NCI Cancer Gene Index

One of our most significant Sophic-Biomax team projects was the 5-year, $2.4M National Cancer Institute (NCI) Cancer Gene Index (CGI) described below and in the CGI White Paper. Documentation for the Cancer Gene Index is available at the NCI Wiki.  Please scroll to the bottom of the Wiki page to view examples of Sophic BioXM Configurations for using CGI to support Cancer Translational Medicine and Biomarker Discovery.  The Cancer Gene Index is an extraordinary, high quality source for information on cancer genes, their relationship with specific cancer diseases and their relationships with chemical compounds and treatments. The Sophic integration and visualization these relationship networks in BioXM provide researchers and oncologists with Scientific Intelligence -  insight to the complexities of cancer that is accurate, powerful and unique.

An accurate and up-to-date inventory of cancer genes is a necessary foundation for advancing cancer research and supporting patient treatment. Clinical researchers and MDs treating patients all need easy access to a reliable core knowledge repository in order to connect “omics” with “oligies”.
 
In 2004, NCI launched the Cancer Gene Index Project (CGI) to provide the cancer community with a complete compendium of all cancer related genes occurring in the biomedical literature with manually annotated gene/disease and gene/compound relationships. The aim was to accelerate discovery of cancer drugs, biomarkers, cures and treatments.
 
A cancer gene was defined as any human gene or gene product that co-occurs in a single Medline® database1 sentence with a cancer disease or compound/treatment term. The Biomax BioLT Linguistics Tool was used to automatically analyze the complete Medline database with more than 18M abstracts and 94M sentences.

During the 5-year project, 6,955 cancer genes were identified and 1.8M sentences were manually validated and annotated with role codes and evidence codes for each gene/disease and gene/compound/treatment relationship by PhD scientists.
 
Sophic has configured and integrated the Cancer Gene Index into the Biomax BioXM Knowledge Management Environment to support research at NCI’s Center for Cancer Research. BioXM and Cancer Gene Index are configured to support translational medicine, biomarker, mRNA and pathway discovery use cases.