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http://kidney.niddk.nih.gov

Information dissemination service of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) established to increase knowledge and understanding about diseases of the kidneys and urologic system among people with these conditions and their families, health care professionals, and the general public: online, in booklets and fact sheets, by email, and over the phone. To carry out this mission, NKUDIC works closely with a coordinating panel of representatives from Federal agencies; voluntary organizations on the national level; professional groups; and State health departments to identify and respond to informational needs about kidney and urologic diseases. NKUDIC provides the following informational products and services: * Response to inquiries about kidney and urologic diseases-ranging from information about available patient and professional education materials to statistical data. By phone (8:30 a.m. to 5 p.m. eastern time, M-F), fax, mail, and email. * Publications about specific kidney and urologic diseases, provided free of copyright, in varying reading levels. Available online or as booklets and brochures. (See our Publications Catalog.) NKUDIC also sends publications to health fairs and community events. Please contact us for more information. * Referrals to health professionals through the National Library of Medicine''''s MEDLINEplus includes a consumer-friendly listing of organizations that will assist you in your search for physicians and other health professionals. * Exhibits at professional meetings specific to kidney and urologic diseases, as well as cross-cutting professional meetings. NKUDIC exhibits at 11 professional meetings, each year, including Society of Urologic Nurses and Associates, American Urologic Association, American Society of Nephrology, National Kidney Foundation, Polycystic Kidney Disease Research Foundation, American Academy of Family Physicians, American Academy of Physician Assistants, American Nurses Association, and the National Conference for Nurse Practitioners.

Proper citation: National Kidney and Urologic Diseases Information Clearinghouse (RRID:SCR_006842) Copy   

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http://www.cidr.jhmi.edu/

Next generation sequencing and genotyping services provided to investigators working to discover genes that contribute to disease. On-site statistical geneticists provide insight into analysis issues as they relate to study design, data production and quality control. In addition, CIDR has a consulting agreement with the University of Washington Genetics Coordinating Center (GCC) to provide statistical and analytical support, most predominantly in the areas of GWAS data cleaning and methods development. Completed studies encompass over 175 phenotypes across 530 projects and 620,000 samples. The impact is evidenced by over 380 peer-reviewed papers published in 100 journals. Three pathways exist to access the CIDR genotyping facility: * NIH CIDR Program: The CIDR contract is funded by 14 NIH Institutes and provides genotyping and statistical genetic services to investigators approved for access through competitive peer review. An application is required for projects supported by the NIH CIDR Program. * The HTS Facility: The High Throughput Sequencing Facility, part of the Johns Hopkins Genetic Resources Core Facility, provides next generation sequencing services to internal JHU investigators and external scientists on a fee-for-service basis. * The JHU SNP Center: The SNP Center, part of the Johns Hopkins Genetic Resources Core Facility, provides genotyping to internal JHU investigators and external scientists on a fee-for-service basis. Data computation service is included to cover the statistical genetics services provided for investigators seeking to identify genes that contribute to human disease. Human Genotyping Services include SNP Genome Wide Association Studies, SNP Linkage Scans, Custom SNP Studies, Cancer Panel, MHC Panels, and Methylation Profiling. Mouse Genotyping Services include SNP Scans and Custom SNP Studies.

Proper citation: Center for Inherited Disease Research (RRID:SCR_007339) Copy   

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http://t1dbase.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 26,2019. In October 2016, T1DBase has merged with its sister site ImmunoBase (https://immunobase.org). Documented on March 2020, ImmunoBase ownership has been transferred to Open Targets (https://www.opentargets.org). Results for all studies can be explored using Open Targets Genetics (https://genetics.opentargets.org). Database focused on genetics and genomics of type 1 diabetes susceptibility providing a curated and integrated set of datasets and tools, across multiple species, to support and promote research in this area. The current data scope includes annotated genomic sequences for suspected T1D susceptibility regions; genetic data; microarray data; and global datasets, generally from the literature, that are useful for genetics and systems biology studies. The site also includes software tools for analyzing the data.

Proper citation: T1DBase (RRID:SCR_007959) Copy   

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https://syllabus.med.unc.edu/courseware/embryo_images/

Tutorial that uses scanning electron micrographs (SEMs) as the primary resource to teach mammalian embryology. The 3-D like quality of the micrographs coupled with selected line drawings and minimal text allow relatively easy understanding of the complex morphological changes that occur in utero. Because early human embryos are not readily available and because embryogenesis is very similar across mammalian species, the majority of micrographs that are utilized in this tutorial are of mouse embryos. The remainder are human. This tutorial is divided into units that may be studied in any order. All of the images have a legend that indicates the age of the embryo. If it is a mouse embryo, the approximate equivalent human age is indicated. To minimize labeling, color-coding is widely used. To view the micrographs without color, the cursor may be placed on the image. The SEMs used in this tutorial are from the Kathleen K. Sulik collection. The line drawings have been used with permission from Lippincott Williams & Wilkins and are from the 6th and 7th editions of Langman''s Medical Embryology by T.W. Sadler.

