BiomarkerKB Wiki - User contributions [en]

Frequently Asked Questions

2026-09-17T18:36:53Z

RajaMazumder: /* What is the difference biomarker types and biomarker roles? */

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 FAQs|biomarker]] and [[#General FAQs|general questions]]. You can also use the BiomarkerKB [https://biomarkerkb.org/contact-us/ 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 [https://biomarkerkb.org/about/ here].

=== Is the project repository publicly available? ===
* You can view all the project repositories [https://github.com/clinical-biomarkers 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 [https://github.com/clinical-biomarkers/biomarker-score-calculator 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 <code>wget -r -l1 -np -nd -R "index.html*" <nowiki>https://data.biomarkerkb.org/ln2data/releases/data/current/reviewed/</nowiki></code>

== Biomarker FAQs ==

=== What is the difference biomarker types and biomarker roles? ===
Biomarker types: Molecular, histologic, radiographic, or physiologic characteristics are types of biomarkers. <nowiki>https://www.fda.gov/drugs/biomarker-qualification-program/about-biomarkers-and-qualification#BEST_Glossary</nowiki>

Biomarker roles: susceptibility/risk, diagnostic, monitoring, prognostic, predictive, pharmacodynamic/response, and safety <nowiki>https://www.fda.gov/drugs/biomarker-qualification-program/about-biomarkers-and-qualification#BEST_Glossary</nowiki> 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 <nowiki>https://github.com/clinical-biomarkers/biomarker-controlled-vocabulary</nowiki>
* 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/
<div style="float: right;"> [[#top|[top]]]</div>

Frequently Asked Questions

2026-09-17T17:27:44Z

RajaMazumder: /* Biomarker FAQs */

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 FAQs|biomarker]] and [[#General FAQs|general questions]]. You can also use the BiomarkerKB [https://biomarkerkb.org/contact-us/ 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 [https://biomarkerkb.org/about/ here].

=== Is the project repository publicly available? ===
* You can view all the project repositories [https://github.com/clinical-biomarkers 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 [https://github.com/clinical-biomarkers/biomarker-score-calculator 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 <code>wget -r -l1 -np -nd -R "index.html*" <nowiki>https://data.biomarkerkb.org/ln2data/releases/data/current/reviewed/</nowiki></code>

== Biomarker FAQs ==

=== What is the difference biomarker types and biomarker roles? ===
Biomarker types: Molecular, histologic, radiographic, or physiologic characteristics are types of biomarkers. <nowiki>https://www.fda.gov/drugs/biomarker-qualification-program/about-biomarkers-and-qualification#BEST_Glossary</nowiki>

Biomarker roles: susceptibility/risk, diagnostic, monitoring, prognostic, predictive, pharmacodynamic/response, and safety <nowiki>https://www.fda.gov/drugs/biomarker-qualification-program/about-biomarkers-and-qualification#BEST_Glossary</nowiki> 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.
* Entity: See entity examples here <nowiki>https://github.com/clinical-biomarkers/biomarker-controlled-vocabulary</nowiki>
* 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/
<div style="float: right;"> [[#top|[top]]]</div>

Frequently Asked Questions

2026-09-17T17:23:27Z

RajaMazumder: /* What is the difference between single-component, multi-component, and composite biomarkers? */

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 FAQs|biomarker]] and [[#General FAQs|general questions]]. You can also use the BiomarkerKB [https://biomarkerkb.org/contact-us/ 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 [https://biomarkerkb.org/about/ here].

