BiomarkerKB Resource Integration: Difference between revisions

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


=CIViC=
= GWAS =
Status: Direct Integration into Data Model
Status: Direct Integration into Data Model


* Clinical Interpretation of Variants in Cancer (CIViC).
* Published genome-wide association studies (GWAS).
* Provides cancer biomarkers in form of DNA mutations (dbSNPs).
* Provides biomarkers in form of SNPs.
* Platform provides clinicians treatment options for patients based on unique tumor profile.
* GWAS Catalog contains SNPs for a vast amount of diseases.
** Preliminary curation only focused on cancer.
** All available biomarkers for conditions in GWAS Catalog are integrated 12/11
* License: Creative Commons Attribution-NonCommercial 4.0 International License.
* License: Creative Commons Attribution-NonCommercial 4.0 International License.


=ClinVar=
= MetaKB =
Status: Direct Integration into Data Model
 
* Provides harmonized associations between cancer genomic variants, diseases, and therapeutic evidence.
* Aggregates and standardizes variant interpretation data from six major knowledgebases:
** CIViC (Clinical Interpretation of Variants in Cancer)  [Already Integrated Directly]
** OncoKB  [Yet to be integrated]
** JAX-CKB (The Jackson Laboratory Clinical Knowledgebase) [Yet to be integrated]
** MolecularMatch [Yet to be integrated]
** PMKB (Precision Medicine Knowledgebase) [Yet to be integrated]
** Cancer Genome Interpreter (CGI) – through its ''Cancer Biomarkers Database'' component .[Integrated]
* Enables mapping of variant–disease–drug relationships with supporting evidence levels, citations, and ontology alignment (e.g., genes, variants, diseases, and drugs).
* Data integration requires review to ensure harmonized entity mappings consistent with the BiomarkerKB data model.
* Focused on somatic variant–based biomarkers; contextual attributes such as tissue type, therapy response, or evidence type can be inferred or imputed where not directly specified.
* Manual curation may be required for entries with incomplete evidence annotation or lacking standard ontology references.
* Integration approach: direct mapping of variant, condition, and evidence entities; cross-references retained to original data sources.
* License: Aggregated data are available for non-commercial, research use only, respecting constituent licenses:
** CIViC – CC0 (Public Domain)
** PMKB – CC-BY 4.0
** CGI – CC0 for biomarkers database, CC-BY-NC 4.0 for tool
** JAX-CKB – CC-BY-NC-SA 4.0
** OncoKB – custom non-commercial license
** MolecularMatch – restricted commercial use
** MetaKB codebase – MIT license
* Overall usage requires adherence to non-commercial research terms; commercial use needs separate permissions from individual data providers.
 
= Glycan LLM Biomarkers =
* LangChain LLM method used to collect biomarkers from PubMed Central abstracts
* Method identifies glycan entities and changes mentioned in them associated to disease
 
= Top 50 Biomarkers =
Status: Direct Integration into Data Model
Status: Direct Integration into Data Model
* Biomarkers collected during Summer Volunteership
* Volunteers identified top 50 biomarker entities from BiomarkerKB
* Using this information the top 50 biomarker entities were searched in PubMed
* 100 biomarkers were manually curated


* 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=
= EDRN =
Status: Sample Integration into Data Model
Status: Sample Integration into Data Model


* Cancer biomarkers.
* Cancer biomarkers.
* Sample of EDRN Biomarkers provided from EDRN LLM method
* Biomarkers are extracted from free text in EDRN publicly available biomarkers


=GWAS=
= LOINC =
Status: Direct Integration into Data Model
Status: Cross-Reference


* Published genome-wide association studies (GWAS).
''Data provided by Metabolomics Workbench''
* 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.


= Glycan LLM Biomarkers =
= OncoKB =
Status: Cross-Reference


* LangChain LLM method used to collect biomarkers from PubMed Central abstracts
* Provides useful information on drugs and therapy options for different biomarker entities.
* Method identifies glycan entities and changes mentioned in them associated to disease
* 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.


=HPO=
=HPO=
Line 53: Line 86:
* Provides cross-reference to OMIM, SNOMED, and MONDO.
* Provides cross-reference to OMIM, SNOMED, and MONDO.


=LOINC=
= UniProtKB =
Status: Cross-Reference
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).
 
= 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


''Data provided by Metabolomics Workbench''
* 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.


=MarkerDB=
= MarkerDB =
Status: Direct Integration into Data Model
Status: Direct Integration into Data Model


