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 biomarker types and biomarker roles?

Biomarker types:  Molecular, histologic, radiographic, or physiologic characteristics are types of biomarkers. https://www.fda.gov/drugs/biomarker-qualification-program/about-biomarkers-and-qualification#BEST_Glossary

Biomarker roles: susceptibility/risk, diagnostic, monitoring, prognostic, predictive, pharmacodynamic/response, and safety https://www.fda.gov/drugs/biomarker-qualification-program/about-biomarkers-and-qualification#BEST_Glossary but we prefer "roles" as opposed to "categories"

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

• These are different biomarker categories.
• What is a biomarker entity: See entity examples here https://github.com/clinical-biomarkers/biomarker-controlled-vocabulary
• What is a biomarker component: Single instance of an entity
• Single-component biomarker: A single biomarker consists of exactly one component (a single measured analyte).
• Multi-component biomarker: A multi-component biomarker (MCB) is a defined combination or defined set of two or more individual biomarkers whose values, when considered together in a specified way (e.g., a lipid panel of total cholesterol, LDL, HDL, and triglycerides). It has two subtypes
  • Integrative biomarker entity - An integrative biomarker entity is composed of multiple component measurements that are generated separately, often using different measurement methods or data sources, rather than as part of a single omics experiment. These components may include, for example, imaging measurements, EEG features, clinical measurements, digital health measurements, genomic results, or laboratory values. A defined mathematical or computational algorithm combines these separate measurements into a single quantitative value, score, or index that is interpreted to have a specific biological, clinical, or diagnostic meaning.
  • Pattern biomarker entity - A pattern biomarker entity is composed of a defined set of component measurements that are generated together or analyzed together to identify a pattern or signature result. This may include omics-derived patterns, such as proteomic, metabolomic, glycomic, transcriptomic, or multi-analyte signatures, as well as other multiplex measurement panels. The key feature is that the component measurements are interpreted collectively, rather than individually, to produce a biomarker result with a specific meaning.

For more details, see Single biomarker, Multicomponent biomarker, and Multi-entity biomarker. Also, please note that these definitions are informed by the FDA-NIH Biomarker Working Group terminology (https://www.ncbi.nlm.nih.gov/books/NBK326791/; https://www.ncbi.nlm.nih.gov/books/NBK610679/), but we have adapted them in some places to better describe the specific biomarker concepts represented in BiomarkerKB.

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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