=== Is the project repository publicly available? ===
* You can view all the project repositories [https://github.com/clinical-biomarkers 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 [https://github.com/clinical-biomarkers/biomarker-score-calculator 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 <code>wget -r -l1 -np -nd -R "index.html*" <nowiki>https://data.biomarkerkb.org/ln2data/releases/data/current/reviewed/</nowiki></code>

== Biomarker FAQs ==
=== What is the difference between single-component, multi-component, and composite biomarkers? ===
* Entity: See entity examples here <nowiki>https://github.com/clinical-biomarkers/biomarker-controlled-vocabulary</nowiki>
* 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/
<div style="float: right;"> [[#top|[top]]]</div>

Frequently Asked Questions

2026-09-17T17:21:03Z

RajaMazumder: /* What is the difference between single-component, multi-component, and composite biomarkers? */

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 FAQs|biomarker]] and [[#General FAQs|general questions]]. You can also use the BiomarkerKB [https://biomarkerkb.org/contact-us/ 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 [https://biomarkerkb.org/about/ here].

=== Is the project repository publicly available? ===
* You can view all the project repositories [https://github.com/clinical-biomarkers 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 [https://github.com/clinical-biomarkers/biomarker-score-calculator 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 <code>wget -r -l1 -np -nd -R "index.html*" <nowiki>https://data.biomarkerkb.org/ln2data/releases/data/current/reviewed/</nowiki></code>

== Biomarker FAQs ==
=== What is the difference between single-component, multi-component, and composite biomarkers? ===
* Entity: See entity examples here <nowiki>https://github.com/clinical-biomarkers/biomarker-controlled-vocabulary</nowiki>
* 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]].

== 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/
<div style="float: right;"> [[#top|[top]]]</div>

Frequently Asked Questions

2026-09-17T17:20:36Z

RajaMazumder: /* What is the difference between single-component, multi-component, and composite biomarkers? */

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 FAQs|biomarker]] and [[#General FAQs|general questions]]. You can also use the BiomarkerKB [https://biomarkerkb.org/contact-us/ 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 [https://biomarkerkb.org/about/ here].

=== Is the project repository publicly available? ===
* You can view all the project repositories [https://github.com/clinical-biomarkers 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 [https://github.com/clinical-biomarkers/biomarker-score-calculator 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 <code>wget -r -l1 -np -nd -R "index.html*" <nowiki>https://data.biomarkerkb.org/ln2data/releases/data/current/reviewed/</nowiki></code>

== Biomarker FAQs ==
=== What is the difference between single-component, multi-component, and composite biomarkers? ===
* Entity: See entity examples here <nowiki>https://github.com/clinical-biomarkers/biomarker-controlled-vocabulary</nowiki>
* 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 multiplex 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]].

== 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/
<div style="float: right;"> [[#top|[top]]]</div>

Frequently Asked Questions

2026-09-17T17:19:34Z

RajaMazumder: /* What is the difference between single-component, multi-component, and composite biomarkers? */

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 FAQs|biomarker]] and [[#General FAQs|general questions]]. You can also use the BiomarkerKB [https://biomarkerkb.org/contact-us/ 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 [https://biomarkerkb.org/about/ here].

=== Is the project repository publicly available? ===
* You can view all the project repositories [https://github.com/clinical-biomarkers 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 [https://github.com/clinical-biomarkers/biomarker-score-calculator 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 <code>wget -r -l1 -np -nd -R "index.html*" <nowiki>https://data.biomarkerkb.org/ln2data/releases/data/current/reviewed/</nowiki></code>

== Biomarker FAQs ==
=== What is the difference between single-component, multi-component, and composite biomarkers? ===
* Entity: See entity examples here <nowiki>https://github.com/clinical-biomarkers/biomarker-controlled-vocabulary</nowiki>
* 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.
** Multiplex biomarker entity - A multiplex 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]].

