Mazumder Research Group (HIVE Lab)

High-performance Integrated Virtual Environment

Transforming Biomarker Data for Breakthrough Discoveries

Biomarker Portal

Biomarker Partnership Project

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:

Benefits Chart

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.

Useful Links

Relevant Publications

  1. 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.
  2. 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.
  3. 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.
  4. 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.

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