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. 2014 Jan;42(Database issue):D215-21.
doi: 10.1093/nar/gkt1128. Epub 2013 Nov 13.

UniCarbKB: building a knowledge platform for glycoproteomics

Matthew P Campbell  1 , Robyn Peterson, Julien Mariethoz, Elisabeth Gasteiger, Yukie Akune, Kiyoko F Aoki-Kinoshita, Frederique Lisacek, Nicolle H Packer
Affiliations

UniCarbKB: building a knowledge platform for glycoproteomics

Matthew P Campbell et al. Nucleic Acids Res. 2014 Jan.

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.

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Figures

Figure 1.
Figure 1.
UniCarbKB offers a number of improved query interfaces. (A) Users can search the database content by monosaccharide composition, attached protein, taxonomy or tissue by using an auto completion feature. (B) The integration of latest version of GlycanBuilder allows users to query UniCarbKB by (sub)structure searching.
Figure 2.
Figure 2.
Screenshot for the Coagulation Factor IX entry in UniCarbKB. The database provides a description of the glycan structures characterized for this glycoprotein and the number of structures associated with experimentally confirmed glycosylation sites. A general description of the glycoprotein is provided that has been derived from the relevant UniProtKB entry in addition to the protein sequence. Users have the Structure Format option to select a preferred graphical format to display the glycan structures that includes the three most commonly used notations. Supporting biological metadata and publication information is also provided. The Biological Associations include details pertinent to the species, the individual protein and tissue/secretory fluid source. Finally, those References that have been manually curated to obtain this information are summarized with appropriate links to PubMed.
Figure 3.
Figure 3.
Navigating from UniProtKB to UniCarbKB. An example is shown for the (A) UniProtKB alpha-2-HS-glycoprotein entry that is linked to (B) the glycan structures on the individual amino acid sites as curated in UniCarbKB, by CAR identifiers. The curated records in the first release of UniCarbKB are being updated and included in the sequence annotation feature records of UniProtKB.
See this image and copyright information in PMC

References

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