- UniCarbKB: building a knowledge platform for glycoproteomics. [PMID: 24234447]
Matthew P Campbell, Robyn Peterson, Julien Mariethoz, Elisabeth Gasteiger, Yukie Akune, Kiyoko F Aoki-Kinoshita, Frederique Lisacek, Nicolle H Packer
Nucleic acids research 2014:42(Database issue)
37 Citations (Google Scholar as of 2016-06-10)
Abstract: 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.
- UniCarbKB: putting the pieces together for glycomics research. [PMID: 21898825]
Matthew P Campbell, Catherine A Hayes, Weston B Struwe, Marc R Wilkins, Kiyoko F Aoki-Kinoshita, David J Harvey, Pauline M Rudd, Daniel Kolarich, Frederique Lisacek, Niclas G Karlsson, Nicolle H Packer
48 Citations (Google Scholar as of 2016-06-10)
Abstract: Despite the success of several international initiatives the glycosciences still lack a managed infrastructure that contributes to the advancement of research through the provision of comprehensive structural and experimental glycan data collections. UniCarbKB is an initiative that aims to promote the creation of an online information storage and search platform for glycomics and glycobiology research. The knowledgebase will offer a freely accessible and information-rich resource supported by querying interfaces, annotation technologies and the adoption of common standards to integrate structural, experimental and functional data. The UniCarbKB framework endeavors to support the growth of glycobioinformatics and the dissemination of knowledge through the provision of an open and unified portal to encourage the sharing of data. In order to achieve this, the framework is committed to the development of tools and procedures that support data annotation, and expanding interoperability through cross-referencing of existing databases. Database URL: http://www.unicarbkb.org. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.