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Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets.
Proper citation: Reactome (RRID:SCR_003485) Copy
http://www.isi.edu/integration/karma/
An information integration software tool that enables users to integrate data from a variety of data sources including databases, spreadsheets, delimited text files, XML, JSON, KML and Web APIs. Users integrate information by modeling it according to an ontology of their choice using a graphical user interface that automates much of the process. Karma learns to recognize the mapping of data to ontology classes and then uses the ontology to propose a model that ties together these classes. Users then interact with the system to adjust the automatically generated model. During this process, users can transform the data as needed to normalize data expressed in different formats and to restructure it. Once the model is complete, users can publish the integrated data as RDF or store it in a database.
Proper citation: Karma (RRID:SCR_003732) Copy
WHOSIS, the WHO Statistical Information System, is an interactive database bringing together core health statistics for the 193 WHO Member States. It comprises more than 100 indicators, which can be accessed by way of a quick search, by major categories, or through user-defined tables. The data can be further filtered, tabulated, charted and downloaded. The data are also published annually in the World Health Statistics Report released in May. The WHO Statistical Information System is the guide to health and health-related epidemiological and statistical information available from the World Health Organization. Most WHO technical programs make statistical information available, and they will be linked from here. Sponsors: WHOSIS is supported by the World Health Organization. Note: The WHO Statistical Information System (WHOSIS) has been incorporated into the Global Health Observatory (GHO) to provide you with more data, more tools, more analysis and more reports.
Proper citation: World Health Organization Statistical Information System (RRID:SCR_008250) Copy
A database, catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. This database resource covers materials in all formats and periods, including printed works from as far back as the 15th century. AGRICOLA is a bibliographic database of citations to the agricultural literature created by the National Agricultural Library and its cooperators. The records describe publications and resources encompassing all aspects of agriculture and allied disciplines, including animal and veterinary sciences, entomology, plant sciences, forestry, aquaculture and fisheries, farming and farming systems, agricultural economics, extension and education, food and human nutrition, and earth and environmental sciences. Although the NAL Catalog (AGRICOLA) does not contain the text of the materials it cites, thousands of its records are linked to full-text documents online, with new links added daily. The NAL Catalog (AGRICOLA) is organized into two bibliographic data sets: *The NAL Online Public Access Catalog (AGRICOLA NAL) contains citations to books, audiovisuals, serials, and other materials, most of which are in the Library''s collection. (The Catalog does contain some records for items not held at NAL.) *The Article Citation Database (AGRICOLA IND) includes citations, many with abstracts, to journal articles (see Journals Indexed in AGRICOLA), book chapters, reports, and reprints, selected primarily from the materials found in the NAL Catalog.
Proper citation: AGRICOLA (RRID:SCR_008158) Copy
Although Haemophilus influenza type b (Hib) diseases and Hepatitis B (Hep B) infections are preventable with one combined life-saving vaccine, both continue to pose risks to the worlds most vulnerable populations, leading to life-long disabilities or even death. Vaccinating against Hib and Hepatitis B represents an essential step towards reaching Millennium Development Goal 4. The Hib bacterium causes meningitis and pneumonia and is considered the third vaccine-preventable cause of death in children aged under five. It is estimated that there are three million cases of serious Hib infection annually, of which 400,000 result in childhood death. The majority of survivors suffer paralysis, deafness, mental retardation and learning disabilities. Babies and young children are most at risk from Hep B, a viral disease, which attacks the liver and can cause both acute and chronic disease. This can lead to chronic liver disease and puts victims at high risk of death from cirrhosis of the liver and liver cancer in later life. More than two billion people are infected by Hep B worldwide of whom 360 million suffer from chronic Hep B infection; the latter is highly prevalent in all countries