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http://cgap.nci.nih.gov/Chromosomes/Mitelman
The web site includes genomic data for humans and mice, including transcript sequence, gene expression patterns, single-nucleotide polymorphisms, clone resources, and cytogenetic information. Descriptions of the methods and reagents used in deriving the CGAP datasets are also provided. An extensive suite of informatics tools facilitates queries and analysis of the CGAP data by the community. One of the newest features of the CGAP web site is an electronic version of the Mitelman Database of Chromosome Aberrations in Cancer. The data in the Mitelman Database is manually culled from the literature and subsequently organized into three distinct sub-databases, as follows: -The sub-database of cases contains the data that relates chromosomal aberrations to specific tumor characteristics in individual patient cases. It can be searched using either the Cases Quick Searcher or the Cases Full Searcher. -The sub-database of molecular biology and clinical associations contains no data from individual patient cases. Instead, the data is pulled from studies with distinct information about: -Molecular biology associations that relate chromosomal aberrations and tumor histologies to genomic sequence data, typically genes rearranged as a consequence of structural chromosome changes. -Clinical associations that relate chromosomal aberrations and/or gene rearrangements and tumor histologies to clinical variables, such as prognosis, tumor grade, and patient characteristics. It can be searched using the Molecular Biology and Clinical (MBC) Associations Searcher -The reference sub-database contains all the references culled from the literature i.e., the sum of the references from the cases and the molecular biology and clinical associations. It can be searched using the Reference Searcher. CGAP has developed six web search tools to help you analyze the information within the Mitelman Database: -The Cases Quick Searcher allows you to query the individual patient cases using the four major fields: aberration, breakpoint, morphology, and topography. -The Cases Full Searcher permits a more detailed search of the same individual patient cases as above, by including more cytogenetic field choices and adding search fields for patient characteristics and references. -The Molecular Biology Associations Searcher does not search any of the individual patient cases. It searches studies pertaining to gene rearrangements as a consequence of cytogenetic aberrations. -The Clinical Associations Searcher does not search any of the individual patient cases. It searches studies pertaining to clinical associations of cytogenetic aberrations and/or gene rearrangements. -The Recurrent Chromosome Aberrations Searcher provides a way to search for structural and numerical abnormalities that are recurrent, i.e., present in two or more cases with the same morphology and topography. -The Reference Searcher queries only the references themselves, i.e., the references from the individual cases and the molecular biology and clinical associations. Sponsors: This database is sponsored by the University of Lund, Sweden and have support from the Swedish Cancer Society and the Swedish Children''s Cancer Foundation
Proper citation: Mitelman Database of Chromosome Aberrations in Cancer (RRID:SCR_012877) Copy
A platform and application suite for bringing together omics and clinical data.
Proper citation: Syapse (RRID:SCR_012023) Copy
https://biolincc.nhlbi.nih.gov/home/
Repository that serves to coordinate searches across data and biospecimen collections from participants in numerous clinical trials and epidemiologic studies and to provide an electronic means for requests for additional information and the submission of requests for collections. The collections, comprising data from more than 80 trials or studies and millions of biospecimens, are available to qualified investigators under specific terms and conditions consistent with the informed consents provided by the individual study participants. Some datasets are presented with studies and supporting materials to facilitate their use in reuse and teaching. Datasets support basic research, clinical studies, observational studies, and demonstrations. Researchers wishing to apply to submit biospecimen collections to the NHLBI Biorepository for sharing with qualified investigators may also use this website to initiate that process.
Proper citation: Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC) (RRID:SCR_013142) Copy
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
A virtual biospecimen registry designed to support and facilitate basic science, clinical, and translational research that will advance understanding of mesothelioma pathophysiology with the goal of expediting the discovery of preventive measures, novel therapeutic interventions, and ultimately, cures for mesothelioma. The NMVB resource is designed to provide mesothelioma tissue samples with high-quality and well-characterized multimodal annotated data to researchers. The NMVB team strongly believes that progress in translational and clinical research - in cancer as well as other disease areas - depends on the ability of researchers to access high-quality tissue that is associated with meaningful annotation. MVB database version 3.0 has been released that provides researchers real-time access to demographic, epidemiologic, pathologic, genotype, and follow-up data associated with biospecimens at no cost. Researchers interested in utilizing NMVB samples for their research may submit an application. All researchers (academic or commercial, United States or foreign) may apply for NMVB tissue specimens. NMVB currently has 966 annotated cases and 1198 biospecimens including: * Paraffin Embedded Tissue * Fresh Frozen Tissue * Blood and DNA Samples The NMVB also has developed mesothelioma tissue microarrays (TMAs) with associated multimodal data annotation. Additional TMAs will be available shortly.
