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.

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