Glycans (sugars) play key roles in all kingdoms of life, being essential for survival, underpinning disease and acting as targets for drug development. Glycan structures are challenging to represent, inhibiting communication and data sharing. The Symbol Nomenclature For Glycans (SNFG) is a robust, simple, shared resource, based on FAIR principles, to depict complex glycan structures using simple geometric shapes. The SNFG acts as a premium medium that enables data sharing and reuse among databases, software, journals, textbooks, and scientists ensuring that data is efficiently and accurately communicated. This resource is broadly accepted and this unfunded volunteer effort is updated regularly at the NCBI-SNFG Page by international experts.
This submission is on behalf of the Symbol Nomenclature For Glycans (SNFG) Discussion group. This quorum is composed of 44 researchers and practitioners from 11 countries and four continents who develop, maintain, and update the glycan symbol nomenclature as part of an unfunded volunteer effort (NCBI-SNFG page). The team consists of members of the IUPAC nomenclature committee, journal editors, members of the NCBI, and leading biochemists, informaticians, NMR and mass spectroscopists, molecular modelers, software developers, and synthetic chemists. Our submission has been endorsed by the entire group, though only those who have participated in the writing have been listed as members of the DataWorks team. The group has an elected chair who acts to oversees maintenance of the SNFG-standard and its updates. When the expertise of the SNFG-group is insufficient, additional members of the community are engaged in curation. This approach results in inclusive interactions that benefit the entire glycoscience field and makes glycoscience knowledge more accessible to the wider scientific community. The SNFG discussion group also coordinates with scientific societies to help communicate new methods to describe glycoscience knowledge.
Goals: For decades, the complexity of glycan structures, i.e. their branched, non-templated, heterogenous structure, resulted in lack of agreement on how to represent them. The SNFG comprises a consensus solution among different groups, that is simple to use and intuitive for experts and non-experts. The goal of the SNFG is to enhance data sharing and reuse among participating databases, journals and texts; and provide a framework for communication, education, and accurate knowledge dissemination.
History: The SNFG standard finds its roots in a nomenclature proposed by Kornfeld and co-workers (1978) to streamline the communication of vertebrate glycan structures. This standard was widely adopted after its usage in The Essentials of Glycobiology (1999, first edition), a landmark textbook (Pub. 1), and promotion by the NIGMS-funded Consortium for Functional Glycomics (2001-2011). In a major revision, the symbol nomenclature was extended to reach beyond vertebrates to invertebrates, in recognition of the impact of glycans across the kingdoms of life (Pub. 2). Since 2015, the SNFG has been curated by an independent community of scientists with diverse expertise. Updates are published periodically (Pub. 3).
Current practice: The SNFG is founded on FAIR principles. To enable findability, the resource is hosted at NCBI-Glycans page, with version history preserved, and glycan accession numbers assigned by glytoucan. The resource is free, accessible, and universally available. The accession numbers are shared by many data portals, enhancing searchability and association of metadata with glycan structure, e.g. enzymes/genes creating them. Interoperability is demonstrated by the use of the SNFG in search results of glycan-centric databases: GlyCosmos, GlyGen, Glyco@Expasy, CSDB. The SNFG is referenced in KEGGGLYCAN and Glycosciences.de, and it is used by the Protein Data Bank and PubChem. These repositories cross-reference additional independent biomedical resources including Reactome and ChEBI. Reuse is demonstrated by the usage of the SNFG in textbooks, journals and databases. While still growing in terms of usage, the SNFG meets domain-relevant community needs.
Compelling features: The acceptance of the SNFG by a broad community of scientists has helped propel the glycosciences from a specialized field into mainstream biomedicine. Its presence at the NCBI is resulting in continued integration of glycan knowledge with gene, protein, pathway, and disease processes.
The SNFG leveraged the momentum of the initial release of a symbol nomenclature by the editors of The Essentials of Glycobiology, along with its adoption by the Consortium for Functional Glycomics, to build a consensus on how to depict glycans using symbols. The timing was right to further develop and formalize a symbol nomenclature that would be broadly applicable. Key to SNFG success was the formation of an international working group with diverse stakeholders and untethered release of the standard to the community. The open-source nature of the resource has been critical for promoting usage. Additional features underpinning success include: i) Adherence to IUPAC and prior paradigms; ii) Deep and deliberative discussion, with considerable consensus building among users, especially database practitioners; iii) Data sharing at the NCBI-SNFG page (Res. 4); iv) Publications that highlight and explain SNFG improvements (Pub. 1-3); v) Incorporation into data-sharing guidelines developed by the community (MIRAGE-Beilstein-Institut); vi) Usage in textbooks (Pub. 1); vii) Improvement of reproducibility and ease of use by development of software tools (Res. 4); viii) Engagement of journals and data repositories to adopt the SNFG, which improves the accuracy of data reporting and facilitates data sharing (Res. 4); ix) Presentations at conferences to enhance awareness. Overall, community engagement and deliberative discussions are key features that enable replication of SNFG success.
The development, sharing, and reuse of the SNFG has resulted in many benefits. First, the representation of complex glycan structures using simple graphics has lowered entry barriers into the glycoscience field. By promoting communication and education between glycoscientists and scientists within allied fields, the SNFG has accelerated ideation, collaboration, and discovery. Second, the association of graphical glycan structures with universal glycan accession numbers, via collaboration with glytoucan.org (Res. 5), has allowed uniform integration and reuse of glycan data across international repositories (e.g. https://www.glygen.org/) including those not focused on glycans (e.g. Protein Data Bank). As a result, new ontologies and methods for generating data queries have emerged. Third, SNFG use is now commonplace in journals, including those requiring this standard, which has improved the quality of scientific output while reducing error (Res. 4). Fourth, the SNFG has promoted the creation of new software for rendering glycans, along with their integration into modeling and mass spectrometry tools (Res. 4). Last, Free teaching slides using the SNFG are available via the Essentials of Glycobiology textbook (Pub. 1).
