
             else if (input.pmids) {
                 for (const prefixed of missingPrefixed) {
-                    const pmid = pmcidToPmid.get(prefixed);
+                    const pmid = pmcidToInputId.get(prefixed);
                     if (pmid)
                         pmidFallbackCandidates.push(pmidContext.get(pmid) ?? { pmid });
                 }
             }
+            else if (input.dois) {
+                for (const prefixed of missingPrefixed) {
+                    const doi = pmcidToInputId.get(prefixed);
+                    if (doi)
+                        doiCandidates.push({ doi });
+                }
+            }
         };
         // ── Stage 1: PMC EFetch ─────────────────────────────────────────────────
         // Wrapped so transient NCBI failures fall through to EPMC/Unpaywall rather
@@ -399,13 +482,13 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
                 }));
                 const returnedPmcIds = new Set(pmcArticles.map((a) => a.pmcId).filter((id) => !!id));
                 for (const prefixed of returnedPmcIds) {
-                    recoveredIds.add(pmcidToPmid.get(prefixed) ?? prefixed);
+                    recoveredIds.add(pmcidToInputId.get(prefixed) ?? prefixed);
                 }
                 const missing = pmcIds
                     .map((id) => withPmcPrefix(id))
                     .filter((id) => !returnedPmcIds.has(id));
                 for (const prefixed of missing) {
-                    const inputId = pmcidToPmid.get(prefixed) ?? prefixed;
+                    const inputId = pmcidToInputId.get(prefixed) ?? prefixed;
                     chainByInput.get(inputId)?.push({ tier: 'pmc', outcome: 'miss' });
                 }
                 routePmcMissesToFallback(missing);
@@ -418,7 +501,7 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
                 });
                 const allPrefixed = pmcIds.map(withPmcPrefix);
                 for (const prefixed of allPrefixed) {
-                    const inputId = pmcidToPmid.get(prefixed) ?? prefixed;
+                    const inputId = pmcidToInputId.get(prefixed) ?? prefixed;
                     chainByInput.get(inputId)?.push({ tier: 'pmc', outcome: 'service-error', detail });
                 }
                 routePmcMissesToFallback(allPrefixed);
@@ -456,7 +539,7 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
                 chainByInput.get(c.pmid)?.push(epmcDisabledEntry);
             for (const c of pmcidFallbackCandidates) {
                 const prefixed = withPmcPrefix(c.pmcid);
-                chainByInput.get(pmcidToPmid.get(prefixed) ?? prefixed)?.push(epmcDisabledEntry);
+                chainByInput.get(pmcidToInputId.get(prefixed) ?? prefixed)?.push(epmcDisabledEntry);
             }
             for (const c of doiCandidates)
                 chainByInput.get(c.doi)?.push(epmcDisabledEntry);
@@ -470,7 +553,7 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
                 chainByInput.get(pmid)?.push(epmcTierFromOutcome(outcome));
             }
             for (const [prefixed, outcome] of epmcOutcomes.pmcidOutcomes) {
-                const inputId = pmcidToPmid.get(prefixed) ?? prefixed;
+                const inputId = pmcidToInputId.get(prefixed) ?? prefixed;
                 if (outcome.kind === 'hit') {
                     recoveredIds.add(inputId);
                     continue;
@@ -495,7 +578,7 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
         // implementation doesn't resolve PMCID → DOI for that branch.
         for (const c of pmcidFallbackCandidates) {
             const prefixed = withPmcPrefix(c.pmcid);
-            chainByInput.get(pmcidToPmid.get(prefixed) ?? prefixed)?.push({
+            chainByInput.get(pmcidToInputId.get(prefixed) ?? prefixed)?.push({
                 tier: 'unpaywall',
                 outcome: 'not-attempted',
                 detail: 'pmcids input does not resolve a DOI for Unpaywall',

