Volunteership Spring 2026 - Revision history

Jeetvora at 15:29, 15 April 2026

2026-04-15T15:29:29Z

← Older revision		Revision as of 15:29, 15 April 2026
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	\|BiomarkerKB		\|BiomarkerKB
	\|Maria Kim; Cyrus Yeung; Jeet Vora		\|Maria Kim; Cyrus Yeung; Jeet Vora
	\|BiomarkerKB~~; PredictMod; GlyGen biocuration~~		\|BiomarkerKB
	\|-		\|-
	\|Venya Gulati		\|Venya Gulati

Hivelabwikiadmin: /* Spring 2026 Symposium */

2026-04-14T16:52:31Z

Spring 2026 Symposium

← Older revision		Revision as of 16:52, 14 April 2026
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	'''Time:''' 4 - 6 PM		'''Time:''' 4 - 6 PM

	'''Zoom Link:''' https://gwu-edu.zoom.us/j/93790551366?pwd=C0aN4b95CUbxahO9By6pTj35D9lFIx.1&jst=2#success		'''Zoom Link:''' [https://gwu-edu.zoom.us/j/93790551366?pwd=C0aN4b95CUbxahO9By6pTj35D9lFIx.1&jst=2#success https://gwu-edu.zoom.us/j/93790551366?pwd=C0aN4b95CUbxahO9By6pTj35D9lFIx.1&jst=2]
	{\| class="wikitable"		{\| class="wikitable"
	!Time		!Time

Hivelabwikiadmin: /* Agenda (All times are in Eastern Standard Time) */

2026-04-14T16:51:38Z

Agenda (All times are in Eastern Standard Time)

← Older revision		Revision as of 16:51, 14 April 2026
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	'''Time:''' 4 - 6 PM		'''Time:''' 4 - 6 PM

	'''Zoom Link''' - ~~TBA~~		'''Zoom Link:''' https://gwu-edu.zoom.us/j/93790551366?pwd=C0aN4b95CUbxahO9By6pTj35D9lFIx.1&jst=2#success

	~~=== Agenda (All times are in Eastern Standard Time) =~~==
	{\| class="wikitable"		{\| class="wikitable"
	!Time		!Time

Lorikrammer: /* Agenda (All times are in Eastern Standard Time) */

2026-04-01T20:00:03Z

Agenda (All times are in Eastern Standard Time)

← Older revision		Revision as of 20:00, 1 April 2026
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	\|Diya Kamalabharathy; Sampurna Chakravorty; Ashley Tien		\|Diya Kamalabharathy; Sampurna Chakravorty; Ashley Tien
	\|-		\|-
	\|5:30-5:~~55PM~~		\|5:30-5:45PM
	\| -		\| PredictMod
	\|		\|
	* 8 + 5 mins QA - presentation #1		* 8 + 5 mins QA - presentation
	* 8 + 5 mins QA - presentation #2		\|Vishal Bakshi
	\|Vishal Bakshi~~; Miao Wang~~
	\|-		\|-
	\|5:55-6:00 PM		\|5:45-6:00 PM
	\| colspan="2" \|Remarks		\| colspan="2" \|Remarks
	\|Raja Mazumder		\|Raja Mazumder
	\|}		\|}

Hivelabwikiadmin at 17:24, 10 March 2026

2026-03-10T17:24:25Z

← Older revision		Revision as of 17:24, 10 March 2026
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	The Spring symposium will be held virtually.		The Spring symposium will be held virtually.

	'''Date:''' April ~~8th~~, 2026 (Wednesday)		'''Date:''' April 15th, 2026 (Wednesday)

	'''Time:''' 4 - 6 PM		'''Time:''' 4 - 6 PM

Hivelabwikiadmin at 19:36, 4 March 2026

2026-03-04T19:36:52Z

← Older revision		Revision as of 19:36, 4 March 2026
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	<nowiki>**</nowiki>Not directly involved in the semester curriculum; long-term volunteer.		<nowiki>**</nowiki>Not directly involved in the semester curriculum; long-term volunteer.

			== Spring 2026 Symposium ==
			The Spring symposium will be held virtually.

