Новая электронная база данных по бактериальным углеводам (BCSDB)

A new free glycomic database (Bacterial Carbohydrate Structure Database) was established. It contains data on the structure, bibliography, NMR spectra, biochemical and other properties of all bacterial carbohydrates reported before 2006. The paper describes the database architecture and interface and BCSDB structure encoding language.Создана открытая структурная база данных по бактериальным углеводам. В работе освещается структура базы данных, ее интерфейс и специально разработанный язык линейной кодировки структур углеводов

Symbol Nomenclature for Graphical Representations of Glycans

ISSN:0959-665

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed

New bacterial carbohydrate structure database (BCSDB)

A new free glycomic database (Bacterial Carbohydrate Structure Database) was established. It contains data on the structure, bibliography, NMR spectra, biochemical and other properties of all bacterial carbohydrates reported before 2006. The paper describes the database architecture and interface and BCSDB structure encoding language

Structural and serological studies of two related O-specific polysaccharides of Proteus vulgaris O21 and Proteus mirabilis O48 having oligosaccharide-phosphate repeating units

In press: YesNRC publication: Ye

GlycoRDF : an ontology to standardize glycomics data in RDF

Motivation: Over the last decades several glycomics-based bioinformatics resources and databases have been created and released to the public. Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored information. Results: An international group of bioinformatics experts in the field of glycomics have worked together to create a standard Resource Description Framework (RDF) representation for glycomics data, focused on glycan sequences and related biological source, publications and experimental data. This RDF standard is defined by the GlycoRDF ontology and will be used by database providers to generate common machine-readable exports of the data stored in their databases. Availability and implementation: The ontology, supporting documentation and source code used by database providers to generate standardized RDF are available online (http://www.glycoinfo.org/GlycoRDF/). Contact: [email protected] or [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.7 page(s