Proper citation: National Mesothelioma Virtual Bank (RRID:SCR_003438) Copy
Consortium to address the increasing demand by researchers for quality-controlled, disease-relevant research grade induced Pluripotent Stem Cell (iPSC) lines, data and cell services by demonstrating an operational banking and distribution service of iPSC lines after 3 years and establishing subsequently for Europe a centralized, not-for-profit bank providing all qualified users with access to scalable, cost-efficient and customized products. The main facility will be at the Babraham Research Campus (Cambridge, UK) and will undertake cell expansion, QC and characterization. The European Cell Culture Collection (ECACC) of Public Health England (Department of Health, UK) will coordinate cell line distribution. The Fraunhofer IBMT (Saarbr��cken, Germany) will provide comprehensive operational back up. In a phased business strategy EBiSC will hot-start distribution of lines contributed by iPSC Centres in 2014, lines collected based on specified user demand, will reach full scale operations in 2016, and with extended funding will become self-sustaining as a not for profit banking operation by 2019. EBiSC will spearhead Europe in the international standardization of iPSC banking by forging collaborative links with similar endeavors in the USA and Asia. It will also provide training to encourage adoption and use of the bank. The project has up to one year after completion to disseminate intellectual property or data created by the project.
Proper citation: EBiSC (RRID:SCR_003856) Copy
http://www.tmf-ev.de/BiobankenRegisterEN/Registry.aspx?udt_2021_param_detail=72
It is the aim of the SepNet initiative to establish a central facility, essential to data and sample quality and homogeneity, that comprises a structured and easily accessible sample bank with probes of homogeneous quality originating from a well-characterized patient population enrolled in independent, innovative and internationally competitive prospective clinical sepsis trials. The SepNetBiobank is a core facility of SepNet. The object of this central sample resource is to organize and handle all relevant aspects of sampling, storage and delivery of samples in the SepNet collaboration to ensure homogeneity of the samples in terms of specimen quality and maintaining sampling standards. This will be achieved through central handling of samples collected in peripheral nationwide 17 regional centers and an additional 36 associated centers according to an agreed sampling scheme and pre-set standards for sample quality, sample handling and banking; quality assurance and all relevant parts of sample handling will be in the hands of the core unit, minimizing pre-analytical steps in the heterogeneous environment of the different regional centers. In the next few months a fully automated sample storage system will be implemented that allows handling of more than 200.000 individual aliquots expected after completion of the different ongoing and planned SepNet Trails. In the next six months a fully automated -80 degree C sample storage system will be implemented. After completion of the plannend and ongoing SepNet trials more than 59.710 expected primary samples (218.040 aliquots) will be stored in this system. This outstanding sample resource will provide the basis for scientific projects aming at improving patient care with sepsis e.g. advancement in diagnostics, risk stratification, therapy and outcome.
Proper citation: SepNet Central Sample Bank (RRID:SCR_004543) Copy
http://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/UCM380961.pdf
An electronically administered patient-reported outcome (PRO) measure that is a qualified measure of symptoms of acute bacterial exacerbation of chronic bronchitis in patients with chronic obstructive pulmonary disease (ABECB-COPD), for use in phase 2 trials. Refer to the proposed context of use, http://www.fda.gov/downloads/Drugs/DevelopmentApprovalProcess/DrugDevelopmentToolsQualificationProgram/UCM399682.pdf. Its intent to quantify frequency, severity, and duration of acute exacerbations in clinical trials of COPD including those with chronic bronchitis. It is designed as an electronic diary made up of fourteen items to be completed by the patient each evening just prior to bedtime. (An item-reduction statistical analysis narrowed the questions from 23 to 14.) For more information see, http://www.fda.gov/downloads/Drugs/DevelopmentApprovalProcess/DrugDevelopmentToolsQualificationProgram/UCM386248.pdf
Proper citation: Exacerbations of Chronic Pulmonary Disease Tool (RRID:SCR_003718) Copy
Repository of person centered measures that evaluates and monitors physical, mental, and social health in adults and children.
Proper citation: Patient-Reported Outcomes Measurement Information System (RRID:SCR_004718) Copy
http://www.kcl.ac.uk/medicine/research/divisions/diiid/centres/pii/biobank/index.aspx
Centralized specimen archiving and molecular analysis facility that assists researchers wishing to undertake cohort-based projects in areas such HIV/AIDS, HCV infection or MRSA. Its aim is to make medical research easier, more efficient and faster to perform. The IDB collects valuable clinical samples from patients with infections who are attending their partner NHS-Trust clinics. Their core collections include blood samples from patients infected with human immunodeficiency virus (HIV), hepatitis B (HBV) & hepatitis C (HCV) viruses or methicillin resistant Staphylococcus aureus (MRSA). Blood samples are separated so that patients������?? DNA, plasmas (cell-free blood) and lymphocytes (white blood cells) can be frozen into a comprehensive library. Medical researchers can access complete sets of samples to answer important clinical questions, if their research project is approved by the IDB''s Management Committee. For this reason they are actively recruiting ''medically interesting'' patients who are infected with HIV, for example: those who remain well ������?? despite being infected for many years; others who are exposed to HIV but remain uninfected; others who develop AIDS very quickly; and, those who are in the process of sero-converting.
