Opentargets vs Medplum MCP
A side-by-side look at the Opentargets and Medplum MCP MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Opentargets for biology & bioinformatics work as a local process; choose Medplum MCP for biology & bioinformatics. You can also run both side by side in one mcpServers block.
Which MCP server should you choose?
Choose Opentargets when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- You prefer a local stdio subprocess transport.
- Its auth model fits you: No auth required.
- You have the keys it needs:
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. - You want tools like
get_target_alternative_genes, get_target_associated_diseases, get_target_chemical_probes.
Choose Medplum MCP when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
Feature & specification comparison
Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology & Bioinformatics | Biology & Bioinformatics |
| Quality signal | 63/100 · Good | 41/100 · Fair |
| Install command | Confirmed | Not confirmed yet |
| Transport | Local subprocess (stdio) | — |
| Auth | No auth required | Not declared |
| Pricing | Free | Not declared |
| Required env vars | MCP_TRANSPORTFASTMCP_SERVER_HOSTFASTMCP_SERVER_PORTOPEN_TARGETS_API_URLOPEN_TARGETS_RATE_LIMIT_RPSOPEN_TARGETS_RATE_LIMIT_BURSTOPEN_TARGETS_RATE_LIMIT_ENABLED | None listed |
| Verified owner | Community listing | Community listing |
| GitHub stars | 19 | 2,760 |
| Directory activity | 4 views 0 installs 0 upvotes | 2 views 0 installs 0 upvotes |
| Tools | 68 | Not listed |
| Full listing | View Opentargets | View Medplum MCP |
Tools & capabilities
Opentargets tools 68
get_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.- +56 more on the listing page
Medplum MCP tools
No tool names declared yet. Check the project README from the listing page.
Ready-to-paste client configs
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.
Opentargets
{
"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"
}
}
}
}
Medplum MCP
No confirmed install command for Medplum MCP yet — follow the setup steps linked from its listing page rather than a guessed package name.
Frequently asked questions
Opentargets is categorized under Biology & Bioinformatics and uses a local stdio subprocess. Medplum MCP belongs to Biology & Bioinformatics and uses an install path we have not confirmed yet. Pick Opentargets for biology & bioinformatics work and Medplum MCP for biology & bioinformatics.
Copy the mcpServers block from the config section on this page into your client's config (for example claude_desktop_config.json or ~/.cursor/mcp.json), then fully restart the client. Medplum MCP has no confirmed install command yet — follow its own setup instructions.
Opentargets is listed as free. Auth: no auth required. Medplum MCP has no declared pricing — check the project's own site. If a server needs environment variables such as API keys, define them under the env key in your client's MCP config.
Yes. MCP clients support multiple servers: add opentargets and mcp-112 as separate keys in the same mcpServers object, and your assistant will call tools from either one.
On AllMCPs, Opentargets has a quality signal of 63/100 (Good) with 4 views, 0 installs and 19 GitHub stars. Medplum MCP has 41/100 (Fair) with 2 views, 0 installs and 2,760 GitHub stars.