Abstract
BackgroundInherited mutations in glyco-related genes can affect the biosynthesis and degradation of glycans and result in severe genetic diseases and disorders. The Glyco-Disease Genes Database (GDGDB), which provides information about these diseases and disorders as well as their causative genes, has been developed by the Research Center for Medical Glycoscience (RCMG) and released in April 2010. GDGDB currently provides information on about 80 genetic diseases and disorders caused by single-gene mutations in glyco-related genes. Many biomedical resources provide information about genetic disorders and genes involved in their pathogenesis, but resources focused on genetic disorders known to be related to glycan metabolism are lacking. With the aim of providing more comprehensive knowledge on genetic diseases and disorders of glycan biosynthesis and degradation, we enriched the content of the GDGDB database and improved the methods for data representation.ResultsWe developed the Genetic Glyco-Diseases Ontology (GGDonto) and a RDF/SPARQL-based user interface using Semantic Web technologies. In particular, we represented the GGDonto content using Semantic Web languages, such as RDF, RDFS, SKOS, and OWL, and created an interactive user interface based on SPARQL queries. This user interface provides features to browse the hierarchy of the ontology, view detailed information on diseases and related genes, and find relevant background information. Moreover, it provides the ability to filter and search information by faceted and keyword searches.ConclusionsFocused on the molecular etiology, pathogenesis, and clinical manifestations of genetic diseases and disorders of glycan metabolism and developed as a knowledge-base for this scientific field, GGDonto provides comprehensive information on various topics, including links to aid the integration with other scientific resources. The availability and accessibility of this knowledge will help users better understand how genetic defects impact the metabolism of glycans as well as how this impaired metabolism affects various biological functions and human health. In this way, GGDonto will be useful in fields related to glycoscience, including cell biology, biotechnology, and biomedical, and pharmaceutical research.
Highlights
Inherited mutations in glyco-related genes can affect the biosynthesis and degradation of glycans and result in severe genetic diseases and disorders
Inherited mutations in glyco-related genes can affect the biosynthesis of glycans as well as their degradation, and this impaired metabolism can result in severe genetic diseases and disorders, such as congenital disorders of glycosylation (CDG) and lysosomal storage diseases (LSD)
As a part of the “Life-Science Database Integration Project” of the National Bioscience Database Center (NBDC) sponsored by the Japan Science and Technology Agency (JST), we developed a knowledge-base of genetic diseases and disorders of glycan metabolism and their causative genes
Summary
Inherited mutations in glyco-related genes can affect the biosynthesis and degradation of glycans and result in severe genetic diseases and disorders. Many relevant information resources and databases are publicly available, including the Online Mendelian Inheritance in Man (OMIM) [1], the Genetics Home Reference [2], the Genetic and Rare Diseases Information Center (GARD) resources [3], the Genetic Testing Registry (GTR) [4], and the Orphanet portal [5], among others These resources provide information on a wide range of known hereditary diseases and disorders as well as their causative genes, and, their contents are not restricted to certain types of metabolic products.
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