seandavi/ci4cc-informatics-resources

Community-maintained list of resources that the CI4CC organization and the larger cancer informatics community have found useful or are developing.

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

• Access to Aggregate Content of ClinicalTrials.gov - Data from ClinicalTrials.gov parsed into an open PostgreSQL database. - [Database]
• ClinicalTrials.gov - ClinicalTrials.gov is a registry and results database of publicly and privately supported clinical studies of human participants conducted around the world. - [API,Database]
• CTRP Clinical Trials API - json-based API that includes CTRP-based clinical trials information, enriched with NCI thesaurus entries. - [API]
• EU Clinical Trials Register - The EU Clinical Trials Register contains information on interventional clinical trials on medicines conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004. - [Database, API]
• OpenTrials.net - Open database and API that is currently hosting data from ClinicalTrials.gov, WHO ITCRP, and the EU Clinical Trials Register. - [Database, API]
• WHO International Clinical Trials Registry Platform (ICTRP) - Search for clinical trials at the ICTRP. - [Database, API]

Policies and Standards

• WHO International Clinical Trials Registry Platform (ICTRP) Standards for Registries - Document describing the WHO ITCRP standards recommendations - [Policy, 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

• NIH Common Data Element (CDE) Resource Portal - National Library of Medicine, National Institutes of Health, Common Data Element (CDE) Resource Portal

Genomics

• List of open cancer variant databases - A community-maintained list of cancer variant databases, including some with evidence-based intervention data.