Browsing by Author "Ramirez, Mário"
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- An ontology and a REST API for sequence based microbial typing dataPublication . Almeida, João; Tiple, João; Ramirez, Mário; Melo-Cristino, José; Vaz, Cátia; Francisco, Alexandre P.; Carrico, JoaoIn the Microbial typing field, the need to have a common understanding of the concepts described and the ability to share results within the community is an increasingly important requisite for the continued development of portable and accurate sequence-based typing methods. These methods are used for bacterial strain identification and are fundamental tools in Clinical Microbiology and Bacterial Population Genetics studies. In this article we propose an ontology designed for the microbial typing field, focusing on the widely used Multi Locus Sequence Typing methodology, and a RESTful API for accessing information systems based on the proposed ontology. This constitutes an important first step to accurately describe, analyze, curate, and manage information for microbial typing methodologies based on sequence based typing methodologies, and allows for the future integration with data analysis Web services.
- PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning treesPublication . Ribeiro-Gonçalves, Bruno; Francisco, Alexandre P.; Vaz, Cátia; Ramirez, Mário; Carrico, JoaoHigh-throughput sequencing methods generated allele and single nucleotide polymorphism information for thousands of bacterial strains that are publicly available in online repositories and created the possibility of generating similar information for hundreds to thousands of strains more in a single study. Minimum spanning tree analysis of allelic data offers a scalable and reproducible methodological alternative to traditional phylogenetic inference approaches, useful in epidemiological investigations and population studies of bacterial pathogens. PHYLOViZ Online was developed to allow users to do these analyses without software installation and to enable easy accessing and sharing of data and analyses results from any Internet enabled computer. PHYLOViZ Online also offers a RESTful API for programmatic access to data and algorithms, allowing it to be seamlessly integrated into any third party web service or software.
- TypOn: the microbial typing ontologyPublication . Vaz, Cátia; Francisco, Alexandre P.; Silva, Mickael; Jolley, Keith A.; Bray, James E.; Pouseele, Hannes; Rothganger, Joerg; Ramirez, Mário; Carriço, João A.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.