GenEpiO aims to provide a single, open-source, globally accessible set of terms to use in databases and software user interfaces, consequently it is called an “application ontology” (as opposed to a taxonomic ontology that specializes in a single domain). It is currently being incorporated into the Integrated Rapid Infectious Disease Analysis www.irida.ca project.

GenEpiO uses the OWL capability to organize terms in a main hierarchy according to the Basic Formal Ontology (BFO) and Ontology for Biomedical Investigations (OBI) schemas. This provides some amount of plug-and-play compatibility with other ontologies in the OBOFoundry family.

In our first pass, most of the terms we have collected pertain to measurements and observables (data) within laboratory practice, genomic analysis, and epidemiology/clinical records. We have focused on placing these terms within BFO/OBI under the “information content entity”category. We provide detail here to encourage feedback about logic implications, interoperability, and relative simplicity.

Data Item
Data Representational Model
Units
n-dimensional specification
Class Inheritance Provides Meaning
Standardization Issues
The Role Of Ontology Imports