Biocuration Workshop 2025

Dynamic changes in protein and lipid glycosylation impact protein homeostasis, membrane functions, development, inflammation, immunity, aging, neural function, pathogen interactions, and almost all aspects of human health from fertilization to death. However, current bioinformatic resources that capture disease and phenotype information focus primarily on the macromolecules represented within the central dogma of molecular biology (DNA, RNA, proteins). In order to gain a more complete understanding of human disease, there is a need to capture the functional impact of glycans and glycosylation on biological processes. We propose a workshop, which would be the third in an ongoing series of workshops sponsored by GlyGen, focused on annotating glycan functions in biological contexts, their digital representation, and integration with existing function annotation efforts.

The third Workshop on Glycan Function Annotation, entitled “Exploring and Enhancing a Glycan Function Ontology”, will be held in conjunction with ISB2025 and will seek the input of participants with expertise in ontologies that describe biological functions. The discussions will build on the outcomes of the first two workshops which identified currently available resources and established an initial ontology for glycan function relationships and associated metadata. It is anticipated that the outcome of the workshop will move the field forward toward finalizing the ontology and its relationships to existing function annotation efforts. This work will lay the foundation for primary data generators and biocurators to collect and organize glycan function annotation as they attempt to enrich our understanding of the impact of glycans and glycosylation across biological domains.

GlyGen is organizing this proposed workshop and expects that it will draw interest from ISB2025 attendees who have experience in gene and protein function, ontology developers, as well as curators that focus on the role of post-translational modifications and metabolism in regulating biological activities.

In addition to welcoming any interested ISB meeting attendees, the organizers are also target a group of specific stakeholders to ensure the highest likelihood of generating impactful workshop outcomes

Background

The first Workshop on Glycan Function Annotation was held in conjunction with the 2023 ISB meeting in Padua, Italy and was entitled “Functional Impact of Glycans and their Annotation.” This workshop brought together subject matter experts, tool developers, and biocurators who annotate content that may directly or unknowingly be related to the functional impact of glycans. The attendees identified areas where curators, data wranglers, and text mining experts could collaborate to address gaps in glycan and glycosylation annotations, leverage each other’s work to improve their respective resources, and encourage data sharing amongst resources. Concrete suggestions were developed for improving the visibility and impact of glycan, glycosylation, and glycoconjugate data. A manuscript describing the discussions and conclusions was published in Database.

Among the recommendations of the first workshop at ISB2023 was a proposal that the bioinformatics community would benefit greatly from the organization of a second workshop that could harvest input from experts in glycobiology and glycan functions. Thus, a second workshop, entitled “Defining Glycan Functions”, was organized and held in conjunction with the 2023 Society for Glycobiology meeting in Kona, Hawaii. The participants, who together possess deep knowledge of a broad range of glycan functions, developed an elemental foundation for describing vocabularies and concepts capable of capturing glycan functions. The participants acknowledged the need for expanding their framework of functions to include hierarchical relationships between glycan types and specific glycan structures, structural motifs, features, and patterns. A manuscript describing the discussions and conclusions is in preparation.

The participants of the first and second workshops jointly recognized the need to expand discussions across the glycoscience, curation, and informatics community in order to hone annotations into forms that are useful across resources.

Organizers

• Mike Tiemeyer (GlySpace, GlyGen)
• Raja Mazumder (GlySpace, GlyGen)
• Rene Ranzinger (GlySpace, GlyGen)
• Nathan Edwards (GlyGen)

Meeting time

Sunday April 6th from 8:30am to 12:30pm CST.

Venue

Stowers Institute
1000 East 50th Street
Kansas City
Missouri 64110
USA

Agenda

Times are in CST

Time	Duration	Topic	Presenters
8:30	10 min	Welcome and Introduction to Purpose of Workshop	Mike Tiemeyer & Rene Ranzinger
8:40	45 min	Introduction into Glycan, GlycoBiology and Glycan Function	Mike Tiemeyer
9:25	15 min	Glycan Function data and object model	Rene Ranzinger
9:40	35 min	Discussion based on use cases (I)	Mike Tiemeyer & Rene Ranzinger
10:15	15 min	Break
10:30	75 min	Discussion based on use cases (II)	Mike Tiemeyer & Rene Ranzinger
11:45	30 min	Summary discussion and next steps	Mike Tiemeyer
12:15pm	10 min	Summary and meeting adjourned	Mike Tiemeyer

Target Audience

• Participants of the ISB2025 meeting with an interest in protein and glycan function.
• Experts who specialize in ontologies that describe biological functions.
• Biocurators who focus on annotating biological data, particularly those interested in post-translational modifications and their functions.
• Researchers and scientists with knowledge of glycan functions and glycosylation.
• Data Wranglers and Text Mining Expert

Expected Outcome

• Building on the initial ontology, the goal is to review and finalize the ontology and its relationships to existing function annotation efforts.
• Improved integration of glycan function annotations with current bioinformatic resources.
• Establishing a framework for primary data generators and biocurators to collect and organize glycan function annotations.
• Facilitating collaboration among experts in different biomedical domains, ontology developers, and curators to foster a multidisciplinary approach to glycan function annotation.
• Identifying key areas for future research and development in glycan function annotation, setting the stage for subsequent workshops and initiatives.

Contact

For questions about the workshop or general inquiries, please contact:
Mike Tiemeyer: mtiemeyer [at] ccrc.uga.edu