cBioPortal consists of the following components:
- MySQL database
- REST API written in Java Spring
- Redis cache for storing frequently used queries (optional)
- validator 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
- REST API written in Java Spring enabling retrieval and writing to the database
- MongoDB database
- cBioPortal also uses the APIs from various
external servicesto provide more information about a variant
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. The backend can be configured to connect to a Redis cache to store database query results for improved performance.
The backend is organized as a multi-module Maven project. See cBioPortal backend code organization.
checks file formats before importing data into the database. There is a wrapper
metaImport.py that validates the data and subsequently calls the
relevant Java classes to import the data.
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.
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.
cBioPortal uses the APIs from several external services to provide more information about a variant:
OncoKB CIVIC Genome Nexus G2S
For privacy concerns see the section:
OncoKB is a precision oncology knowledge base that contains information about the effects and treatment implications of specific cancer gene alterations. See the section OncoKB Data Access for how to configure external OncoKB service.
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 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 (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.