A side-by-side look at the Clinicaltrialsgov MCP Server and Opentargets MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Clinicaltrialsgov MCP Server for biology, medicine and bioinformatics work as a local process; choose Opentargets for biology, medicine and bioinformatics as a local process. You can also run both side by side in one mcpServers block.
clinicaltrials_search_studies, clinicaltrials_get_study_record, clinicaltrials_get_study_count.MCP_TRANSPORT, FASTMCP_SERVER_HOST, FASTMCP_SERVER_PORT, OPEN_TARGETS_API_URL, OPEN_TARGETS_RATE_LIMIT_RPS, OPEN_TARGETS_RATE_LIMIT_BURST, OPEN_TARGETS_RATE_LIMIT_ENABLED.get_target_alternative_genes, get_target_associated_diseases, get_target_chemical_probes.Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology, Medicine and Bioinformatics | Biology, Medicine and Bioinformatics |
| Quality signal | 61/100 · Good | 61/100 · Good |
| Install command | Confirmed | Confirmed |
| Transport | Local subprocess (stdio) | Local subprocess (stdio) |
| Auth | Not declared | No auth required |
| Pricing | Not declared | Free |
| Required env vars | None listed | MCP_TRANSPORTFASTMCP_SERVER_HOSTFASTMCP_SERVER_PORTOPEN_TARGETS_API_URLOPEN_TARGETS_RATE_LIMIT_RPSOPEN_TARGETS_RATE_LIMIT_BURSTOPEN_TARGETS_RATE_LIMIT_ENABLED |
| Verified owner | Community listing | Community listing |
| GitHub stars | 99 | 19 |
| Directory activity | 1 views 0 installs 0 upvotes | 3 views 0 installs 0 upvotes |
| Tools | 7 | 68 |
| Full listing | View Clinicaltrialsgov MCP Server | View Opentargets |
clinicaltrials_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 criteriaget_target_alternative_genesList alternate gene symbols and database cross-references for a target.get_target_associated_diseasesList diseases linked to a target with association scores.get_target_chemical_probesList available chemical probes and their quality metrics.get_target_classReturn ChEMBL target class annotations for a gene.get_target_depmap_essentialityFetch DepMap CRISPR essentiality scores across cell lines.get_target_expressionReturn baseline expression measurements for a target across biosamples.get_target_genetic_constraintFetch genetic constraint metrics (gnomAD) for a target.get_target_hallmarksReturn cancer hallmark annotations associated with a target.get_target_homologuesRetrieve cross-species homologues for a target gene.get_target_infoRetrieve core identity details for a target gene.get_target_interactionsRetrieve protein interaction partners for a target from curated databases.get_target_known_drugsReturn compounds with known activity on the target.Paste 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": {
"clinicaltrialsgov-mcp-server": {
"command": "bunx",
"args": [
"clinicaltrialsgov-mcp-server@latest"
]
}
}
}
{
"mcpServers": {
"opentargets": {
"command": "uvx",
"args": [
"--from",
"git+https://github.com/nickzren/opentargets-mcp",
"opentargets-mcp"
],
"env": {
"MCP_TRANSPORT": "YOUR_MCP_TRANSPORT_HERE",
"FASTMCP_SERVER_HOST": "YOUR_FASTMCP_SERVER_HOST_HERE",
"FASTMCP_SERVER_PORT": "YOUR_FASTMCP_SERVER_PORT_HERE",
"OPEN_TARGETS_API_URL": "YOUR_OPEN_TARGETS_API_URL_HERE",
"OPEN_TARGETS_RATE_LIMIT_RPS": "YOUR_OPEN_TARGETS_RATE_LIMIT_RPS_HERE",
"OPEN_TARGETS_RATE_LIMIT_BURST": "YOUR_OPEN_TARGETS_RATE_LIMIT_BURST_HERE",
"OPEN_TARGETS_RATE_LIMIT_ENABLED": "YOUR_OPEN_TARGETS_RATE_LIMIT_ENABLED_HERE"
}
}
}
}