Pistoia Alliance

Ontologies Guidelines for Best Practice

By Pistoia Alliance Ontologies Mapping Project team


These guidelines for best practice support the application and mapping of ontologies in the life sciences as part of the Pistoia Alliance Ontologies Mapping project which creates better tools and services for mapping
ontologies to facilitate their exploitation.

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. The Ontologies Mapping Project will give users access to standardised tools and methodologies to map and visualise ontologies, to understand ontology structure, potential overlaps and equivalence of meaning. The outcome of this project will be to help users to better integrate, understand and analyse their data more effectively.

Motivation and purpose

This document describes the best practice guidelines that are designed to check how suitable source ontologies are for mapping. It places emphasis on the application of ontologies in the Life Science industry to encourage best practice and to explain how this relates to the mapping of ontologies in a particular domain. In some areas of Life Science such as Clinical Sciences, best practice is mature enough to be governed by appropriate authorities (e.g. FDA, CDISC, EMA, IDMP etc.), whereas in Preclinical and Translational Research areas, best practices and data standards tend to be much less mature and can even be absent. These guidelines will identify and align with existing communities and authorities, especially those that are relevant to research and early development for particular ontology domains regarded as critical to industry needs rather than the vast field of Life Science.

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