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Found 142 result(s)

China National GeneBank DataBase

国家基因库生命大数据平台

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The China National GeneBank database (CNGBdb) is a unified platform for biological big data sharing and application services. CNGBdb has now integrated a large amount of internal and external biological data from resources such as CNGB, NCBI, and the EBI. There are several sub-databases in CNGBdb, including literature, variation, gene, genome, protein, sequence, organism, project, sample, experiment, run, and assembly. Based on underlying big data and cloud computing technologies, it provides various data services, including archive, analysis, knowledge search, and management authorization of biological data. CNGBdb adopts data structures and standards of international omics, health, and medicine, such as The International Nucleotide Sequence Database Collaboration (INSDC), The Global Alliance for Genomics and Health GA4GH (GA4GH), Global Genome Biodiversity Network (GGBN), American College of Medical Genetics and Genomics (ACMG), and constructs standardized data and structures with wide compatibility. All public data and services provided by CNGBdb are freely available to all users worldwide. CNGB Sequence Archive (CNSA) is the bionomics data repository of CNGBdb. CNGB Sequence Archive (CNSA) is a convenient and efficient archiving system of multi-omics data in life science, which provides archiving services for raw sequencing reads and further analyzed results. CNSA follows the international data standards for omics data, and supports online and batch submission of multiple data types such as Project, Sample, Experiment/Run, Assembly, Variation, Metabolism, Single cell, and Sequence. Moreover, CNSA has achieved the correlation of sample entities, sample information, and analyzed data on some projects. Its data submission service can be used as a supplement to the literature publishing process to support early data sharing.CNGB Sequence Archive (CNSA) is a convenient and efficient archiving system of multi-omics data in the life science of CNGBdb, which provides archiving services for raw sequencing reads and further analyzed results. CNSA follows the international data standards for omics data, and supports online and batch submission of multiple data types such as Project, Sample, Experiment/Run, Assembly, Variation, Metabolism, Single cell, Sequence. Its data submission service can be used as a supplement to the literature publishing process to support early data sharing.

PATRIC

Pathosystems Resource Integration Center

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<<<!!!<<< This repository is no longer available. >>>!!!>>> PATRIC will go offline by mid-December2022. Here is what you need to know. As announced previously, PATRIC, the bacterial BRC, and IRD / ViPR, the viral BRCs, are being merged into the new Bacterial and Viral Bioinformatics Resource Center (BV-BRC). BV-BRC combines the data, tools, and technologies from these BRCs to provide an integrated resource for bacterial and viral genomics-based infectious disease research.

dbSNP

SNV

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The NCBI Short Genetic Variations database, commonly known as dbSNP, catalogs short variations in nucleotide sequences from a wide range of organisms. These variations include single nucleotide variations, short nucleotide insertions and deletions, short tandem repeats and microsatellites. Short Genetic Variations may be common, thus representing true polymorphisms, or they may be rare. Some rare human entries have additional information associated withthem, including disease associations, genotype information and allele origin, as some variations are somatic rather than germline events. ***NCBI will phase out support for non-human organism data in dbSNP and dbVar beginning on September 1, 2017***

Tropical Rainfall Measuring Mission

TRMM

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<<<!!!<<< This repository is no longer available. >>>!!!>>> TRMM is a research satellite designed to improve our understanding of the distribution and variability of precipitation within the tropics as part of the water cycle in the current climate system. By covering the tropical and sub-tropical regions of the Earth, TRMM provides much needed information on rainfall and its associated heat release that helps to power the global atmospheric circulation that shapes both weather and climate. In coordination with other satellites in NASA's Earth Observing System, TRMM provides important precipitation information using several space-borne instruments to increase our understanding of the interactions between water vapor, clouds, and precipitation, that are central to regulating Earth's climate. The TRMM mission ended in 2015 and final TRMM multi-satellite precipitation analyses (TMPA, product 3B42/3B43) data processing will end December 31st, 2019. As a result, this TRMM webpage is in the process of being retired and some TRMM imagery may not be displaying correctly. Some of the content will be moved to the Precipitation Measurement Missions website https://gpm.nasa.gov/ and our team is exploring ways to provide some of the real-time products using GPM data. Please contact us if you have any additional questions.

OceanSITES

Taking the pulse of the global ocean

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OceanSITES is a worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. Since 1999, the international OceanSITES science team has shared both data and costs in order to capitalize on the enormous potential of these moorings. The growing network now consists of about 30 surface and 30 subsurface arrays. Satellite telemetry enables near real-time access to OceanSITES data by scientists and the public. OceanSITES moorings are an integral part of the Global Ocean Observing System. They complement satellite imagery and ARGO float data by adding the dimensions of time and depth.

