The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

The 10th International Conference on Biomedical Ontology (ICBO 2019), was held at the Jacobs School of Medicine and Biomedical Sciences of the University at Buffalo, in Buffalo, NY, USA. It was the 10-year anniversary of the ICBO series, and the return of the conference to Buffalo after the first two ICBO conferences were held in Buffalo in 2009 and 2011. ICBO 2019 was well attended, with 115 registered attendees and additional walk-ins from the local academic community. The program included excellent (...) keynote talks by Barry Smith, “International Standard Ontology,” and Bjoern Peters, “Putting principles into practice: OBO ontologies and applications in immunology,” as well as 23 oral presentations, 26 posters, and one software presentation. There were 53 papers and abstracts submitted for peer-review to ICBO 2019. Each submission was reviewed by three members chosen from the Program Committee. Of these submissions, 43 were accepted for this volume: 19 full papers, 23 poster abstracts, and 1 software demonstration extended abstract. We thank our program committee for their thoughtful reviews. There were also three workshops and four tutorials (listed below) held in conjunction with the main ICBO 2019 meeting. (shrink)