Glycan Function Workshop at SfG 2023: Difference between revisions

Revision as of 17:26, 2 October 2023

The workshop on "Glycan Function Annotation" associated with the annual meeting of the Society for GlycoBiology 2023 will be held on November 4th at Hilton Waikoloa Village Resort, on the big island of Hawaii. The workshop is organized and chaired by Dr. Mike Tiemeyer and Dr. René Ranzinger from the Complex Carbohydrate Research Center and sponsored by the GlyGen project with the support of NIH. This workshop follows the workshop on "Glycan Function" held in Padova, Italy in May 2023. While the workshop in Italy was pretty much focused on the bioinformatics and biocuration aspects of glycan function the workshop in Hawaii will focus on the biology and chemistry aspects.

Organization Committee

Dr. Mike Tiemeyer and Dr. René Ranzinger organizing and chairing the workshop. Other people that helped in planning the agenda and organizing the meeting are:

Raja Mazumder (GlyGen)
Karina Martinez (GlyGen)
Anna Bighta (Complex Carbohydrate Research Center)

Venue

Hilton Waikoloa Village

69-425 Waikoloa Beach Drive

Waikoloa, HI 96738

Travel information

Airport

Kona International Airport (KOA) is a 20-minute (19 miles) car ride from the hotel.

Uber & Lyft

Rides from Kona International Airport range from $21–$37.

Taxi

Approx. $55-$65 (one way) Parking Self-Parking: $39/night Valet Parking: $55/night

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 9:55	20 min 45 min	Q1. How would your resource extract glycan related data from literature or other sources? Presentations Discussions (All attendees)	Hiren Joshi	Yukie Akune Kristian Axelsen James Urban	Rene Ranzinger Cecilia Arighi	Vijay Shanker
10:40	15 min	Coffee Break
10:55 11:15	20 min 45 min	Q2. What type of glycan related data would be useful to your resource, that you don’t currently have access to? Presentations Discussions (All attendees)	Maria Martin	Randi Vita Paul Thomas Yan Liu	Yasunori Yamamoto Nathan Edwards	Emily Bordeleau
12:00	60 min	Lunch
1:00 1:20	20 min 45 min	Q3. What type of data, that you do have, might enhance glycan related data? Presentations Discussions (All attendees)	Deepti Jaiswal Kundu	Ted Groth Ten Feizi Kiyoko F. Aoki-Kinoshita	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 Discussions (All attendees)	Mike Tiemeyer	Adnan Malik Kalpana Panneerselvam Susan Bello	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

Attendees


	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)

Contact

For questions about registration or general inquiries, please contact:

Mike Tiemeyer: mtiemeyer@ccrc.uga.edu

Rene Ranzinger: rene@ccrc.uga.edu

@@ Line 1: / Line 1: @@
-'''There were 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:'''
+The workshop on "Glycan Function Annotation" associated with the annual meeting of the Society for GlycoBiology 2023 will be held on November 4th at Hilton Waikoloa Village Resort, on the big island of Hawaii. The workshop is organized and chaired by Dr. Mike Tiemeyer and Dr. René Ranzinger from the [https://ccrc.uga.edu/ Complex Carbohydrate Research Center] and sponsored by the [https://www.glygen.org/ GlyGen project] with the support of NIH. This workshop follows the [[Glycan Function Workshop 2023|workshop on "Glycan Function"]] held in Padova, Italy in May 2023. While the workshop in Italy was pretty much focused on the bioinformatics and biocuration aspects of glycan function the workshop in Hawaii will focus on the biology and chemistry aspects.
+=== Organization Committee ===
+Dr. Mike Tiemeyer and Dr. René Ranzinger organizing and chairing the workshop. Other people that helped in planning the agenda and organizing the meeting are:
-<u>'''[[BioCuration Workshop 2023#All Day Pre-Workshop (Sunday April 23)|All Day Pre-Workshop]]'''</u>
+* Raja Mazumder ([https://www.glygen.org/ GlyGen])
+* Karina Martinez ([https://www.glygen.org/ GlyGen])
+* Anna Bighta ([https://ccrc.uga.edu/ Complex Carbohydrate Research Center])
-'''Sunday April 23, 2023, 9:00am - 5:00pm'''
+=== Venue ===
+'''Hilton Waikoloa Village'''
-'''Hotel NH Padova, Padua, Italy'''
+-425 Waikoloa Beach Drive
-'''Registration:''' https://www.eventbrite.com/e/workshop-on-functional-impact-of-glycans-and-their-curation-tickets-489922931677
+Waikoloa, HI 96738
-'''''This event is separate from the 2023 Biocuration Conference.'''''
+=== Travel information ===
+'''Airport'''
+Kona International Airport (KOA) is a 20-minute (19 miles) car ride from the hotel.
-'''<u>[[BioCuration Workshop 2023#2-Hour Biocuration Workshop (Monday April 24)|2-Hour Biocuration Workshop]]</u>'''
+'''Uber & Lyft'''
-'''Monday April 24, 2023, 11:00am - 1:00pm'''
+Rides from Kona International Airport range from $21–$37.
-'''Cultural Center Altinate San Gaetano, Padua, Italy'''
+'''Taxi'''
-'''Registration:''' https://biocuration2023.github.io/
+Approx. $55-$65 (one way)
+'''Parking'''
+Self-Parking: $39/night
+Valet Parking: $55/night
-'''''This event is hosted by the 2023 Biocuration Conference.'''''
+=== Schedule ===
-'''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)
-===='''<big><u>All Day Pre-Workshop (Sunday April 23)</u></big>'''====
-[https://glygen.org/ GlyGen] and the [https://www.glycobiology.org/ Society for Glycobiology] are sponsoring a special pre-workshop prior to the [https://biocuration2023.github.io/ 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/ 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/ 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 [https://www.nh-hotels.com/hotel/nh-padova Hotel NH Padova] from Saturday, April 22nd onwards. Additional lodging suggestions can be found on the 2023 Biocuration Conference website [https://biocuration2023.github.io/lodging here].
-=====Schedule=====
 {| class="wikitable"
 |+
@@ Line 245: / Line 209: @@
 *Group members - Will join chair, presenters & reporters in preparing summary for their question
+=== Attendees ===
-=====Presentation/Discussion Sessions=====
+  {| class="wikitable"
-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)=====
-{| class="wikitable"
 |+
 !
@@ Line 370: / Line 321: @@
 |}
+=== '''Contact''' ===
-===='''<big><u>2-Hour Biocuration Workshop (Monday April 24)</u></big>'''====
-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
+Mike Tiemeyer: mtiemeyer@ccrc.uga.edu
-Karina Martinez: karinamartinez@gwu.edu
-Jeet Vora: jeetvora@gwu.edu
+Rene Ranzinger: rene@ccrc.uga.edu