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. | ||
=MarkerDB= | =MarkerDB= | ||
Status: Cross Reference | Status: Cross Reference | ||
| Line 18: | Line 6: | ||
* License: Creative Commons Attribution-NonCommercial 4.0 International License. | * License: Creative Commons Attribution-NonCommercial 4.0 International License. | ||
* Information includes: panel information, abnormal levels of biomarkers by disease, structural information, etc | * Information includes: panel information, abnormal levels of biomarkers by disease, structural information, etc | ||
* Annotations that can be cross | * 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 | ||
| Line 29: | Line 17: | ||
* 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 | ||
=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 | |||
Latest revision as of 14:42, 11 March 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.
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
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
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
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