This repository provides practical use cases and resources for the Cancer Epitope Database and Analysis Resource (CEDAR) Query API. It includes Python Notebooks and Entity-Relationship Diagrams (ERDs) designed to help users programatically perform novel and complex queries.
This information is complementary to the official documentation:
The use cases are implemented as Jupyter Notebooks located in the /python directory. They reproduce search scenarios and queries from Koşaloğlu-Yalçın, Z. et al. (2025).
Important: Since CEDAR's database is actively updated with new data, query results vary over time and might not exactly match the outputs documented in the notebooks and book chapter.
CEDAR_API_I.ipynb- Demonstrates how to retrieve all publication references for a specific antigen (e.g., Prostate-specific antigen).CEDAR_API_II.ipynb- Shows how to investigate the experimental evidence for the immunogenicity of a specific neoepitope (e.g., "SYLDSGIHF").CEDAR_API_III.ipynb- Provides a method to find viral antigens and epitopes associated with a specific cancer type (e.g., head and neck cancer).CEDAR_API_IV.ipynb- Explains how to identify neoantigens that have been used in therapeutic cancer vaccines for human patients.
To better understand the database structure, the /diagrams directory contains ERDs that visualize table keys and relationships. These diagrams are a valuable reference for constructing your own custom queries.
cedar_api_epitope_antigen_reference_keys_submodel.png- EPITOPE / ANTIGEN / REFERENCE Keys Sub-Modelcedar_api_tcell_tcr_keys_submodel.png- TCELL / TCR Keys Sub-Modelcedar_api_bcell_bcr_keys_submodel.png- BCELL / BCR Keys Sub-Modelcedar_api_mhc_keys_submodel.png- MHC Keys Sub-Model
If you have any questions or feedback, please contact the CEDAR team at cedar@lji.org.