The GlySpace Alliance: toward a collaborative global glycoinformatics community

Aoki‐Kinoshita, Kiyoko F.; Lisacek, Frédérique; Mazumder, Raja; York, William S.; Packer, Nicolle H.

doi:10.1093/glycob/cwz078

Cited by 31 publications

(17 citation statements)

References 4 publications

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“…We are also planning on contacting lipid ontology and database developers to discuss where concepts could be combined or mapped with one another. Eventually, all of these integrated data will be available from the members of the GlySpace Alliance ( Aoki-Kinoshita et al. 2020 ).…”

Section: Discussionmentioning

confidence: 99%

The glycoconjugate ontology (GlycoCoO) for standardizing the annotation of glycoconjugate data and its application

et al. 2021

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Recent years have seen great advances in the development of glycoproteomics protocols and methods resulting in a sustainable increase in the reporting proteins, their attached glycans and glycosylation sites. However, only very few of these reports find their way into databases or data repositories. One of the major reasons are the absence of digital standard to represent glycoproteins and the challenging annotations with glycans. Depending on the experimental method, such a standard must be able to represent glycans as complete structures or as compositions, store not just single glycans but also represent glycoforms on a specific glycosylation side, deal with partially missing site information if no site mapping was performed, and store abundances or ratios of glycans within a glycoform of a specific site. In order to support the above, we have developed the GlycoConjugate Ontology (GlycoCoO) as a standard semantic framework to describe and represent glycoproteomics data. GlycoCoO can be used to represent glycoproteomics data in triplestores and can serve as a basis for data exchange formats. The ontology, database providers and supporting documentation are available online (https://github.com/glycoinfo/GlycoCoO).

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Section: Discussionmentioning

confidence: 99%

The glycoconjugate ontology (GlycoCoO) for standardizing the annotation of glycoconjugate data and its application

et al. 2021

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“…Even glycan-mediated ECM [126] and host-pathogen [127] interactions are registered. To increase the utility and interoperability, efforts are underway to unify datasets throughout the Glycomics@ExPASy [128], GlyGen [129], and GlyCosmos [130] datahubs as the GlyspaceAliance [131]. Despite this progress, consistent formats have yet to be globally adopted, hindering data sharing and collaboration within glycobiology and with adjacent collaborators in proteomics.…”

Section: High-throughput Measurement Of Glycomesmentioning

confidence: 99%

Big-Data Glycomics: Tools to Connect Glycan Biosynthesis to Extracellular Communication

Kellman

Lewis

2021

Trends in Biochemical Sciences

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Characteristically, cells must sense and respond to environmental cues. Despite the importance of cell-cell communication, our understanding remains limited and often lacks glycans. Glycans decorate proteins and cell membranes at the cell-environment interface, and modulate intercellular communication, from development to pathogenesis. Providing further challenges, glycan biosynthesis and cellular behavior are co-regulating systems. Here, we discuss how glycosylation contributes to extracellular responses and signaling. We further organize approaches for disentangling the roles of glycans in multicellular interactions using newly available datasets and tools, including glycan biosynthesis models, omics datasets, and systems-level analyses. Thus, emerging tools in big data analytics and systems biology are facilitating novel insights on glycans and their relationship with multicellular behavior. Extracellular Glycans Influence Intercellular BehaviorEvery cell and many viruses are wrapped in a sugar-coating of functional glycans (see Glossary) and glycoconjugates that helps modulate cell-cell communication, the glycocalyx. Glycans are bound to peptide or lipid glycoconjugates and matured in the endomembrane system. They then reside on the cell surface or diffuse into the extracellular matrix (ECM). The emergence, recycling, and dispersion of glycans is often slow, variable, and glycoconjugate dependent (2-1000 h); therefore, environmentally responsive nascent glycans do not transform the cell surface immediately [1,2]. Instead, the glycocalyx constitutes a composite memory of recent and current responses to intercellular exchanges. Together, the glycocalyx, the communication-modulating glycans and glycoconjugates between conversing cells form a rich resource that can be leveraged to improve our understanding of how cells communicate (Figure 1, Key Figure ).ECM glycans are voluminous, ubiquitous, and diverse, extending to 2-3 times the cell diameter [3]. With 4549 of 20 365 reviewed human proteins (UniProtKB) corresponding to~250 000 proteoforms per cell type [4], there are~50 glycoforms for every glycoprotein. Glycan metabolism uses 342 documented [5] human glycosyltransferases and glycosidases, each performing interdependent and distinct monosaccharide additions and removals. Borrowing from epigenetics, lectins, glycosyltransferases, and glycosidases have been described as the readers, writers, and erasers of the glycocalyx [6,7]. These encapsulating carbohydrates moderate many cellular responses, including development, growth, differentiation, migration, signaling, and morphogenesis (Table 1) making few biological discussions complete outside the glycan context (Figure 2) [8].Today, we are seeing glycan essentiality and neglect in the study of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the COVID-19 causative agent (Figure 2C). Because cells and viruses are wrapped in glycans, glycans moderate the first host-pathogen interactions, including immune evasion through viral glycosylation [9,10] and h...

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“…This information needs to be not only that acquired by the technologies of glycomics and glycoproteomics, but the seamless integration of such datasets with information delivered by well-established genomics, transcriptomics, proteomics, metabolomics and/or lipidomics technologies for an integrated and holistic understanding of cellular biology in health and disease, such as has now begun with the international glycoinformatics initiatives of GlyConnect (https:// glyconnect.expasy.org/), Glygen (https:// glygen.org/) and GlyCosmos (https://gly cosmos.org/) under the collaborative Gly-Space Alliance. 32 Once the dynamics and functional glycan features are determined on proteins within a complex biological system it is important to translate these findings into useful practice. Coordinated efforts in glycobiotechnology and clinical glycoscience that aim to connect fundamental and applied glycobiology and to translate findings in this field into products including new therapeutic targets to treat, cure and ultimately prevent disease and new biomarkers to diagnose and prognose diseases, are ongoing.…”

Section: Future Directions Of the Fieldmentioning

confidence: 99%