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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...

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Autores principales: Campbell, Matthew P., Peterson, Robyn, Mariethoz, Julien, Gasteiger, Elisabeth, Akune, Yukie, Aoki-Kinoshita, Kiyoko F., Lisacek, Frederique, Packer, Nicolle H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
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.
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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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