== 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/
<div style="float: right;"> [[#top|[top]]]</div>

Frequently Asked Questions

2026-09-17T17:11:33Z

RajaMazumder: /* What is the difference between single-component, multi-component, and composite biomarkers? */

Frequently Asked Questions

2026-09-17T17:09:43Z

RajaMazumder: /* What is the difference between single-component, multi-component, and composite biomarkers? */

Frequently Asked Questions

2026-09-17T17:09:12Z

RajaMazumder: /* What is the difference between single-component, multi-component, and composite biomarkers? */

Frequently Asked Questions

2026-09-17T17:08:27Z

RajaMazumder: /* What is the difference between single-component, multi-component, and composite biomarkers? */

Frequently Asked Questions

2026-09-17T17:05:37Z

RajaMazumder: /* What is the difference between single, multicomponent, and multi-entity biomarkers? */

Data Release Notes

2025-12-15T17:41:14Z

RajaMazumder: /* Versioning Format */

== Versioning Format ==
The versioning format follows a three-digit structure: X.Y.Z.
* The first digit (X) changes when a major update is introduced, such as changes in the data model.
* The second digit (Y) increments when new data is added.
* The third digit (Z) is updated for bug fixes or minor changes.

== Version 2.1.0 ==
Date: December 11, 2025
=== Data Updates ===
* Added the LLM-extracted glycan biomarker dataset provided by Cyrus Chun Hong Au Yeung.
=== Backend and Infrastructure Updates ===
* The incorrect download links on the [https://data.biomarkerkb.org Data Portal] have been fixed.
* LOINC codes are no longer tied to specimen IDs.

== Version 2.0.2 ==
Date: December 4, 2025
=== Bug Fixes ===
* LOINC codes are no longer tied to specimen (UBERON) IDs.
* For biomarkers that could not be mapped to [[Controlled Vocabulary and Keywords|Controlled Vocabulary]] the original biomarker name is displayed, followed by "in review".

== Version 2.0.1 ==
=== Data Updates ===
* Added cross-references to the Common Fund Data Ecosystem ([https://commonfund.nih.gov/dataecosystem CFDE]) Data Coordinating Centers and other resources:
** [https://www.gtexportal.org/home/ GTEx]
** [https://pharos.nih.gov/ Pharos]
** [https://reactome.org/ Reactome]
** [https://undiagnosed.hms.harvard.edu/ Undiagnosed Diseases Network]
** [https://idg.reactome.org/ Illuminating the Druggable Genome (IDG) Reactome Portal]
** [https://www.metabolomicsworkbench.org/ Metabolomics Workbench]
** [https://maayanlab.cloud/sigcom-lincs SigCom LINCS]

== Version 2.0.0 ==
=== Data Updates ===
* The biomarker field is now standardized using controlled vocabulary terms.
* Added metabolite as an <code>assessed_entity_type</code> to <code>mw_loinc_biomarkers.tsv</code>.
* Added [https://rnacentral.org/ RNAcentral] cross-reference support.
* Added Electronic Health Records Normal ranges data from Oracle Health for Troponin I as an example.

== Version 1.0.6 ==
=== Data Updates ===
* Added a new dataset: MW LOINC biomarkers (<code>mw_loinc_biomarkers.tsv</code>).
* Added [https://ncithesaurus.nci.nih.gov/ National Cancer Institute Thesaurus] and [https://www.rcsb.org/ Protein Data Bank] cross-references.
=== Backend and Infrastructure Updates ===
* Added the <code>display_name</code> field to the <code>format-converter</code> so data source names appear with correct casing.

== Version 1.0.5 ==
=== Data Updates ===
* Updated the Troponin biomarker value <code>assessed_biomarker_entity</code> for consistency.
* Added normal ranges from Electronic Health Records provided by the University of New Mexico for Troponin biomarkers.
* Added Cell Ontology and Protein Ontology cross-references.
=== Backend and Infrastructure Updates ===
* Updated all script paths to use <code>data_source.conf</code> and validated data source names.

== Version 1.0.4 ==
This release introduces new datasets, cross-references, and bug fixes.
=== Data Updates ===
* Added Cancer Genome Interpreter data on cancer biomarkers from MetaKB.
* Added Metabolomics Workbench LOINC data on metabolite biomarkers.
* Added Cell Ontology and Protein Ontology cross-references.
=== Bug Fixes ===
* Fixed issue where cookie preferences weren't being saved when selecting "Allow".