that GAVI supports. Children are most vulnerable to infection with 90 percent of infants infected in the first months of their lives developing chronic Hep B infection. Infections in the developing world are mostly from mother to child, or from child to child, mainly through cuts, bites, scrapes and scratches. Vaccinating against Hib and Hep B represents an essential step towards reaching Millennium Development Goal 4, which is to reduce the under-five mortality rate by two thirds by 2015. GAVI uses two mechanisms that draw heavily on private-sector thinking to help overcome historic limitations to development funding for immunisation. These mechanisms are the AMC and the IFFIm. The former reflects the need to meet disproportionately high costs in the early stages of implementing aid programmes; the latter developing countries'' need for sustainable predictable funding., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GAVI (RRID:SCR_008528) Copy
Our genes and lifestyle factors, such as calorie rich diets and a lack of exercise, contribute to the development of Type 2 diabetes. But what we dont know is the exact nature of the genetic risk and how this interacts with lifestyle factors to cause diabetes. The Diabetes UK Warren 2 Group was formed in 1992 to investigate the genetic basis of Type 2 diabetes. The Group, comprising of researchers from six UK diabetes research centres, began by recruiting families into the study enriched for Type 2 diabetes ie having two or more siblings with the condition. With over 2000 individuals from 843 families in the collection, it is now being used to search for the genes that make people susceptible to Type 2 diabetes. When identifying susceptibility genes it is important to know how the gene affects normal metabolism in relatives without diabetes. In 1999. the Warren 2 Extension study recruited first degree relatives (siblings and children) of the original Warren 2 families, who did not have diabetes, in the knowledge that they would also be enriched with the same susceptibility genes. This study recruited 811 relatives without diabetes (586 offspring and 225 siblings) all of whom have undergone detailed metabolic assessment. A similar study was undertaken in Oxford called the Diabetes In Families (DIF) Study. In 2001, the Warren 2 Trios and Duos Study recruited 500 families from around the country consisting of an individual with Type 2 diabetes and both their parents (trios) or an individual with diabetes, one of their parents and at least 2 siblings (duos). In addition to this, a further 1500 individuals with diabetes were recruited as part of the Warren 2 Cases study. This website is run by the Diabetes Research department and the Centre for Molecular Genetics at the Peninsula Medical School and Royal Devon and Exeter Hospital, Exeter, UK.
Proper citation: Diabetes Genes (RRID:SCR_008639) Copy
http://blaster.docking.org/zinc/
Welcome to ZINC, a free database of commercially-available compounds for virtual screening. ZINC contains over 13 million purchasable compounds in ready-to-dock, 3D formats. ZINC is provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF). To cite ZINC, please reference: Irwin and Shoichet, J. Chem. Inf. Model. 2005;45(1):177-82 PDF, DOI. We thank NIGMS for financial support (GM71896). There are release notes for ZINC 10. - We have a survey where you can give us feedback.
Proper citation: Zinc (RRID:SCR_008596) Copy
GOstat is a tool that allows you to find statistically overrepresented Gene Ontologies within a group of genes. The Gene-Ontology database (GO: http://www.geneontology.org) provides a useful tool to annotate and analyze the function of large numbers of genes. Modern experimental techniques, as e.g. DNA microarrays, often result in long lists of genes. To learn about the biology in this kind of data it is desirable to find functional annotation or Gene-Ontology groups which are highly represented in the data. This program (GOstat) should help in the analysis of such lists and will provide statistics about the GO terms contained in the data and sort the GO annotations giving the most representative GO terms first. Run GOstat: * Go to search form - Computes GO statistics of a list of genes selected from a microarray. * GOstat Display - You can store results from a previously run and view them here, either by uploading them as a file or putting them on a selected URL. * Upload Custom GO Annotations - This allows you to upload your own GO annotation database and use it with GOstat. Variants of GOstat: * Rank GOstat - Takes input from all genes on microarray instead of using a fixed cutoff and uses ranks using a Wilcoxon test or either ranks or pvalues to score GOs using Kolmogorov-Smirnov statistics. * Gene Abundance GOstats - Takes input from all genes on microarray and sums up the gene abundances for each GO to compute statistics. * Two list GOstat - Compares GO statistics in two independent lists of genes, not necessarily one of them being the complete list the other list is sampled from. Platform: Online tool, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GOstat (RRID:SCR_008535) Copy