package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts CHANGED Viewed

@@ -1,6 +1,6 @@
 /**
  * @fileoverview PubMed citation tool — generates formatted citations (APA, MLA,
- * BibTeX, RIS) for one or more PubMed articles.
+ * BibTeX, RIS, Vancouver) for one or more PubMed articles.
  * @module src/mcp-server/tools/definitions/format-citations.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
@@ -11,11 +11,13 @@ export declare const formatCitationsTool: import("@cyanheads/mcp-ts-core").ToolD
         mla: "mla";
         bibtex: "bibtex";
         ris: "ris";
+        vancouver: "vancouver";
     }>, z.ZodArray<z.ZodEnum<{
         apa: "apa";
         mla: "mla";
         bibtex: "bibtex";
         ris: "ris";
+        vancouver: "vancouver";
     }>>]>>;
 }, z.core.$strip>, z.ZodObject<{
     citations: z.ZodArray<z.ZodObject<{
@@ -56,5 +58,7 @@ export declare const formatCitationsTool: import("@cyanheads/mcp-ts-core").ToolD
     readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
     readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
     readonly retryable: false;
-}], undefined>;
+}], {
+    readonly notice: z.ZodOptional<z.ZodString>;
+}>;
 //# sourceMappingURL=format-citations.tool.d.ts.map

package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAejD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwH9B,CAAC"}

package/dist/mcp-server/tools/definitions/format-citations.tool.js CHANGED Viewed

@@ -1,6 +1,6 @@
 /**
  * @fileoverview PubMed citation tool — generates formatted citations (APA, MLA,
- * BibTeX, RIS) for one or more PubMed articles.
+ * BibTeX, RIS, Vancouver) for one or more PubMed articles.
  * @module src/mcp-server/tools/definitions/format-citations.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
@@ -11,9 +11,9 @@ import { parseFullArticle } from '../../../services/ncbi/parsing/article-parser.
 import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
 import { conceptMeta, EDAM_DATA_FORMATTING, SCHEMA_CREATIVE_WORK } from './_concepts.js';
 import { pmidStringSchema } from './_schemas.js';
-const CitationStyleEnum = z.enum(['apa', 'mla', 'bibtex', 'ris']);
+const CitationStyleEnum = z.enum(['apa', 'mla', 'bibtex', 'ris', 'vancouver']);
 export const formatCitationsTool = tool('pubmed_format_citations', {
-    description: 'Get formatted citations for PubMed articles in one or more styles (apa, mla, bibtex, ris). Pass a single style as a string or multiple as an array.',
+    description: 'Get formatted citations for PubMed articles in one or more styles (apa, mla, bibtex, ris, vancouver). Pass a single style as a string or multiple as an array.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     _meta: conceptMeta([SCHEMA_CREATIVE_WORK, EDAM_DATA_FORMATTING]),
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/format-citations.tool.ts',
@@ -22,14 +22,14 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
         pmids: z.array(pmidStringSchema).min(1).max(50).describe('PubMed IDs to cite'),
         format: z
             .union([
-            CitationStyleEnum.describe('Single citation style. One of: apa, mla, bibtex, ris.'),
+            CitationStyleEnum.describe('Single citation style. One of: apa, mla, bibtex, ris, vancouver.'),
             z
                 .array(CitationStyleEnum)
                 .min(1)
-                .describe('Multiple citation styles to generate. Each entry: apa, mla, bibtex, or ris.'),
+                .describe('Multiple citation styles to generate. Each entry: apa, mla, bibtex, ris, or vancouver.'),
         ])
             .default('apa')
-            .describe('Citation format(s) to generate — single style as a string or multiple as an array. Allowed values: apa, mla, bibtex, ris.'),
+            .describe('Citation format(s) to generate — single style as a string or multiple as an array. Allowed values: apa, mla, bibtex, ris, vancouver.'),
     }),
     output: z.object({
         citations: z
@@ -48,6 +48,14 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
             .optional()
             .describe('Requested PMIDs that did not return article metadata'),
     }),
+    // Recovery guidance when nothing could be formatted — agent-facing context, surfaced
+    // via ctx.enrich.notice() to both structuredContent and content[]; absent on success.
+    enrichment: {
+        notice: z
+            .string()
+            .optional()
+            .describe('Optional guidance when no citations were produced — points to discovery tools. Absent when at least one citation was produced.'),
+    },
     async handler(input, ctx) {
         const formats = Array.isArray(input.format) ? input.format : [input.format];
         ctx.log.debug('Fetching articles for citation generation', {
@@ -66,6 +74,9 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
         });
         const returnedPmids = new Set(citations.map((entry) => entry.pmid));
         const unavailablePmids = input.pmids.filter((pmid) => !returnedPmids.has(pmid));
+        if (citations.length === 0) {
+            ctx.enrich.notice('No articles were returned for the submitted PMIDs. They may be invalid, unpublished, or withdrawn. Try pubmed_search_articles to discover valid PMIDs, or pubmed_spell_check if these came from a noisy source.');
+        }
         return {
             citations,
             totalSubmitted: input.pmids.length,
@@ -81,9 +92,6 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
         if (result.unavailablePmids?.length) {
             lines.push(`**Unavailable PMIDs:** ${result.unavailablePmids.join(', ')}`);
         }
-        if (result.totalFormatted === 0) {
-            lines.push(`\n> No articles were returned for the submitted PMIDs. They may be invalid, unpublished, or withdrawn. Try \`pubmed_search_articles\` to discover valid PMIDs, or \`pubmed_spell_check\` if these came from a noisy source.`);
-        }
         for (const entry of result.citations) {
             lines.push(`\n## PMID ${entry.pmid}`);
             if (entry.title)

