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ci4cc-informatics-resources

This is a community-maintained list of resources that the CI4CC organization and larger cancer informatics have found useful or are developing. Contributions welcome...

Clinical Trials

Databases and APIs

Policies and Standards

Cancer Registries

Databases and APIs

  • SEER - The Surveillance, Epidemiology, and End Results (SEER) Program of the National Cancer Institute provides information on cancer statistics in an effort to reduce the cancer burden among the U.S. population. - [Database, API]

Data Engineering and Analytics

Natural Language Processing

  • Apache cTAKES - Apache cTAKES™ is a natural language processing system for extraction of information from electronic medical record clinical free-text. - [OSS]

Analytics

Image Informatics

  • 3D Slicer - 3D Slicer is an extensible open source software platform for medical image informatics, image processing, and three-dimensional visualization. - [Imaging, OSS]
  • dcmqi - DICOM for Quantitative Imaging (dcmqi) is a free, open source library that implements conversion of the quantitative imaging analysis results stored in commonly used research formats into the standard DICOM representation. - [Imaging, OSS, Standards]
  • ePAD - open source web-based radiology image and annotation tool for cancer lesion assessment and radiomics. - [Imaging, OSS, Web]
  • QIFP - freely available web based platform for executing pipelines of radiomics image processing. - [Imaging, OSS]
  • QuIP — Quantitative Imaging In Pathology (QUIP) is an integrated software platform designed to support analysis, management, and exploration of whole slide tissue images for cancer research. The QuIP software platform consists of a set of docker containers, which provide analysis execution and data management backend services, and web applications to load and visualize whole slide tissue images (stored in supported file formats) and explore analysis results. - [Imaging, Pathology, OSS]

Data Platforms

Genomics

  • Genomic Data Commons - The NCI's Genomic Data Commons (GDC) provides the cancer research community with a unified data repository that enables data sharing across cancer genomic studies in support of precision medicine. - [Genomics, Clinical Data, Precision Oncology]

Imaging

  • The Cancer Imaging Archive - The Cancer Imaging Archive (TCIA) is NCI’s primary resource for acquiring, curating, managing and distributing images and related data to support Cancer Research. It contains multiple collections of imaging data, and associated non-imaging data for various cancer disease sites. - [Imaging, Precison Oncology, Pathology, Radiomics]

Clinical

Data Sharing and Open Data Efforts

Genomics