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http://purl.bioontology.org/ontology/NPO
An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.
Proper citation: NanoParticle Ontology (RRID:SCR_010369) Copy
http://bg.upf.edu/transfic/home
A method to transform Functional Impact scores taking into account the differences in basal tolerance to germline SNVs of genes that belong to different functional classes.
Proper citation: TransFIC (RRID:SCR_010788) Copy
https://proteomics.cancer.gov/programs/cptac
Clinical proteomic tumor analysis consortium to systematically identify proteins that derive from alterations in cancer genomes and related biological processes, in order to understand molecular basis of cancer that is not possible through genomics and to accelerate translation of molecular findings into clinic. Operates through Proteome Characterization Centers, Proteogenomic Translational Research Centers, and Proteogenomic Data Analysis Centers. CPTAC investigators collaborate, share data and expertise across consortium, and participate in consortium activities like developing standardized workflows for reproducible studies.
Proper citation: CPTAC (RRID:SCR_017135) Copy
http://cancer.gov/cancertopics/pdq/cancerdatabase
NCI''s comprehensive cancer database that contains summaries on a wide range of cancer topics; a registry of 8,000+ open and 19,000+ closed cancer clinical trials from around the world; a directory of professionals who provide genetics services; the NCI Dictionary of Cancer Terms, with definitions for 6,800+ cancer and medical terms; and the NCI Drug Dictionary, which has information on 2,300+ agents used in the treatment of cancer or cancer-related conditions. The PDQ cancer information summaries are peer reviewed and updated monthly by six editorial boards comprised of specialists in adult treatment, pediatric treatment, supportive care, screening and prevention, genetics, and complementary and alternative medicine. The Boards review current literature from more than 70 biomedical journals, evaluate its relevance, and synthesize it into clear summaries. Many of the summaries are also available in Spanish.
Proper citation: Physician Data Query (RRID:SCR_006833) Copy
A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data.
Proper citation: Synapse (RRID:SCR_006307) Copy
A cancer research center whose goal is to offer innovative technoligies to spur the develpment of new methods of diagnosing and treating cancer. CNIO contains a variety of programs of investigation, including a biotechnology program, a clinical research program, and a molecular oncology program. CNIO also provides services that allow researchers to access and use technologies and tools such as cytogenetics and monoclonal antibodies, and hosts a biomedical biobank.
Proper citation: Spanish National Cancer Research Center (RRID:SCR_014054) Copy
Portal provides tools for visualizing, querying, and downloading cancer data, which is released on quarterly schedule.
Proper citation: ICGC Data Portal (RRID:SCR_021722) Copy
http://bioinfo-out.curie.fr/projects/snp_gap/
Software for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured by single-nucleotide polymorphism (SNP) arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. The method performs well even for poor-quality data, low tumor content, and highly rearranged tumor genomes.
Proper citation: Genome Alteration Print (RRID:SCR_012016) Copy
Biomedical research institute in Germany that investigates the mechanisms of cancer and works to identify cancer risk factors. They provide the foundations for developing novel approaches in the prevention, diagnosis, and treatment of cancer and are a member of the Helmholtz Association of National Research Centers. Professor Harald zur Hausen was awarded the Nobel Prize for Medicine for his outstanding scientific contribution to the study of human papillomaviruses (HPV). In addition, the staff of the Cancer Information Service (KID) offers information about the widespread disease of cancer for patients, their families, and the general public. The Center is funded by the German Federal Ministry of Education and Research (90%) and the State of Baden-Württemberg (10%).
Proper citation: German Cancer Research Center (RRID:SCR_012942) Copy
Ratings or validation data are available for this resource
http://pubs.rsc.org/en/content/articlehtml/2017/LC/C7LC00703E
Equipment that is a magnetic micropore chip for rapid unbiased circulating tumor cell isolation and in situ RNA analysis. The chip detects tumor cells and can help doctors treat patients with these tumors.
