UniCarbKB: a glycobioinformatics infrastructure for data discovery — ASN Events
  1. Schedule
  2. Symposium Two: Glycoproteomics
  3. UniCarbKB: a glycobioinformatics infrastructure for data discovery

UniCarbKB: a glycobioinformatics infrastructure for data discovery (#7)

Matthew P Campbell 1 , Robyn Peterson 1 , Yukie Akune 2 , Jodie L Abrahams 1 , Chi-Hung Lin 1 , Julien Mariethoz 3 , Elisabeth Gasteige 4 , Kiyoko F Aoki-Kinoshita 2 , Frederique Lisacek 3 , Nicolle H Packer 1
  1. Biomolecular Frontiers Research Centre, Macquarie University, Sydney, NSW, Australia
  2. Department of Bioinformatics, Soka University, Tokyo, Japan
  3. Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Switzerland

  4. Swiss Institute of Bioinformatics, Geneva, Switzerland

In partnership with leading international research groups we are involved with the development of the UniCarb KnowledgeBase (UniCarbKB); an effort to develop and provide an informatic framework for the storage of high-quality data collections including informative meta-data and annotated experimental datasets.

UniCarbKB is a new database that aids the exploration of glycoproteins pertinent to current research strategies that strives to be a comprehensive resource. To sufficiently address research questions we aim to: 1) build on the knowledge originating from GlycoSuiteDB by carefully including selected and filtered glycoprotein data; 2) organise data to enable user-friendly interaction and querying by adopting standardisation and ontology guidelines; and 3) build a platform that will support the inclusion of new data mining tools and connect disparate resources. Here, we shall demonstrate the functionality of UniCarbKB and our strategy to increase the content and value of data provided by UniCarbKB, and our efforts to build and provide open APIs for the glycobioinformatic community.

Glycobioinformatics databases and tools are co-operatively adopting semantic technologies for managing data content, called GlycoRDF. The availability of GlycoRDF and access to RDFized databases is opening new and exciting avenues for connecting and interrogating large volumes of publicly accessible data. Examples of the capability of UniCarbKB-RDF for exploring and correlating glycomics structural and experimental data will be presented. Furthermore, the utility of semantic technologies to connect glycan-related knowledge bases with other omics resources (UniProtKB and NeXtProt) to enhance data discovery and inference of protein and glycan biological function will be highlighted.

The development of UniCarbKB and supporting technologies continues to provide a new perspective on glycobioinformatics, which extends access to high-quality annotations with interfaces to supporting analytical data sets. The initiative will be driven as a community endeavour to promote data sharing to ensure its future development and growth. Especially, our efforts to align data capture with the GlycoRDF, MIRAGE and international glycan repository initiatives.

  1. Campbell MP, Peterson R, Mariethoz J, Gasteiger E, Akune Y, Aoki-Kinoshita KF, Lisacek F, Packer NH. UniCarbKB: building a knowledge platform for glycoproteomics.Nucleic Acids Res. 2014 Jan;42(Database issue):D215-21