GlycoStore to GlyGen: Computational and Informatics Resources for Glycoscience Data Integration
Dr Matthew Campbell - Senior Research Fellow, the Institute for Glycomics, Griffith University, Australia
GlyGen is a collaborative open science effort that aims to integrate and curate structural, experimental and functional information from many species and sources to support precision medicine, disease modelling, and systems biology. Over the last few years, we have created an integrated knowledge graph, analytic tools, and web services that enable users to explore structures, pathways and networks involved in glycosylation and glyco-mediated processes.
An increase in accumulated knowledge necessitates the development of creative bioinformatics resources that facilitate research data discovery. However, the lack of agreed upon standards with respect to formatting of glycomics data and annotations, as well as the heterogeneity of language used to describe metadata poses major challenges to the comprehensive analysis of such information.
In this presentation, I will discuss recent advances and share our experiences – good and bad – in developing technologies that are opening new and exciting avenues for connecting and interrogating glycomics and glycoproteomics data collections. I will introduce GlyGen and UniCarbKB and provide an overview of data collections available including quality control mechanisms and biocuration efforts, and progress in building an intuitive user interfaces. This will include a description of GlycoStore a chromatographic and electrophoretic retention database of N-, O- and GSL glycans released and characterised from a range of glycoproteins, glycolipids and biotherapeutics; and the implementation of GlycoRDF and GlycoCoO (sematic technologies) to standardise and connect data sets. Finally, I will discuss how curated data can be used to build machine learning platforms to improve the prediction and validation of N-/O-linked glycosylation sites incorporating deep learning neural networks and Support Vector Machine (SVM) classifiers.
Date: Tuesday 2nd March 2021 - 3.15-4.30pm
Registration: The symposium is free to attend and open to all. To register your attendance, please email Stuart M Haslam (s.haslam@imperial.ac.uk), Yan Liu (yan.liu2@imperial.ac.uk) or Ben Schumann (b.schumann@imperial.ac.uk).
Dr Campbell Bio
Dr Campbell is Research Fellow at the Institute for Glycomics, Griffith University (Australia) leading the joint NIH Glycoscience GlyGen and UniCarbKB glycoinformatics initiative.
He started his research career at the Oxford Glycobiology Institute under the mentorship of Prof. Pauline Rudd as part of the EUROCarbDB project. During this time the Oxford Glycobiology Glycan Sequencing Group moved to Dublin as part of the newly established National Institute for Bioprocessing Research and Training (NIBRT). While at NIBRT Dr Campbell coordinated the development of UniCarb-DB, and the continued growth of GlycoBase in support of industrial collaborations.
In 2010, he joined Professor Packer’s research group at Macquarie University (Sydney, Australia) to develop an infrastructure for linking mass spectrometry data with a glycomics repository, which led to the development of the UniCarbKB platform. In 2017, to strengthen analytical glycobiolgy research in Australia members of the Packer group relocated to the Institute for Glycomics (Gold Coast, Australia), expanding national glycoinformatics and analytical capabilities and establishing the Australian Centre for Cancer Glycomics and to. The Institute for Glycomics is a flagship biomedical research institute that represents a unique resource with a multi-disciplinary and translational approach with a particular focus on chemical biology, infectious disease, and cancer.