Biomarker Partnership - Revision history

JeetVora at 21:04, 4 March 2026

2026-03-04T21:04:46Z

← Older revision		Revision as of 21:04, 4 March 2026
Line 17:		Line 17:
	* Data mining: The project will use data mining techniques to extract and organize biomarker data from public sources.		* Data mining: The project will use data mining techniques to extract and organize biomarker data from public sources.
	* Software development: The project will develop software tools to support the management and analysis of biomarker data.		* Software development: The project will develop software tools to support the management and analysis of biomarker data.
	* Training and outreach: The project will provide training and outreach materials to help researchers use the data and tools developed by the project.		* Training and outreach: The project will provide training and outreach materials to help researchers use the data and tools developed by the project. Xy

	== Benefits ==		== Benefits ==

Rehmam: /* Principal Investigators */

2026-01-22T20:55:09Z

Principal Investigators

← Older revision		Revision as of 20:55, 22 January 2026
Line 36:		Line 36:
	== Collaborators ==		== Collaborators ==

	===== ~~Principal Investigators =====~~		===== [https://www.glygen.org/ GlyGen - The George Washington University] =====
	* Raja Mazumder ([https://www.glygen.org/ GlyGen])		* Raja Mazumder (Principal Investigator)
	* ~~Michael Tiemeyer~~ (~~[https://www.glygen.org/ GlyGen]~~)		* Jeet Vora (Program Manager)
	* ~~Christophe Lambert~~ (~~[https://commonfund~~.~~nih~~.~~gov/idg IDG]~~)		* Daniall Masood (Ph.D. student \| Data Curator)
	* ~~Jeremy Yang~~ (~~[https://commonfund.nih.gov/idg IDG]~~)		* Maria Kim (Backend Developer)
	* ~~Shankar Subramaniam~~ (~~[https://www.metabolomicsworkbench.org/ MW]~~)		* Sean Kim (Backend Developer)

	===== ~~Project Manager =====~~		===== [https://www.glygen.org/ GlyGen - CCRC The University of Georgia, Athens] =====
	* Jeet Vora ([https://www.glygen.org/ GlyGen])		* Rene Ranzinger (Subrecipient PI \| Project Manager)
			* Michael Tiemeyer (Co-Investigator)
			* Sujeet Kulkarni (Full Stack Develoepr)

	===== ~~Backend Developers~~ =====		===== [https://www.metabolomicsworkbench.org/ Metabolomics Workbench (MW) - University of California, San Diego] =====
	* ~~Maria Kim~~		* Shankar Subramaniam (Subrecipient PI)
	* Sean ~~Kim~~		* Srinivasan Ramachandran (Project Manager)
			* Mano Maurya (Software Developer)
			* Shakti Gupta (Bioinformatics Researcher)

			===== [https://edrn.cancer.gov/ Early Detection Research Network (EDRN) - NASA JPL - California Institute of Technology] =====

			* Ashish Mahabal (Subrecipient PI)
			* Daniel Crichton (Project Manager)
			* Sean Kelly (Software Developer)
			* Heather Kincaid (Bioinformatics Researcher)

			===== [https://commonfund.nih.gov/idg Illuminating Druggable Genome (IDG) - University of New Mexico] =====

			* Jeremy Yang (Subrecipient PI)
			* Christophe Lambert (Subrecipient PI)
			* Vincent Metzger (Co-Investigator)
			* Cristian Bologa (Co-Investigator)
			* Noah Reboul (Student Research Assistant)

Rehmam at 20:42, 22 January 2026

2026-01-22T20:42:36Z

← Older revision		Revision as of 20:42, 22 January 2026
Line 12:		Line 12:
	* Disseminating the results of this project to the research community.		* Disseminating the results of this project to the research community.

	~~The benefits of this project include:~~

	This project is expected to have a significant impact on the field of biomarker research. It will make biomarker data more accessible and understandable, and it will facilitate the use of biomarkers in drug development and clinical trials. This will ultimately lead to improved personalized medicine for patients.

