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https://www.bips-institut.de/en/research/cancer-registry.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. A population based database collecting incident cases of cancer diagnosed since January 1998 in the population of the Federal state of Bremen. The Registry provides data for the analysis of * age specific time trends and geographical patterns of cancer incidence in men and women * cancer causes (e.g. work-related, environmental and personal risk factors) * epidemiological evaluation of screening programs * survival analysis of cancer patients. Since the incidence year of 2001, the Registry has a completeness level of > 95 %, based on expected values provided by the Robert Koch Institute.

Proper citation: Bremen Cancer Registry (RRID:SCR_004093) Copy   

•   Source: SciCrunch Registry

https://seer.cancer.gov/siterecode/icdo3_dwhoheme/index.html

Website describing International Classification of Diseases-Oncology codes that corresponds to different cancer sites in the Surveillance, Epidemiology, and End Results (SEER) registry.

Proper citation: NCI Site Recode ICD-O-3/WHO 2008 Definition (RRID:SCR_024687) Copy   

•   Source: SciCrunch Registry

http://oncokb.org

Precision oncology knowledge base which contains information about the effects and treatment implications of specific cancer gene alterations. OncoKB contains detailed information about specific alterations in 418 cancer genes. Each variant entry contains biological effect, prevalence, prognostic information, and treatment implications. Information is curated from various sources, such as guidelines from the FDA, ClinicalTrials.gov, and scientific literature by a network of clinical fellows, research fellows, and faculty members at Memorial Sloan Kettering Cancer Center.

Proper citation: OncoKB (RRID:SCR_014782) Copy   

•   Source: SciCrunch Registry

http://galaxy.cineca.it/fusion/main

Portal provides an easy access to a comprehensive database designed for storing, displaying and annotating gene fusion events detected from NGS data. It can query a database of somatic fusion genes events predicted and annotated starting from paired-end RNA-seq data.

Proper citation: LiGeA (RRID:SCR_015940) Copy   

•   Source: SciCrunch Registry

http://cancergenome.nih.gov/

Project exploring the spectrum of genomic changes involved in more than 20 types of human cancer that provides a platform for researchers to search, download, and analyze data sets generated. As a pilot project it confirmed that an atlas of changes could be created for specific cancer types. It also showed that a national network of research and technology teams working on distinct but related projects could pool the results of their efforts, create an economy of scale and develop an infrastructure for making the data publicly accessible. Its success committed resources to collect and characterize more than 20 additional tumor types. Components of the TCGA Research Network: * Biospecimen Core Resource (BCR); Tissue samples are carefully cataloged, processed, checked for quality and stored, complete with important medical information about the patient. * Genome Characterization Centers (GCCs); Several technologies will be used to analyze genomic changes involved in cancer. The genomic changes that are identified will be further studied by the Genome Sequencing Centers. * Genome Sequencing Centers (GSCs); High-throughput Genome Sequencing Centers will identify the changes in DNA sequences that are associated with specific types of cancer. * Proteome Characterization Centers (PCCs); The centers, a component of NCI's Clinical Proteomic Tumor Analysis Consortium, will ascertain and analyze the total proteomic content of a subset of TCGA samples. * Data Coordinating Center (DCC); The information that is generated by TCGA will be centrally managed at the DCC and entered into the TCGA Data Portal and Cancer Genomics Hub as it becomes available. Centralization of data facilitates data transfer between the network and the research community, and makes data analysis more efficient. The DCC manages the TCGA Data Portal. * Cancer Genomics Hub (CGHub); Lower level sequence data will be deposited into a secure repository. This database stores cancer genome sequences and alignments. * Genome Data Analysis Centers (GDACs) - Immense amounts of data from array and second-generation sequencing technologies must be integrated across thousands of samples. These centers will provide novel informatics tools to the entire research community to facilitate broader use of TCGA data. TCGA is actively developing a network of collaborators who are able to provide samples that are collected retrospectively (tissues that had already been collected and stored) or prospectively (tissues that will be collected in the future).

