Frequently Asked Questions

The frequently asked questions are a collection of user questions related to the BiomarkerKB frontend, backend, and data. The answers to these questions contain definition and explanations of terms, such as Single Biomarker or Multicomponent Biomarker. The list of questions is subdivided into questions related to biomarker and general questions. You can also use the BiomarkerKB contact page to reach out to us with any additional questions or queries.

General FAQs

Where can I find more information on the project?

• The project webpage can be found here.

Is the project repository publicly available?

• You can view all the project repositories here.

What are the biomarker scores and how are scores assigned for the biomarkers?

• The biomarker-score-calculator and default scoring algorithm can be found here. The biomarker scores can be seen on the full JSON data model responses from the API.

Why are some biomarkers assigned a score of 0?

• Biomarkers with a default score of 0 are manually assigned a 0 score and are pending a manual review. The review of the biomarker can include a spot check, full manual quality checking, NLP based methods, and discussions with the submitter/resource. Until the review is complete the biomarker will keep a score of 0 and after the review is complete the biomarker will be scored using the biomarker score calculator tool.

How to download all the current dataset files using CLI?

• The BiomarkerKB dataset can be downloaded using the command wget -r -l1 -np -nd -R "index.html*" https://data.biomarkerkb.org/ln2data/releases/data/current/reviewed/

Biomarker FAQs

What is the difference between single-component, multi-component, and composite biomarkers?

• A single biomarker consists of exactly one component and one entity (a single measured analyte).
• A multicomponent biomarker combines two or more independently measured components assessed together, each having a distinct component_index (e.g., a lipid panel of total cholesterol, LDL, HDL, and triglycerides).
• A multi-entity biomarker occurs when at least one of those components is itself made up of multiple molecular entities sharing the same component_index but distinct entity_index values (e.g., a glycan bound to a protein)
• A biomarker can be multicomponent, multi-entity, or both at once.

For more details, see Single biomarker, Multicomponent biomarker, and Multi-entity biomarker.

References

Daniall Masood, Mariia Kim, Jeet Vora, Robel Kahsay, Patrick McNeely, Sean Kim, Cyrus Chun Hong Au Yeung, Sujeet Kulkarni, Darren A. Natale, Srinivasan Ramachandran, Shakti Gupta, Mano Maurya, Cristian G. Bologa, Thomas S. DeNapoli, Vincent T. Metzger, Praveen Kumar, Nasheath Ahmed, John Erol Evangelista, Nia Lingam, Sean C. Kelly, Jorge L. Sepulveda, Avi Ma’ayan, Jonathan Silverstein, Deanne M. Taylor, Daniel J. Crichton, Ashish Mahabal, Jeremy J. Yang, Christophe G. Lambert, Shankar Subramaniam, Michael Tiemeyer, Rene Ranzinger, Raja Mazumder (2026). "BiomarkerKB: An Integrated Knowledgebase Supporting Biomarker-Centric Exploration of Biomedical Data". Patterns, DOI 10.1016/j.patter.2026.101636.

External links

• BiomarkerKB: https://biomarkerkb.org/

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