Solovieva Elena, Shikanai Toshihide, Fujita Noriaki, Narimatsu Hisashi
Glycoscience and Glycotechnology Research Group, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.
GlycoBiomarker Leading Innovation Co. Ltd. (GL-i), Tsukuba, Japan.
J Biomed Semantics. 2018 Apr 18;9(1):14. doi: 10.1186/s13326-018-0182-0.
Inherited 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.
We 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.
Focused 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.
糖相关基因的遗传突变会影响聚糖的生物合成和降解，导致严重的遗传疾病和病症。糖病基因数据库（GDGDB）由医学糖科学研究中心（RCMG）开发，并于2010年4月发布，该数据库提供了有关这些疾病和病症及其致病基因的信息。GDGDB目前提供了约80种由糖相关基因单基因突变引起的遗传疾病和病症的信息。许多生物医学资源提供了有关遗传疾病及其发病机制中涉及的基因的信息，但缺乏专注于已知与聚糖代谢相关的遗传疾病的资源。为了提供关于聚糖生物合成和降解的遗传疾病和病症的更全面知识，我们丰富了GDGDB数据库的内容并改进了数据表示方法。
我们使用语义网技术开发了遗传糖病本体（GGDonto）和基于RDF/SPARQL的用户界面。特别是，我们使用RDF、RDFS、SKOS和OWL等语义网语言表示GGDonto的内容，并基于SPARQL查询创建了一个交互式用户界面。该用户界面提供了浏览本体层次结构、查看疾病和相关基因的详细信息以及查找相关背景信息的功能。此外，它还提供了通过分面搜索和关键词搜索来过滤和搜索信息的能力。
GGDonto专注于聚糖代谢遗传疾病和病症的分子病因、发病机制和临床表现，并作为该科学领域的知识库而开发，它提供了关于各种主题的全面信息，包括有助于与其他科学资源整合的链接。这些知识的可用性和可访问性将帮助用户更好地理解遗传缺陷如何影响聚糖代谢，以及这种受损的代谢如何影响各种生物学功能和人类健康。通过这种方式，GGDonto将在与糖科学相关的领域中发挥作用，包括细胞生物学、生物技术、生物医学和药物研究。
