12  Controlled vocabularies and ontologies

For data to be reusable, the metadata and documentation must use consistent terminology that is clearly explained so that different users can understand its meaning unambiguously. We recommend starting with simple, controlled vocabularies before moving on to more complex structures, such as taxonomies or ontologies. As with other metadata and documentation elements, standard or widely used vocabularies or ontologies should be used where available.

12.1 Controlled vocabularies

Controlled vocabularies are standardized and organized arrangements of words and phrases presented as alphabetical lists of terms or as thesauri and taxonomies with a hierarchical structure of broader and narrower terms (see ‘controlled vocabulary’ concept in EU vocabulary).

  • Consistency: they provide a common language for researchers, minimizing variations and ambiguities

  • Interoperability: they facilitate integration and sharing of data across systems, disciplines, and organizations, enabling seamless collaboration (human and machine actionable).

  • Reusability: Research data annotated with standard vocabularies are easier to interpret and reuse

12.2 Taxonomies

A taxonomy is a controlled vocabulary in which all the terms belong to a single hierarchical structure and have parent/child or broader/narrower relationships to other terms. The structure is sometimes referred to as a ‘tree’. The addition of non-preferred terms/synonyms may or may not be part of a taxonomy. (see ‘taxonomy’ concept in EU vocabularies).

12.3 Ontologies

An ontology is a formal way of representing knowledge about a specific domain, using a structured framework of concepts and their relationships see ‘ontology’ in EU vocabularies. It can also be seen as a hierarchical graph covering a specific subject area or domain. An ontology has classes (i.e., concepts, terms, etc) as basic units and relations or inks between the classes.

12.4 Selected resources

  • Open Biological and Biomedical Ontology Foundry is a community that develops interoperable ontologies for the biological sciences

  • Ontobee is a server that aims to facilitate ontology data sharing, visualization, query integration and analysis.

  • FairSharing is a platform to look for standards, policies and databases. It can also be used to search for ontologies and controlled vocabularies