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.
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)
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.
- Because of this license we can directly integrate data from MarkerDB into BiomarkerKB
- Information includes: panel information, abnormal levels of biomarkers by disease, structural information, etc
- Annotations that can be cross reference 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
Other resources to be added: CADSR Cancer Center, https://themarker.idrblab.cn/, biomarker.org, ResMarkerDB