Functional Impact of Glycans and their Curation
There will be two glycan function events in Padua, Italy. We encourage everyone who is attending the Sunday pre-workshop to also join us Monday, if they plan to stay for the conference:
Sunday April 23, 2023, 9:00am - 5:00pm
Hotel NH Padova, Padua, Italy
Registration: https://www.eventbrite.com/e/workshop-on-functional-impact-of-glycans-and-their-curation-tickets-489922931677
This event is separate from the 2023 Biocuration Conference.
Monday April 24, 2023, 11:00am - 1:00pm
Cultural Center Altinate San Gaetano, Padua, Italy
Registration: https://biocuration2023.github.io/
This event is hosted by the 2023 Biocuration Conference.
Abstract
Dynamic changes in protein glycosylation impact human health and disease progression. However, current resources that capture disease and phenotype information such as MIM, Monarch Initiative, UniProt, and Genomics England, and others focus primarily on the macromolecules 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. While the aforementioned resources include glycan-related genes, such as biosynthetic and degradative enzymes, the function and disease annotations are usually associated with the gene product rather than with the relevant glycosylation and glycan structural changes. Expression of glycan-related genes represents only a subset of factors affecting protein glycosylation. The functional impact of a specific glycan structure may depend on the protein to which it is bound, site of attachment, truncation or loss of the entire glycan structure. A catalog of glycosylation combinations, their relationship with other biomolecules, and their functional implications will provide insight into the biological roles of glycans and the impact of genetic and environmental factors on their expression. The purpose of this workshop is to bring together subject matter experts, tool developers and biocurators from resources that annotate content that is related to the functional impact of glycans. Each resource will do a short presentation on their data of interest, including types of annotations, what impact glycan function might have on these annotations, and standards and ontologies they are using. This will be followed by a jamboree/hackathon where we will discuss selected publications to identify commonalities and gaps in our current curation practices, and provide potential solutions. The attendees will help identify areas where curators, data wranglers, and text mining experts can 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.
Organization Committee
Raja Mazumder (GlySpace, GlyGen), Mike Tiemeyer (GlySpace, GlyGen), Rene Ranzinger (GlyGen), Maria Martin (UniProt, GlyGen), Kiyoko Aoki-Kinoshita (GlySpace, GlyCosmos, GlyTouCan), Frederique Lisacek (GlySpace, GlyConnect), Cecilia Arighi (PIR, BioCreative, UniProt), Randi Vita (IEDB), Jeet Vora (GlyGen), Karina Martinez (GlyGen)
All Day Pre-Workshop (Sunday April 23)
GlyGen and the Society for Glycobiology are sponsoring a special pre-workshop prior to the 2023 International Biocuration Conference in Padua, Italy. The purpose of this workshop is to focus on community building and learning what each resource is doing related to the functional impact of glycans.
Venue
Hotel NH Padova, Via Niccolò Tommaseo, 61, 35131 Padova, Italy
https://www.nh-hotels.com/hotel/nh-padova
16 minute walking time to Centro Culturale San Gaetano (Conference venue)
Cost
Free, with lunch and coffee provided. Travel and accommodation are not included.
Accommodations
You can book a room at Hotel NH Padova from Saturday, April 22nd onwards. Additional lodging suggestions can be found on the 2023 Biocuration Conference website here.
Schedule
| Time | Session | Agenda |
|---|---|---|
| 8:30am - 9:00am | Breakfast | |
| 9:00am - 12:00pm | Morning session | Introductions & Overview (30 minutes) Presentation/Discussion Question #1 (1.25 hours) |
| 12:00 - 1:00pm | Lunch | |
| 1:00pm - 3:30pm | Afternoon session | Presentation/Discussion Question #3 (1.25 hours) Coffee break (5 mins) |
| 3:30pm - 5:00pm | Final Discussion | Prepare summaries (30 mins) Presentations from each question (40 mins) |
Presentation/Discussion Sessions
Each presentation/discussion session will focus on one of the four questions below. These sessions will be divided into a presentation section (~30mins) followed by a whole-group discussion (~45 mins).
For each question, selected resources will give short presentations (~5 mins) on their ideas and strategic thoughts related to how their data of interest can intersect with glycan-related data, including useful annotations, standards, and ontologies. The goal of the discussions will be to improve coordination amongst resources to harmonize and enhance the impact of data related to glycans and glycoconjugates, including structures, functions, biosynthesis, pathophysiology, etc.
Two chairs will be selected to facilitate each of the presentation/discussion sessions and 2 reporters per question will be selected to prepare and present the results during the final session and the Monday Biocuration workshop.
| Question | Chairs | Presenters | Reporters |
|---|---|---|---|
| How would your resource extract glycan-related data from literature or other sources? | TBD | TBD | TBD |
| What type of glycan-related data would be useful to your resource–that you don’t currently have access to? | TBD | TBD | TBD |
| What type of data–that you do have–might enhance glycan-related data? | TBD | TBD | TBD |
| What standards does your resource use for the glycan-related annotations? | TBD | TBD | TBD |
Registered Attendees (Resource/Project)
| Resource/Project | Attendees | Presentation/s | |
|---|---|---|---|
| 1 | GlyGen | Karina, Rene, Vijay, Nathan, Mike, Raja
Jeet (remote) |
Intro, Questions 1-4 |
| 2 | GlyConnect | Frederique | ? |
| 3 | IEDB | Randi | ? |
| 4 | UniProt, BioCreative | Cecilia | ? |
| 5 | GlyCosmos | Kiyoko, Yasunori | ? |
| 6 | IntAct | Kalpana | ? |
| 7 | MGI | Susan | ? |
| 8 | UniProt | Maria | ? |
| 9 | Microarray curation | Ten, Liu, Yukie | ? |
| 10 | GlycoShape-3D | Ives | ? |
| 11 | Glycan structure software | Jon A | ? |
| 12 | Glyco.me | Hiren | ? |
| 13 | GO, PANTHER | Paul | ? |
| 14 | Rhea | Kristian | ? |
| 15 | Glycowork | Jon L, James, Thomes | ? |
| 16 | ELIBIO | Krishna | ? |
| 17 | PRIDE | Deepti | ? |
| 18 | GlycoEnzOnto | Ted | ? |
| 19 | ChEBI | Adnan | ? |
2-Hour Biocuration Workshop (Monday April 24)
Biocuration 2023 will be hosting 5 workshops, including Functional impact of glycans and their curation, at the main conference venue. For additional information, visit the Biocuration website here: https://biocuration2023.github.io/workshops#glycans
Contact
For questions about registration or general inquiries, please contact:
Raja Mazumder: mazumder@gwu.edu
Karina Martinez: karinamartinez@gwu.edu
Jeet Vora: jeetvora@gwu.edu