package/dist/mcp-server/tools/definitions/format-citations.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/ncbi/formatting/citation-formatter.d.ts CHANGED Viewed

@@ -1,12 +1,12 @@
 /**
  * @fileoverview Hand-rolled citation formatters for PubMed articles.
- * Supports APA 7th, MLA 9th, BibTeX, and RIS formats.
+ * Supports APA 7th, MLA 9th, BibTeX, RIS, and Vancouver (ICMJE/NLM) formats.
  * Pure TypeScript, zero dependencies, Workers-compatible.
  * @module src/services/ncbi/formatting/citation-formatter
  */
 import type { ParsedArticle } from '../types.js';
 /** Supported citation output formats. */
-export type CitationStyle = 'apa' | 'mla' | 'bibtex' | 'ris';
+export type CitationStyle = 'apa' | 'mla' | 'bibtex' | 'ris' | 'vancouver';
 /**
  * Format a PubMed article as an APA 7th edition citation.
  *
@@ -46,6 +46,20 @@ export declare function formatBibtex(article: ParsedArticle): string;
  * Record ends with `ER  - ` (trailing spaces per spec).
  */
 export declare function formatRis(article: ParsedArticle): string;
+/**
+ * Format a PubMed article as a Vancouver (ICMJE/NLM) reference — the numbered
+ * style used by NEJM, Lancet, JAMA, BMJ, and most biomedical journals.
+ *
+ * Pattern (the leading list number is the consumer's responsibility — entries
+ * are formatted independently, so this returns the unnumbered reference body):
+ * ```
+ * Surname AB, Surname CD, et al. Article title. Abbrev J Name. Year;Vol(Issue):Pages. doi: 10.x/y
+ * ```
+ * Journal name uses the NLM/ISO abbreviation when available; pages are used as
+ * PubMed supplies them (often elided, e.g. "583-9"); the DOI carries no trailing
+ * period so it stays copy-pasteable.
+ */
+export declare function formatVancouver(article: ParsedArticle): string;
 /**
  * Format a single article in the requested citation style.
  * Throws on unsupported style.

