Biomarker Partnership: Difference between revisions
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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. | ||
| Line 11: | Line 12: | ||
* Disseminating the results of this project to the research community. | * Disseminating the results of this project to the research community. | ||
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. | |||
== Benefits == | |||
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. | |||
== 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: [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: [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; [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]. | |||
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 == | |||
===== [https://www.glygen.org/ GlyGen - The George Washington University] ===== | |||
* Raja Mazumder (Principal Investigator) | |||
* Jeet Vora (Program Manager) | |||
* Daniall Masood (Ph.D. student | Data Curator) | |||
* Maria Kim (Backend Developer) | |||
* Sean Kim (Backend Developer) | |||
===== [https://www.glygen.org/ GlyGen - CCRC The University of Georgia, Athens] ===== | |||
* Rene Ranzinger (Subrecipient PI | Project Manager) | |||
* Michael Tiemeyer (Co-Investigator) | |||
* Sujeet Kulkarni (Full Stack Develoepr) | |||
===== [https://www.metabolomicsworkbench.org/ Metabolomics Workbench (MW) - University of California, San Diego] ===== | |||
* Shankar Subramaniam (Subrecipient PI) | |||
* 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) | |||
Latest revision as of 20:55, 22 January 2026
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 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 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.
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
- 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: 10.1200/CCI.19.00117. PMID: 32142370.
The CFDE Biomarker Partnership is funded by the National Institutes of Health Office of Strategic Coordination - The Common Fund under the grant # 1OT2OD032092.
Collaborators
GlyGen - The George Washington University
- Raja Mazumder (Principal Investigator)
- Jeet Vora (Program Manager)
- Daniall Masood (Ph.D. student | Data Curator)
- Maria Kim (Backend Developer)
- Sean Kim (Backend Developer)
GlyGen - CCRC The University of Georgia, Athens
- Rene Ranzinger (Subrecipient PI | Project Manager)
- Michael Tiemeyer (Co-Investigator)
- Sujeet Kulkarni (Full Stack Develoepr)
Metabolomics Workbench (MW) - University of California, San Diego
- Shankar Subramaniam (Subrecipient PI)
- Srinivasan Ramachandran (Project Manager)
- Mano Maurya (Software Developer)
- Shakti Gupta (Bioinformatics Researcher)
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)
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)