	The project will use a variety of methods to achieve its goals, including:		The project will use a variety of methods to achieve its goals, including:

Rehmam at 20:42, 22 January 2026

2026-01-22T20:42:06Z

← Older revision		Revision as of 20:42, 22 January 2026
Line 21:		Line 21:
	* Software development: The project will develop software tools to support the management and analysis of biomarker data.		* Software development: The project will develop software tools to support the management and analysis of biomarker data.
	* Training and outreach: The project will provide training and outreach materials to help researchers use the data and tools developed by the project.		* Training and outreach: The project will provide training and outreach materials to help researchers use the data and tools developed by the project.

			== Benefits ==
			The benefits of this project include:


			This project is expected to have a significant impact on the field of biomarker research. It will make biomarker data more accessible and understandable, and it will facilitate the use of biomarkers in drug development and clinical trials. This will ultimately lead to improved personalized medicine for patients.

	== Relevant Publications ==		== Relevant Publications ==

Rehmam at 20:39, 22 January 2026

2026-01-22T20:39:23Z

← Older revision		Revision as of 20:39, 22 January 2026
Line 1:		Line 1:
	Biomarker Partnership is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that will organize and integrate biomarker data from different public sources. The data will be connected to contextual information to show a novel systems-level view of biomarkers.		Biomarker Partnership is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that will organize and integrate biomarker data from different public sources. The data will be connected to contextual information to show a novel systems-level view of biomarkers.

			== About the Partnership Project ==
	The motivation for this project is to improve the harmonization and organization of biomarker data. This will be done by mapping biomarkers from public sources to, and across, CF data elements. This mapping will bridge knowledge across multiple Data Coordinating Centers (DCCs) and biomedical disciplines.		The motivation for this project is to improve the harmonization and organization of biomarker data. This will be done by mapping biomarkers from public sources to, and across, CF data elements. This mapping will bridge knowledge across multiple Data Coordinating Centers (DCCs) and biomedical disciplines.

Rehmam at 20:38, 22 January 2026

2026-01-22T20:38:34Z

← Older revision		Revision as of 20:38, 22 January 2026
Line 23:		Line 23:
	== Relevant Publications ==		== Relevant Publications ==

