The environment ontology: contextualising biological and biomedical entities

Abstract

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO; http://www.environmentontology.org) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO's motivation, content, structure, adoption, and governance approach. The ontology is available from http://purl.obolibrary.org/obo/envo.owl - an OBO format version is also available by switching the file suffix to "obo".

Figure 1

Subclasses of ENVO’s environmental condition may be used as differentiae when defining subclasses of classes in the biome (shown), environmental feature, or environmental material hierarchies. Retrieval of entities annotated with ENVO classes that satisfy a given condition is thus facilitated.

Figure 2

ENVO’s feature hierarchy includes classes describing entities of geographic and mesoscopic scale. Classes created during term capture exercises (marine feature, organic feature; marked with asterisks) temporarily house subclasses which will be curated and redistributed into more appropriate classes as needed.