The Ontology Lookup Service (OLS) hosted at the EMBL European Bioinformatics Institute has been providing ontology search and visualisation services for over ten years. In this time the range and diversity of ontologies has changed dramatically. One of the major shifts has been the increasing use of the W3C Web Ontology Language (OWL) for representing biomedical ontologies. The OLS has been reengineered in order to accommodate the OWL standard and provide a wider range of ontology-based services to the community.
This first iteration of the new OLS provides the following functionality: 1) An ontology crawler that detects when external ontologies have changed 2) A search engine for querying ontology term meta-data 3) Web services for querying the structure of the ontology 4) A user interface for exploring and visualising the ontologies 5) A versioning system to track ontology evolution.
The EU funded DIACHRON project4 has been developing a framework for managing the evolution of data on the Semantic Web. The move to OWL means that OLS can utilise DIACHRON technology to monitor ontologies for changes so that the system can be updated when new ontologies become available. DIACHRON is also providing tooling to detect changes at the level of individual terms between ontology releases. OLS has adopted the OBO foundry YAML-LD format for registering metadata about how to access ontologies.
The OLS search index has been developed as part of the BioSolr5 project that is exploring optimal ways to index ontologies in open source search engines such as Apache-Solr. OSL provides a generic ontology indexing application for Solr that is also available as a standalone Solr application. To complement the search index we provide a RESTful API to ontology and entity (class, property and instance) metadata. The ontology is persisted in a Neo4J database and the REST API was built using the Spring Data framework. This API supports the generation of Hypertext Application Language (HAL) JSON documents that contain links to related document for programmatically navigating the ontology structures. All of the ontologies in OLS will also be loaded into the EBI RDF platform6 and made available via a SPARQL endpoint.
Finally a new Website has been developed that includes Javascript based ontology widgets for searching and visualising ontologies. These widgets can be easily integrated into third-party websites. 2.1
Availability
The OLS beta can be viewed at http://www.ebi.ac.uk/ols/beta. The source code is available from https://github.com/EBISPOT/OLS. 3
We acknowledge funds EMBL and the DIACHON, BioMedBridges and CORBEL projects funded by the European Commission (grant agreement numbers 601043, 284209, 654248). BioSolr is funded by the BBSRC (BB/M013146/1).