== Version 1.0.3 ==
This release introduces new cross-references and updates to ensure compatibility with external resources.
=== Data Updates ===
* NCBI cross-references added across gene biomarker entries.
* ChEBI cross-references integrated for small molecules and metabolites.
=== Backend and Infrastructure Updates ===
* ChEBI API migration: Updated all programmatic links from the legacy SOAP services to the new REST API endpoints, following ChEBI’s platform migration.
** Old services retired 1 September 2025.
** New stable API: [https://www.ebi.ac.uk/chebi/backend/api/docs ChEBI REST API docs]
** New data products and beta interface available at [https://www.ebi.ac.uk/chebi/beta/ ChEBI 2.0].
== Version 1.0.2 ==
=== Data Updates ===
* Published updated [https://www.metabolomicsworkbench.org/ Metabolomics Workbench] data.
* Published sample data from the [https://edrn.nci.nih.gov/ Early Detection Research Network].
=== Backend and Infrastructure Updates ===
* <code>evidence_source</code> database names now retain their original casing for accuracy and consistency.
* EDRN identifiers were added to the [https://github.com/clinical-biomarkers/format-converter/blob/main/mapping_data/namespace_map.json namespace map].
* [https://www.genenames.org/ HUGO Gene Nomenclature Committee] (HGNC) was added to the cross-reference JSON file.
* Fixed an issue where <code>evidence_source</code> values without tags were previously dropped; these are now preserved.
* Added a user-guided spelling correction function to improve data entry quality.
* The TSV-to-JSON converter now automatically checks for header spelling errors.
* Introduced <code>_suggest_header_corrections</code> to flag and propose fixes for misspelled headers.
* Enhanced <code>_stream_tsv</code> with a call to <code>_check_header_spelling</code> to prevent invalid headers from being processed.

== Version 1.0.1 ==
=== Data Updates ===
* Added <code> xrefs.tsv</code> to the list of datasets.
=== Backend & Infrastructure Updates ===
* Fixed ID formatting issues in NCBI and UniProt references within <code> oncomx.tsv</code>, removing erroneous spaces (e.g., <code> NCBI: 3288</code> → <code> NCBI:3288</code>) and extraneous text (e.g., <code>"(composition)"</code>). Affected biomarkers included AN6295-1, AN6756-1, AN6728-1, and others.
* Merged assessed entity type synonyms.

== Version 1.0.0 ==
* BiomarkerKB data portal available with OncoMX, OpenTargets, MarkerDB, ClinVar, PubMed Central Biomarker Gene Set Curation, MW, UniProtKB, GWAS, CIViC biomarker data.

BiomarkerKB Resource Integration

2025-10-23T19:25:46Z

RajaMazumder:

BiomarkerKB collects data from many different resources. The data that is collected is not always directly integrated into the data model and data from a resource is sometimes just added as valuable contextual annotations or cross references.

Other resources to be explored: [https://search.cancervariants.org/ MetaKB], [https://cadsr.cancer.gov/onedata/Home.jsp CADSR Cancer], https://themarker.idrblab.cn/, biomarker.org, ResMarkerDB, SalivaDB, https://glycanage.com/publications, https://www.cancergenomeinterpreter.org/biomarkers, [https://github.com/issues/assigned?issue=clinical-biomarkers%7Cbiomarker-issue-repo%7C248 Glycan Biomarkers] ([https://github.com/glygener/CarboCurator code])

Please contact us at mazumder_lab@gwu.edu and daniallmasood@gwu.edu if you have any other resources that may contain biomarker data

=CIViC=
Status: Direct Integration into Data Model

* Clinical Interpretation of Variants in Cancer (CIViC).
* Provides cancer biomarkers in form of DNA mutations (dbSNPs).
* Platform provides clinicians treatment options for patients based on unique tumor profile.
* License: Creative Commons Attribution-NonCommercial 4.0 International License.

