Navigating the Glycome Space and Connecting the Glycoproteome.
UniCarbKB ( http://unicarbkb.org ) is a comprehensive resource for mammalian glycoprotein and annotation data. In particular, the database provides information on the oligosaccharides characterized from a glycoprotein at either the global or site-specific level. This evidence is accumulated from a peer-reviewed and manually curated collection of information on oligosaccharides derived from membrane and secreted glycoproteins purified from biological fluids and/or tissues. This information is further supplemented with experimental method descriptions that summarize important sample preparation and analytical strategies. A new release of UniCarbKB is published every three months, each includes a collection of curated data and improvements to database functionality. In this Chapter, we outline the objectives of UniCarbKB, and describe a selection of step-by-step workflows for navigating the information available. We also provide a short description of web services available and future plans for improving data access. The information presented in this Chapter supplements content available in our knowledgebase including regular updates on interface improvements, new features, and revisions to the database content ( http://confluence.unicarbkb.org ).
Department of Chemistry and Biomolecular Sciences, Research Drive, Building E8C, Macquarie University, North Ryde, Sydney, 2109, NSW, Australia.
Matthew P
MP
Campbell
Department of Chemistry and Biomolecular Sciences, Research Drive, Building E8C, Macquarie University, North Ryde, Sydney, 2109, NSW, Australia.
Robyn A
RA
Peterson
Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Battelle - Building A7, Route de Drize, 1227 Carouge, Switzerland.
Elisabeth
E
Gasteiger
Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Battelle - Building A7, Route de Drize, 1227 Carouge, Switzerland.
Julien
J
Mariethoz
Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Battelle - Building A7, Route de Drize, 1227 Carouge, Switzerland.|Computer Science Department, University of Geneva, Battelle - Building A7, Route de Drize, 1227 Carouge, Switzerland.
Frederique
F
Lisacek
Department of Chemistry and Biomolecular Sciences, Research Drive, Building E8C, Macquarie University, North Ryde, Sydney, 2109, NSW, Australia. nicki.packer@mq.edu.au.
Nicolle H
NH
Packer
D000818:Animals; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D054794:Glycomics / Q000379:methods*; D006023:Glycoproteins; D006801:Humans; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D057386:Search Engine; D012984:Software; D014584:User-Computer Interface; D064878:Web Browser
D006023:Glycoproteins; D020543:Proteome
Curation; Database; Glycan; Glycobioinformatics; Glycomics; Glycoproteomics