Proper citation: Embryo Images Normal and Abnormal Mammalian Development (RRID:SCR_006297) Copy   

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http://www.autoimmunitycenters.org/

Nine centers that conduct clinical trials and basic research on new immune-based therapies for autoimmune diseases. This program enhances interactions between scientists and clinicians in order to accelerate the translation of research findings into medical applications. By promoting better coordination and communication, and enabling limited resources to be pooled, ACEs is one of NIAID''''s primary vehicles for both expanding our knowledge and improving our ability to effectively prevent and treat autoimmune diseases. This coordinated approach incorporates key recommendations of the NIH Autoimmune Diseases Research Plan and will ensure progress in identifying new and highly effective therapies for autoimmune diseases. ACEs is advancing the search for effective treatments through: * Diverse Autoimmunity Expertise Medical researchers at ACEs include rheumatologists, neurologists, gastroenterologists, and endocrinologists who are among the elite in their respective fields. * Strong Mechanistic Foundation ACEs augment each clinical trial with extensive basic studies designed to enhance understanding of the mechanisms responsible for tolerance initiation, maintenance, or loss, including the role of cytokines, regulatory T cells, and accessory cells, to name a few. * Streamlined Patient Recruitment The cooperative nature of ACEs helps scientists recruit patients from distinct geographical areas. The rigorous clinical and basic science approach of ACEs helps maintain a high level of treatment and analysis, enabling informative comparisons between patient groups.

Proper citation: Autoimmunity Centers of Excellence (RRID:SCR_006510) Copy   

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http://www.ebi.ac.uk/pdbe/emdb/

Repository for electron microscopy density maps of macromolecular complexes and subcellular structures at Protein Data Bank in Europe. Covers techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography.

Proper citation: Electron Microscopy Data Bank at PDBe (MSD-EBI) (RRID:SCR_006506) Copy   

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https://repository.niddk.nih.gov/home/

NIDDK Central Repositories are two separate contract funded components that work together to store data and samples from significant, NIDDK funded studies. First component is Biorepository that gathers, stores, and distributes biological samples from studies. Biorepository works with investigators in new and ongoing studies as realtime storage facility for archival samples.Second component is Data Repository that gathers, stores and distributes incremental or finished datasets from NIDDK funded studies Data Repository helps active data coordinating centers prepare databases and incremental datasets for archiving and for carrying out restricted queries of stored databases. Data Repository serves as Data Coordinating Center and website manager for NIDDK Central Repositories website.

Proper citation: NIDDK Central Repository (RRID:SCR_006542) Copy   

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http://www.informatics.jax.org/expression.shtml

Community database that collects and integrates the gene expression information in MGI with a primary emphasis on endogenous gene expression during mouse development. The data in GXD are obtained from the literature, from individual laboratories, and from large-scale data providers. All data are annotated and reviewed by GXD curators. GXD stores and integrates different types of expression data (RNA in situ hybridization; Immunohistochemistry; in situ reporter (knock in); RT-PCR; Northern and Western blots; and RNase and Nuclease s1 protection assays) and makes these data freely available in formats appropriate for comprehensive analysis. There is particular emphasis on endogenous gene expression during mouse development. GXD also maintains an index of the literature examining gene expression in the embryonic mouse. It is comprehensive and up-to-date, containing all pertinent journal articles from 1993 to the present and articles from major developmental journals from 1990 to the present. GXD stores primary data from different types of expression assays and by integrating these data, as data accumulate, GXD provides increasingly complete information about the expression profiles of transcripts and proteins in different mouse strains and mutants. GXD describes expression patterns using an extensive, hierarchically-structured dictionary of anatomical terms. In this way, expression results from assays with differing spatial resolution are recorded in a standardized and integrated manner and expression patterns can be queried at different levels of detail. The records are complemented with digitized images of the original expression data. The Anatomical Dictionary for Mouse Development has been developed by our Edinburgh colleagues, as part of the joint Mouse Gene Expression Information Resource project. GXD places the gene expression data in the larger biological context by establishing and maintaining interconnections with many other resources. Integration with MGD enables a combined analysis of genotype, sequence, expression, and phenotype data. Links to PubMed, Online Mendelian Inheritance in Man (OMIM), sequence databases, and databases from other species further enhance the utility of GXD. GXD accepts both published and unpublished data.

