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UniCarbKB: building a knowledge platform for glycoproteomics
The UniCarb KnowledgeBase (UniCarbKB; http://unicarbkb.org) offers public access to a growing, curated database of information on the glycan structures of glycoproteins. UniCarbKB is an international effort that aims to further our understanding of structures, pathways and networks involved in glyco...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Oxford University Press
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964942/ https://www.ncbi.nlm.nih.gov/pubmed/24234447 http://dx.doi.org/10.1093/nar/gkt1128 |
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author | Campbell, Matthew P. Peterson, Robyn Mariethoz, Julien Gasteiger, Elisabeth Akune, Yukie Aoki-Kinoshita, Kiyoko F. Lisacek, Frederique Packer, Nicolle H. |
author_facet | Campbell, Matthew P. Peterson, Robyn Mariethoz, Julien Gasteiger, Elisabeth Akune, Yukie Aoki-Kinoshita, Kiyoko F. Lisacek, Frederique Packer, Nicolle H. |
author_sort | Campbell, Matthew P. |
collection | PubMed |
description | The UniCarb KnowledgeBase (UniCarbKB; http://unicarbkb.org) offers public access to a growing, curated database of information on the glycan structures of glycoproteins. UniCarbKB is an international effort that aims to further our understanding of structures, pathways and networks involved in glycosylation and glyco-mediated processes by integrating structural, experimental and functional glycoscience information. This initiative builds upon the success of the glycan structure database GlycoSuiteDB, together with the informatic standards introduced by EUROCarbDB, to provide a high-quality and updated resource to support glycomics and glycoproteomics research. UniCarbKB provides comprehensive information concerning glycan structures, and published glycoprotein information including global and site-specific attachment information. For the first release over 890 references, 3740 glycan structure entries and 400 glycoproteins have been curated. Further, 598 protein glycosylation sites have been annotated with experimentally confirmed glycan structures from the literature. Among these are 35 glycoproteins, 502 structures and 60 publications previously not included in GlycoSuiteDB. This article provides an update on the transformation of GlycoSuiteDB (featured in previous NAR Database issues and hosted by ExPASy since 2009) to UniCarbKB and its integration with UniProtKB and GlycoMod. Here, we introduce a refactored database, supported by substantial new curated data collections and intuitive user-interfaces that improve database searching. |
format | Online Article Text |
id | pubmed-3964942 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-39649422014-03-25 UniCarbKB: building a knowledge platform for glycoproteomics Campbell, Matthew P. Peterson, Robyn Mariethoz, Julien Gasteiger, Elisabeth Akune, Yukie Aoki-Kinoshita, Kiyoko F. Lisacek, Frederique Packer, Nicolle H. Nucleic Acids Res II. Protein sequence and structure, motifs and domains The UniCarb KnowledgeBase (UniCarbKB; http://unicarbkb.org) offers public access to a growing, curated database of information on the glycan structures of glycoproteins. UniCarbKB is an international effort that aims to further our understanding of structures, pathways and networks involved in glycosylation and glyco-mediated processes by integrating structural, experimental and functional glycoscience information. This initiative builds upon the success of the glycan structure database GlycoSuiteDB, together with the informatic standards introduced by EUROCarbDB, to provide a high-quality and updated resource to support glycomics and glycoproteomics research. UniCarbKB provides comprehensive information concerning glycan structures, and published glycoprotein information including global and site-specific attachment information. For the first release over 890 references, 3740 glycan structure entries and 400 glycoproteins have been curated. Further, 598 protein glycosylation sites have been annotated with experimentally confirmed glycan structures from the literature. Among these are 35 glycoproteins, 502 structures and 60 publications previously not included in GlycoSuiteDB. This article provides an update on the transformation of GlycoSuiteDB (featured in previous NAR Database issues and hosted by ExPASy since 2009) to UniCarbKB and its integration with UniProtKB and GlycoMod. Here, we introduce a refactored database, supported by substantial new curated data collections and intuitive user-interfaces that improve database searching. Oxford University Press 2014-01-01 2013-11-13 /pmc/articles/PMC3964942/ /pubmed/24234447 http://dx.doi.org/10.1093/nar/gkt1128 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | II. Protein sequence and structure, motifs and domains Campbell, Matthew P. Peterson, Robyn Mariethoz, Julien Gasteiger, Elisabeth Akune, Yukie Aoki-Kinoshita, Kiyoko F. Lisacek, Frederique Packer, Nicolle H. UniCarbKB: building a knowledge platform for glycoproteomics |
title | UniCarbKB: building a knowledge platform for glycoproteomics |
title_full | UniCarbKB: building a knowledge platform for glycoproteomics |
title_fullStr | UniCarbKB: building a knowledge platform for glycoproteomics |
title_full_unstemmed | UniCarbKB: building a knowledge platform for glycoproteomics |
title_short | UniCarbKB: building a knowledge platform for glycoproteomics |
title_sort | unicarbkb: building a knowledge platform for glycoproteomics |
topic | II. Protein sequence and structure, motifs and domains |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964942/ https://www.ncbi.nlm.nih.gov/pubmed/24234447 http://dx.doi.org/10.1093/nar/gkt1128 |
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