BiomarkerKB Resource Integration
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: MetaKB, CADSR Cancer, https://themarker.idrblab.cn/, biomarker.org, ResMarkerDB, SalivaDB, https://glycanage.com/publications, https://www.cancergenomeinterpreter.org/biomarkers
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
- License: Creative Commons Attribution-NonCommercial 4.0 International License.
- 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
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
- License is Creative Commons Attribution 4.0 International (CC BY 4.0)
- In UniProt there are found_in and entries that are actual biomarkers
- found_in will get an cross reference
- actual biomarkers will be directly integrated
- Manual curation of 56 reviewed entries with mention of "biomarker" in flat text file