Proper citation: Gene Expression Database (RRID:SCR_006539) Copy   

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http://www.nkdep.nih.gov/lab-evaluation/gfr-calculators.shtml

Glomerular Filtration Rate (GFR) calculators to estimate kidney function for adults (MDRD GFR Calculator) and children (Schwartz GFR Calculator). In adults, the recommended equation for estimating glomerular filtration rate (GFR) from serum creatinine is the Modification of Diet in Renal Disease (MDRD) Study equation. The IDMS-traceable version of the MDRD Study equation is used. Currently the best equation for estimating glomerular filtration rate (GFR) from serum creatinine in children is the Bedside Schwartz equation for use with creatinine methods with calibration traceable to IDMS. Using the original Schwartz equation with a creatinine value from a method with calibration traceable to IDMS will overestimate GFR.

Proper citation: Glomerular Filtration Rate Calculators (RRID:SCR_006443) Copy   

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http://www.nkdep.nih.gov/lab-evaluation/gfr/creatinine-standardization.shtml

Standard specification to reduce inter-laboratory variation in creatinine assay calibration and therefore enable more accurate estimates of glomerular filtration rate (eGFR). Created by NKDEP''''s Laboratory Working Group in collaboration with the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) and the European Communities Confederation of Clinical Chemistry (now called the European Federation of Clinical Chemistry and Laboratory Medicine), the effort is part of a larger NKDEP initiative to help health care providers better identify and treat chronic kidney disease in order to prevent or delay kidney failure and improve patient outcomes. Recommendations are intended for the USA and other countries or regions that have largely completed standardization of creatinine calibration to be traceable to an isotope dilution mass spectrometry (IDMS) reference measurement procedure. The program''''s focus is to facilitate the sharing of information to assist in vitro diagnostic manufacturers, clinical laboratories, and others in the laboratory community with calibrating their serum creatinine measurement procedures to be traceable to isotope dilution mass spectrometry (IDMS). The program also supports manufacturers'''' efforts to encourage their customers in the laboratory to coordinate use of standardized creatinine methods with implementation of a revised GFR estimating equation appropriate for use with standardized creatinine methods. Communication resources and other information for various segments of the laboratory community are available in the Creatinine Standardization Recommendations section of the website. Also available is a protocol for calibrating creatinine measurements using whole blood devices. The National Institute for Standards and Technology (NIST) released a standard reference material (SRM 967 Creatinine in Frozen Human Serum) for use in establishing calibrations for routine creatinine measurement procedures. SRM 967 was validated to be commutable with native serum samples for many routine creatinine procedures and is useful to establish or verify traceability to an IDMS reference measurement procedure. Establishing calibrations for serum creatinine methods using SRM 967 not only provides a mechanism for ensuring more accurate measurement of serum creatinine, but also enables more accurate estimates of GFR. For clinical laboratories interested in independently checking the calibration supplied by their creatinine reagent suppliers/manufacturers, periodic measurement of NIST SRM 967 should be considered for inclusion in the lab''''s internal quality assurance program. To learn more about SRM 967, including how to purchase it, visit the NIST website, https://www-s.nist.gov/srmors/quickSearch.cfm

Proper citation: Creatinine Standardization Program (RRID:SCR_006441) Copy   

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http://www.thegpm.org/

The Global Proteome Machine Organization was set up so that scientists involved in proteomics using tandem mass spectrometry could use that data to analyze proteomes. The projects supported by the GPMO have been selected to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results. The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. This database has been integrated into GPM server pages, allowing users to quickly compare their experimental results with the best results that have been previously observed by other scientists.

Proper citation: Global Proteome Machine Database (GPM DB) (RRID:SCR_006617) Copy   

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http://www.usrds.org/

Annual report, standard analysis files and an online query system from the national data registry on the end-stage renal disease (ESRD) population in the U.S., including treatments and outcomes. The Annual Data Report is divided into two parts. The Atlas section displays data using graphs and charts. Specific chapters address trends in ESRD patient populations, quality of ESRD care, kidney transplantation outcomes, costs of ESRD care, Healthy People 2010 objectives, chronic kidney disease, pediatric ESRD, and cardiovascular disease special studies. The Reference Tables are devoted entirely to the ESRD population. The RenDER (Renal Data Extraction and Referencing) online data query system allows users to build data tables and maps for the ESRD population. National, state, and county level data are available. USRDS staff collaborates with members of Centers for Medicare & Medicaid Services (CMS), the United Network for Organ Sharing (UNOS), and the ESRD networks, sharing datasets and actively working to improve the accuracy of ESRD patient information.

Proper citation: United States Renal Data System (RRID:SCR_006699) Copy   

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https://www.fludb.org/brc/home.spg?decorator=influenza

The Influenza Research Database (IRD) serves as a public repository and analysis platform for flu sequence, experiment, surveillance and related data.

