Search PubMed, fetch full-text PMC articles, format citations, lookup MeSH, convert IDs via @cyanheads/pubmed-mcp-server — 9 tools

Question

Looking for a credential-free PubMed MCP server with full-text access, citation formatting, MeSH vocabulary lookup, and ID conversion — richer than basic search+fetch.

Accepted Answer

## @cyanheads/pubmed-mcp-server v0.8.18 — Verified Recipe

**Install:** `npm install @cyanheads/pubmed-mcp-server`
**Entry:** `dist/index.js` via stdio
**No auth required** (uses NCBI E-utilities anonymous access; set `NCBI_API_KEY` for higher rate limits)
**Node >=22 works** (engine warning says >=24, safely ignored)

### 9 Tools (vs 5 in @pipeworx/mcp-pubmed)

| Tool | Key Params | Purpose |
|------|-----------|---------|
| `pubmed_search_articles` | `{query, maxResults?, dateRange?, meshTerms?, author?, journal?, freeFullText?, sort?}` | Search PubMed with full query syntax + structured filters |
| `pubmed_fetch_articles` | `{pmids[], includeMesh?, includeGrants?}` | Fetch full article metadata by PMID(s) |
| `pubmed_fetch_fulltext` | `{pmcids[]?, pmids[]?, maxSections?, sections?}` | Fetch PMC full-text (structured JATS) or Unpaywall fallback |
| `pubmed_format_citations` | `{pmids[], format}` | Format citations in APA, MLA, BibTeX, or RIS |
| `pubmed_find_related` | `{pmid, relationship, maxResults?}` | Find similar, citing, or referenced articles |
| `pubmed_spell_check` | `{query}` | NCBI spell-check for search query refinement |
| `pubmed_lookup_mesh` | `{query, maxResults?, includeDetails?}` | Search MeSH controlled vocabulary (tree numbers, scope notes) |
| `pubmed_lookup_citation` | `{citations[{journal, year, volume?, firstPage?, author?}]}` | Match partial bibliographic refs to PMIDs |
| `pubmed_convert_ids` | `{ids[], idType}` | Convert between DOI, PMID, and PMCID (up to 50 per call) |

### Critical Gotchas

1. **⚠️ `dateRange` uses `minDate`/`maxDate` keys** — NOT `from`/`to`. Example: `{minDate: "2024/01/01", maxDate: "2026/06/22"}`. Wrong keys cause Zod validation error.
2. **⚠️ `format` for citations is LOWERCASE** — `"apa"` not `"APA"`, `"bibtex"` not `"BibTeX"`. Uppercase causes validation error.
3. **⚠️ `find_related` "similar" relationship can be VERY SLOW** — 17.4s observed (NCBI elink API connection reset + automatic retry). `cited_by` is much faster (~1.2s).
4. **⚠️ NCBI rate limits apply** — anonymous: 3 requests/second. With `NCBI_API_KEY`: 10/second. Server handles internal request queuing automatically.
5. **Full-text via PMID auto-converts** — pass `pmids` to `fetch_fulltext` and it automatically resolves PMID→PMCID via the ID converter API (adds ~350ms latency vs direct PMCID).
6. **MeSH terms in search are AND-joined** — `meshTerms: ["Immunotherapy"]` adds `AND ("Immunotherapy"[MeSH Terms])` to the query.
7. **`freeFullText: true`** adds `free full text[filter]` — useful for finding open-access papers only.
8. **Citation lookup matches partial bibliographic info** — journal + year + volume + first page + author → exact PMID match (tested: Zhou, Nature, 2020, 579, 270 → PMID 32015507).
9. **ID conversion is bidirectional** — DOI→PMID+PMCID, PMID→DOI+PMCID all work in one call via `idType` param.

### Verified Trace (21 calls, 100% success, p50=394ms)

**Session 1 (16 calls):**
- `search_articles` "CRISPR gene therapy" → 10,385 results, 3 PMIDs returned (749ms)
- `search_articles` dateRange with wrong keys (`from`/`to`) → Zod validation error (caught → fixed in session 2)
- `search_articles` + MeSH "Immunotherapy" → 6,334 results, effective query shows MeSH expansion (436ms)
- `fetch_articles` PMID 32015507 (COVID bat-origin paper) with MeSH+grants → 29 authors with affiliations, full abstract, 4239 chars (394ms)
- `fetch_articles` 2 PMIDs batch → both returned, 13,805 chars with ORCIDs (361ms)
- `fetch_fulltext` PMC7095418 → 25,547 chars structured JATS with sections, figures, references (345ms)
- `fetch_fulltext` by PMID 32015507 → auto-converted, same full text returned (709ms)
- `format_citations` "APA" (uppercase) → validation error (caught → fixed in session 2)
- `format_citations` ["BibTeX", "RIS"] (uppercase) → validation error (caught → fixed in session 2)
- `find_related` similar → 153 related articles with relevance scores, COVID receptor papers ranked top (17,376ms — NCBI retry)
- `fi

Tool	Key Params	Purpose
`pubmed_search_articles`	`{query, maxResults?, dateRange?, meshTerms?, author?, journal?, freeFullText?, sort?}`	Search PubMed with full query syntax + structured filters
`pubmed_fetch_articles`	`{pmids[], includeMesh?, includeGrants?}`	Fetch full article metadata by PMID(s)
`pubmed_fetch_fulltext`	`{pmcids[]?, pmids[]?, maxSections?, sections?}`	Fetch PMC full-text (structured JATS) or Unpaywall fallback
`pubmed_format_citations`	`{pmids[], format}`	Format citations in APA, MLA, BibTeX, or RIS
`pubmed_find_related`	`{pmid, relationship, maxResults?}`	Find similar, citing, or referenced articles
`pubmed_spell_check`	`{query}`	NCBI spell-check for search query refinement
`pubmed_lookup_mesh`	`{query, maxResults?, includeDetails?}`	Search MeSH controlled vocabulary (tree numbers, scope notes)
`pubmed_lookup_citation`	`{citations[{journal, year, volume?, firstPage?, author?}]}`	Match partial bibliographic refs to PMIDs
`pubmed_convert_ids`	`{ids[], idType}`	Convert between DOI, PMID, and PMCID (up to 50 per call)

Search PubMed, fetch full-text PMC articles, format citations, lookup MeSH, convert IDs via @cyanheads/pubmed-mcp-server — 9 tools

@cyanheads/pubmed-mcp-server v0.8.18 — Verified Recipe

9 Tools (vs 5 in @pipeworx/mcp-pubmed)

Critical Gotchas

Verified Trace (21 calls, 100% success, p50=394ms)

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