GlyGen: Computational and informatics resources and tools for glycosciences research

Although ongoing technical advances are accelerating the pace and sophistication of data acquisition in glycoscience, the transformation of these data to glycobiology knowledge, insight, and understanding is slowed by the limited number of tools that facilitate their integration with biological knowledge. Thus, to fill in the critical gaps, there is a need for a broadly relevant and sustainable glycoinformatics resource that can provide tools and data to address specific glycoscience questions. GlyGen is an integrated, extendable and cross-disciplinary glycoinformatics resource that will facilitate knowledge discovery in basic and translational glycobiology by integrating multidisciplinary data and knowledge from diverse resources. It will address glycobiology questions that can currently be answered only by extensive literature-based research and manual collection of data from disparate resources. The aims of the GlyGen project includes integrating and exchange of up-to-date glycobiology-related information and data with partnering data sources such as EMBL-EBI, NCBI, UniProt, UniCarbKB, and others; creating an intuitive web portal to search and browse for glycoscience knowledge that will also include off-line data analysis, data exploration, and mining. Furthermore, the GlyGen project includes the development of essential new information resources, namely the Glycan Microarray Database that will provide key information about the interactions of glycans with other biomolecules and a Glycan Naming Ontology (GNOme) that facilitates interpretation of incomplete structural information in the context of biological functions. GlyGen\u27s comprehensive data integration framework and valuable user\u27s feedback will provide unprecedented support for complex queries spanning diverse data types relevant to glycobiology, extending its scope beyond the mapping of glycan data to genes and proteins. The resource would be publicly available and will facilitate the sharing and dissemination of glycobiology knowledge. It will provide new opportunities for a systems-level understanding of glycobiology in disease and development, even for scientists who do not specialize in glycobiology

Functional implications of glycans and their curation:insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy

Dynamic changes in protein glycosylation impact human health and disease progression. However, current resources that capture disease and phenotype information focus primarily on the macromolecules within the central dogma of molecular biology (DNA, RNA, proteins). To gain a better understanding of organisms, there is a need to capture the functional impact of glycans and glycosylation on biological processes. A workshop titled "Functional impact of glycans and their curation" was held in conjunction with the 16th Annual International Biocuration Conference to discuss ongoing worldwide activities related to glycan function curation. This workshop brought together subject matter experts, tool developers, and biocurators from over 20 projects and bioinformatics resources. Participants discussed four key topics for each of their resources: (i) how they curate glycan function-related data from publications and other sources, (ii) what type of data they would like to acquire, (iii) what data they currently have, and (iv) what standards they use. Their answers contributed input that provided a comprehensive overview of state-of-the-art glycan function curation and annotations. This report summarizes the outcome of discussions, including potential solutions and areas where curators, data wranglers, and text mining experts can collaborate to address current gaps in glycan and glycosylation annotations, leveraging each other's work to improve their respective resources and encourage impactful data sharing among resources. Database URL: https://wiki.glygen.org/Glycan_Function_Workshop_2023

Vora, Jeet Kiran's Quick Files

The Quick Files feature was discontinued and it’s files were migrated into this Project on March 11, 2022. The file URL’s will still resolve properly, and the Quick Files logs are available in the Project’s Recent Activity

GlyGen

GlyGen (gly-glycobiology; gen-information), is an advanced glycoinformatics resource developed to facilitate discovery in basic and translational glycobiology research along with enhancing the integration of multidisciplinary information from diverse resources. GlyGen will include knowledge about molecular, biophysical and functional properties of glycans, genes, and proteins organized in pathways and ontologies, plus a rapidly growing body of biological big data related to cancer mutation and expression. GlyGen adopts an innovative user driven approach for implementing, prioritizing and knowledge disseminating tools to address the questions and needs of glycobiology community. Website: www.glygen.or

Slides

Slides from internal and external presentation

GlyGen GitHub

GitHub repositories for GlyGen code and script

Enhancing the interoperability of glycan data flow between ChEBI, PubChem, and GlyGen.

Glycans play a vital role in health, disease, bioenergy, biomaterials, and bio-therapeutics. As a result, there is keen interest to identify and increase glycan data in bioinformatics databases like ChEBI and PubChem, and connecting them to resources at the EMBL-EBI and NCBI to facilitate access to important annotations at a global level. GlyTouCan is a comprehensive archival database that contains glycans obtained primarily through batch upload from glycan repositories, glycoprotein databases, and individual laboratories. In many instances, the glycan structures deposited in GlyTouCan may not be fully defined or have supporting experimental evidence and citations. Databases like ChEBI and PubChem were designed to accommodate complete atomistic structures with well-defined chemical linkages. As a result, they cannot easily accommodate the structural ambiguity inherent in glycan databases. Consequently, there is a need to improve the organization of glycan data coherently to enhance connectivity across the major NCBI, EMBL-EBI, and glycoscience databases. This paper outlines a workflow developed in collaboration between GlyGen, ChEBI, and PubChem to improve the visibility and connectivity of glycan data across these resources. GlyGen hosts a subset of glycans (~29,000) from the GlyTouCan database and has submitted valuable glycan annotations to the PubChem database and integrated over 10,500 (including ambiguously defined) glycans into the ChEBI database. The integrated glycans were prioritized based on links to PubChem and connectivity to glycoprotein data. The pipeline provides a blueprint for how glycan data can be harmonized between different resources. The current PubChem, ChEBI, and GlyTouCan mappings can be downloaded from GlyGen (https://data.glygen.org)