package/dist/services/ncbi/formatting/citation-formatter.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"citation-formatter.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/formatting/citation-formatter.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,aAAa,EAAuB,MAAM,aAAa,CAAC;AAEtE,yCAAyC;AACzC,MAAM,MAAM,aAAa,GAAG,KAAK,GAAG,KAAK,GAAG,QAAQ,GAAG,KAAK,GAAG,WAAW,CAAC;AAgM3E;;;;;;;GAOG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CA6CxD;AAMD;;;;;;;GAOG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CAkDxD;AAMD;;;;;;;;;;;;GAYG;AACH,wBAAgB,YAAY,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CAkF3D;AAMD;;;;;GAKG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CA4FxD;AA4CD;;;;;;;;;;;;GAYG;AACH,wBAAgB,eAAe,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CAuC9D;AAMD;;;GAGG;AACH,wBAAgB,cAAc,CAAC,OAAO,EAAE,aAAa,EAAE,KAAK,EAAE,aAAa,GAAG,MAAM,CAanF;AAED;;;GAGG;AACH,wBAAgB,eAAe,CAC7B,OAAO,EAAE,aAAa,EACtB,MAAM,EAAE,aAAa,EAAE,GACtB,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAMxB"}

package/dist/services/ncbi/formatting/citation-formatter.js CHANGED Viewed

@@ -1,6 +1,6 @@
 /**
  * @fileoverview Hand-rolled citation formatters for PubMed articles.
- * Supports APA 7th, MLA 9th, BibTeX, and RIS formats.
+ * Supports APA 7th, MLA 9th, BibTeX, RIS, and Vancouver (ICMJE/NLM) formats.
  * Pure TypeScript, zero dependencies, Workers-compatible.
  * @module src/services/ncbi/formatting/citation-formatter
  */
@@ -370,8 +370,12 @@ export function formatBibtex(article) {
         if (m.descriptorName)
             keywordSet.add(m.descriptorName);
     }
+    // Brace-wrap each term so MeSH descriptors that carry internal commas in
+    // their inverted form (e.g. "Databases, Protein") stay a single keyword —
+    // biblatex's comma-separated list parser reads a braced item as one element.
     if (keywordSet.size > 0) {
-        fields.push(['keywords', escapeBibtex([...keywordSet].join(', '))]);
+        const keywords = [...keywordSet].map((k) => `{${escapeBibtex(k)}}`).join(', ');
+        fields.push(['keywords', keywords]);
     }
     // Build entry
     const maxKeyLen = Math.max(...fields.map(([k]) => k.length));
@@ -468,6 +472,100 @@ export function formatRis(article) {
     return lines.join('\n');
 }
 // ---------------------------------------------------------------------------
+// Vancouver (ICMJE / NLM)
+// ---------------------------------------------------------------------------
+/**
+ * Format a single author in Vancouver style: `Surname AB` — surname, a space,
+ * then initials with no periods or internal spaces. Collective/group authors
+ * return their name directly.
+ */
+function formatAuthorVancouver(author) {
+    if (author.collectiveName)
+        return author.collectiveName;
+    const last = author.lastName ?? '';
+    const initialsSource = author.initials ??
+        author.firstName
+            ?.split(/[\s-]+/)
+            .filter(Boolean)
+            .map((part) => part[0])
+            .join('');
+    // Letters only (Unicode-aware), uppercased, no separators: "AB", not "A. B."
+    const initials = initialsSource
+        ? Array.from(initialsSource)
+            .filter((c) => /\p{L}/u.test(c))
+            .join('')
+            .toUpperCase()
+        : '';
+    if (!last)
+        return initials;
+    if (!initials)
+        return last;
+    return `${last} ${initials}`;
+}
+/**
+ * Format the full author list for Vancouver: list every author for six or
+ * fewer; for seven or more, list the first six followed by `et al.` (ICMJE).
+ */
+function formatAuthorsVancouver(authors) {
+    const names = authors.map(formatAuthorVancouver).filter(Boolean);
+    if (names.length === 0)
