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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
http://inparanoid.sbc.su.se/cgi-bin/index.cgi
Collection of pairwise comparisons between 100 whole genomes generated by a fully automatic method for finding orthologs and in-paralogs between TWO species. Ortholog clusters in the InParanoid are seeded with a two-way best pairwise match, after which an algorithm for adding in-paralogs is applied. The method bypasses multiple alignments and phylogenetic trees, which can be slow and error-prone steps in classical ortholog detection. Still, it robustly detects complex orthologous relationships and assigns confidence values for in-paralogs. The original data sets can be downloaded.
Proper citation: InParanoid: Eukaryotic Ortholog Groups (RRID:SCR_006801) Copy
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
http://rice.plantbiology.msu.edu/
Database and resource that provides sequence and annotation data for the rice genome. This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. All structural and functional annotation is viewable through our Rice Genome Browser which currently supports 75 tracks of annotation. Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads. Rice is a model species for the monocotyledonous plants and the cereals which are the greatest source of food for the world''s population. While rice genome sequence is available through multiple sequencing projects, high quality, uniform annotation is required in order for genome sequence data to be fully utilized by researchers. The existence of a common gene set and uniform annotation allows researchers within the rice community to work from a common resource so that their results can be more easily interpreted by other scientists. The objective of this project has always been to provide high quality annotation for the rice genome. They generated, refined and updated gene models for the estimated 40,000-60,000 total rice genes, provided standardized annotation for each model, linked each model to functional annotation including expression data, gene ontologies, and tagged lines. They have provided a resource to extend the annotation of the rice genome to other plant species by providing comparative alignments to other plant species. Analysis/Tools are available including: BLAST, Locus Name Search, Functional Term Search, Protein Domain Search, Anatomy Expression Viewer, Highly Expressed Genes
Proper citation: Rice Genome Annotation (RRID:SCR_006663) Copy
http://www.ensemblgenomes.org/
Database portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualization platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Many of the databases supporting the portal have been built in close collaboration with the scientific community - essential for maintaining the accuracy and usefulness of the resource. A common set of user interfaces (which include a graphical genome browser, FTP, BLAST search, a query optimized data warehouse, programmatic access, and a Perl API) is provided for all domains. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualized in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site.
Proper citation: Ensembl Genomes (RRID:SCR_006773) Copy
Publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralized resource. The database can be mined as a knowledgebase or used with the integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response. Although InnateDB curation focuses on innate immunity-relevant interactions and pathways, it also incorporates detailed annotation on the entire human, mouse and bovine interactomes by integrating data (178,000+ interactions & 3,900+ pathways) from several of the major public interaction and pathway databases. InnateDB also has integrated human, mouse and bovine orthology predictions generated using Ortholgue software. Ortholgue uses a phylogenetic distance-based method to identify possible paralogs in high-throughput orthology predictions. Integrated human and mouse conserved gene order and synteny information has also been determined to provide further support for orthology predictions. InnateDB Capabilities: * View statistics for manually-curated innate immunity relevant molecular interactions. New manually curated interactions are submitted weekly. * Search for genes and proteins of interest. * Search for experimentally-verified molecular interactions by gene/protein name, interaction type, cell type, etc. * Search genes/interactions belonging to 3,900 pathways. * Visualize interactions using an intuitive subcellular localization-based layout in Cerebral. * Upload your own list of genes along with associated gene expression data (from up to 10 experimental conditions) to interactively analyze this data in a molecular interaction network context. Once you have uploaded your data, you will be able to interactively visualize interaction networks with expression data overlaid; carry out Pathway, Gene Ontology and Transcription Factor Binding Site over-representation analyses; construct orthologous interaction networks in other species; and much more. * Access curated interaction data via a dedicated PSICQUIC webservice.