Proper citation: The Cancer Genome Atlas (RRID:SCR_003193) Copy   

•   Source: SciCrunch Registry

http://www.bcgsc.ca/project/pleiades-promoter-project

Project to generate human DNA promoters of less than 4 kb (MiniPromoters) to drive gene expression in defined brain regions of therapeutic interest for diseases such as Alzheimer, Parkinson, Huntington, Amyotrophic Lateral Sclerosis, Multiple Sclerosis, Spinocerebellar Ataxia, Depression, Autism, and Cancer. Project develops and shares tools like human MiniPromoters that drive region- and cell-specific gene expression in the mouse brain, expression constructs, mouse embryonic stem cell lines, and knock-in mice all of which carry brain-specific MiniPromoters. Project is daughter of Genome Canada Project, Atlas of Gene Expression in Mouse Development, within which mouse brain gene expression data have already been gathered. Project team has collaborated with International BioPharma Solutions Ltd., management and communications consulting company specializing in product development and commercialization advice. Project will explore challenging interface between science and journalism with focus on genomics and gene therapy.

Proper citation: Pleiades Promoter Project: Genomic Resources Advancing Therapies for Brain Disorders (RRID:SCR_003282) Copy   

•   Source: SciCrunch Registry

http://www.kreftregisteret.no/en/Research/Janus-Serum-Bank/

The Janus Serum Bank has blood samles from 317 000 Norwegians. The biobank is reserved for cancer research, and is internationally unique regarding size and number of cancer cases. The Janus Serum Bank is a population based biobank reserved for cancer research. The specimens are collected during the period from 1972-2004 and are stored at 25 degrees Celsius. The samples originate from 317 000 persons in Norway who have participated in health studies and also from blood donors in and around Oslo. Today, samples are only collected from earlier donors in the Janus Serum Bank who have developed cancer. The Bank is internationally unique regarding size and number of cancer cases. Annual linkage to the Cancer Registry shows that 52 500 donors are diagnosed with cancer as of December 31, 2009. The main goals of the biobank are to make the material available to cancer researchers over the whole world and deliver quality assured samples and data. The Janus Serum Bank is registered in the Biobank Register (Notification number 737)

Proper citation: Janus Serum Bank (RRID:SCR_005885) Copy   

•   Source: SciCrunch Registry

http://ki.se/en/research/ki-biobank

KI Biobank is an accredited core facility offering sample collection services. KI Biobank is located at the Department of Medical Epidemiology and Biostatistics. KI Biobank offer infrastructure for pre analytical sample handling and provide researchers guidance on how samples should be taken and labeled. The processes comprise registration, handling, storage and distribution of samples. KI Biobank also offers DNA-extraction from blood and saliva. In order to insure complete traceability on samples and belonging information all processes are controlled by a Laboratory Information Management System (LIMS). For every new study a contract is established describing the study and the disposition rights. We also help in writing Biobank agreements including multicenteravtal and Material Transfer Agreement. KI Biobank is, according to the Biobank law, responsible for all sample collections handled within the core facility and those that are stored on the departments on KI campus. Clinical sample collections are handled by the Biobank units at the respective hospitals within the Stockholm County Council. Besides the samples that are stored centrally at KI Biobank, KI Biobank is also the administrative biobank for research sample collections at Karolinska Institutet that are stored and administrated at the departments. All research sample collections must be reported to KI Biobank. The following types of sample collections are registered in the biobank; sample collections taken within the regular health care that has been transferred to Karolinska Institutet with an agreement of transfer, samples taken from healthy individuals or other persons out of the regular health care and samples that have been taken abroad.