+        return '';
+    if (names.length <= 6)
+        return names.join(', ');
+    return `${names.slice(0, 6).join(', ')}, et al.`;
+}
+/**
+ * Format a PubMed article as a Vancouver (ICMJE/NLM) reference — the numbered
+ * style used by NEJM, Lancet, JAMA, BMJ, and most biomedical journals.
+ *
+ * Pattern (the leading list number is the consumer's responsibility — entries
+ * are formatted independently, so this returns the unnumbered reference body):
+ * ```
+ * Surname AB, Surname CD, et al. Article title. Abbrev J Name. Year;Vol(Issue):Pages. doi: 10.x/y
+ * ```
+ * Journal name uses the NLM/ISO abbreviation when available; pages are used as
+ * PubMed supplies them (often elided, e.g. "583-9"); the DOI carries no trailing
+ * period so it stays copy-pasteable.
+ */
+export function formatVancouver(article) {
+    const segments = [];
+    // Authors — terminate with a period unless the list already ends in "et al."
+    const authorStr = article.authors?.length ? formatAuthorsVancouver(article.authors) : '';
+    if (authorStr) {
+        segments.push(authorStr.endsWith('.') ? authorStr : `${authorStr}.`);
+    }
+    // Title — sentence case as supplied, single terminating period
+    if (article.title) {
+        segments.push(`${article.title.replace(/\.\s*$/, '')}.`);
+    }
+    // Journal — NLM/ISO abbreviation preferred, full title as fallback
+    const journal = article.journalInfo;
+    const journalName = journal?.isoAbbreviation ?? journal?.title;
+    if (journalName) {
+        segments.push(`${journalName.replace(/\.\s*$/, '')}.`);
+    }
+    // Source — "Year;Volume(Issue):Pages."
+    const year = getYear(article);
+    let source = year !== 'n.d.' ? year : '';
+    if (journal?.volume) {
+        source += source ? `;${journal.volume}` : journal.volume;
+        if (journal.issue)
+            source += `(${journal.issue})`;
+        if (journal.pages)
+            source += `:${journal.pages}`;
+    }
+    else if (journal?.pages) {
+        source += source ? `:${journal.pages}` : journal.pages;
+    }
+    if (source)
+        segments.push(`${source}.`);
+    // DOI — NLM "doi: <doi>" form; no trailing period (would corrupt the DOI)
+    if (article.doi) {
+        segments.push(`doi: ${article.doi}`);
+    }
+    return segments.join(' ');
+}
+// ---------------------------------------------------------------------------
 // Dispatchers
 // ---------------------------------------------------------------------------
 /**
@@ -484,6 +582,8 @@ export function formatCitation(article, style) {
             return formatBibtex(article);
         case 'ris':
             return formatRis(article);
+        case 'vancouver':
+            return formatVancouver(article);
     }
 }
 /**

package/dist/services/ncbi/formatting/citation-formatter.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/ncbi/parsing/pmc-article-parser.d.ts CHANGED Viewed

@@ -18,7 +18,11 @@ export declare function extractJatsAuthors(contribGroup: JatsNode | undefined):
  * in manuscript-submitted PMC deposits) preserve their main text.
  */
 export declare function extractBodySections(body: JatsNode | undefined): ParsedPmcSection[];
-/** Extract references from a `<back>` node. Prefers mixed-citation over element-citation. */
+/**
+ * Extract references from a `<back>` node. Prefers mixed-citation over
+ * element-citation, descending into `<citation-alternatives>` when a ref carries
+ * both forms there rather than as direct children of `<ref>`.
+ */
 export declare function extractReferences(back: JatsNode | undefined): ParsedPmcReference[];
 /**
  * Parse a single JATS `<article>` node (from PMC EFetch via the ordered parser)

