Architecture overview

cBioPortal consists of the following components:

  • backend written in Java

  • MySQL database that the backend uses

  • validator

    which checks file formats before importing data into the database

  • frontend

    built with React, Mobx and Bootstrap

  • session service for storing

    user saved data such as virtual studies and groups

  • Mongo database which session service uses

  • cBioPortal also uses the APIs from various external services to provide more information about a variant

Backend

The backend is written in Java and connects to a MySQL database to serve a REST API following the OpenAPI specification (https://www.cbioportal.org/api/). Note that the repo where this lives in (https://github.com/cBioPortal/cbioportal) also contains Java classes to import data as well as the validator.

Validator

The validator checks file formats before importing data into the database. There is a wrapper script metaImport.py that validates the data and subsequently calls the relevant Java classes to import the data.

Session Service

The session service is used for storing user saved data such as virtual studies and groups. See the tutorials section to read more about these features. Session service is a Java app that serves a REST API backed by a Mongo database. The session service is served as a proxy through the cBioPortal backend REST API. The backend is therefore the only component that needs to be able to connect to it. The frontend does not connect to it directly.

Frontend

The frontend is a single page app built with React, Mobx and Bootstrap. The data gets pulled from the backend REST API. The frontend is by default included with the backend so no extra setup is required.

External Services

cBioPortal uses the APIs from several external services to provide more information about a variant:

For privacy concerns see the section: A note on privacy.

OncoKB

OncoKB is a precision oncology knowledge base that contains information about the effects and treatment implications of specific cancer gene alterations. For information on how to deploy this service yourself see: https://github.com/oncokb/oncokb.

CIVIC

CIVIC is a community-edited forum for discussion and interpretation of peer-reviewed publications pertaining to the clinical relevance of variants (or biomarker alterations) in cancer. For information on how to deploy this service yourself see: https://github.com/griffithlab/civic-server. It is also possible to disable showing CIVIC in cBioPortal by setting show.civic=false in the portal.properties (See portal.properties reference).

Genome Nexus

Genome Nexus is a comprehensive one-stop resource for fast, automated and high-throughput annotation and interpretation of genetic variants in cancer. For information on how to deploy this service yourself see: https://github.com/genome-nexus/genome-nexus. For more information on the various annotation sources and versions provided by Genome Nexus see: https://docs.genomenexus.org/annotation-sources.

G2S

G2S (Genome to Structure) maps genomic variants to 3D structures. cBioPortal uses it on the mutations tab to show the variants on a 3D structure. For information on how to deploy this service yourself see: https://github.com/genome-nexus/g2s.

A note on privacy

cBioPortal calls these services with variant information from the cBioPortal database. It however does not send over information that links a variant to a particular sample or patient. If this is a concern for your use case we recommmend to deploy your own versions of these services. See the sections above to linkouts for instructions on how to do this.