Proper citation: CaTCh FISH Chip (RRID:SCR_015810) Copy
Project to create network based understanding of biology by cataloging changes in gene expression and other cellular processes when cells are exposed to genetic and environmental stressors. Program to develop therapies that might restore pathways and networks to their normal states. Has LINCS Data Coordination and Integration Center and six Data and Signature Generation Centers: Drug Toxicity Signature Generation Center, HMS LINCS Center, LINCS Center for Transcriptomics, LINCS Proteomic Characterization Center for Signaling and Epigenetics, MEP LINCS Center, and NeuroLINCS Center.
Proper citation: LINCS Project (RRID:SCR_016486) Copy
Portal to make cancer related proteomic datasets easily accessible to public. Facilitates multiomic integration in support of precision medicine through interoperability with other resources. Developed to advance our understanding of how proteins help to shape risk, diagnosis, development, progression, and treatment of cancer. One of several repositories within NCI Cancer Research Data Commons which enables researchers to link proteomic data with other data sets (e.g., genomic and imaging data) and to submit, collect, analyze, store, and share data throughout cancer data ecosystem. PDC provides access to highly curated and standardized biospecimen, clinical, and proteomic data, intuitive interface to filter, query, search, visualize and download data and metadata. Provides common data harmonization pipeline to uniformly analyze all PDC data and provides advanced visualization of quantitative information. Cloud based (Amazon Web Services) infrastructure facilitates interoperability with AWS based data analysis tools and platforms natively. Application programming interface (API) provides cloud-agnostic data access and allows third parties to extend functionality beyond PDC. Structured workspace that serves as private user data store and also data submission portal. Distributes controlled access data, such as patient-specific protein fasta sequence databases, with dbGaP authorization and eRA Commons authentication.
Proper citation: Proteomic Data Commons (RRID:SCR_018273) Copy
https://portal.imaging.datacommons.cancer.gov
Portal for finding and analyzing cancer imaging data. Part of Cancer Research Data Commons to support cancer imaging research. Provides cloud based access to medical imaging data and library of analytical tools and workflows to share, analyze, and visualize multi modal imaging data from both clinical and basic cancer research studies.
Proper citation: NCI Imaging Data Commons (RRID:SCR_019127) Copy
https://datacommons.cancer.gov
Cloud based data science infrastructure that provides secure access to cancer research data from NCI programs and key external cancer programs. Serves as coordinated resource for public data sharing of NCI funded programs. Users can explore and use analytical and visualization tools for data analysis. Enables to search and aggregate data across repositories including Cancer Data Service, Clinical Trial Data Commons, Genomic Data Commons, Imaging Data Commons, Integrated Canine Data Commons, Proteomic Data Commons.
Proper citation: Cancer Research Data Commons (RRID:SCR_019128) Copy
http://cahub.cancer.gov/about/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented July 5, 2018. A national center for biospecimen science and standards to advance cancer research and treatment. It was created in response to the critical and growing need for high-quality, well-documented biospecimens for cancer research. The initiative builds on resources already developed by the NCI, including the Biospecimen Research Network and the NCI Best Practices for Biospecimen Resources, both of which were developed to address challenges around standardization of the collection and dissemination of quality biospecimens. caHUB will develop the infrastructure for collaborative biospecimen research and the production of evidence-based biospecimen standard operating procedures.
Proper citation: caHUB (RRID:SCR_009657) Copy
Initiative to enable cancer discovery and treatment based on complete elucidation of molecular networks underlying cancer. CCMI leverages advanced interaction mapping and computational facilities to generate and analyze cancer networks.
Proper citation: Cancer Cell Map Initiative (RRID:SCR_023043) Copy
Medical wiki of interventions, regimens, and general information relevant to fields of hematology and oncology. Knowledge base for hematology and oncology providers, containing details about hematology/oncology drugs and treatment regimens. Any healthcare professional can sign up to contribute. Acuracy and completeness of content is overseen by Editorial Board.
