A side-by-side look at the Biolit and Clinicaltrialsgov 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 Clinicaltrialsgov 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.clinicaltrials_search_studies, clinicaltrials_get_study_record, clinicaltrials_get_study_count.Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology, Medicine and Bioinformatics | Biology, Medicine and Bioinformatics |
| Quality signal | 53/100 · Good | 61/100 · 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 | 99 |
| Directory activity | 1 views 0 installs 0 upvotes | 1 views 0 installs 0 upvotes |
| Tools | 12 | 7 |
| Full listing | View Biolit | View Clinicaltrialsgov 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 versionclinicaltrials_search_studiesSearch studies with full-text and field-specific queries, status/phase/geographic filters, pagination, sorting, and field selectionclinicaltrials_get_study_recordFetch a single study by NCT ID — full protocol record with optional location/outcome/reference capsclinicaltrials_get_study_countFast total study count for a query, without fetching dataclinicaltrials_get_field_valuesDiscover valid values for API fields, with per-value study countsclinicaltrials_get_field_definitionsResolve valid field names — keyword search, path drill-down, or top-level overviewclinicaltrials_get_study_resultsFetch posted results — outcomes, adverse events, participant flow, baseline — for completed studiesclinicaltrials_find_eligibleMatch patient demographics and conditions to candidate recruiting trials, without checking inclusion/exclusion criteriaPaste 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": {
"clinicaltrialsgov-mcp-server": {
"command": "bunx",
"args": [
"clinicaltrialsgov-mcp-server@latest"
]
}
}
}