CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, prevention, and treatment. We emphasize CIDO development relevant to COVID-19

CLO: The cell line ontology

Abstract Background Cell lines have been widely used in biomedical research. The community-based Cell Line Ontology (CLO) is a member of the OBO Foundry library that covers the domain of cell lines. Since its publication two years ago, significant updates have been made, including new groups joining the CLO consortium, new cell line cells, upper level alignment with the Cell Ontology (CL) and the Ontology for Biomedical Investigation, and logical extensions. Construction and content Collaboration among the CLO, CL, and OBI has established consensus definitions of cell line-specific terms such as ‘cell line’, ‘cell line cell’, ‘cell line culturing’, and ‘mortal’ vs. ‘immortal cell line cell’. A cell line is a genetically stable cultured cell population that contains individual cell line cells. The hierarchical structure of the CLO is built based on the hierarchy of the in vivo cell types defined in CL and tissue types (from which cell line cells are derived) defined in the UBERON cross-species anatomy ontology. The new hierarchical structure makes it easier to browse, query, and perform automated classification. We have recently added classes representing more than 2,000 cell line cells from the RIKEN BRC Cell Bank to CLO. Overall, the CLO now contains ~38,000 classes of specific cell line cells derived from over 200 in vivo cell types from various organisms. Utility and discussion The CLO has been applied to different biomedical research studies. Example case studies include annotation and analysis of EBI ArrayExpress data, bioassays, and host-vaccine/pathogen interaction. CLO’s utility goes beyond a catalogue of cell line types. The alignment of the CLO with related ontologies combined with the use of ontological reasoners will support sophisticated inferencing to advance translational informatics development.http://deepblue.lib.umich.edu/bitstream/2027.42/109554/1/13326_2013_Article_185.pd

Vaxjo: A Web-Based Vaccine Adjuvant Database and Its Application for Analysis of Vaccine Adjuvants and Their Uses in Vaccine Development

Vaccine adjuvants are compounds that enhance host immune responses to co-administered antigens in vaccines. Vaxjo is a web-based central database and analysis system that curates, stores, and analyzes vaccine adjuvants and their usages in vaccine development. Basic information of a vaccine adjuvant stored in Vaxjo includes adjuvant name, components, structure, appearance, storage, preparation, function, safety, and vaccines that use this adjuvant. Reliable references are curated and cited. Bioinformatics scripts are developed and used to link vaccine adjuvants to different adjuvanted vaccines stored in the general VIOLIN vaccine database. Presently, 103 vaccine adjuvants have been curated in Vaxjo. Among these adjuvants, 98 have been used in 384 vaccines stored in VIOLIN against over 81 pathogens, cancers, or allergies. All these vaccine adjuvants are categorized and analyzed based on adjuvant types, pathogens used, and vaccine types. As a use case study of vaccine adjuvants in infectious disease vaccines, the adjuvants used in Brucella vaccines are specifically analyzed. A user-friendly web query and visualization interface is developed for interactive vaccine adjuvant search. To support data exchange, the information of vaccine adjuvants is stored in the Vaccine Ontology (VO) in the Web Ontology Language (OWL) format

Rational Vaccine Design by Reverse & Structural Vaccinology and Ontology

Vaccination is one of the most successful public health interventions in modern medicine. However, it is still challenging to develop effective vaccines against many infectious diseases such as tuberculosis, HIV, and malaria. There are challenges in integrating the high volume, variety, and variability of vaccine-related data and rationally designing effective and safe vaccines efficiently. In my thesis study, I systematically and comprehensively analyzed manually annotated protective vaccine antigens in the Protegen database and identified these protective antigens' enriched patterns. I then created Vaxign-ML, a novel machine learning-based reverse vaccinology method based on the curated Protegen data for rational vaccine design. Vaxign-ML was used to successfully predict vaccine antigens for tuberculosis and Coronavirus Disease 2019 (COVID-19). I also developed a new structural vaccinology design program that optimizes COVID-19 spike glycoprotein as a vaccine candidate for enhanced vaccine protection via T cell epitope engineering. The vaccine antigens selected and optimized by Reverse and Structural Vaccinology in this dissertation are subjected to future experimental verification. Furthermore, I created a community-based Ontology of Host-Pathogen Interactions (OHPI), which served as a platform to semantically represent the interactions between host and virulence factors that are also protective antigens. I developed the Vaccine Investigation Ontology (VIO) for standardized metadata representation for high throughput vaccine OMICS data analysis. Overall, my thesis research aims to uncover protective antigen patterns, create methods/tools to effectively develop vaccines against infectious diseases of public health significance, and strengthen our understanding of vaccine protection mechanisms. These works can be further expanded and integrated with other technologies such as epitope prediction, molecular epidemiology, and high-throughput sequencing to build the foundation of precision vaccinology.PHDBioinformaticsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/167997/1/edong_1.pd