Proper citation: Influenza Research Database (IRD) (RRID:SCR_006641) Copy   

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http://diabetes.niddk.nih.gov/dm/pubs/america/

A compilation and assessment of epidemiologic, public health, and clinical data on diabetes and its complications in the United States. Published by the National Diabetes Data Group of the National Institute of Diabetes and Digestive and Kidney Diseases, the book contains 36 chapters organized in five areas: * the descriptive epidemiology of diabetes in the United States based on national surveys and community-based studies, including prevalence, incidence, sociodemographic and metabolic characteristics, risk factors for developing diabetes, and mortality * the myriad complications that affect patients with diabetes * characteristics of therapy and medical care for diabetes * economic aspects, including health insurance and health care costs * diabetes in special populations, including African Americans, Hispanics, Asian and Pacific Islanders, Native Americans, and pregnant women. Diabetes in America, 2nd Edition, has been designed to serve as a reliable scientific resource for assessing the scope and impact of diabetes and its complications, determining health policy and priorities in diabetes, and identifying areas of need in research. The intended audience includes health policy makers at the local and Federal levels who need a sound quantitative base of knowledge to use in decision making; clinicians who need to know the probability that their patients will develop diabetes and the prognosis of the disease for complications and premature mortality; persons with diabetes and their families who need sound information on which to make decisions about their life with diabetes; and the research community which needs to identify areas where important scientific knowledge is lacking.

Proper citation: Diabetes in America (RRID:SCR_006754) Copy   

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http://www.peptideatlas.org

Multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences. All results of sequence and spectral library searching are subsequently processed through the Trans Proteomic Pipeline to derive a probability of correct identification for all results in a uniform manner to insure a high quality database, along with false discovery rates at the whole atlas level. The raw data, search results, and full builds can be downloaded for other uses. All results of sequence searching are processed through PeptideProphet to derive a probability of correct identification for all results in a uniform manner ensuring a high quality database. All peptides are mapped to Ensembl and can be viewed as custom tracks on the Ensembl genome browser. The long term goal of the project is full annotation of eukaryotic genomes through a thorough validation of expressed proteins. The PeptideAtlas provides a method and a framework to accommodate proteome information coming from high-throughput proteomics technologies. The online database administers experimental data in the public domain. You are encouraged to contribute to the database.

Proper citation: PeptideAtlas (RRID:SCR_006783) Copy   

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https://zenodo.org/

Repository for all research outputs from across all fields of science in any file format as well as both positive and negative results. They assign all publicly available uploads a Digital Object Identifier (DOI) to make the upload easily and uniquely citeable. They further support harvesting of all content via the OAI-PMH protocol. They promote peer-reviewed openly accessible research, and curate uploads. ZENODO allows users to create their own collection and accept or reject all uploads to it. They allow for uploading under a multitude of different licenses and access levels.

Proper citation: ZENODO (RRID:SCR_004129) Copy   

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http://dkcoin.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented October 13, 2014. The resource has moved to the NIDDKInformation Network (dkNET) project. Contact them at info_at_dknet.org with any questions. Database of large pools of data relevant to the mission of NIDDKwith the goal of developing a community-based network for integration across disciplines to include the larger DKuniverse of diseases, investigators, and potential users. The focus is on greater use of this data with the objective of adding value by breaking down barriers between sites to facilitate linking of different datasets. To date (2013/06/10), a total of 1,195 resources have been associated with one or more genes. Of 11,580 total genes associated with resources, the ten most represented are associated with 359 distinct resources. The main method by which they currently interconnect resources between the providers is via EntrezGene identifiers. A total of 780 unique genes provide the connectivity between 3,159 resource pairs across consortia. To further increase interconnectivity, the groups have been further annotating their data with additional gene identifiers, publications, and ontology terms from selected Open Biological and Biomedical Ontologies (OBO).

Proper citation: dkCOIN (RRID:SCR_004438) Copy   

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http://www.cure.med.ucla.edu/

Center whose interests and activities encompass several facets of gastrointestinal regulatory physiology and cell biology. It provides an infrastructure to support basic, translational and clinical research and to facilitate interdisciplinary research and training activities in digestive diseases.

Proper citation: CURE - Digestive Diseases Research Center (RRID:SCR_004238) Copy   

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http://www.ncbi.nlm.nih.gov/pcsubstance?db=pcsubstance

As one of three primary databases of PubChem (Pcsubstance, Pccompound, and PCBioAssay), PubChem Substance Database contains descriptions of chemical samples, from a variety of sources, and links to PubMed citations, protein 3D structures, and biological screening results that are available in PubChem BioAssay. If the contents of a chemical sample are known, the description includes links to PubChem Compound. A PubChem FTP is available and new data is accepted into the repository. Pcsubstance contains more than 81 million records (2011).

Proper citation: PubChem Substance (RRID:SCR_004742) Copy   

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http://www.rcsb.org/#Category-welcome

Collection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results.

Proper citation: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (RRID:SCR_012820) Copy   

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