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  • UniCarbKB: New database features for integrating glycan structure abundance, compositional glycoproteomics data, and disease associations

    Author(s)
    Campbell, Matthew P.
    Packer, Nicolle H.
    Griffith University Author(s)
    Packer, Nicki
    Year published
    2016
    Metadata
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    Abstract
    Background: UniCarbKB aims to provide a resource for the representation of mammalian glycobiology knowledge by providing a curated database of structural and experimental data, supported by a web application that allows users to easily find and view richly annotated information. The database comprises two levels of annotation (i) global-specific data of oligosaccharides released and characterised from single purified glycoproteins and (ii) information pertaining to site-specific glycan heterogeneity. Additional, contextual information is provided including structural, bibliographic, and taxonomic information for each ...
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    Background: UniCarbKB aims to provide a resource for the representation of mammalian glycobiology knowledge by providing a curated database of structural and experimental data, supported by a web application that allows users to easily find and view richly annotated information. The database comprises two levels of annotation (i) global-specific data of oligosaccharides released and characterised from single purified glycoproteins and (ii) information pertaining to site-specific glycan heterogeneity. Additional, contextual information is provided including structural, bibliographic, and taxonomic information for each entry. Methods: Since the launch of UniCarbKB in 2012, we have continued to improve the organisation of our data model. Recently, we have extended our pipeline to collate structural and abundance changes of oligosaccharides in different human disease states and experimental models to extend our coverage of the human glycome. Results: In this manuscript, we demonstrate the capability of UniCarbKB to store and query relative glycan abundance data using a set of published colorectal and prostate cancer cell lines as examples. Furthermore, we outline our strategy for managing large-scale glycoproteomics data, site-specific and glycan compositional data, and how this information is adding value to UniCarbKB. Finally, we summarise our efforts to improve the efficient representation of disease terms and associated changes in glycan heterogeneity by integrating the Disease Ontology. Conclusions: Updates and improvements to UniCarbKB have introduced unique features for storing and displaying glycosylation features of mammalian glycoproteins. The integration of site-specific glycosylation data obtained from large-scale glycoproteomics and introduction of cell line studies will improve the analysis of glycoproteins and entire glycomes.
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    Journal Title
    Biochimica et Biophysica Acta. General Subjects
    Volume
    1860
    Issue
    8
    DOI
    https://doi.org/10.1016/j.bbagen.2016.02.016
    Subject
    Biochemistry and cell biology
    Biochemistry and cell biology not elsewhere classified
    Pharmacology and pharmaceutical sciences
    Publication URI
    http://hdl.handle.net/10072/336555
    Collection
    • Journal articles

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