Proper citation: Karolisnka Biobank (RRID:SCR_004355) Copy   

•   Source: SciCrunch Registry

http://www.rbcsyd.se/

To meet the law requirements and regulations of the National Board of the Southern Health Care Region, Region Skane and Lund University agreed to establish a common biobanking center for Southern healthcare region. Regional biobanksrcentrum will develop and maintain systems for quality assurance and integrity protected using biobanks. The Regional Biobank center is responsible for matters relating to the collection, storage and use of samples stored in biobanks in the Southern healthcare region. Regional Biobank center operations consist of: * to promote the use of biobank material is in accordance with legal requirements biobank * to promote integrity protected and safe storage of repository material * to provide information about the biobank law and biobank materials used for individual sample donors, health professionals, researchers and the public * to handle requests for modified consent and desire to destroy or de test * maintaining a current and privacy protected records of repository material in the region * work to the individual''s integrity will be strengthened in relation to research on biobank material. Tissue samples available to other parties, by surrendering, or by sending tissue samples for analysis, requiring the return or destruction, after completion of the analysis. Regional Biobank Centre (RBC) for the southern healthcare region was established in 2004 and was until 2010 in the Oncology Centre. As of January 1, 2011 it is under the management of RBC Labmedicin Skane.

Proper citation: Swedish Regional Biobank (RRID:SCR_004503) Copy   

•   Source: SciCrunch Registry

http://www.cancerbiobank.org/

CCPRB (Cancer Control using Population-based Registries and Biobanks) is a Network of Excellence project within the sixth framework programme of the European Union. It is aiming at improved control of cancer by facilitating research linking biobanks and cancer registries. The project involves a systematic quality assurance and continuous development of standards and norms for human sample biobanks in Europe, as well as development of improved integrity-protection standards in the handling of sensitive information in connection with biobank-based research. The samples in the biobanks will be used in large-scale cancer research searching for genetic and infectious causes to cancer, in particular in the areas of breast and colorectal cancer and childhood leukemia. Project objectives: * Provide the study base for uniquely large population-based prospective studies on cancer * Define and implement a generally applicable European Quality Standard for Biobanking that will include improved data and specimen standardization, acquisition and analysis, reliable and standardized statistical analysis as well as improved management and co-ordination of European biobanks. * Define and promote the implementation of integrity-proof methods for biobank-based research involving well defined and secure third party code-keeping systems. * Enable large-scale, population-based research on: ** evaluation of cancer treatment and role of molecular markers in treatment selection ** use over-generation registry linkages applied to large biobank cohorts to identify and evaluate genetic predisposition associated with increased cancer risk as well as interactions with common environmental exposures. ** use over-generation registry linkages applied to large biobank cohorts to explore and evaluate intrauterine exposures associated with increased cancer risk ** exploit the power of large population cohorts for design of optimal strategies for cancer prevention and its evaluation. * Establish a Europe-wide network for spreading the awareness of i) the data, samples and knowledge generated European biobank-based research ii) possibilities for future biobank-based research and iii) the best practice quality standards for biobank-based research.

Proper citation: Cancer Control using Population-based Registries and Biobanks (RRID:SCR_004902) Copy   

