BiomarkerKB Resource Integration: Difference between revisions
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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. | 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://cadsr.cancer.gov/onedata/Home.jsp CADSR Cancer], https://themarker.idrblab.cn/, biomarker.org, ResMarkerDB, SalivaDB | |||
Please contact us at mazumder_lab@gwu.edu if you have any other | |||
=CIViC= | |||
=ClinVar= | |||
=GWAS= | |||
=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 | |||
=MarkerDB= | =MarkerDB= | ||
Status: Cross Reference | Status: Cross Reference | ||
| Line 8: | Line 30: | ||
* Annotations that can be cross-referenced include the above | * 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 | * 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= | |||
=OncoKB= | =OncoKB= | ||
| Line 17: | Line 41: | ||
* Paid license is required | * Paid license is required | ||
* Cross reference from biomarkers in BiomarkerKB to the appropriate drug information and therapy information is the best solution | * Cross reference from biomarkers in BiomarkerKB to the appropriate drug information and therapy information is the best solution | ||
=OncoMX= | |||
=OpenTargets= | |||
=PubMed Central Biomarker Gene Set Curation= | |||
=UniProtKB= | =UniProtKB= | ||
| Line 29: | Line 60: | ||
** actual biomarkers will be directly integrated | ** actual biomarkers will be directly integrated | ||
*Manual curation of 56 reviewed entries with mention of "biomarker" in flat text file | *Manual curation of 56 reviewed entries with mention of "biomarker" in flat text file | ||
Revision as of 13:37, 10 June 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
Please contact us at mazumder_lab@gwu.edu if you have any other
CIViC
ClinVar
GWAS
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
MarkerDB
Status: Cross Reference
- 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
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
OpenTargets
PubMed Central Biomarker Gene Set Curation
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