title: TypOn: the microbial typing ontology.
abstract: Bacterial identification and characterization at subspecies level is commonly known as Microbial Typing. Currently, these methodologies are fundamental tools in Clinical Microbiology and bacterial population genetics studies to track outbreaks and to study the dissemination and evolution of virulence or pathogenicity factors and antimicrobial resistance. Due to advances in DNA sequencing technology, these methods have evolved to become focused on sequence-based methodologies. The need to have a common understanding of the concepts described and the ability to share results within the community at a global level are increasingly important requisites for the continued development of portable and accurate sequence-based typing methods, especially with the recent introduction of Next Generation Sequencing (NGS) technologies. In this paper, we present an ontology designed for the sequence-based microbial typing field, capable of describing any of the sequence-based typing methodologies currently in use and being developed, including novel NGS based methods. This is a fundamental step to accurately describe, analyze, curate, and manage information for microbial typing based on sequence based typing methods.
authors.affiliation: INESC-ID, R. Alves Redol 9, 1000-029 Lisboa, Portugal ; Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Cons. Emídio Navarro 1, 1959-007 Lisboa, Portugal.
authors.forename: Cátia
authors.initials: C
authors.lastname: Vaz
authors.affiliation: INESC-ID, R. Alves Redol 9, 1000-029 Lisboa, Portugal ; Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal.
authors.forename: Alexandre P
authors.initials: AP
authors.lastname: Francisco
authors.affiliation: Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal.
authors.forename: Mickael
authors.initials: M
authors.lastname: Silva
authors.affiliation: Department of Zoology, University of Oxford, Oxford, UK.
authors.forename: Keith A
authors.initials: KA
authors.lastname: Jolley
authors.affiliation: Department of Zoology, University of Oxford, Oxford, UK.
authors.forename: James E
authors.initials: JE
authors.lastname: Bray
authors.affiliation: Applied Maths NV, Keistraat 120, 98308 Sint-Martens-Latem, Belgium.
authors.forename: Hannes
authors.initials: H
authors.lastname: Pouseele
authors.affiliation: Ridom GmbH, Mendelstr. 11, D-48149 Münster, Germany.
authors.forename: Joerg
authors.initials: J
authors.lastname: Rothganger
authors.affiliation: Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal.
authors.forename: Mário
authors.initials: M
authors.lastname: Ramirez
authors.affiliation: Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal.
authors.forename: João A
authors.initials: JA
authors.lastname: Carriço
keywords: Knowledge representation; Microbial typing methods; Ontology