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CIViC: Clinical Interpretations of Variants in Cancer

CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer, available online at civicdb.org. Our goal is to enable precision medicine by providing an educational forum for dissemination of knowledge and active discussion of the clinical significance of cancer genome alterations. For more details and to cite CIViC please refer to the CIViC publication in Nature Genetics.

Description

The CIViC knowledgebase project seeks to advance cancer precision medicine with community collaboration. Precision medicine refers to the use of prevention and treatment strategies that are tailored to the unique features of each individual and their disease. In the context of cancer this might involve the identification of specific mutations shown to predict response to a targeted therapy. The biomedical literature describing these associations is large and growing rapidly. Currently these interpretations exist largely in private or encumbered databases resulting in extensive repetition of effort. Realizing precision medicine will require this information to be centralized, debated, and interpreted for application in the clinic.

All content created in CIViC is, and will continue to be, freely available, without restriction with a Public Domain License. Anyone can contribute to CIViC by simply registering for an account. Users join the community with “Curator” level privileges that allow them to comment or propose additions or revisions on any knowledge in CIViC. Proposed additions and revisions are then reviewed by users with “Editor” level privileges before gaining “Accepted” status. Submitted content, not yet accepted, should be interpreted/used with caution. Community Curators work together with Editors towards comprehensive and accurate interpretations of the clinical relevance of variants in cancer.

Getting Started

CIViC is a Rails backend serving a GraphQL API to an Angular frontend. The same API that powers the frontend is available for anyone to use. The easiest way to get started is to experiment in the GraphiQL user interface. You can also browse autogenerated documentation here.

Dependencies

  • Ruby >= 3.0 (recommended install via rbenv)
  • PostgreSQL >= 14
  • Node >= 14

Installing

  • In server/

    • gem install bundler && rbenv rehash
    • bundle install
    • rails db:create
    • rails db:schema:load
    • rails s to start the server. It will be running on 127.0.0.1:3000.

  • In client/

    • npm install -g yarn
    • yarn install
    • yarn start will start the dev server at 127.0.0.1:4200 and proxy API requests to the backend

Version History

See Releases Page

License

The content of CIViC, hosted by The McDonnell Genome Institute at Washington University School of Medicine is released under the Creative Commons Public Domain Dedication (CC0 1.0 Universal) and the source code for the CIViC server and client is licensed under the MIT License.