A side-by-side look at the Biolit and Pubmed MCP Server MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Biolit for biology, medicine and bioinformatics work as a local process; choose Pubmed MCP Server for biology, medicine and bioinformatics as a local process. You can also run both side by side in one mcpServers block.
ANTHROPIC_API_KEY, OPENAI_API_KEY, LLM_PROVIDER, LLM_MODEL, CORE_API_KEY, BIOLIT_CUSTOM_RESOLVERS.run_pipeline, fetch_pubmed_metadata, fetch_geo_record.pubmed_search_articles, pubmed_fetch_articles, pubmed_fetch_fulltext.Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology, Medicine and Bioinformatics | Biology, Medicine and Bioinformatics |
| Quality signal | 53/100 · Good | 57/100 · Good |
| Install command | Confirmed | Confirmed |
| Transport | Local subprocess (stdio) | Local subprocess (stdio) |
| Auth | Not declared | Not declared |
| Pricing | Not declared | Not declared |
| Required env vars | ANTHROPIC_API_KEYOPENAI_API_KEYLLM_PROVIDERLLM_MODELCORE_API_KEYBIOLIT_CUSTOM_RESOLVERS | None listed |
| Verified owner | Community listing | Community listing |
| GitHub stars | 2 | 159 |
| Directory activity | 1 views 0 installs 0 upvotes | 1 views 0 installs 0 upvotes |
| Tools | 12 | 11 |
| Full listing | View Biolit | View Pubmed MCP Server |
run_pipelineFetch, optionally screen, and optionally extract a mixed list of PMIDs, DOIs, and/or GEO accessions; write results CSV (and optionally a `.md` summary when `markdown=True`). Accepts `ids` (comma-separated), `bib_path` (`.bib` file), or `ids_file` (plain-text identifier file). Pass `sections` (comma…fetch_pubmed_metadataFetch PubMed metadata by PMIDfetch_geo_recordFetch and parse a GEO record by accessionfetch_fulltextRetrieve full text for a PMID (6-step chain)fetch_geo_fulltextRetrieve full text for a GEO accession via its linked PMIDsfetch_supplementaryRetrieve & extract text from a paper's supplementary files (supplementary methods, tables) via Europe PMCscreen_paperLLM relevance screen given pre-fetched textextract_fieldsStructured field extraction given pre-fetched textresolve_doiResolve a DOI to PMID + PMCID via the NCBI ID Converterlookup_s2_pdfCheck whether Semantic Scholar has an open-access PDF for a DOIread_pmids_from_emlParse PMIDs from a PubMed alert `.eml` fileget_versionReturn the installed biolit package versionpubmed_search_articlesSearch PubMed with full query syntax, structured filters, date ranges, and optional summariespubmed_fetch_articlesFetch article metadata by PMID: abstract, authors, journal, MeSH terms, grants, linked retraction and correction noticespubmed_fetch_fulltextFetch full text by PMID, PMCID, or DOI, falling back from PMC to Europe PMC to Unpaywallpubmed_europepmc_searchSearch Europe PMC for preprints, patents, Agricola, and open-access records PubMed doesn't carrypubmed_europepmc_fetchFetch complete Europe PMC records, including the untruncated abstract, by `source` + `epmcIdpubmed_format_citationsFormat citations in APA 7th, MLA 9th, BibTeX, RIS, or Vancouver (ICMJE/NLM)pubmed_find_relatedFind similar articles, citing articles, or references for a PMIDpubmed_spell_checkCorrect a misspelled PubMed query via NCBI ESpellpubmed_lookup_meshLook up MeSH headings with tree numbers, scope notes, and entry termspubmed_lookup_citationResolve partial references, up to 25 at a time, to PMIDs via ECitMatchpubmed_convert_idsConvert between DOI, PMID, and PMCID via the PMC ID ConverterPaste either block (or both) into your client config, e.g. claude_desktop_config.json or ~/.cursor/mcp.json. We only show a config when the install command is confirmed.
{
"mcpServers": {
"biolit": {
"command": "uvx",
"args": [
"biolit"
],
"env": {
"ANTHROPIC_API_KEY": "YOUR_ANTHROPIC_API_KEY_HERE",
"OPENAI_API_KEY": "YOUR_OPENAI_API_KEY_HERE",
"LLM_PROVIDER": "YOUR_LLM_PROVIDER_HERE",
"LLM_MODEL": "YOUR_LLM_MODEL_HERE",
"CORE_API_KEY": "YOUR_CORE_API_KEY_HERE",
"BIOLIT_CUSTOM_RESOLVERS": "YOUR_BIOLIT_CUSTOM_RESOLVERS_HERE"
}
}
}
}
{
"mcpServers": {
"pubmed-mcp-server-2": {
"command": "bunx",
"args": [
"@cyanheads/pubmed-mcp-server@latest"
]
}
}
}