You can begin your search immediately using the Quick form on the home page or you can access the other specialized search forms in Embase. You can choose any section from the options on the top menu bar: Search, Emtree, Journals, Authors, or Help. You can start to search without logging in but if you would like to set up an email alert or save a search, then you may Login or Register from the upper-right part of the screen. Note: if you are outside your institution IP range, you will first be directed to the info site before accessing the Embase Home page. For more information on remote access, please see Login section. Search Forms Search is at the core of Embase and all search forms are designed to allow you to look for biomedical and pharmaceutical clinical and research information easily and quickly, whether you are a new or experienced searcher. The Embase search engine allows Boolean searching with wildcard and truncation features, as well as many predefined search limits. Search is divided into five options: Quick, Advanced, Drug, Disease and Article. Quick lets you perform easy yet powerful searches without having to learn a complex search language. It is perfect if you are starting your research and looking for an overview of the literature or good terms to include in your search strategy. Autocomplete will help you to search using the bext terminology. Advanced incorporates options from Emtree term mapping including explosion searching for maximum precision in subject searching (see Emtree) and Drug and Disease provide access to specialized features useful to search these topics, such as ''Adverse Drug Reaction''''Drug Combination''. Generally speaking, drug searches are best carried out in the Drug form, diseases in the Disease form and non-drug and disease searches in the Advanced form. Article allows you to pinpoint individual articles. Embase is owned and operated by Elsevier B.V., Radarweg 29, 1043 NX Amsterdam, The Netherlands, Reg. No. 33156677, BTW No. 002967455B65 (Elsevier).
Proper citation: Embase Biomedical Answers (RRID:SCR_008498) Copy
A complete online Product Catalog of chemicals, supplies, accessories, and equipment for Electron and Light Microscopy, Histology, Cell Biology, Neuroscience, and all biological related research fields. At the site, you can find technical tips and recommended articles of interest, technical and product data sheets, Material Safety Data Sheets, and many revolutionary new products and exclusive items. A complete product catalog of the entire Diatome collection of Diamond knives, tools, and accessories for Electron and Light microscopy for Biological and Materials Science at room and cryo temperatures. Available on-line as well is information on our services, programs, specials, and policies. The complete handling and use technical manual as well as troubleshooting can also be found at our site. The Summers Optical on-line catalog including a complete line of optical cements and adhesives, decementing agents, hardness testers, ultrasonic baths and UV lights as well as technical and transmission data and problem solving can be found at this site. As well as, our unique bonding manual including troubleshooting and charts for how to choose a cement for specific applications and a complete set of MSDS on all of our products can be seen here. EMS Contract Packaging is a total service contract manufacturer, packager, and formulator with over 40 years experience in drug and cosmetic formulating and packaging. Negafile furniture quality wood filing systems and storage cases for grids, negatives, film and microscope glass slides. And a full line of shipping and packaging solutions for all your traditional or digital media.
Proper citation: Emsdiasum (RRID:SCR_008497) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Retrieve-ensembl-seq is included in the software suite regulatory sequence analysis tools (RSAT), allowing instant submission of retrieved sequences to further analysis tools. AVAILABILITY: retrieve-ensembl-seq is integrated in the RSAT suite: http://rsat.ulb.ac.be/rsat. Web site: http://rsat.ulb.ac.be/rsat/retrieve-ensembl-seq_form.cgi. Web services: http://rsat.ulb.ac.be/rsat/web_services/RSATWS.wsdl. Stand-alone distribution: freely available under an academic licence to download from the RSAT web site. The complete manual, a convenient tutorial and demos are available from the RSAT website. Additional help can be found on the RSAT public forum.
