The Infectious Disease Ontology in the Age of COVID-19

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research

An ontological analysis of drug prescriptions

International audienceThe ambiguities and overspecificities of prescription semantics along with their lack of standardization hinders the adoption of electronic prescriptions in some countries, limit data interoperability and are potential sources of error. An ontology of drug prescriptions could help overcome such difficulties and ultimately reduce adverse drug events. This article presents the Prescription of Drugs Ontology (PDRO), a reference ontology founded on the Open Biomedical Ontology Foundry (OBO Foundry) realist principles and built on the upper ontology Basic Formal Ontology (BFO). It imports by the methodology Minimum Information to Reference an External Ontology Term (MIREOT) classes and object properties from the Information Artifact Ontology (IAO), the Ontology for Biomedical Investigations (OBI), the Ontology for General Medical Science (OGMS), the Ontology for Medically Related Social Entities (OMRSE) and the Drug Ontology (DRON). It categorizes a prescription and its parts as information content entities. It defines a key component of prescriptions, a drug administration specification, as an action specification that directs a process of drug administration. This article also discusses how to deal with synonymy and provides a pre-formal analysis of the social ontology underlying drug prescriptions, involving entities such as permissions, recommendations or mild obligations