Actes des 25es journées francophones d'Ingénierie des Connaissances (IC 2014)

National audienceLes Journées Francophones d'Ingénierie des Connaissances fêtent cette année leurs 25 ans. Cette conférence est le rendez-vous annuel de la communauté française et francophone qui se retrouve pour échanger et réfléchir sur des problèmes de recherche qui se posent en acquisition, représentation et gestion des connaissances. Parmi les vingt et un articles sélectionnés pour publication et présentation à la conférence, un thème fondateur de l'ingénierie des connaissances domine : celui de la modélisation de domaines. Six articles traitent de la conception d'ontologies, trois articles de l'annotation sémantique et du peuplement d'ontologies et deux articles de l'exploitation d'ontologies dans des systèmes à base de connaissances. L'informatique médicale est le domaine d'application privilégié des travaux présentés, que l'on retrouve dans sept articles. L'ingénierie des connaissances accompagne l'essor des technologies du web sémantique, en inventant les modèles, méthodes et outils permettant l'intégration de connaissances et le raisonnement dans des systèmes à base de connaissances sur le web. Ainsi, on retrouve les thèmes de la représentation des connaissances et du raisonnement dans six articles abordant les problématiques du web de données : le liage des données, leur transformation et leur interrogation ; la représentation et la réutilisation de règles sur le web de données ; la programmation d'applications exploitant le web de données. L'essor des sciences et technologies de l'information et de la communication, et notamment des technologies du web, dans l'ensemble de la société engendre des mutations dans les pratiques individuelles et collectives. L'ingénierie des connaissances accompagne cette évolution en plaçant l'utilisateur au cœur des systèmes informatiques, pour l'assister dans le traitement de la masse de données disponibles. Quatre articles sont dédiés aux problématiques du web social : analyse de réseaux sociaux, détection de communautés, folksonomies, personnalisation de recommandations, représentation et prise en compte de points de vue dans la recherche d'information. Deux articles traitent de l'adaptation des systèmes aux utilisateurs et de l'assistance aux utilisateurs et deux autres de l'aide à la prise de décision. Le taux de sélection de cette édition de la conférence est de 50%, avec dix-neuf articles longs et deux articles courts acceptés parmi quarante-deux soumissions. S'y ajoutent une sélection de neuf posters et démonstrations parmi douze soumissions, présentés dans une session dédiée et inclus dans les actes. Enfin, une innovation de cette édition 2014 de la conférence est la programmation d'une session spéciale " Projets et Industrie ", animée par Frédérique Segond (Viseo), à laquelle participeront Laurent Pierre (EDF), Alain Berger (Ardans) et Mylène Leitzelman (Mnemotix). Trois conférencières invitées ouvriront chacune des journées de la conférence que je remercie chaleureusement de leur participation. Nathalie Aussenac-Gilles (IRIT) retracera l'évolution de l'ingénierie des connaissances en France depuis 25 ans, de la pénurie à la surabondance. A sa suite, Frédérique Segond (Viseo) abordera le problème de " l'assouvissement " de la faim de connaissances dans la nouvelle ère des connaissances dans laquelle nous sommes entrés. Enfin, Marie-Laure Mugnier (LIRMM) présentera un nouveau cadre pour l'interrogation de données basée sur une ontologie, fondé sur des règles existentielles