Proper citation: InnateDB (RRID:SCR_006714) Copy
canSAR is an integrated database that brings together biological, chemical, pharmacological (and eventually clinical) data. Its goal is to integrate this data and make it accessible to cancer research scientists from multiple disciplines, in order to help with hypothesis generation in cancer research and support translational research. This cancer research and drug discovery resource was developed to utilize the growing publicly available biological annotation, chemical screening, RNA interference screening, expression, amplification and 3D structural data. Scientists can, in a single place, rapidly identify biological annotation of a target, its structural characterization, expression levels and protein interaction data, as well as suitable cell lines for experiments, potential tool compounds and similarity to known drug targets. canSAR has, from the outset, been completely use-case driven which has dramatically influenced the design of the back-end and the functionality provided through the interfaces. The Web interface provides flexible, multipoint entry into canSAR. This allows easy access to the multidisciplinary data within, including target and compound synopses, bioactivity views and expert tools for chemogenomic, expression and protein interaction network data.
Proper citation: canSAR (RRID:SCR_006794) Copy
Web server to provide germplasm information about plants, animals, microbes, invertebrates and access to databases that maintain passport, characterization, evaluation, inventory, and distribution data for the management and utilization of national germplasm collections. Under control of the U.S. Department of Agriculture's Agricultural Research Service to support the National Genetic Resources Program (NGRP). Operated by the Database Management Unit of the National Germplasm Resource Laboratory in Beltsville, Maryland.
Proper citation: Germplasm Resources Information Network (RRID:SCR_006675) Copy
The Drugs.com mission is to be the Internets most trusted resource for drug and related health information. We will achieve this aim by presenting independent, objective, comprehensive and up-to-date information in a clear and concise format for both consumers and healthcare professionals. Their goal is to provide clear information about drugs sold in the USA, at a level everyone can comprehend. For consumers, we provide product information in non-technical language. Health professionals will find what they need in the FDA Product Label Professional Information database. The Care Guide provides information about the treatment of common illnesses and injuries. The Drug Interactions checker details drug-drug interaction mechanisms, severity and management, and also outlines drug-food interactions. Drugs.com is NOT an online pharmacy and does not condone the sale of prescription medicines over the Internet without a prescription. Drugs.com simply provides a free drug-information service to help you better understand how medicines work: their uses, side effects and potential to interact with other medicines. For information on purchasing prescription medicines online please visit the FDAs Buying Prescription Medicine Online: A Consumer Safety Guide. Drugs.com medical dictionary is powered by Stedmans. Since 1911, Stedmans Medical Dictionary has been the medical professions most trusted source for medical definitions. A complete medical terms dictionary, Steadmans Electronic Medical Dictionary contains over 107,000 medical terms taken directly from Stedmans Medical Dictionary, 28th Edition. Most search engines cover the entire Internet, and searches on these engines may produce many results that are not specific to your drug question. On Drugs.com, you can search by medical condition or by drug, and get the answer you need right away. Searches by drug can be made using the brand name or the generic name of the drug. Searches by medical condition will return a list of medications used to treat that condition. Sponsors: The Drugs.com drug information service is supported by donations and revenue from site advertisers. The Drugs.com staff endeavor to source ads that are medically or community-service oriented. All ads must be appropriate for all-age family viewing, and we screen banner ads for family-appropriate content before the ads go live.
Proper citation: Drugs.com (RRID:SCR_000656) Copy
http://www.nitrc.org/projects/atp
Autism research program that makes available post-mortem brain tissue to qualified scientists all over the world. Working directly with tissue banks, organ procurement agencies, medical examiners and the general public, this is the largest program dedicated to increasing and enhancing the availability of post-mortem brain tissue for basic research in autism. To date, the ATP has collected and stored more than 170 brains in their repositories at Harvard (US) and Oxford (UK). These brains are processed by formalin fixation and/or snap frozen to properly provide high quality tissue of all brain regions, in support of biological research in autism. The ATP is unique in that they diligently pursue all available clinical data (pre and post mortem) on tissue donors in order to create the most biologically relevant brain repository for autism research. These data, together with tissue resources from both banks and associated repositories, are presented to all interested researchers through their extensive web-based data portal (login required). The ATP is not a brain bank, but works directly with the Harvard Brain Tissue Resource Center in Boston (HBTRC), Massachusetts to serve as its tissue repository. This program augments brain bank functions by: * Creating the most biologically relevant brain tissue repository possible * Fully covering all costs associated with brain extraction and transfer to the repositories at Harvard (US and Canada) and Oxford (UK). * Providing scientific oversight of tissue distributions * Overseeing and managing all tissue grants * Clinically phenotyping and acquiring extensive medical data on all of their donors * Providing continuing family support and communication to all of their donors * Directly supporting researchers to facilitate autism research * Maintaining a robust web based data management and secure on-line global interface system * Developing and supporting ATP established scientific initiatives * Actively providing public outreach and education The ATP is not a clinical organ procurement agency, but rather they facilitate the wishes of donors and families to donate their tissue to autism research. Through the ATP's established international infrastructure, they work with any accredited tissue bank, organ procurement agency, or medical examiner that receives a family's request to donate their loved one's tissue to the program. Once contacted, the ATP will insure that the family's request to donate their loved one's tissue is faithfully met, covering all costs to the family and partnering agency as well as ensuring the tissues' proper and rapid transport to the ATP's repository at the Harvard Brain Tissue Resource Center (HBTRC) in Boston, Massachusetts.
