ols4
by EBISPOT·★ 89·Score 47
EMBL-EBI's Ontology Lookup Service provides an MCP server for biomedical ontologies via REST API.
Overview
The OLS4 (Ontology Lookup Service) is a comprehensive repository for biomedical ontologies, providing a single point of access to the latest versions. It features a website, REST API, and MCP server endpoint at https://www.ebi.ac.uk/ols4/api/mcp. The service uses specialized databases (Solr for full-text search and Neo4j for graph queries) to handle complex ontology queries efficiently. Developed in Java with a React frontend, it's designed for both public use and private deployment of custom ontologies.
Try asking AI
After installing, here are 5 things you can ask your AI assistant:
When to choose this
Choose OLS when you need access to standardized biomedical ontologies through MCP, especially for AI applications in bioinformatics or healthcare.
When NOT to choose this
Not suitable if you need ontology reasoning capabilities, as OLS assumes pre-reasoned ontologies and doesn't perform any OWL reasoning.
Comparable tools
Installation
Installation
- **Docker Compose (Recommended)**:
``bash HOST_UID=$(id -u) HOST_GID=$(id -g) docker compose up ``
- **Kubernetes with Helm**:
``bash export KUBECONFIG=<K8S_CONFIG> helm install ols4 <OLS4_DIR>/k8chart/ols4 --set imageTag=dev ``
- **Claude Desktop Configuration**:
Add to your Claude Desktop config.json: ``json { "mcpServers": { "ols": { "command": "curl", "args": ["-s", "https://www.ebi.ac.uk/ols4/api/mcp"] } } } ``
FAQ
- What ontologies are available in OLS?
- OLS hosts a variety of biomedical ontologies including EFO, GO, CHEBI, and many others. You can see a complete list through the web interface at https://www.ebi.ac.uk/ols4/
- Can I host my own ontology with OLS?
- Yes, you can configure OLS to host your own OWL or RDFS ontologies by creating a configuration file and following the deployment instructions in the README.
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Last updated · Auto-generated from public README + GitHub signals.