EBI Ontology Lookup Service — 250+ biomedical ontologies
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Config is the same across clients — only the file and path differ.
{
"mcpServers": {
"io-github-pipeworx-io-ebi-ols": {
"command": "<see-readme>",
"args": []
}
}
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EBI Ontology Lookup Service — 250+ biomedical ontologies
No automated test available for this server. Check the GitHub README for setup instructions.
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EBI OLS4 MCP — Ontology Lookup Service.
Part of Pipeworx — an MCP gateway connecting AI agents to 673+ live data sources.
| Tool | Description |
|---|---|
list_ontologies | List loaded ontologies (paginated). |
get_ontology | Ontology metadata by id (e.g. "efo", "mondo", "go"). |
search | Full-text search across all ontologies (or one). |
get_term | Term details. Pass either iri, short_form, or obo_id (the latter two require ontology). |
term_ancestors | Transitive ancestors of a term. |
term_children | Direct children of a term. |
Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
{
"mcpServers": {
"ebi-ols": {
"url": "https://gateway.pipeworx.io/ebi-ols/mcp"
}
}
}
Or connect to the full Pipeworx gateway for access to all 673+ data sources:
{
"mcpServers": {
"pipeworx": {
"url": "https://gateway.pipeworx.io/mcp"
}
}
}
Instead of calling tools directly, you can ask questions in plain English:
ask_pipeworx({ question: "your question about Ebi Ols data" })
The gateway picks the right tool and fills the arguments automatically.
MIT