MCP server

Ebi Ols

io.github.pipeworx-io/ebi-ols

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

EBI OLS4 MCP — Ontology Lookup Service.

Working at last checkOfficial: pipeworx.io's GitHub account (pipeworx-io)About 27,009 tokens per request once connected48 tools

https://gateway.pipeworx.io/ebi-ols/mcp

At a glance

Type: MCP server
Publisher: pipeworx.io (verified by the MCP Registry)
Status: Working at last check
Tools: 48
Token cost: About 27,009 tokens per request
Sets up in: Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok
Last checked: 26 Oct 2026, 08:29 UTC

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http ebi-ols https://gateway.pipeworx.io/ebi-ols/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.ebi-ols]
url = "https://gateway.pipeworx.io/ebi-ols/mcp"

Gemini CLI

{"mcpServers":{"ebi-ols":{"httpUrl":"https://gateway.pipeworx.io/ebi-ols/mcp"}}}

Cursor

{"mcpServers":{"ebi-ols":{"url":"https://gateway.pipeworx.io/ebi-ols/mcp"}}}

VS Code

{"servers":{"ebi-ols":{"type":"http","url":"https://gateway.pipeworx.io/ebi-ols/mcp"}}}

Antigravity

agy mcp add ebi-ols https://gateway.pipeworx.io/ebi-ols/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"ebi-ols","server_url":"https://gateway.pipeworx.io/ebi-ols/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"ebi-ols","server_url":"https://gateway.pipeworx.io/ebi-ols/mcp"}

get_ontology ~66 tokens
Ontology metadata by id (e.g. "efo", "mondo", "go").
get_term ~143 tokens
Term details. Pass either iri, short_form, or obo_id (the latter two require ontology).
list_ontologies ~176 tokens
EMBL-EBI Ontology Lookup Service (OLS4) — page through every biomedical ontology loaded into OLS, such as GO, EFO, MONDO, ChEBI, HPO and UBERON. Returns each ontology's id, title, description, term count, version and status, with size/page controls. Answers which biomedical ontologies are searchable
search ~160 tokens
Full-text search across all ontologies (or one).
term_ancestors ~81 tokens
Transitive ancestors of a term.
term_children ~80 tokens
Direct children of a term.

Mondo
Mondo — condition-string resolver onto the Mondo Disease Ontology.
EventTrader MCP
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Bioportal
BioPortal — NCBO's biomedical ontology repository (data.bioontology.org).
Delx Commerce — Pay-per-Result APIs for Agents
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Beyond Wine
Claims-based knowledge base for no/low ABV specialty beverages (producers, beverages, people).
Hpo Api
HPO API MCP.
Opentargets
Open Targets MCP — disease/target/drug knowledge graph.
Quickgo
QuickGO (EBI) MCP — Gene Ontology browser.

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