•   Source: SciCrunch Registry

http://www.ucl.ac.uk/biobank/

Two University College London (UCL) biobanks, one based at the Royal Free Hospital (RFH) Campus and the other based at Bloomsbury supporting Pathology and the Cancer Institute, will act as physical repositories for collections of biological samples and data from patients consented at UCLH, Partners Hospitals and external sources. This will incorporate collections of existing stored samples and new collections. UCL-RFH BioBank, the physical repository at the Royal Free, presents a unique opportunity to advance medical research through making access to research tissue easier, faster and much more efficient. The BioBank is both a physical repository, with capacity for up to 1 million cryogenically stored samples and a virtual repository for all tissue, cell, plasma, serum, DNA and RNA samples stored throughout UCLP. In particular, samples considered "relevant material", such as tissues and cells, that are licensed by the Human Tissue Authority, can be stored long term. Existing holdings of tissues and cells where appropriate can be transferred to the Physical BioBank at the Royal Free. UCL - Royal Free BioBank provides a flexible approach to banking, allowing the Depositor to pick and choose services that are tailored to fit their requirements. Collaborations arising from publicizing of the existence of the holdings are entirely at the discretion of the depositor, as the facility ensures that access to the deposits remains at the decision of the Depositor/User. UCL Biobank for studying Health and Disease (based at Pathology-Rockefeller building and the UCL-Cancer Institute will support projects principally involved in the study of human disease. The aim is to support primarily, research in the Pathology Department, UCLH and the UCL-Cancer Institute but it will also support other UCLH partners. The biobank will store normal and pathological specimens, surplus to diagnostic requirements, from relevant tissues and bodily fluids. Stored tissues will include; snap-frozen or cryopreserved tissue, formalin-fixed tissue, paraffin-embedded tissues, and slides prepared for histological examination. Tissues will include resection specimens obtained surgically or by needle core biopsy. Bodily fluids will include; whole blood, serum, plasma, urine, cerebrospinal fluid, milk, saliva and buccal smears and cytological specimens such as sputum and cervical smears. Fine needle aspirates obtained from tissues and bodily cavities (e.g. pleura and peritoneum) will also be collected. Where appropriate the biobank will also store separated cells, protein, DNA and RNA isolated from collected tissues and bodily fluids described above. Some of the tissue and aspirated samples will be stored in the diagnostic archive.

Proper citation: UCL Biobank (RRID:SCR_000517) Copy   

•   Source: SciCrunch Registry

http://wiki.chasmsoftware.org/index.php/Main_Page

CHASM is a method that predicts the functional significance of somatic missense mutations observed in the genomes of cancer cells, allowing mutations to be prioritized in subsequent functional studies, based on the probability that they give the cells a selective survival advantage. SNV-Box is a database of pre-computed features of all possible amino acid substitutions at every position of the annotated human exome. Users can rapidly retrieve features for a given protein amino acid substitution for use in machine learning.

Proper citation: CHASM/SNV-Box (RRID:SCR_006445) Copy   

•   Source: SciCrunch Registry

http://p53.fr

The UMD TP53 Mutation Database is a novel web site exclusively dedicated to mutant TP53. The following datasets, analytical tools and software are available. * The TP53 UMD mutation database in human cancer (2012 release). This novel release (35,000 mutations, 3,600 publications) has been highly curated using an original and novel statistical procedure (See Edlung et al. PNAS 2012). * TP53MUTLOAD (MUTant Loss Of Activity Database), a novel database dedicated to detailed analysis of the properties of each TP53 mutant, ranging from transactivation to cell growth properties, change of conformation, localization or various gains of functions. The database contains more than 110,000 different entries. * TP53 Mut assessor, a novel stand-alone software available for both Windows and Mac users. Check your favorite TP53 mutants and get an instant identity card. Very useful to analyze any newly discovered TP53 mutants, as the software checks for every possible TP53 mutation. * MUT-TP53 2.0, an accurate and powerful tool that automatically manages p53 mutations and generate tables ready for publication, decreasing the risk of typing errors. MUT-TP53 2.0 also provides specific information for each TP53 mutation, allowing the user to assess the quality of the data. Up to 500 TP53 mutations can be managed simultaneously.

Proper citation: UMD p53 Mutation Database (RRID:SCR_006720) Copy   

•   Source: SciCrunch Registry

http://www.proteinatlas.org/

Open access resource for human proteins. Used to search for specific genes or proteins or explore different resources, each focusing on particular aspect of the genome-wide analysis of the human proteins: Tissue, Brain, Single Cell, Subcellular, Cancer, Blood, Cell line, Structure and Interaction. Swedish-based program to map all human proteins in cells, tissues, and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome.