Database of Interacting Proteins

DIP

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The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Please, check the reference page to find articles describing the DIP database in greater detail. The Database of Ligand-Receptor Partners (DLRP) is a subset of DIP (Database of Interacting Proteins). The DLRP is a database of protein ligand and protein receptor pairs that are known to interact with each other. By interact we mean that the ligand and receptor are members of a ligand-receptor complex and, unless otherwise noted, transduce a signal. In some instances the ligand and/or receptor may form a heterocomplex with other ligands/receptors in order to be functional. We have entered the majority of interactions in DLRP as full DIP entries, with links to references and additional information

AceView

AceView genes

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AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals’ transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated.

UCSD Signaling gateway

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<<<!!!<<< This repository is no longer available. >>>!!!>>>

Alberta Biodiversity Monitoring Institute Data & Analytics Portal

ABMI Data & Analytics Portal

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Data Download section provides easy access to the ABMI’s data and innovative data products ranging from raw field data, to species habitat associations, to remote sensing and geospatial products, to animal camera trap data, and more.

Pfam Protein Families

Pfam

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The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). !!! Powering down the Pfam website On October 5th, redirecting the traffic from Pfam (pfam.xfam.org) to InterPro (www.ebi.ac.uk/interpro) will start. The Pfam website will be available at legacy.pfam.xfam.org until January 2023, when it will be decommissioned. You can read more about the sunset period in the blog post (https://xfam.wordpress.com/2022/08/04/pfam-website-decommission/). !!!

BigBrain Database

Big Brain

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The BigBrain Project repository contains data from BigBrain: A high-resolution, 3D model of a human post-mortem brain, which was obtained in accordance with ethical requirements of the University of Düsseldorf. The brain of a 65-year-old body donor was sectioned, stained for cell bodies, scanned at very high resolution, and then digitally reconstructed in 3D. The full dataset of images, volumes, and surfaces are available for download on the project's ftp site, while a subset of files offering different spatial resolutions can be accessed via LORIS. The web-based 3D interactive atlas viewer is capable of displaying very large brain volumes, including oblique slicing, a whole brain overview, surface meshes, and maps. It enables navigating the BigBrain in 3D, exploring the growing set of highly detailed maps for cortical layers and cytoarchitectonic areas, and finding related neuroscience data.

TOXNET

Toxicology Data Network

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<<<!!!<<<The repository is no longer available <<<!!!<<< TOXNET has moved. Most content will continue to be collected and reviewed; selected information is accessible through PubChem, PubMed, and Bookshelf. If you have questions, please contact NLM Customer Support at https://support.nlm.nih.gov/ >>>!!!>>>

Nucleic Acid Database

NDB

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The NDB is a resource for nucleic acid research and education. The NDB assembles and distributes information about the three-dimensional structures of nucleic acids through a variety of resources, including a searchable database, Atlas, and software

Conserved Domain database

CDD

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The Conserved Domain Database is a resource for the annotation of functional units in proteins. Its collection of domain models includes a set curated by NCBI, which utilizes 3D structure to provide insights into sequence/structure/function relationships

UniGene

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<<<!!!<<< This repository is no longer available>>>!!!>>>. Although the web pages are no longer available, you will still be able to download the final UniGene builds as static content from the FTP site https://ftp.ncbi.nlm.nih.gov/repository/UniGene/. You will also be able to match UniGene cluster numbers to Gene records by searching Gene with UniGene cluster numbers. For best results, restrict to the “UniGene Cluster Number” field rather than all fields in Gene. For example, a search with Mm.2108[UniGene Cluster Number] finds the mouse transthyretin Gene record (Ttr). You can use the advanced search page https://www.ncbi.nlm.nih.gov/gene/advanced to help construct these searches. Keep in mind that the Gene record contains selected Reference Sequences and GenBank mRNA sequences rather than the larger set of expressed sequences in the UniGene cluster.

SMOKA Science Archive

SMOKA

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SMOKA provides public science data obtained at Subaru Telescope, 188cm telescope at Okayama Astrophysical Observatory, 105cm Schmidt telescope at Kiso Observatory (University of Tokyo), MITSuME, and KANATA Telescope at Higashi-Hiroshima Observatory. It is intended mainly for astronomical researchers.

Reciprocal Net

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The Reciprocal Net is a distributed database used by research crystallographers to store information about molecular structures; much of the data is available to the general public. The Reciprocal Net project is still under development. Currently, there are 18 participating crystallography laboratories online. The project is funded by the National Science Foundation (NSF) and part of the National Science Digital Library. The contents of this collection will come principally from structures contributed by participating crystallography laboratories, thus providing a means for teachers, students, and the general public to connect better with current chemistry research. The Reciprocal Net's emphasis is on obtaining structures of general interest and usefulness to those several classes of digital library users.