package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"pmc-article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/pmc-article-parser.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EACV,gBAAgB,EAChB,eAAe,EAEf,kBAAkB,EAClB,gBAAgB,EACjB,MAAM,aAAa,CAAC;AACrB,OAAO,EAKL,KAAK,QAAQ,EAGd,MAAM,sBAAsB,CAAC;AAmB9B,iGAAiG;AACjG,wBAAgB,kBAAkB,CAAC,YAAY,EAAE,QAAQ,GAAG,SAAS,GAAG,eAAe,EAAE,CA2BxF;AA2HD;;;;;GAKG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,gBAAgB,EAAE,CA2BlF;AA0BD~~,6FAA6F~~;~~AAC7F~~,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,kBAAkB,EAAE,~~CAsBlF~~;AAID;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,WAAW,EAAE,QAAQ,GAAG,gBAAgB,CA4CvE"}
1	+ {"version":3,"file":"pmc-article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/pmc-article-parser.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EACV,gBAAgB,EAChB,eAAe,EAEf,kBAAkB,EAClB,gBAAgB,EACjB,MAAM,aAAa,CAAC;AACrB,OAAO,EAKL,KAAK,QAAQ,EAGd,MAAM,sBAAsB,CAAC;AAmB9B,iGAAiG;AACjG,wBAAgB,kBAAkB,CAAC,YAAY,EAAE,QAAQ,GAAG,SAAS,GAAG,eAAe,EAAE,CA2BxF;AA2HD;;;;;GAKG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,gBAAgB,EAAE,CA2BlF;AA0BD;;;;GAIG;AACH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,kBAAkB,EAAE,CA4BlF;AAID;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,WAAW,EAAE,QAAQ,GAAG,gBAAgB,CA4CvE"}

package/dist/services/ncbi/parsing/pmc-article-parser.js CHANGED Viewed

@@ -206,7 +206,11 @@ function extractSection(sec) {
     };
 }
 // ─── References ─────────────────────────────────────────────────────────────
-/** Extract references from a `<back>` node. Prefers mixed-citation over element-citation. */
+/**
+ * Extract references from a `<back>` node. Prefers mixed-citation over
+ * element-citation, descending into `<citation-alternatives>` when a ref carries
+ * both forms there rather than as direct children of `<ref>`.
+ */
 export function extractReferences(back) {
     if (!back)
         return [];
@@ -215,7 +219,12 @@ export function extractReferences(back) {
         return [];
     const results = [];
     for (const ref of findAll(refList, 'ref')) {
-        const citationNode = findOne(ref, 'mixed-citation') ?? findOne(ref, 'element-citation');
+        // JATS wraps the two citation forms in <citation-alternatives> (the NLM
+        // construct carrying both a structured <element-citation> and a readable
+        // <mixed-citation>). findOne matches direct children only, so resolve that
+        // container first; refs with a direct citation node fall through to `ref`.
+        const container = findOne(ref, 'citation-alternatives') ?? ref;
+        const citationNode = findOne(container, 'mixed-citation') ?? findOne(container, 'element-citation');
         if (!citationNode)
             continue;
         const citation = textContent(citationNode);

package/dist/services/ncbi/parsing/pmc-article-parser.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.7.10",
+  "version": "2.8.0",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
   "type": "module",
@@ -92,7 +92,7 @@
   },
   "devDependencies": {
     "@biomejs/biome": "^2.4.16",
-    "@types/node": "^25.9.1",
+    "@types/node": "^25.9.2",
     "@types/sanitize-html": "^2.16.1",
     "@vitest/coverage-istanbul": "^4.1.8",
     "depcheck": "^1.4.7",

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.7.10",
+  "version": "2.8.0",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.7.10",
+      "version": "2.8.0",
       "packageArguments": [
         {
           "type": "positional",
@@ -66,7 +66,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.7.10",
+      "version": "2.8.0",
       "packageArguments": [
         {
           "type": "positional",