Proper citation: Regulatory Sequence Analysis Tools (RRID:SCR_008560) Copy
http://recombineering.ncifcrf.gov/
Recombineering (recombination-mediated genetic engineering) is a powerful method for fast and efficient construction of vectors for subsequent manipulation of the mouse genome or for use in cell culture experiments. It is also an efficient way of manipulating the bacterial genome directly. Recombineering is a method based on homologous recombination in E. Coli using recombination proteins provided from ? phage. Our bacterial strains contain a defective ? prophage inserted into the bacterial genome. The phage genes of interest, exo, bet, and gam, are transcribed from the ?PL promoter. This promoter is repressed by the temperature-sensitive repressor cI857 at 32C and derepressed (the repressor is inactive) at 42C. When bacteria containing this prophage are kept at 32C no recombination proteins are produced. However, after a brief (15 minutes) heat-shock at 42C a sufficient amount of recombination proteins are produced. exo is a 5''-3'' exonuclease that creates single-stranded overhangs on introduced linear DNA. bet protects these overhangs and assists in the subsequent recombination process. gam prevents degradation of linear DNA by inhibiting E. Coli RecBCD protein. Linear DNA (PCR product, oligo, etc.) with sufficient homology in the 5'' and 3'' ends to a target DNA molecule already present in the bacteria (plasmid, BAC, or the bacterial genome itself) can be introduced into heat-shocked and electrocompetent bacteria using electroporation. The introduced DNA will now be modified by exo and bet and undergo homologous recombination with the target molecule. The method is so efficient that co-electroporation of a supercoiled plasmid and a linear piece of DNA into heat-shocked, electrocompetent bacteria will work as well.
Proper citation: Recombineering Information (RRID:SCR_008556) Copy
A large multi-site pediatric MRI and genetics data resource to facilitate studies of the genomic landscape of the developing human brain. It includes information about the developing mental and emotional functions of the children to understand the genetic basis of individual differences in brain structure and connectivity, cognition, and personality. Investigators on the project are studying 1400 children between the ages of 3 and 20 years so that links between genetic variation and developing patterns of brain connectivity can be examined. Investigators interested in the effects of a particular gene will be able to search the database for any brain areas or connections between areas that differ as a function of variation in a particular gene, and also to determine if the genes appear to affect the course of brain development at some point during childhood. A data exploration tool has been created for mapping and analyzing MRI data sets collected for PING and related developmental studies. Approved investigators will be able to view raw image sets and derived 3D brain maps of MRI and DTI data, conduct hypothesis testing, and graph brain area measures as they change across the time course of development. PING Cores * Coordinating Core: Functions include project management, screening of participants and maintaining the database * Neuroimaging Core: applying a standardized high-resolution structural MRI protocol involving 3-D T1-weighted scans, a T2-weighted volume, and a set of diffusion-weighted scans with multiple b values and diffusion directions, scans to estimate MRI relaxation rates, and gradient echo EPI scans for resting state fMRI. Importantly, adaptive motion compensation, using ����??PROMO����??, a novel real-time motion correction algorithm will be used. Specific PING protocols for each scanner manufacturer: ** PING MRI Protocol - GE ** PING MRI Protocol - Philips ** PING MRI Protocol - Siemens * Assessment Core: Cognitive assessments for the PING project are conducted using the NIH Toolbox for Cognition. * Genomics Core: functions as a central repository for receipt of saliva samples collected for each study participant. Once received, samples are catalogued, maintained, and DNA is extracted using state-of-the-field laboratory techniques. Ultimately, genome-wide genotyping is performed on the extracted DNA using the Illumina Human660W-Quad BeadChip. PING involves 10 sites throughout the country including UCSD, University of Hawaii, Scripps Genomics, UCLA, UC Davis, Kennedy Krieger Institute/Johns Hopkins, Sacker Institute/Cornell University, University of Massachusetts, Massachusetts General Hospital/Harvard, and Yale. Families who may want to participate in the study, or others who want to know more about it, may email questions to ping (at) ucsd.edu.