Proper citation: Autism Tissue Program (RRID:SCR_000651) Copy
International collaborative research project and database of annotated mammalian genome. Used to improve estimates of total number of genes and their alternative transcript isoforms in both human and mouse. Consortium to assign functional annotations to full length cDNAs that were collected during Mouse Encyclopedia Project at RIKEN.
Proper citation: Functional Annotation of the Mammalian Genome (RRID:SCR_000788) Copy
http://www.genome.jp/kegg/expression/
Database for mapping gene expression profiles to pathways and genomes. Repository of microarray gene expression profile data for Synechocystis PCC6803 (syn), Bacillus subtilis (bsu), Escherichia coli W3110 (ecj), Anabaena PCC7120 (ana), and other species contributed by the Japanese research community.
Proper citation: Kyoto Encyclopedia of Genes and Genomes Expression Database (RRID:SCR_001120) Copy
Project aggregates and provides experimental gene expression data from genito-urinary system. International consortium providing molecular atlas of gene expression for developing organs of GenitoUrinary (GU) tract. Mouse strains to facilitate developmental and functional studies within GU system. Experimental protocols and standard specifications. Tutorials describing GU organogenesis and primary data via database. Data are from large-scale in situ hybridization screens (wholemount and section) and microarray gene expression data of microdissected, laser-captured and FACS-sorted components of developing mouse genitourinary (GU) system.
Proper citation: GenitoUrinary Development Molecular Anatomy Project (RRID:SCR_001554) Copy
https://scicrunch.org/scicrunch/data/source/nlx_154697-1/search?q=*&l=
Integrated Animals is a virtual database currently indexing available animal strains and mutants from: AGSC (Ambystoma), BCBC (mice), BDSC (flies), CWRU Cystic Fibrosis Mouse Models (mice), DGGR (flies), FlyBase (flies), IMSR (mice), MGI (mice), MMRRC (mice), NSRRC (pig), NXR (Xenopus), RGD (rats), Sperm Stem Cell Libraries for Biological Research (rats), Tetrahymena Stock Center (Tetrahymena), WormBase (worms), XGSC (Xiphophorus), ZFIN (zebrafish), and ZIRC (zebrafish).
Proper citation: Integrated Animals (RRID:SCR_001421) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Duke Image Analysis Laboratory (DIAL) is committed to providing comprehensive imaging support in research studies and clinical trials to various agencies. The capabilities of the lab include protocol development, site training and certification, and image archival and analysis for a variety of modalities including magnetic resonance imaging, magnetic resonance spectroscopy, computed tomography and nuclear medicine. DIAL uses the latest technologies to analyze Magnetic Resonance Imaging (MRI) data sets of the brain. Currently the lab is engaged in measurement of the hippocampus, amygdala, caudate, ventricular system, and other brain regional volumes. Each of these techniques have undergone a rigorous validation process. The measurements of brain structures provide a useful means of non-invasively testing for changes in the brain of the patient. Changes over time in the brain can be detected, and evaluated with respect to the treatment that the patient is receiving. Magnetic Resonance Spectroscopy (MRS) allows DIAL to obtain an accurate profile of the chemical content of the brain. This sensitive technique can detect small changes in the metabolic state of the brain; changes that vary in response to administration of therapeutic agents. The ability to detect these subtle shifts in brain chemistry allows DIAL to identify changes in the brain with more sensitivity than allowed by image analysis. In this respect, NMR spectroscopy can provide early detection of changes in the brain, and serves to compliment the data obtained from image analysis. Additionally, DIAL also contains SQUID (Scalable Query Utility and Image Database). It is an image management system developed to facilitate image management in research and clinical trials: SQUID offers secure, redundant image storage and organizational functions for sorting and searching digital images for a variety of modalities including MRI, MRS, CAT Scan, X-Ray and Nuclear Medicine. SQUID can access images directly from DUMC scanners. Data can also be loaded via DICOM CDs, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Duke University Medical Center: Duke Image Analysis Laboratory (RRID:SCR_001716) Copy
Suite of motif-based sequence analysis tools to discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences; search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN; compare a motif to all motifs in a database of motifs; associate motifs with Gene Ontology terms via their putative target genes, and analyze motif enrichment using SpaMo or CentriMo. Source code, binaries and a web server are freely available for noncommercial use.