			'''Date:''' April 8th, 2026 (Wednesday)

			'''Time:''' 4 - 6 PM

			'''Zoom Link''' - TBA

			=== Agenda (All times are in Eastern Standard Time) ===
			{\| class="wikitable"
			!Time
			!Project
			!Presentation Title
			!Presenter(s)
			\|-
			\|4:00-4:05 PM
			\| colspan="2" \|Welcome & Introduction
			\|Raja Mazumder
			\|-
			\|4:05-4:30 PM
			\|GlyGen
			\|
			* 8 + 5 mins QA - presentation #1
			* 8 + 5 mins QA - presentation #2
			\|Diya Kamalabharathy; Isaac Kim
			\|-
			\|4:30-4:45 PM
			\|ARGOS
			\|
			* 8 + 5 mins QA - presentation #1
			\|Venya Gulati
			\|-
			\|4:45-5:10 PM
			\|BiomarkerKB
			\|
			* 8 + 5 mins QA - presentation #1
			* 8 + 5 mins QA - presentation #2
			\|Vishal Muthusekaran; Conner Cognata
			\|-
			\|5:10-5:30 PM
			\|PredictMod
			\|
			* 15 + 5 mins QA - group presentation
			\|Diya Kamalabharathy; Sampurna Chakravorty; Ashley Tien
			\|-
			\|5:30-5:55PM
			\| -
			\|
			* 8 + 5 mins QA - presentation #1
			* 8 + 5 mins QA - presentation #2
			\|Vishal Bakshi; Miao Wang
			\|-
			\|5:55-6:00 PM
			\| colspan="2" \|Remarks
			\|Raja Mazumder
			\|}

Lorikrammer: /* Volunteers (TBD) */

2026-02-13T19:11:13Z

Volunteers (TBD)

@@ Line 193: / Line 193: @@
 |Urnisha Bhuiyan; Rene Ranzinger
 |PredictMod; GlyGen biocuration; ARGOS
 |}
 <nowiki>*</nowiki>Returning volunteer.

Lorikrammer: /* Volunteers (TBD) */

2026-02-13T19:09:05Z

Volunteers (TBD)

← Older revision		Revision as of 19:09, 13 February 2026
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	\|-		\|-
	\|[https://www.linkedin.com/in/diya-kamalabharathy-62557935a/ Diya Kamalabharathy*]		\|[https://www.linkedin.com/in/diya-kamalabharathy-62557935a/ Diya Kamalabharathy*]
	\|PredictMod		\|PredictMod; GlyGen
	\|Lori Krammer; Urnisha Bhuiyan; Rene Ranzinger		\|Lori Krammer; Urnisha Bhuiyan; Rene Ranzinger
	\|PredictMod; Glyco web development		\|PredictMod; Glyco web development
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	\|-		\|-
	\|Isaac Kim		\|Isaac Kim
	\|		\|GlyGen
	\|		\|Urnisha Bhuiyan; Rene Ranzinger
	\|PredictMod; GlyGen biocuration; ARGOS		\|PredictMod; GlyGen biocuration; ARGOS
	\|}		\|}
	<nowiki>*</nowiki>Returning volunteer.		<nowiki>*</nowiki>Returning volunteer.

Hivelabwikiadmin: /* Volunteers (TBD) */

2026-02-10T19:16:59Z

Volunteers (TBD)

← Older revision		Revision as of 19:16, 10 February 2026
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	\|		\|
	\|PredictMod; GlyGen biocuration; ARGOS		\|PredictMod; GlyGen biocuration; ARGOS
	\|-
	~~\|Yashitha Pobbareddy~~
	~~\|ARGOS~~
	~~\|Christie Woodside~~
	~~\|ARGOS; GlyGen biocuration; BiomarkerKB~~
	\|}		\|}
	<nowiki>*</nowiki>Returning volunteer.		<nowiki>*</nowiki>Returning volunteer.

