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

Matthew P. Campbell*, Nicolle H. Packer

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

20 Citations (Scopus)

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 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. General significance Continuing advancements in analytical technologies and new data types are advancing disease-related glycomics. It is increasingly necessary to ensure all the data are comprehensively annotated. UniCarbKB was established with the mission of providing a resource for human glycobiology by capturing a wide range of data with corresponding annotations. This article is part of a Special Issue entitled Glycans in personalised medicine Guest Editor: Professor Gordan Lauc.

Original languageEnglish
Pages (from-to)1669-1675
Number of pages7
JournalBiochimica et Biophysica Acta - General Subjects
Volume1860
Issue number8
DOIs
Publication statusPublished - 1 Aug 2016

Keywords

  • Database
  • Disease
  • Glycans
  • Glycobioinformatics
  • Glycomics
  • Glycoproteins
  • Relative abundance

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