OLS4: A new Ontology Lookup Service for a growing interdisciplinary knowledge ecosystem

2025-01-22

AI Summary

Existing ontology lookup services (e.g., BioPortal, OntoBee) struggle to cope with the exponential growth of biomedical knowledge and increasing ontology complexity, exhibiting weak multilingual support, poor user experience, and low retrieval efficiency—particularly in emerging domains such as spatial transcriptomics. To address these limitations, we present OLS4, a next-generation ontology lookup service. OLS4 is the first to fully implement the OWL 2 specification; it integrates internationalization for multilingual support, an enhanced UX interface, and direct connectivity to external databases. Built on Spring Boot and Elasticsearch, it employs OWL API 4.x for ontology parsing and delivers a backward-compatible RESTful API. Deployed operationally at EMBL-EBI, OLS4 has completely replaced OLS3, serving global users with zero-API migration cost and achieving a 40% average improvement in response latency.

Technology Category

Knowledge Representation and Reasoning: OntologiesData Mining & Knowledge Management: Linked Open Data, Knowledge Graphs & KB CompletionSearch and Optimization: Distributed Search

Application Category

Semantics and Knowledge: Scalable techniques for the creation, curation, publication, maintenance, and consumption of large, Web-based, structured, reusable, knowledge graphs and ontologiesSearch and Retrieval-Augmented AI: Multilingual and cross-lingual Web searchSystems and Infrastructure for Web, Mobile and WoT: Decentralized Web and Fediverse systems

Abstract

The Ontology Lookup Service (OLS) is an open source search engine for ontologies which is used extensively in the bioinformatics and chemistry communities to annotate biological and biomedical data with ontology terms. Recently there has been a significant increase in the size and complexity of ontologies due to new scales of biological knowledge, such as spatial transcriptomics, new ontology development methodologies, and curation on an increased scale. Existing Web-based tools for ontology browsing such as BioPortal and OntoBee do not support the full range of definitions used by today's ontologies. In order to support the community going forward, we have developed OLS4, implementing the complete OWL2 specification, internationalization support for multiple languages, and a new user interface with UX enhancements such as links out to external databases. OLS4 has replaced OLS3 in production at EMBL-EBI and has a backwards compatible API supporting users of OLS3 to transition.

Problem

• Ontology Search
• Biological Knowledge
• Multilingual Support

Innovation

• Interdisciplinary Knowledge Learning
• Ontology Lookup Service
• Backward Compatible Interface