	# Lyman DF, Bell A, Black A, Dingerdissen H, Cauley E, Gogate N, Liu D, Joseph A, Kahsay R, Crichton DJ, Mehta A, Mazumder R. Modeling and integration of N-glycan biomarkers in a comprehensive biomarker data model. Glycobiology. 2022 Sep 19;32(10):855-870. doi: /glycob/cwac046. PMID: 35925813.		# Lyman DF, Bell A, Black A, Dingerdissen H, Cauley E, Gogate N, Liu D, Joseph A, Kahsay R, Crichton DJ, Mehta A, Mazumder R. Modeling and integration of N-glycan biomarkers in a comprehensive biomarker data model. Glycobiology. 2022 Sep 19;32(10):855-870. doi: [https://academic.oup.com/glycob/article/32/10/855/6655823?login=true /glycob/cwac046]. PMID: [https://pubmed.ncbi.nlm.nih.gov/35925813/ 35925813].
	# Gogate N, Lyman D, Bell A, Cauley E, Crandall KA, Joseph A, Kahsay R, Natale DA, Schriml LM, Sen S, Mazumder R. COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model. Brief Bioinform. 2021 Nov 5;22(6):bbab191. doi: /bib/bbab191. PMID: 34015823.		# Gogate N, Lyman D, Bell A, Cauley E, Crandall KA, Joseph A, Kahsay R, Natale DA, Schriml LM, Sen S, Mazumder R. COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model. Brief Bioinform. 2021 Nov 5;22(6):bbab191. doi: [https://academic.oup.com/bib/article/22/6/bbab191/6278606?login=true /bib/bbab191]. PMID: [https://pubmed.ncbi.nlm.nih.gov/34015823/ 34015823].
	# Lyman D, Natale D, Schriml L, Anton K, Crichton DC, Mazumder R. Analysis of Biomarker Data Towards Development of a Molecular Biomarker Ontology. Proceedings of the International Conference on Biomedical Ontologies 2021 (ICBO 2021) co-located with the Workshop on Ontologies for the Behavioural and Social Sciences (OntoBess 2021) as part of the Bolzano Summer of Knowledge (BOSK 2021) Bozen-Bolzano, Italy. 2021 Sep 16-18; ceur-ws.org.		# Lyman D, Natale D, Schriml L, Anton K, Crichton DC, Mazumder R. Analysis of Biomarker Data Towards Development of a Molecular Biomarker Ontology. Proceedings of the International Conference on Biomedical Ontologies 2021 (ICBO 2021) co-located with the Workshop on Ontologies for the Behavioural and Social Sciences (OntoBess 2021) as part of the Bolzano Summer of Knowledge (BOSK 2021) Bozen-Bolzano, Italy. 2021 Sep 16-18; [https://ceur-ws.org/ ceur-ws.org].
	# Dingerdissen HM, Bastian F, Vijay-Shanker K, Robinson-Rechavi M, Bell A, Gogate N, Gupta S, Holmes E, Kahsay R, Keeney J, Kincaid H, King CH, Liu D, Crichton DJ, Mazumder R. OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data. JCO Clin Cancer Inform. 2020 Mar;4:210-220. doi: [https://ascopubs.org/doi/10.1200/CCI.19.00117 10.1200/CCI.19.00117]. PMID: [https://pubmed.ncbi.nlm.nih.gov/32142370/ 32142370].		# Dingerdissen HM, Bastian F, Vijay-Shanker K, Robinson-Rechavi M, Bell A, Gogate N, Gupta S, Holmes E, Kahsay R, Keeney J, Kincaid H, King CH, Liu D, Crichton DJ, Mazumder R. OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data. JCO Clin Cancer Inform. 2020 Mar;4:210-220. doi: [https://ascopubs.org/doi/10.1200/CCI.19.00117 10.1200/CCI.19.00117]. PMID: [https://pubmed.ncbi.nlm.nih.gov/32142370/ 32142370].

Line 31:		Line 31:

	== Collaborators ==		== Collaborators ==
	~~Principal Investigators~~

			===== Principal Investigators =====
	* Raja Mazumder ([https://www.glygen.org/ GlyGen])		* Raja Mazumder ([https://www.glygen.org/ GlyGen])
	* Michael Tiemeyer ([https://www.glygen.org/ GlyGen])		* Michael Tiemeyer ([https://www.glygen.org/ GlyGen])
Line 39:		Line 39:
	* Shankar Subramaniam ([https://www.metabolomicsworkbench.org/ MW])		* Shankar Subramaniam ([https://www.metabolomicsworkbench.org/ MW])

	Project Manager		===== Project Manager =====

	* Jeet Vora ([https://www.glygen.org/ GlyGen])		* Jeet Vora ([https://www.glygen.org/ GlyGen])

	Backend Developers		===== Backend Developers =====

	* Maria Kim		* Maria Kim
	* Sean Kim		* Sean Kim

Rehmam at 20:35, 22 January 2026

2026-01-22T20:35:33Z

← Older revision		Revision as of 20:35, 22 January 2026
Line 20:		Line 20:
	* Software development: The project will develop software tools to support the management and analysis of biomarker data.		* Software development: The project will develop software tools to support the management and analysis of biomarker data.
	* Training and outreach: The project will provide training and outreach materials to help researchers use the data and tools developed by the project.		* Training and outreach: The project will provide training and outreach materials to help researchers use the data and tools developed by the project.

