Establishing best practices and use cases for the application and management of ontologies and their mappings for Life Science industry

Project deliverables

After delivering guidelines and tools recommendations, the project has defined the requirements for an enterprise quality, ontologies mapping service. We are implementing a prototype Ontologies Mappings Service for the phenotype and disease domain by working with the Samples, Phenotypes and Ontologies Team at EMBL-EBI.

The mapping algorithm and predicted mappings for phenotype and disease ontologies will be openly available along with full documentation and publication of the methodology and results in an appropriate journal. The mapping service is now being extended to public ontologies relevant to laboratory analytics for biology and chemistry. EMBL-EBI plan to make the predicted mappings available through the OxO repository of ontology mappings.

Why is this important?

Ontologies can include hierarchical relationships; taxonomies; classifications and/or vocabularies which are becoming increasingly important for support of research and development. They have numerous applications such as knowledge management, data integration and text mining where researchers need to analyse large quantities of complex data as part of their daily work.

What will the project achieve?

The Ontologies Mapping Project will help users to select top performing tools, methodologies and services for mapping and visualisation of ontologies, to understand ontology structure, potential overlaps and equivalent or similar meaning. The impact of this project will be to help users to better integrate, understand and analyse their data more effectively through better usage of public ontologies and mappings between them.

How will the project do this?

The project has built a Community of Interest of considerable size and influence in the ontologies field. It has delivered a set of guidelines for use as a checklist to facilitate the selection of ontologies for application. The Ontologies Guidelines for Best Practice are available on a publicly accessible wiki:-

We have evaluated ontology mapping tools and algorithms through and organised the phenotype track of the Ontology Alignment Evaluation Initiative ( We are now collaborating with EMBL-EBI to demonstrate a prototype ontology mapping service for public ontologies in the  phenotype and disease domain, which is being extended to the lab analytics domain.