TypOn: the microbial typing ontology

Journal of Biomedical Semantics

João A Carriço³  Mário Ramirez³  Joerg Rothganger²  Hannes Pouseele⁴  James E Bray⁵  Keith A Jolley⁵  Mickael Silva³  Alexandre P Francisco¹  Cátia Vaz⁶ 

[1] Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal;Ridom GmbH, Mendelstr. 11, D-48149 Münster, Germany;Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal;Applied Maths NV, Keistraat 120, 98308 Sint-Martens-Latem, Belgium;Department of Zoology, University of Oxford, Oxford, UK;Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Cons. Emídio Navarro 1, 1959-007 Lisboa, Portugal

关键词: Microbial typing methods;    Knowledge representation;    Ontology;   

Others  :  1133530
DOI  :  10.1186/2041-1480-5-43

 received in 2014-06-20, accepted in 2014-10-06,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Vaz et al.; licensee BioMed Central Ltd.

【 图 表 】

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