			== Relevant Publications ==

			# Lyman DF, Bell A, Black A, Dingerdissen H, Cauley E, Gogate N, Liu D, Joseph A, Kahsay R, Crichton DJ, Mehta A, Mazumder R. Modeling and integration of N-glycan biomarkers in a comprehensive biomarker data model. Glycobiology. 2022 Sep 19;32(10):855-870. doi: /glycob/cwac046. PMID: 35925813.
			# Gogate N, Lyman D, Bell A, Cauley E, Crandall KA, Joseph A, Kahsay R, Natale DA, Schriml LM, Sen S, Mazumder R. COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model. Brief Bioinform. 2021 Nov 5;22(6):bbab191. doi: /bib/bbab191. PMID: 34015823.
			# Lyman D, Natale D, Schriml L, Anton K, Crichton DC, Mazumder R. Analysis of Biomarker Data Towards Development of a Molecular Biomarker Ontology. Proceedings of the International Conference on Biomedical Ontologies 2021 (ICBO 2021) co-located with the Workshop on Ontologies for the Behavioural and Social Sciences (OntoBess 2021) as part of the Bolzano Summer of Knowledge (BOSK 2021) Bozen-Bolzano, Italy. 2021 Sep 16-18; ceur-ws.org.
			# Dingerdissen HM, Bastian F, Vijay-Shanker K, Robinson-Rechavi M, Bell A, Gogate N, Gupta S, Holmes E, Kahsay R, Keeney J, Kincaid H, King CH, Liu D, Crichton DJ, Mazumder R. OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data. JCO Clin Cancer Inform. 2020 Mar;4:210-220. doi: [https://ascopubs.org/doi/10.1200/CCI.19.00117 10.1200/CCI.19.00117]. PMID: [https://pubmed.ncbi.nlm.nih.gov/32142370/ 32142370].

			The [https://commonfund.nih.gov/dataecosystem CFDE] Biomarker Partnership is funded by the [https://commonfund.nih.gov/ National Institutes of Health Office of Strategic Coordination - The Common Fund] under the grant # 1OT2OD032092.

			== Collaborators ==
			Principal Investigators

			* Raja Mazumder ([https://www.glygen.org/ GlyGen])
			* Michael Tiemeyer ([https://www.glygen.org/ GlyGen])
			* Christophe Lambert ([https://commonfund.nih.gov/idg IDG])
			* Jeremy Yang ([https://commonfund.nih.gov/idg IDG])
			* Shankar Subramaniam ([https://www.metabolomicsworkbench.org/ MW])

			Project Manager

			* Jeet Vora ([https://www.glygen.org/ GlyGen])

			Backend Developers

			* Maria Kim
			* Sean Kim

Rehmam at 16:32, 12 November 2025

2025-11-12T16:32:54Z

← Older revision		Revision as of 16:32, 12 November 2025
Line 12:		Line 12:

	The benefits of this project include:		The benefits of this project include:

			This project is expected to have a significant impact on the field of biomarker research. It will make biomarker data more accessible and understandable, and it will facilitate the use of biomarkers in drug development and clinical trials. This will ultimately lead to improved personalized medicine for patients.

			The project will use a variety of methods to achieve its goals, including:

			* Data mining: The project will use data mining techniques to extract and organize biomarker data from public sources.
			* Software development: The project will develop software tools to support the management and analysis of biomarker data.
			* Training and outreach: The project will provide training and outreach materials to help researchers use the data and tools developed by the project.

Rehmam at 16:09, 12 November 2025

2025-11-12T16:09:51Z

← Older revision		Revision as of 16:09, 12 November 2025
Line 1:		Line 1:
	~~jvdh~~		Biomarker Partnership is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that will organize and integrate biomarker data from different public sources. The data will be connected to contextual information to show a novel systems-level view of biomarkers.

			The motivation for this project is to improve the harmonization and organization of biomarker data. This will be done by mapping biomarkers from public sources to, and across, CF data elements. This mapping will bridge knowledge across multiple Data Coordinating Centers (DCCs) and biomedical disciplines.

			The scope of this project includes the following:

			* Mapping biomarkers from public sources to relevant data elements.
			* Mapping contextual data from participating DCCs.
			* Developing a framework for organizing biomarker data.
			* Creating tools for querying and exploring biomarker data.
			* Disseminating the results of this project to the research community.

			The benefits of this project include:

Rehmam: Created page with "jvdh"

2025-11-11T20:04:42Z

Created page with "jvdh"

New page

jvdh