ols

is an Aggregator.

The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. Users can browse ontologies through the website and programmatically via the OLS REST API and an MCP server. As of 2026-09-30 it served 287 ontologies with about 10.8 million classes, loaded from the OBO Foundry registry plus ontologies curated by EMBL-EBI. Maintained by the Samples, Phenotypes and Ontologies Team (SPOT) at EMBL-EBI.

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Domains

biomedical, biological systems, information technology

License

Apache License 2.0 (software; loaded ontologies carry their own licenses)

Homepage

ols

Repository

GitHub

External IDs

Product Summary

Products

From this Resource
ID Name URL Category Format Description
ols.portal OLS Web Portal ols4 Graphical Interface http Web interface for browsing and search...
ols.api OLS REST API api-docs Programming Interface http RESTful API for programmatic access t...
ols.json OLS Ontologies JSON latest Product json Gzipped tar archive (ontology_jsons.t...
ols.json-linked OLS Linked Ontology JSON latest Product json Gzipped tar archive (ontology_jsons_l...
ols.embeddings OLS Term Embeddings embeddings Product parquet Precomputed ontology term embeddings ...
ols.mcp OLS MCP Server mcp Programming Interface http Model Context Protocol (MCP) server f...
ols.mappings OLS SSSOM Mappings latest Mapping sssom Ontology mappings extracted from all ...
From other Resources
ID Name URL Category Format Relation Description
service-kp.trapi Service Provider TRAPI Service%20Provider Programming Interface http had primary source TRAPI endpoint for the Service Provid...
bioregistry.registry.json Bioregistry JSON Export registry.json (768.2 KB) Product json was influenced by Full Bioregistry export as JSON, with...
bioregistry.sssom Bioregistry SSSOM Mappings bioregistry.sssom.tsv (133.1 KB) Mapping sssom was influenced by SSSOM mappings between Bioregistry pr...

Details

Ontology Lookup Service

Overview

The Ontology Lookup Service (OLS) is a comprehensive repository for biomedical ontologies maintained by EMBL-EBI. It provides a single point of access to the latest versions of numerous biomedical ontologies, making it easier for researchers to browse, search, and access ontology data. OLS supports both human browsing through its web interface and programmatic access through its REST API.

Data Content

OLS aggregates and provides access to numerous biomedical ontologies from various sources, including:

  • Anatomy and Development: Uberon, Cell Ontology (CL), and others
  • Diseases: Disease Ontology (DOID), Mondo, Human Phenotype Ontology (HPO)
  • Chemistry: ChEBI
  • Molecular Biology: Gene Ontology (GO), Sequence Ontology (SO)
  • And many more biomedical domain ontologies

The service provides:

  • Latest ontology versions with automatic updates
  • Cross-references between ontologies
  • Links to external databases
  • Ontology metadata and provenance information
  • Term definitions, synonyms, and hierarchical relationships

Key Features

  • Web Interface: User-friendly browsing and searching with filtering options
  • REST API: Comprehensive programmatic access to all ontology data
  • Search Capabilities: Full-text search with exact match and obsolete term options
  • Cross-References: Linked data between different ontologies and external databases
  • Multiple Formats: Data available as OLS JSON, linked JSON, SSSOM mappings and term embeddings
  • Regular Updates: Continuous integration of latest ontology versions
  • SSSOM Mappings: Standardized ontology-to-ontology mappings

Access Methods

  • Web Portal: Browse and search through https://www.ebi.ac.uk/ols4/
  • REST API: Programmatic access documented at https://www.ebi.ac.uk/ols4/api-docs
  • FTP Downloads: Data dumps available at https://ftp.ebi.ac.uk/pub/databases/spot/ols/
  • MCP Server: Model Context Protocol access for AI assistants
  • MCP Server: Model Context Protocol server for AI integration

Data Formats

OLS provides data in multiple formats:

  1. JSON: Internal ontology representation (~50 GB uncompressed)
  2. Linked JSON: With cross-references added (~150 GB uncompressed)
  3. Embeddings: Precomputed term embeddings in Parquet format
  4. SSSOM: Standard Simple Standard for Ontology Mappings format

Use Cases

  1. Ontology Browsing: Explore biomedical ontologies interactively
  2. Programmatic Integration: Access ontology data in applications via API
  3. Local Deployment: Set up local OLS instances for development
  4. Mapping Analysis: Study cross-ontology mappings and relationships
  5. Data Annotation: Use ontology terms for standardized data annotation
  6. AI Integration: Access ontology knowledge through MCP server

The SPOT team also provides complementary services:

  • OxO: Cross-ontology mapping service between terms from different ontologies
  • ZOOMA: Service to assist in mapping data to ontologies in OLS

Management

Organization: EMBL-EBI Samples, Phenotypes and Ontologies Team (SPOT)

Repository: https://github.com/EBISPOT/ols4

Contact:

  • GitHub Issues: https://github.com/EBISPOT/ols4/issues
  • Email: ols-support@ebi.ac.uk
  • Mailing List: ols-announce@ebi.ac.uk (for announcements)

Funding

OLS has been supported by:

  • EMBL-EBI Core Funds
  • European Union HORIZON program (grant 101131959)
  • Chan-Zuckerberg Initiative (Human Cell Atlas Data Coordination Platform)
  • NIH Office of the Director (R24-OD011883, OT2OD033756)
  • NIH National Human Genome Research Institute (5RM1 HG010860)
  • European Union’s Horizon 2020 (grants 824087, 825575, 654248)
  • EVORA project (grant 101131959)

Privacy and Terms

  • Privacy Policy: Available at https://www.ebi.ac.uk/ols4/Privacy_notice_for_EMBL-EBI_Public_Website.pdf
  • Terms of Use: https://www.ebi.ac.uk/about/terms-of-use
  • License: EMBL-EBI licensing terms apply

Citation

Please cite: OLS4: a new Ontology Lookup Service for a growing interdisciplinary knowledge ecosystem. Bioinformatics, Volume 41, Issue 5, May 2025, btaf279. PMID: 40323307

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Created: October 30, 2025 | Last modified: October 04, 2026