Proper citation: HemOnc Knowledgebase (RRID:SCR_023436) Copy
http://www.rrcancer.ca/en/publique/accueil
An infrastructure to allow Quebec researchers to have at their disposal tumor banks and the services that support large scale research in genomics and proteomics. The database and the tissue bank of the research network was created to allow rapid access to biological samples and their clinical data. It is spread out over many hospital institutions (in Montreal, Quebec and Sherbrooke). The members of the RRCancer-BTD supply normal, benign and malignant samples from routine surgeries and blood tests. Blood and tissue samples are collected by the provincial biobanks on a regular basis and are coded, classified and stored. The samples can be supplied to a researcher either fresh or frozen or blocks of paraffin or on slices. The sharing of information and biological material is managed according to ethical rules and contributes to increasing the value of research in Quebec. The network has mobilized a significant number of researchers in the area of cancer that unite their efforts to pursue high caliber multidisciplinary research. They are a group of researchers from many different Qu��bec Universities all working in the branch of cancer research. They are located in four hospital centers in Quebec, namely the University of Montreal Hospital Centre (CHUM), the University of Quebec Hospital Centre (CHUQ), the University of Sherbrooke Hospital Centre (CHUS) and the McGill University Hospital Centre (CUSM), as well as in the affiliated research and university centers (Sacr��-Coeur, Maisonneuve-Rosemont and the Montreal Jewish Hospital). The collaborative efforts created and maintained in this network have allowed transfer of knowledge and the sharing of cutting edge technologies. RRCancer favors multidisciplinary cancer research in both fundamental and clinical scopes. The network is based on the desire researchers to work together to prevent cancer and improve therapeutic strategies, all the while continuing the very important task of raining new specialists and graduate students.
Proper citation: Cancer Research Network of the FRSQ (RRID:SCR_004225) Copy
An independent, not-for-profit biobanking and biotechnology foundation designed to facilitate new, high quality medical research. The IBBL collects, stores, and analyzes biological samples and associated data, which are then made available to research organizations investigating new treatments for diseases. It houses a biospecimen collection and biorepository that contains high quality tissues and maintains quality control of the specimens and the clinical data associated with the tissue samples, while maintaining biobanking ethical standards. It also provides biorefinery analyses and research services that can make analytes from tissues (e.g. DNA, RNA and protein), maintains technology for high throughput gene sequencing and gene expression, and conducts biospecimen research. An informatics platform maintains the clinical and biospecimens data in a secure fashion for additional analysis. Samples are collected by IBBL personnel from hospitals in a targeted manner. The IBBL collaborates with research and health organizations in North America, Europe and the Middle East, and with the major international biobanking societies.
Proper citation: Integrated Biobank of Luxembourg (RRID:SCR_004211) Copy
http://www.itor-ghs.org/biorepository.php
From the type of mutation causing cancer to specific gene expression levels, genetic biomarkers are becoming an indispensable tool for developing new treatment models for cancer. The ITOR Biorepository Services tissue bank initiatives are critical to the continued development of an organized research infrastructure that will attract leading biotechnology and pharmaceutical companies interested in developing the next generation of cancer therapies. Ultimately, by linking the laboratory and clinical settings through innovative research investigations, USC, Greenville Hospital System University Medical Center, and private partners can identify the most novel ways to find and couple these biomarkers to patient drug trials and eventually, the most effective treatments & cures for cancer. The ITOR Biorepository Services Department ����?����������?? in conjunction with the Greenville Hospital System''s surgical oncologists, pathologists and staff ����?����������?? have developed tissue bank sample processing guidelines for frozen tissue, fresh tissue and peripheral blood and include flash freezing in liquid nitrogen within 15 minutes of harvest to maximize cell viability for basic science research. The department has a dedicated staff, including two research nurses and a data coordinator, which facilitate the logistics of tissue handling and submit outcomes data on participating patients. The ITOR Biorepository staff is in the process of adopting a universal consent for all patients of the Greenville Hospital System to have the option of donating excess tissue for research, should they desire. ITOR of GHS has several tissue-based patient initiatives & programs under development and ongoing. At the forefront of cancer care are two specific programs, Total Cancer Care and Caris Target Now.
Proper citation: ITOR Biorepository Services (RRID:SCR_004191) Copy
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