SkyView

SkyView Virtual Observatory

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SkyView is a Virtual Observatory on the Net generating images of any part of the sky at wavelengths in all regimes from Radio to Gamma-Ray.

Berkeley Drosophila Genome Project insitu

BDGP insitu homepage

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In early 2010 we updated the site to facilitate more rapid transfer of our data to the public database and focus our efforts on the core mission of providing expression pattern images to the research community. The original database https://www.fruitfly.org/index.html reproduced functions available on FlyBase, complicating our updates by the requirement to re-synchronize with FlyBase updates. Our expression reports on the new site still link to FlyBase gene reports, but we no longer reproduce FlyBase functions and therefore can update expression data on an ongoing basis instead of more infrequent major releases. All the functions relating to the expression patterns remain and we soon will add an option to search expression patterns by image similarity, in addition to annotation term searches. In a transitional phase we will leave both the old and the new sites up, but the newer data (post Release 2) will appear only on the new website. We welcome any feedback or requests for additional features. - The goals of the Drosophila Genome Center are to finish the sequence of the euchromatic genome of Drosophila melanogaster to high quality and to generate and maintain biological annotations of this sequence. In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community.

NCBI BioSystems Database

NCBI BioSystems

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<<<!!!<<< The NCBI BioSystems Database will be retired in March 2022. >>>!!!>>> This retirement includes the representation of BioSystems records in the NCBI Entrez system and viewers of BioSystems content. NCBI now provides metabolic pathway and other biosystems data through the regularly updated PubChem Pathways resource (https://pubchemdocs.ncbi.nlm.nih.gov/pathways) that offers a fresh, extended, and more modern interface.

National Cryosphere Desert Data Center

国家冰川冻土沙漠科学数据中心

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The National Cryosphere Desert Data Center (hereinafter referred to as NCDC) is supported by the Institute of environment and Engineering in the cold and dry areas of the Chinese Academy of Sciences, in cooperation with Xinjiang Institute of ecology and geography of the Chinese Academy of Sciences, Chengdu Institute of mountain land disaster and environment of the Ministry of water resources of the Chinese Academy of Sciences, Qinghai Salt Lake Research Institute of the Chinese Academy of Sciences and Qinghai Gao of the Chinese Academy of Sciences The Institute of protobiology and other units were jointly established. The supporting units of glacier permafrost desert data center have formed a scientific research and support system of seven research laboratories and three research systems, highlighting the research characteristics of glacier, permafrost, desert, atmosphere, water and soil, ecology, environment, resources, engineering and sustainable development in the dry areas of cold regions.

SURFRAD

Surface Radiation

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To understand the global surface energy budget is to understand climate. Because it is impractical to cover the earth with monitoring stations, the answer to global coverage lies in reliable satellite-based estimates. Efforts are underway at NASA and universities to develop algorithms to do this, but such projects are in their infancy. In concert with these ambitious efforts, accurate and precise ground-based measurements in differing climatic regions are essential to refine and verify the satellite-based estimates, as well as to support specialized research. To fill this niche, the Surface Radiation Budget Network (SURFRAD) was established in 1993 through the support of NOAA's Office of Global Programs.

PSD Climate and Weather Data

NOAA, ESRL, PSD, CWD

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The NOAA/ESRL Physical Sciences Division (PSD) conducts weather and climate research to observe and understand Earth's physical environment, and to improve weather and climate predictions on global-to-local scales. PSD archives a wide range of data ranging from gridded climate datasets extending hundreds of years to real-time wind profiler data at a single location. The data or products derived from this data, organized by type, are available to scientists and the general public .

GAPHYOR

GAz-PHYsics-ORsay

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The repository is no longer available. <<<!!!<<< 2018-08-29: no more access to GAPHYOR >>>!!!>>> Important note: The database was no longer feeded with data or updated in the years 2005-2007. The financial support of the project had been stopped a few yers ahead that time. The maintainance of the IT system couldn't be ensured anymore and system was shutdown in 2015. Please see the other databases in the field.

database of Sequence Tagged Sites

dbSTS

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<<<!!!<<< The page is no longer available. This database was already retired, and on this page users could find information on how to search and use these sequences. dbSTS was an NCBI resource that contained sequence data for short genomic landmark sequences or Sequence Tagged Sites. STS sequences are incorporated into the STS Division of GenBank. >>>!!!>>>