MicroGlycoDB: A database of microbial glycans using Semantic Web technologies
Glycoconjugates are present on microbial surfaces and play critical roles in modulating interactions with the environment and the host. Extensive research on microbial glycans, including elucidating the structural diversity of the glycan moieties of glycoconjugates and polysaccharides, has been carr...
Saved in:
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2024-01-01
|
| Series: | BBA Advances |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2667160324000140 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850118985935224832 |
|---|---|
| author | Sunmyoung Lee Louis-David Leclercq Yann Guerardel Christine M. Szymanski Thomas Hurtaux Tamara L. Doering Takane Katayama Kiyotaka Fujita Kazuhiro Aoki Kiyoko F. Aoki-Kinoshita |
| author_facet | Sunmyoung Lee Louis-David Leclercq Yann Guerardel Christine M. Szymanski Thomas Hurtaux Tamara L. Doering Takane Katayama Kiyotaka Fujita Kazuhiro Aoki Kiyoko F. Aoki-Kinoshita |
| author_sort | Sunmyoung Lee |
| collection | DOAJ |
| description | Glycoconjugates are present on microbial surfaces and play critical roles in modulating interactions with the environment and the host. Extensive research on microbial glycans, including elucidating the structural diversity of the glycan moieties of glycoconjugates and polysaccharides, has been carried out to investigate the function of glycans in modulating the interactions between the host and microbes, to explore their potential applications in the therapeutic targeting of pathogenic species, and in the use as probiotics in gut microbiomes. However, glycan-related information is dispersed across numerous databases and a vast amount of literature, which makes it laborious and time-consuming to identify and gather the relevant information about microbial glycosylation. This challenge can be addressed by a comprehensive database, which could offer insight into the fundamental processes underlying glycosylation. We have developed a MicroGlycoDB database to provide integrated glycan information on important model microorganisms. The data is described using Semantic Web Technologies, which allow microbial glycan data to be represented in a structured format accessible by machines, thus facilitating data sharing and integration with other resources that catalog features such as pathways, diseases, or interactions. This semantic data based on ontologies will contribute to the discovery of new knowledge in the field of microbiology, along with the expansion of information on the glycosylation of other microorganisms. |
| format | Article |
| id | doaj-art-311d9b4d017747c5b5e9074f35fdcecf |
| institution | OA Journals |
| issn | 2667-1603 |
| language | English |
| publishDate | 2024-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | BBA Advances |
| spelling | doaj-art-311d9b4d017747c5b5e9074f35fdcecf2025-08-20T02:35:44ZengElsevierBBA Advances2667-16032024-01-01610012610.1016/j.bbadva.2024.100126MicroGlycoDB: A database of microbial glycans using Semantic Web technologiesSunmyoung Lee0Louis-David Leclercq1Yann Guerardel2Christine M. Szymanski3Thomas Hurtaux4Tamara L. Doering5Takane Katayama6Kiyotaka Fujita7Kazuhiro Aoki8Kiyoko F. Aoki-Kinoshita9Glycan and Life Systems Integration Center (GaLSIC), Soka University, Hachioji, Tokyo, JapanFrench National Center for Scientific Research (CNRS), University of Lille, Lille, FranceFrench National Center for Scientific Research (CNRS), University of Lille, Lille, FranceComplex Carbohydrate Research Center (CCRC), University of Georgia, Athens, GA, USADepartment of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USADepartment of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USAGraduate School of Biostudies, Kyoto University, Kyoto, JapanThe United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, JapanDepartment of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USAGlycan and Life Systems Integration Center (GaLSIC), Soka University, Hachioji, Tokyo, Japan; Graduate School of Science and Engineering, Soka University, Hachioji, Tokyo, Japan; Corresponding author at: 1 Chome-236 Tangimachi, Hachioji, Tokyo, Japan.Glycoconjugates are present on microbial surfaces and play critical roles in modulating interactions with the environment and the host. Extensive research on microbial glycans, including elucidating the structural diversity of the glycan moieties of glycoconjugates and polysaccharides, has been carried out to investigate the function of glycans in modulating the interactions between the host and microbes, to explore their potential applications in the therapeutic targeting of pathogenic species, and in the use as probiotics in gut microbiomes. However, glycan-related information is dispersed across numerous databases and a vast amount of literature, which makes it laborious and time-consuming to identify and gather the relevant information about microbial glycosylation. This challenge can be addressed by a comprehensive database, which could offer insight into the fundamental processes underlying glycosylation. We have developed a MicroGlycoDB database to provide integrated glycan information on important model microorganisms. The data is described using Semantic Web Technologies, which allow microbial glycan data to be represented in a structured format accessible by machines, thus facilitating data sharing and integration with other resources that catalog features such as pathways, diseases, or interactions. This semantic data based on ontologies will contribute to the discovery of new knowledge in the field of microbiology, along with the expansion of information on the glycosylation of other microorganisms.http://www.sciencedirect.com/science/article/pii/S2667160324000140MicrobesGlycosylationDatabaseData integrationSemantic data |
| spellingShingle | Sunmyoung Lee Louis-David Leclercq Yann Guerardel Christine M. Szymanski Thomas Hurtaux Tamara L. Doering Takane Katayama Kiyotaka Fujita Kazuhiro Aoki Kiyoko F. Aoki-Kinoshita MicroGlycoDB: A database of microbial glycans using Semantic Web technologies BBA Advances Microbes Glycosylation Database Data integration Semantic data |
| title | MicroGlycoDB: A database of microbial glycans using Semantic Web technologies |
| title_full | MicroGlycoDB: A database of microbial glycans using Semantic Web technologies |
| title_fullStr | MicroGlycoDB: A database of microbial glycans using Semantic Web technologies |
| title_full_unstemmed | MicroGlycoDB: A database of microbial glycans using Semantic Web technologies |
| title_short | MicroGlycoDB: A database of microbial glycans using Semantic Web technologies |
| title_sort | microglycodb a database of microbial glycans using semantic web technologies |
| topic | Microbes Glycosylation Database Data integration Semantic data |
| url | http://www.sciencedirect.com/science/article/pii/S2667160324000140 |
| work_keys_str_mv | AT sunmyounglee microglycodbadatabaseofmicrobialglycansusingsemanticwebtechnologies AT louisdavidleclercq microglycodbadatabaseofmicrobialglycansusingsemanticwebtechnologies AT yannguerardel microglycodbadatabaseofmicrobialglycansusingsemanticwebtechnologies AT christinemszymanski microglycodbadatabaseofmicrobialglycansusingsemanticwebtechnologies AT thomashurtaux microglycodbadatabaseofmicrobialglycansusingsemanticwebtechnologies AT tamaraldoering microglycodbadatabaseofmicrobialglycansusingsemanticwebtechnologies AT takanekatayama microglycodbadatabaseofmicrobialglycansusingsemanticwebtechnologies AT kiyotakafujita microglycodbadatabaseofmicrobialglycansusingsemanticwebtechnologies AT kazuhiroaoki microglycodbadatabaseofmicrobialglycansusingsemanticwebtechnologies AT kiyokofaokikinoshita microglycodbadatabaseofmicrobialglycansusingsemanticwebtechnologies |