Line 74: Line 131:
* Metabolite biomarkers utilized in the uniform newborn screening program.
* 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.
* 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=
=OncoMX=
Line 117: Line 165:
* Biomarker data was collected and incorporated however biomarker field was incomplete and data integrated was given a score of -2
* Biomarker data was collected and incorporated however biomarker field was incomplete and data integrated was given a score of -2
* Data is still valuable as contextual data and can be revisited to complete biomarker field in future
* Data is still valuable as contextual data and can be revisited to complete biomarker field in future
= Top 50 Biomarkers =
Status: Direct Integration into Data Model
* Biomarkers collected during Summer Volunteership
* Volunteers identified top 50 biomarker entities from BiomarkerKB
* Using this information the top 50 biomarker entities were searched in PubMed
* 100 biomarkers were manually curated
=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).
=MetaKB=
Status: Direct Integration into Data Model
* Provides harmonized associations between cancer genomic variants, diseases, and therapeutic evidence.
* Aggregates and standardizes variant interpretation data from six major knowledgebases:
** CIViC (Clinical Interpretation of Variants in Cancer)  [Already Integrated Directly]
** OncoKB  [Yet to be integrated]
** JAX-CKB (The Jackson Laboratory Clinical Knowledgebase) [Yet to be integrated]
** MolecularMatch [Yet to be integrated]
** PMKB (Precision Medicine Knowledgebase) [Yet to be integrated]
** Cancer Genome Interpreter (CGI) – through its ''Cancer Biomarkers Database'' component .[Integrated]
* Enables mapping of variant–disease–drug relationships with supporting evidence levels, citations, and ontology alignment (e.g., genes, variants, diseases, and drugs).
* Data integration requires review to ensure harmonized entity mappings consistent with the BiomarkerKB data model.
* Focused on somatic variant–based biomarkers; contextual attributes such as tissue type, therapy response, or evidence type can be inferred or imputed where not directly specified.
* Manual curation may be required for entries with incomplete evidence annotation or lacking standard ontology references.
* Integration approach: direct mapping of variant, condition, and evidence entities; cross-references retained to original data sources.
* License: Aggregated data are available for non-commercial, research use only, respecting constituent licenses:
** CIViC – CC0 (Public Domain)
** PMKB – CC-BY 4.0
** CGI – CC0 for biomarkers database, CC-BY-NC 4.0 for tool
** JAX-CKB – CC-BY-NC-SA 4.0
** OncoKB – custom non-commercial license
** MolecularMatch – restricted commercial use
** MetaKB codebase – MIT license
* Overall usage requires adherence to non-commercial research terms; commercial use needs separate permissions from individual data providers.

Latest revision as of 16:20, 16 December 2025

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: CADSR Cancer, https://themarker.idrblab.cn/, biomarker.org, ResMarkerDB, SalivaDB, https://glycanage.com/publications, https://www.c, Glycan Biomarkers (code), Alliance Genome


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

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.
    • All available biomarkers for conditions in GWAS Catalog are integrated 12/11
  • License: Creative Commons Attribution-NonCommercial 4.0 International License.

MetaKB

Status: Direct Integration into Data Model

  • Provides harmonized associations between cancer genomic variants, diseases, and therapeutic evidence.
  • Aggregates and standardizes variant interpretation data from six major knowledgebases:
    • CIViC (Clinical Interpretation of Variants in Cancer) [Already Integrated Directly]
    • OncoKB [Yet to be integrated]
    • JAX-CKB (The Jackson Laboratory Clinical Knowledgebase) [Yet to be integrated]
    • MolecularMatch [Yet to be integrated]
    • PMKB (Precision Medicine Knowledgebase) [Yet to be integrated]
    • Cancer Genome Interpreter (CGI) – through its Cancer Biomarkers Database component .[Integrated]
  • Enables mapping of variant–disease–drug relationships with supporting evidence levels, citations, and ontology alignment (e.g., genes, variants, diseases, and drugs).
  • Data integration requires review to ensure harmonized entity mappings consistent with the BiomarkerKB data model.
  • Focused on somatic variant–based biomarkers; contextual attributes such as tissue type, therapy response, or evidence type can be inferred or imputed where not directly specified.
  • Manual curation may be required for entries with incomplete evidence annotation or lacking standard ontology references.
  • Integration approach: direct mapping of variant, condition, and evidence entities; cross-references retained to original data sources.
  • License: Aggregated data are available for non-commercial, research use only, respecting constituent licenses:
    • CIViC – CC0 (Public Domain)
    • PMKB – CC-BY 4.0
    • CGI – CC0 for biomarkers database, CC-BY-NC 4.0 for tool
    • JAX-CKB – CC-BY-NC-SA 4.0
    • OncoKB – custom non-commercial license
    • MolecularMatch – restricted commercial use
    • MetaKB codebase – MIT license
  • Overall usage requires adherence to non-commercial research terms; commercial use needs separate permissions from individual data providers.

Glycan LLM Biomarkers

  • LangChain LLM method used to collect biomarkers from PubMed Central abstracts
  • Method identifies glycan entities and changes mentioned in them associated to disease

Top 50 Biomarkers

Status: Direct Integration into Data Model

  • Biomarkers collected during Summer Volunteership
  • Volunteers identified top 50 biomarker entities from BiomarkerKB
  • Using this information the top 50 biomarker entities were searched in PubMed
  • 100 biomarkers were manually curated

EDRN

Status: Sample Integration into Data Model

  • Cancer biomarkers.
  • Sample of EDRN Biomarkers provided from EDRN LLM method
  • Biomarkers are extracted from free text in EDRN publicly available biomarkers

LOINC

Status: Cross-Reference

Data provided by Metabolomics Workbench

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.

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.

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).

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.

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.

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.

SenNet Biomarker Data

Status: Direction Integration Into Data Model

  • Cell senescence biomarkers from SenNet group
  • Biomarker data was collected and incorporated however biomarker field was incomplete and data integrated was given a score of -2
  • Data is still valuable as contextual data and can be revisited to complete biomarker field in future
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