Proper citation: The Human Protein Atlas (RRID:SCR_006710) Copy   

•   Source: SciCrunch Registry

http://www.hms.harvard.edu/NEPRC/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. A U.S. Regional Primate Research Center that focuses on AIDS, cancer, neuropsychiatric disorders, drug addiction, and neurodegenerative disease. The Division of Primate Resources provides researchers with the services and facilities to support biomedical research. It offers a broad spectrum of services ranging from analysis of tissue specimens to partnership investigations with leading biomedical research institutions. Outside investigators have access to tissue specimens, organs, blood, skeletal structures, and viral specimens. Services include veterinary services, animals and animal care, surgical and radiographic services, timed mating, biocontainment, pathology services, and professional and technical expertise. Additional diagnostic and research services at NEPRC include testing for antiviral antibodies, DNA cloning, and DNA sequencing. The colony of nine species includes rhesus macaques and other Old World monkeys and New World species including the common marmoset and squirrel monkey. Other species can be obtained. Animals with exceptional characteristics (specific-pathogen-free, timed pregnancy, surgically altered, etc.) can be made available if needed. Scientists wishing to conduct research at the center must have projects reviewed and approved by the center animal allocation committee.

Proper citation: New England National Primate Research Center (RRID:SCR_002887) Copy   

•   Source: SciCrunch Registry

http://www.dna-network.ac.uk/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on October 6, 2011. A project to collect, store and study DNA samples from tens of thousands of healthy volunteers and patients with diseases of major public importance. It aims to identify genes that are risk factors for the conditions. The network consists of 13 collections led by different clinicians throughout the UK. At its heart is an archive infrastructure which manages the DNA and the information associated with it. The European Collection of Cell Cultures in Porton Down handles the blood, peripheral blood lymphocytes and EBV-transformed cell lines, while the Centre for Integrated Genomic Medical Research at Manchester University manages the DNA. These banked samples are available to UK and international researchers, who can examine data and set up collaborative work by registering at the DNA Network's website. The conditions for which samples are currently collected and stored are: Acute leukemia, Asthma and eczema, Late onset Alzheimer's disease, Breast cancer, Colorectal cancer, Coronary artery disease, Glomerulonephritis, Hypertension, Age-related macular degeneration, Multiple sclerosis, Parkinson's disease, Type 2 diabetes, Unipolar depression.

Proper citation: UK DNA Banking Network (RRID:SCR_010619) Copy   

•   Source: SciCrunch Registry

http://www.istge.it/crb/english.htm

The Centro di Risorse Biologiche (CRB-IST), institutional facility of IST, has been recently established by the General Director (Deliberation number 624 July 11, 2008). It aims at co-ordinating already existing biobanking activities, and participating in the European Infrastructure of Biobanks and Biomolecular Resources (BBMRI), in preparation in the frame of the 7th FP of the European Community. Aims: * to facilitate high quality translational research dependent on biological material and data * to address ethical issues on biobanking * to promote the project at the population level * to co-ordinate the IST biobanks and cell banks * to harmonize technical and management SOPs, according to international best practices * to help reduce costs for collection and storage of biological material * to favor institutional recognition at a regional, national and international level - to sustain the role of the Institute in the European infrastructure.

Proper citation: Biological Resource Centre - National Institute for Cancer Research (RRID:SCR_010548) Copy   

•   Source: SciCrunch Registry

http://lincs.hms.harvard.edu/db/

Database that contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents and experimental and data analysis protocols. Experimental reagents include small molecule perturbagens, cells, antibodies, and proteins.

Proper citation: HMS LINCS Database (RRID:SCR_006454) Copy   

•   Source: SciCrunch Registry

http://dgidb.genome.wustl.edu/

A database of drug-gene relationships that provides drug-gene interactions and potential druggability data given list of genes. There are about 15 data sources that are being aggregated by DGIdb, with update date and these data sources are listed on this page: http://dgidb.genome.wustl.edu/sources, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DGIdb (RRID:SCR_006608) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/CANCO

A vocabulary that is able to describe and semantically interconnect the different paradigms of the cancer chemoprevention domain.

Proper citation: Cancer Chemoprevention Ontology (RRID:SCR_006966) Copy   

•   Source: SciCrunch Registry