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), Karina Martinez (GlyGen), Jeet Vora (GlyGen), Maria Martin (UniProt, GlyGen), Kiyoko Aoki-Kinoshita (GlySpace, GlyCosmos, GlyTouCan), Frederique Lisacek (GlySpace, GlyConnect), Cecilia Arighi (PIR, BioCreative, UniProt), Randi Vita (IEDB)
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)
Getting there
From the Marco Polo airport:
Bus only: Busitalia (https://www.fsbusitalia.it) offers a direct bus from the airport. Take bus line E015 towards Padova Autostazione for 14 stops, get off at Padova Fiera R. The hotel is 181 meters away. The trip is about 65 min and is €8.50.
Bus/Train: Take ATVO (https://www.atvo.it) bus line no. 25a to Venezia P.Roma for 5 stops, get off at Mestre Stazione FS. From there, take a train to Bologna Centrale and get off at Padova stop. Then, take the bus U18 to San Marco for 3 stops, get off at Tommaseo 114. You will find the hotel 130 metres away. It's a 1H 15 min trip and is € 7.50 + 3.40€ + 1,80€.
Taxi: It's a 1H 30 minutes trip and is around 98€.
From Padova train station:
Take the bus U18 to San Marco for 3 stops, get off at Tommaseo 114. You will find the hotel 130 metres away. Ticket (75 min): 1,30€ Ticket (24H): 3,80€
By Car:
The hotel's GPS Coordinates: 45.412671°N 11.892378000000008°E
Parking: Onsite, Indoor and is €10 / day. Parking cannot be reserved in advance
Cost
Free, with lunch and coffee provided. Travel, accommodation and breakfast 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 | Duration | Topic | Chair | Presenters | Reporters | Group Members |
|---|---|---|---|---|---|---|
| 9:00 | 15 min | Welcome | Raja Mazumder Rene Ranzinger |
|||
| 9:15 | 20 min | Glycan Function Overview | Mike Tiemeyer | |||
9:35 |
20 min |
Q1. How would your resource extract glycan related data from literature or other sources? Presentations |
Hiren Joshi | Yukie Akune Kristian Axelsen |
Rene Ranzinger Cecilia Arighi |
Vijay Shanker |
| 10:40 | 15 min | Coffee Break | ||||
10:55 |
20 min |
Q2. What type of glycan related data would be useful to your resource, that you don’t currently have access to? Presentations |
Maria Martin | Randi Vita Paul Thomas |
Yasunori Yamamoto Nathan Edwards |
Emily Bordeleau |
| 12:00 | 60 min | Lunch | ||||
1:00 |
20 min |
Q3. What type of data, that you do have, might enhance glycan related data? Presentations |
Deepti Jaiswal Kundu | Ted Groth Ten Feizi |
Frederique Lisacek Callum Ives |
Raja Mazumder |
| 2:05 2:25 |
20 min 45 min |
Q4. What standards does your resource use for the glycan related annotations? Presentations |
Mike Tiemeyer | Adnan Malik Kalpana Panneerselvam |
Krishna Khakurel Karina Martinez |
Taciana Manso |
| 3:10 | 50 min | Break out session: Chair, presenters, reporters and group members meet with their designated group and prepare a summary/presentation for their question (coffee will be provided) | ||||
| 4:00 | 60 min | 15 min presentations by each group | Mike Tiemeyer Raja Mazumder |
Karina Martinez Rene Ranzinger |
Participant Roles
- Chair - Facilitate discussion sessions
- Presenters - Give short ~5 minute presentation on their response to discussion question
- Reporters - Take notes, prepare and present summary for discussion question
- Group members - Will join chair, presenters & reporters in preparing summary for their question
Presentation/Discussion Sessions
Each presentation/discussion session will focus on one of the four questions above. These sessions will be divided into a presentation section (~20mins) followed by a discussion among all attendees (~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.
One chair will be selected to facilitate each of the presentation/discussion sessions and 2 reporters per question will be responsible for recording and presenting the results during the final session and the Monday Biocuration workshop.
During the summary session at 3:10, each discussion question group (consisting of chair, presenters, reporters and group members) will meet to summarize the findings for their question, and prepare a presentation.
Registered Attendees (Resource/Project)
| Resource/Project | Attendees | |
|---|---|---|
| 1 | GlyGen | Karina Martinez, Rene Ranzinger, Vijay Shanker, Nathan Edwards, Mike Tiemeyer, Raja Mazumder, Jeet Vora (remote) |
| 2 | Glyco@Expasy | Frederique Lisacek |
| 3 | Immune Epitope Database and Analysis Project (IEDB) | Randi Vita |
| 4 | UniProt/iPTMnet/BioCreative | Cecilia Arighi |
| 5 | GlyCosmos | Kiyoko F. Aoki-Kinoshita, Yasunori Yamamoto |
| 6 | IntAct | Kalpana Panneerselvam |
| 7 | MGI | Susan Bello (remote) |
| 8 | UniProt | Maria Martin |
| 9 | Microarray curation | Ten Feizi, Yan Liu, Yukie Akune |
| 10 | GlycoShape-3D | Callum Ives |
| 11 | Glyco.me | Hiren Joshi |
| 12 | GO/PANTHER | Paul Thomas |
| 13 | Rhea | Kristian Axelsen, Alan Bridge (remote) |
| 14 | Glycowork | James Urban |
| 15 | ELIBIO Project | Krishna Khakurel (remote) |
| 16 | PRIDE | Deepti Jaiswal Kundu |
| 17 | GlycoEnzOnto | Ted Groth |
| 18 | ChEBI | Adnan Malik |
| 19 | University of British Columbia | Emily Bordeleau |
| 20 | University of York | Jon Agirre (remote) |
| 21 | Glycosciences.de/MonosaccharideDB | Thomas Lütteke (remote) |
| 22 | Glycan microarrays | Akul Mehta (remote) |
| 23 | IMGT | Taciana Manso (remote), Sofia Kossida (remote) |
| 24 | O-GlcNAcAtlas | Junfeng Ma (remote) |
| 25 | PubChem | Evan Bolton (remote) |
| 26 | VirtualGlycome/SNFG | Sriram Neelamegham (remote) |
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