=ClinVar=
Status: Direct Integration into Data Model

* Public archive of reports of human variations classified for diseases and drug responses.
* Provides biomarkers for all disease, but we have only curated cancer biomarkers for now.
** dbSNPs
** File is really big but will go back and use existing script to map all biomarkers from here into the data model.
* License: Creative Commons Attribution-NonCommercial 4.0 International License.

=EDRN=
Status: Sample Integration into Data Model

* Cancer biomarkers.

=GWAS=
Status: Direct Integration into Data Model

* Published genome-wide association studies (GWAS).
* Provides biomarkers in form of SNPs.
* GWAS Catalog contains SNPs for a vast amount of diseases.
** Preliminary curation only focused on cancer.
** Will use existing script to map all biomarkers into data model.
* License: Creative Commons Attribution-NonCommercial 4.0 International License.

=HPO=

Status: Cross-Reference

* HPO provides disease and entity associations.
* Does not provide a change within the entity so we cannot collect biomarker data from here.
* However we can use it as a cross-reference within our cross-referencing section.
* Provides cross-reference to OMIM, SNOMED, and MONDO.

=LOINC=
Status: Cross-Reference

''Data provided by Metabolomics Workbench''

=MarkerDB=
Status: Direct Integration into Data Model

* Provides a lot of useful biomarker data and cross-references other resources as well.
* Information includes: panel information, abnormal levels of biomarkers by disease, structural information, etc.
* Annotations that can be cross-referenced include the above.
* By cross-referencing, BiomarkerKB will allow users to find more information for specific biomarkers and move towards the goal of being a comprehensive resource for biomarkers.
* License: Creative Commons Attribution-NonCommercial 4.0 International License.

=Metabolomics Workbench=
Status: Direct Integration into Data Model

''Data provided by Metabolomics Workbench''

* Metabolite biomarkers utilized in the uniform newborn screening program.
* Detect treatable disorders that are life threatening or having long-term morbidity, before they become symptomatic.

=OncoKB=
Status: Cross-Reference

* Provides useful information on drugs and therapy options for different biomarker entities.
* Also provides information based on what condition the entity is related to.
* License: A license is required to use OncoKB for commercial and/or clinical purposes, and to access OncoKB data programmatically for academic purposes.
* Paid license is required
* Cross-reference from biomarkers in BiomarkerKB to the appropriate drug information and therapy information is the best solution.

=OncoMX=
Status: Direct Integration into Data Model

* integrated cancer mutation and expression resource for exploring cancer biomarkers
* Manual curation effort by GWU and JPL
* Over 600 single and panel biomarkers
* License: Creative Commons Attribution-NonCommercial 4.0 International License.

=OpenTargets=
Status: Direct Integration into Data Model

* Collects potential drug targets and therapeutic targets.
* Some effort was required to find the correct biomarker data.
* 1200 biomarkers collected.
** dbSNPs related to cancer and other disease
* License: Creative Commons Attribution-NonCommercial 4.0 International License.

=PubMed Central Biomarker Gene Set Curation=
Status: Direct Integration into Data Model

''Data provided by Avi Ma'ayan's LINCS group''

* This data set was created through manual curation of biomarker gene sets on Pubmed Central using the results of gene sets returned from Rummagene.
* Using the outputted search results within the Rummagene web server, we manually identified publications that associated different conditions and environmental exposures to biomarker gene sets.
* The biomarker gene sets were retrieved through the validation of the gene mentioned within each of the publications.
* The primary use case for this data is to identify biomarker panels/ gene sets associated with conditions.

=UniProtKB=

Status: Direct Integration into Data Model

* Can provide biomarker (change in entity), entity, condition, and sampling data.
* This data is in a text file that has to be reviewed fully and to make sure it will be able to be automatically extracted.
* Contextual information can be imputed if necessary.
* In UniProt there are found_in and entries that are actual biomarkers:
** found_in will get a cross-reference;
** actual biomarkers will be directly integrated.
* Manual curation of 56 reviewed entries with mention of "biomarker" in flat text file.
* License is Creative Commons Attribution 4.0 International (CC BY 4.0).