Giacomo De Colle

Mark Jensen, Giacomo De Colle, Sean Kindya et al.

The Common Core Ontologies (CCO) are designed as a mid-level ontology suite that extends the Basic Formal Ontology. CCO has since been increasingly adopted by a broad group of users and applications and is proposed as the first standard mid-level ontology. Despite these successes, documentation of the contents and design patterns of the CCO has been comparatively minimal. This paper is a step toward providing enhanced documentation for the mid-level ontology suite through a discussion of the contents of the eleven ontologies that collectively comprise the Common Core Ontology suite.

Shane Babcock, Carter Benson, Giacomo De Colle et al.

Infectious diseases remain a critical global health challenge, and the integration of standardized ontologies plays a vital role in managing related data. The Infectious Disease Ontology (IDO) and its extensions, such as the Coronavirus Infectious Disease Ontology (CIDO), are essential for organizing and disseminating information related to infectious diseases. The COVID-19 pandemic highlighted the need for updating IDO and its virus-specific extensions. There is an additional need to update IDO extensions specific to bacteria, fungus, and parasite infectious diseases. We adopt the "hub and spoke" methodology to generate pathogen-specific extensions of IDO: Virus Infectious Disease Ontology (VIDO), Bacteria Infectious Disease Ontology (BIDO), Mycosis Infectious Disease Ontology (MIDO), and Parasite Infectious Disease Ontology (PIDO). The creation of pathogen-specific reference ontologies advances modularization and reusability of infectious disease data within the IDO ecosystem. Future work will focus on further refining these ontologies, creating new extensions, and developing application ontologies based on them, in line with ongoing efforts to standardize biological and biomedical terminologies for improved data sharing and analysis.

John Beverley, Giacomo De Colle, Mark Jensen et al.

Mid-level ontologies are used to integrate terminologies and data across disparate domains. There are, however, no clear, defensible criteria for determining whether a given ontology should count as mid-level, because we lack a rigorous characterization of what the middle level of generality is supposed to contain. Attempts to provide such a characterization have failed, we believe, because they have focused on the goal of specifying what is characteristic of those single ontologies that have been advanced as mid-level ontologies. Unfortunately, single ontologies of this sort are generally a mixture of top- and mid-level, and sometimes even of domain-level terms. To gain clarity, we aim to specify the necessary and sufficient conditions for a collection of one or more ontologies to inhabit what we call a mid-level architecture.