Platforms EOI: UniCarbKB: Building a Standardised and Scalable Informatics Platform for Glycosciences Research

20 September 2019 at 13:02

Project title

UniCarbKB: Building a Standardised and Scalable Informatics Platform for Glycosciences Research

Field of Research code(s)

03 CHEMICAL SCIENCES 06 BIOLOGICAL SCIENCES 08 INFORMATION AND COMPUTING SCIENCES 11 MEDICAL AND HEALTH SCIENCES

EOI Lead Name

Matthew Campbell

EOI lead Research Group

Institute for Glycomics

EOI lead Organisation

Institute for Glycomics, Griffith University

EOI lead Email

Collaborator details

Name Research Group Organisation

Malcolm Wolski eResearch Services Griffith University

Project description

Over the last few years the glycomics knowledge platform UniCarbKB has contributed to the growth of international glycoinformatics resources by providing access to data collections, web services and software applications supported by biocuration activities. However, UniCarbKB has continued to develop as a single monolithic resource. This proposed project will improve the growth and scalability of UniCarbKB by breaking down the platform into smaller and composable pieces. This will be achieved through the adoption of a more decentralised approach and a microservice architecture that will allow components of the platform to scale at different rates.

This architecture will allow us is to build an extendable and cross-disciplinary resource by integrating existing data with new analysis tools. The adoption of international resources (e.g. NIH GlyGen), will allow not just mapping of glycan data to genes and proteins but also pathways, gene ontology, publications and a wide variety of data from EBI, NCBI and other sources. Additionally, we propose to integrate glycan array data and develop ontologies that can serve as tools for integration and subsequently analysis of glycan-associated Existing technology

Adopt

The proposed project will adopt a multi-tier application architecture in which applications will be developed and deployed as microservices. The services will include: i) data analysis and workflow tools (Galaxy-plugin and QC pipelines); ii) APIs (GraphQL) and SPARQL endpoints; iii) web application front-end; and iv) data feeds from international resources. These services will be encapsulated in self-contained environments (Docker) leading to quicker deployments and improved sustainability. Kubernetes will be adopted for orchestrating containers and will be coordinated with ARDC e.g. QCIF.

Adapt

The proposed project aims to adapt infrastructure developed by three leading glycosciences focused platforms: i) GlyGen (USA/UK/Japan/Australia), ii) UniCarbKB (Australia) and iii) GlySpace Alliance (international). In addition, we will adapt data formats, ontologies, and reporting guidelines described by the MIRAGE commission, the GlycoRDF initiative, and HELM for encoding complex. The project will extend existing open-access software applications for glycan-array analysis (GRITS and GMADB) to improve the identification binding determinants involved in disease and host-pathogen interactions.

Build

We aim to build a scalable and sustainable glycoinformatics platform to connect glycoscience with other biomolecular information (focused on cancer and infectious diseases). The platform will adhere to / incorporate agreed upon data standards importantly innovative software will be built that enable researchers to analyse their own data. Furthermore, we shall build a comprehensive data model that harmonises glycomics related data whilst establishing cross-references with platforms spanning multiple domains, addressing a key impediment in data- interoperability within the life sciences. Anticipated requirements

Annual funding

$200,000 - $299,000

Proposed length

2 years Other information

Other information you wish to provide

The proposed project will be supported by researchers from leading Australian glycomics and glycoproteomics centres (Institute for Glycomics Griffith University, Macquarie University, University of Queensland and University of Melbourne), and international advocates from UK, USA, Japan and Taiwan. The project will integrate and extend platforms being developed by international researchers and subsequently will be supported by a leading team of developers. The full proposal will define the role of collaborators and the scientific advisory board. Terms

I agree to the terms

Yes