Skip to content

Cancercelllines Resource Documentation

The cancercelllines.org genomic information resource contains genome profiling data, somatic mutation information and associated metadata for thousands of human cancer cell lines. It has its origins in genomic copy number variation (CNV) profiling data of cell lines originally collected as part of the more than 100’000 individual datasets in the Progenetix oncogenomic resource. However, by providing genome mapped, annotated data for many types of genomic mutations, together with CNV profiles for a subset of the overall more than 16'000 cell lines, cancercelllines.org goes beyond the original scope of Progenetix and provides an entry point for the comparative analysis of genomic variants in cell lines as well as for the exploration of related publications.

Citation

  • cancercelllines.org: Cancer cell line oncogenomic online resource (2023)
Additional Articles & Citation Options
  • Huang Q, Carrio-Cordo P, Gao B, Paloots R, Baudis M. (2021) The Progenetix oncogenomic resource in 2021. Database (Oxford). 2021 Jul 17
  • progenetix.org: Progenetix oncogenomic online resource (2022)
  • Baudis M, Cleary ML. (2001) Progenetix.net: an online repository for molecular cytogenetic aberration data. Bioinformatics. 17:1228-1229
  • Cai H, Kumar N, Ai N, Gupta S, Rath P, Baudis M. Progenetix: 12 years of oncogenomic data curation. Nucleic Acids Res (2014) Jan;42
  • Cai H, Kumar N, Baudis M. (2012) arrayMap: a reference resource for genomic copy number imbalances in human malignancies. PLoS One. 7:e36944.
  • Baudis M. (2007) Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data. BMC Cancer. 7:226.
  • Baudis M. (2006) Online database and bioinformatics toolbox to support data mining in cancer cytogenetics. Biotechniques. 40:296-272.
Registration & Licenses

As of March 2012, no registration is required for using Progenetix and related resources such as cancercelllines.org. While the data is licensed under CC-BY 4.0 we suggest that you contact Michael Baudis if you plan any commercial use of the database or are interested to incorporate the data into your research projects, for optional collaborative support.

Progenetix The Progenetix database and cancer genomic information resource provides a comprehensive collection of genomic copy number profiling data for the majority of cancer types (ca. 800 diagnostic codes as of 2023). It was publicly launched in 2001, abnnounced through an article in Bioinformatics. The database & software are developed by the group of Michael Baudis at the University of Zurich and the Swiss Institute of Bioinformatics (SIB).

Additional information - e.g. about contacts or related publications - is available through the group page of the Baudis group at the University of Zürich. For a list of publication by the Baudis group you can go to the group's website, EuropePMC or any of the links here.

Beacon The Beacon project of the Global Alliance for Genomics and Health GA4GH develops a framework and default data model for the discovery and exchange of genomic variants and associated biomedical annotations. cancercelllines.org makes extensive use of the Beacon protocol for its API and also as engine behind its front end (see below).

Progenetix Source Code

With exception of some utility scripts and external dependencies (e.g. MongoDB) the following projects provide the vast majority of the software (from database interaction to website) behind Progenetix and Beacon+.

bycon

  • Python based service based on the GA4GH Beacon protocol
  • software powering the cancercelllines.org and Progenetix resources
  • Beacon+ implementation(s) use the same code base

cancercelllines-web

  • website for cancercelllines.org
  • implemented as React / Next.js project
  • contains this documentation tree here as mkdocs project, with files in the docs directory

byconaut

  • extensions (server services...) and management tools for bycon-based installations

progenetix-web

  • website for Progenetix and its Beacon+ implementations
  • provides Beacon interfaces for the bycon server, as well as other Progenetix sevices (e.g. the publications repository)
  • implemented as React / Next.js project
  • contains this documentation tree here as mkdocs project, with files in the docs directory

Additional Projects

icdot2uberon

  • mappings between ICD-O 3 topographies and UBERON anatomical sites

ICDOntologies

  • mappings between ICD-O 3 morphology / topography pairs and NCIt neoplasm core cancer ontology