Proper citation: MEME Suite - Motif-based sequence analysis tools (RRID:SCR_001783) Copy
http://amigo.geneontology.org/
Web tool to search, sort, analyze, visualize and download data of interest. Along with providing details of the ontologies, gene products and annotations, features a BLAST search, Term Enrichment and GO Slimmer tools, the GO Online SQL Environment and a user help guide.Used at the Gene Ontology (GO) website to access the data provided by the GO Consortium. Developed and maintained by the GO Consortium.
Proper citation: AmiGO (RRID:SCR_002143) Copy
Database of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus including information about genes and proteins of Aspergillus nidulans and Aspergillus fumigatus; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Sgenus species. Also available are Gene Ontology (GO) and community resources. Based on the Candida Genome Database, the Aspergillus Genome Database is a resource for genomic sequence data and gene and protein information for Aspergilli. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). Search options allow you to: *Search AspGD database using keywords. *Find chromosomal features that match specific properties or annotations. *Find AspGD web pages using keywords located on the page. *Find information on one gene from many databases. *Search for keywords related to a phenotype (e.g., conidiation), an allele (such as veA1), or an experimental condition (e.g., light). Analysis and Tools allow you to: *Find similarities between a sequence of interest and Aspergillus DNA or protein sequences. *Display and analyze an Aspergillus sequence (or other sequence) in many ways. *Navigate the chromosomes set. View nucleotide and protein sequence. *Find short DNA/protein sequence matches in Aspergillus. *Design sequencing and PCR primers for Aspergillus or other input sequences. *Display the restriction map for a Aspergillus or other input sequence. *Find similarities between a sequence of interest and fungal nucleotide or protein sequences. AspGD welcomes data submissions.
Proper citation: ASPGD (RRID:SCR_002047) Copy
National marine phytoplankton collection, maintaining over 2700 strains from around the world, most are marine phytoplankton but they also have benthic, macrophytic, freshwater and heterotrophic organisms - now incorporating bacteria and viruses. Strain records have (when available): * collection and isolation information * culturing medium recipes and growth conditions * photographs * GenBank accession link * collection site map * link to the taxonomic database Micro*scope The deposition of new strains are welcome if the strains are a valuable addition to the collection. Examples include strains that are referred to in publications, contain interesting molecular, biochemical or physiological properties, are the basis for taxonomic descriptions, are important for aquaculture, or are from an unusual geographical location or ecological habitat. The NCMA offers a course in phytoplankton culturing techniques and facilities for visiting scientists are available at the new laboratories in East Boothbay, Maine. Services include: Mass Culturing DNA and RNA, Purification, Private Holdings, Culture Techniques Course, Visiting Scientists, Single Cell Genomics, Flow Cytometry, Corporate Alliances and Technology Transfer.
Proper citation: National Center for Marine Algae and Microbiota (RRID:SCR_002120) Copy
http://hymenopteragenome.org/beebase/
Gene sequences and genomes of Bombus terrestris, Bombus impatiens, Apis mellifera and three of its pathogens, that are discoverable and analyzed via genome browsers, blast search, and apollo annotation tool. The genomes of two additional species, Apis dorsata and A. florea are currently under analysis and will soon be incorporated.BeeBase is an archive and will not be updated. The most up-to-date bee genome data is now available through the navigation bar on the HGD Home page.
Proper citation: BeeBase (RRID:SCR_008966) Copy
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