Proper citation: Kings College London Infectious Diseases BioBank (RRID:SCR_004827) Copy
http://ki.se/ki/jsp/polopoly.jsp?d=29328&a=30572&l=en
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016.
Proper citation: KI Biobank - NOAK (RRID:SCR_006008) Copy
Collects and stores genetic (DNA) samples along with associated healthcare information from patients of Northwestern-affiliated hospitals and clinics. This resource is available to scientists to conduct groundbreaking genetic research. The information and blood samples provided will be used by researchers to examine the role genes play in the development and treatment of common diseases. The NUgene Project seeks to increase the understanding of genetic mechanisms underlying common diseases, assist in the development of DNA-based technology for diagnosis and treatment of disease, and aid physicians and other healthcare providers in the application of genetics to the practice of medicine. NUgene participants are recruited throughout the Northwestern-affiliated healthcare community in order to create an ethnically and medically diverse population for research. Participants must be 18 years of age or older and receive their medical care from a Northwestern-affiliated provider, regardless of health status. Consenting individuals complete all aspects of enrollment in a single meeting with a research coordinator. The enrollment process includes the donation of a single sample of blood and the completion of a self-administered questionnaire. Participants also sign a consent form during this encounter. The NUgene Project is an interdisciplinary project that relies on the expertise of individuals working in a variety of fields, including science, medicine, clinical research, statistics, epidemiology, and computational biology. NUgene''s multidisciplinary approach has spurred collaborations within Northwestern-affiliated institutions and with other outside institutions. This collaboration of ideas is the future of genetics and genomic research., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: NUgene Project (RRID:SCR_007426) Copy
http://www.niaid.nih.gov/about/organization/dait/pages/csgadp.aspx
Collaborative network of investigators with a focus on prevention of autoimmune disease, defined as halting the development of autoimmune disease prior to clinical onset by means other than global immunosuppression, and an emphasis on Type 1 diabetes. Its mission is to engage in scientific discovery that significantly advances knowledge for the prevention and regulation of autoimmune disease. The specific goals enunciated in pursuit of this mission are: * To create improved models of disease pathogenesis and therapy to better understand immune mechanisms that will provide opportunities for prevention strategies * To use these models as validation platforms with which to test new tools applicable to human studies * To encourage core expertise and collaborative projects designed for rapid translation from animal to human studies, emphasizing the development of surrogate markers for disease progression and/or regulation which can be utilized in the context of clinical trials
Proper citation: Cooperative Study Group for Autoimmune Disease Prevention (RRID:SCR_006803) Copy
Database and biorepository from a multi-site, multi-disciplinary study characterizing the familial transmission of alcoholism and related phenotypes and identifying susceptibility genes using genetic linkage. Investigators have assembled a collection of over 300 extended families densely affected by alcoholism (more than 3000 individuals), including clinical, neuropsychological, electrophysiological, biochemical, and genetic data, and established a repository of immortalized cell lines from these individuals, to serve as a permanent source of DNA for genetic studies. NIAAA has funded the Collaborative Studies on Genetics of Alcoholism (COGA) since 1989, with the goal of identifying the specific genes underlying this vulnerability. Data and biomaterials are available to qualified investigators in the broader scientific community. Recipients of data and biomaterials will be responsible for defraying the cost of their distribution. Pedigrees densely affected with alcoholism (DSM-III-R) have been ascertained at six sites (SUNY Downstate Health Sciences Center, University of Connecticut, Indiana University, Washington University, University of Iowa, and The University of California at San Diego). Diagnoses of alcohol dependence according to several diagnostic systems (e.g., DSM-III-R, Feighner, ICD-10) are made based on examination of medical records and direct assessment using the Semi-Structured Assessment for Genetics of Alcoholism (SSAGA). Nuclear and extended pedigrees containing at least two alcohol-dependent first-degree relatives in addition to an alcohol dependent proband (with all affected individuals meeting both DSM-IIIR and Feighner criteria) have been ascertained. Clinical data comprises anonymous data on family structure, age, sex, vital status, psychopathology, diagnosis, other clinically relevant information, are stored, maintained, and distributed by Washington University. Research data, consist of data on blood biochemistry and psychological test performance, which are stored, maintained, and distributed by Washington University, and brain electrophysiological data, which are stored, maintained, and distributed by SUNY. Genetic analysis data, consisting of marker genotypes, along with results of previous genetic analyses of COGA data, are stored, maintained, and distributed by Washington University. Biomaterials, consisting of lymphoblastoid cell lines and DNA from participating subjects are stored, maintained, and distributed by Rutgers University. Researchers may gain access to clinical data, research data, genetic analysis data, and biomaterials, subject to NIAAA approval, by completing an application details available from the website. After access certification, the principal investigator will be given access to electronic data files and other documentation.