Proper citation: Pediatric Imaging Neurocognition and Genetics (RRID:SCR_008953) Copy
http://www.cs.tau.ac.il/~spike/
Database of curated human signaling pathways with an associated interactive software tool for analysis and dynamic visualization of pathways. Individual pathway maps can be viewed and downloaded; the entire database may be browsed, or launched via a map viewer tool that allows dynamic visualization of the database and save networks in XGMML format that can be viewed in all generic XGMML viewers. Map Topics * Cell cycle progress and check points * DNA damage response * Programmed cell death related processes * Stress-activated transcription factors * Mitogen-activated protein kinase pathways * Immune response signaling * HEarSpike: hearing related pathways
Proper citation: SPIKE (RRID:SCR_010466) Copy
A public repository of metabolite information as well as tandem mass spectrometry data is provided to facilitate metabolomics experiments. It contains structures and represents a data management system designed to assist in a broad array of metabolite research and metabolite identification. An annotated list of known metabolites and their mass, chemical formula, and structure are available. Each metabolite is linked to outside resources for further reference and inquiry. MS/MS data is also available on many of the metabolites.
Proper citation: METLIN (RRID:SCR_010500) Copy
http://www-amdis.iaea.org/ALADDIN/
Numerical database of atomic and molecular processes and particle-surface interactions. It has formatted data on atomic structure and spectra (energy levels,wave lengths, and transition probabilities); electron and heavy particle collisions with atoms, ions, and molecules (cross sections and/or rate coefficients, including, in most cases, analytic fit to the data); sputtering of surfaces by impact of main plasma constituents and self sputtering; particle reflection from surfaces; thermophysical and thermomechanical properties of beryllium and pyrolytic graphites.
Proper citation: ALADDIN (RRID:SCR_010476) Copy
http://tools.neb.com/NEBcutter2/
This tool will take a DNA sequence and find the large, non-overlapping open reading frames using the E.coli genetic code and the sites for all Type II and commercially available Type III restriction enzymes that cut the sequence just once. By default, only enzymes available from NEB are used, but other sets may be chosen. Just enter your sequence and submit. Further options will appear with the output. The maximum size of the input file is 1 MByte, and the maximum sequence length is 300 KBases. NEBcutter produces a variety of outputs including restriction enzyme maps, theoretical digests and links into the restriction enzyme database, REBASE (http://rebase.neb.com/rebase/rebase.html). Importantly, its table of recognition sites is updated daily from REBASE and it marks all sites that are potentially affected by DNA methylation (Dam, Dcm, etc.). Many options exist to choose the enzymes used for digestion, including all known specificities, subsets of those that are commercially available or sets of enzymes that produce compatible termini.
Proper citation: NEBcutter (RRID:SCR_010664) Copy
A website which assigns molecular functional effects of non-synonymous SNPs based on structure and sequence analysis.
Proper citation: SNPs3D (RRID:SCR_010787) Copy
https://genome-cancer.ucsc.edu/
A suite of web-based tools to visualize, integrate and analyze cancer genomics and its associated clinical data. It is possible to display your own clinical data within one of their datasets.
Proper citation: UCSC Cancer Genomics Browser (RRID:SCR_011796) Copy
GABI-Kat is a database of flanking sequence tags (FSTs) from T-DNA mutagenised A. thaliana plants. Over time, an increasing number of lines will become available from NASC. The "show sequence" page of SimpleSearch will display if a GABI-Kat line for a given FST has already been donated to NASC. Lines that have so far not been regrown and confirmed are only available from GABI-Kat directly. We have used four vectors: pAC106 (GenBank:AJ537513), pAC161 (GenBank:AJ537514), pGABI1 (GenBank:AY529716) and pADIS1 (GenBank:AY529717). Sequence and overview map data of all vectors are available from the download page. Features of interest which are not included in the map should be deduced from the sequence. For a specified line, the vector is displayed in the "Show Sequence" page of SimpleSearch.
Proper citation: GABI-KAT (RRID:SCR_012751) Copy
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