Urnisha.bhuiyan: /* 2. GlyGen Biocuration Project Ideas */

2026-01-28T13:36:16Z

2. GlyGen Biocuration Project Ideas

← Older revision		Revision as of 13:36, 28 January 2026
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	==== 2. GlyGen Biocuration Project Ideas ====		==== 2. GlyGen Biocuration Project Ideas ====
	POC: Rene Ranzinger, Urnisha Bhuiyan~~, Kate Warner~~		POC: Rene Ranzinger, Kate Warner, Urnisha Bhuiyan

	Over the last three decades, numerous glycomics database projects have been initiated to collect valuable information about glycans, proteins, and their interactions. Some of these databases have been discontinued due to the end of project funding~~. However~~, the data within ~~these databases~~ remains highly valuable to the community. Integrating these datasets into modern databases or knowledgebases, such as GlyGen, presents a challenge because much of the ~~valuable~~ metadata (e.g., species, tissue, disease, cell line) ~~annotations are~~ free-text ~~terms~~ that do not ~~align with established standard~~ dictionaries and ontologies used ~~in modern~~ resources. Automated matching of this information with dictionaries or ontologies is often not possible due to the use of synonyms, spelling errors, or abbreviations. For example, "human," "man," and "h. sapiens" all map to the scientific species name "Homo sapiens."		Over the last three decades, numerous glycomics database projects have been initiated to collect valuable information about glycans, proteins, and their interactions. Some of these databases have been discontinued due to the end of project funding; however, the data contained within them remains highly valuable to the research community. Integrating these legacy datasets into modern databases or knowledgebases, such as GlyGen, presents a significant challenge because much of the associated metadata (e.g., species, tissue, disease, cell line) is recorded as free-text that does not conform to the standardized dictionaries and ontologies used by current resources.

	~~The GlyGen~~ project ~~aims~~ to ~~make datasets~~ from ~~two older~~ databases (~~CarbBank~~, ~~CFG~~) ~~accessible by migrating the data~~ and metadata into ~~our database~~. ~~For this~~ project, ~~we are seeking curators~~ with a ~~medical or biology background who are interested in helping map metadata terms from these old databases~~ to ~~standard dictionaries~~ and ~~ontologies~~.		To address this challenge, this project will leverage large language models (LLMs) to automate the mapping of free-text metadata from legacy databases, specifically CarbBank and CFG, to standardized accessions in authoritative resources such as NCBI Taxonomy, Disease Ontology, and Cellosaurus. The LLM-based workflow will identify and normalize synonyms, abbreviations, and spelling variants (e.g., “human,” “man,” or “h. sapiens” mapped to Homo sapiens), enabling scalable and reproducible metadata harmonization that would otherwise require extensive manual curation. The LLM tasks will be performed using OpenAI resources integrated into the GlyGen curation pipeline. The project involves the development of Python scripts to read and write data, invoke the OpenAI API and compare results with manual curated data. Another aspect of the work is the development and finetunning of a prompt for ChatGPT to ensure reliable and accurate mapping is produced.

	~~The project involves:~~		While the mapping process will be largely automated, manual validation will be incorporated as a quality-control step to assess model performance, verify correctness, and identify edge cases requiring refinement. This hybrid approach significantly reduces curator burden while ensuring high-quality, ontology-aligned annotations.

	~~# Using internet resources (e.g., Google, Wikipedia)~~ to ~~identify terms used in the old database.~~		The goal of this effort is to migrate and modernize datasets from CarbBank and CFG, making them interoperable with GlyGen and other contemporary glycoinformatics resources through a scalable, AI-assisted curation strategy.
	~~# Mapping identified terms to corresponding dictionaries~~ and ~~ontologies using the webpages~~ and ~~search interfaces of these projects.~~
	~~# Finding papers based on titles and author lists that may contain spelling errors.~~
	~~# Interacting~~ and ~~discussing with~~ other ~~curators in case terms are mapped differently~~.

	~~If you have~~ any ~~other ideas or methods you would like to focus on~~, please ~~reach out to~~ rene@ccrc.uga.edu ~~to discuss them~~.		For any questions, please contact Rene Ranzinger (rene@ccrc.uga.edu) or Kate Warner (k.warner1@email.gwu.edu).

	'''3. GlyGen Publication Analysis Project Ideas'''		'''3. GlyGen Publication Analysis Project Ideas'''