Proper citation: Collaborative Studies on Genetics of Alcoholism (RRID:SCR_006841) Copy
An observational longitudinal clinical study partnership to identify and validate biomarkers of Parkinson disease (PD) progression and provide easy and open web-based access to the comprehensive set of correlated clinical data and biospecimens, information, and biosamples acquired from PD and age and gender matched healthy control subjects to the research community. The data and specimens have been collected in a standardized manner under strict protocols and includes clinical (demographic, motor and non-motor, cognitive and neurobehavioral), imaging (raw and processed MRI, SPECT and DAT), and blood chemistry and hematology subject assessments and biospecimen inventories (serum, plasma, whole blood, CSF, DNA, RNA and urine). All data are de-identified to protect patient privacy. PPMI will be carried out over five years at 21 clinical sites in the United States and Europe and requires the participation of 400 Parkinson's patients and 200 control participants. The PPMI database provides researchers with access to correlated clinical and imaging data, along with annotated biospecimens, all available within an open access system that encourages data sharing (http://www.ppmi-info.org/access-data-specimens/). The website hosts an Ongoing Analysis section to keep the scientific community apprised of analyses being completed, in hopes of stimulating collaborations between researchers who are using PPMI data and specimens.
Proper citation: Parkinson's Progression Markers Initiative (RRID:SCR_006431) Copy
Program provides advanced graduate training to veterinarians who wish to pursue careers in comparative medicine. Trainees may combine one year of residency training in clinical, administrative and diagnostic laboratory animal medicine with two or more years of research training. Alternatively, trainees with experience in laboratory animal medicine, comparative pathology or related disciplines may begin research training at the time of admission. Training is designed to prepare individuals for a variety of careers including comparative medicine research, clinical and administrative laboratory animal medicine and comparative and diagnostic laboratory animal pathology. Students may either pursue an MS or PhD. Research opportunities are available in several areas including infectious disease, pathology, molecular biology, mouse biology and cardiovascular physiology. Resources available include the University of Missouri Office of Animal Resources (OAR) and Research Animal Diagnostic Laboratory (RADIL) and Mutant Mouse and Rat Resource and Research Centers. The University of Missouri Comparative Medicine Program (CMP) is post Doctor of Veterinary Medicine training that combines graduate residency training, course work and research. Trainees with relevant experience in laboratory animal medicine or comparative pathology may pursue research training without residency training. In the residency year of training, two rotations are performed: diagnostic laboratory animal pathology in the Research Animal Diagnostic Laboratory (RADIL); clinical medicine and animal resource management in the Office of Animal Resources (OAR). The remaining two to four years focus on research training under an established investigator. After three years, trainees successfully fulfilling program requirements receive a certificate of residency training. MS students complete their program while PhD students continue to pursue research training. Sponsors: CMP is supported by the University of Missouri comparative, medicine, veterinarian, residency, training, clinical, administrative, diagnostic, laboratory, animal, pathology, cardiovascular, molecular, biology, mouse, physiology
Proper citation: University of Missouri Comparative Medicine Program (RRID:SCR_008298) Copy
Semi-automated and manually curated database of gene/variant annotations, therapy knowledge, diagnostic/prognostic information, and oncology clinical trials. Users can search CKB via gene, gene variants, drug, drug class, indication, and clinical trials.
Proper citation: Jackson Laboratory Clinical Knowledgebase (RRID:SCR_014965) Copy
http://diabetes.wisc.edu/index.php
Interactive database of gene expression and diabetes related clinical phenotypes. Allows to search gene expression in tissues as a function of obesity, strain, and age, in a mouse.
Proper citation: Attie Lab Diabetes Database (RRID:SCR_016639) Copy
https://www.cdc.gov/nchs/ndi/index.htm
Database of death record information on file in state vital statistics offices. Working with these state offices, the National Center for Health Statistics (NCHS) established the NDI as a resource to aid epidemiologists and other health and medical investigators with their mortality ascertainment activities.
Proper citation: National Death Index (RRID:SCR_016369) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23,2022. A database that lists, reviews, and rates resources for teaching neuroscience at the graduate and undergraduate level.
Proper citation: Educational Resources in Neuroscience (RRID:SCR_000169) Copy
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
