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Found 24 result(s)
dbEST is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. Expressed Sequence Tags (ESTs) are short (usually about 300-500 bp), single-pass sequence reads from mRNA (cDNA). Typically they are produced in large batches. They represent a snapshot of genes expressed in a given tissue and/or at a given developmental stage. They are tags (some coding, others not) of expression for a given cDNA library. Most EST projects develop large numbers of sequences. These are commonly submitted to GenBank and dbEST as batches of dozens to thousands of entries, with a great deal of redundancy in the citation, submitter and library information. To improve the efficiency of the submission process for this type of data, we have designed a special streamlined submission process and data format. dbEST also includes sequences that are longer than the traditional ESTs, or are produced as single sequences or in small batches. Among these sequences are products of differential display experiments and RACE experiments. The thing that these sequences have in common with traditional ESTs, regardless of length, quality, or quantity, is that there is little information that can be annotated in the record. If a sequence is later characterized and annotated with biological features such as a coding region, 5'UTR, or 3'UTR, it should be submitted through the regular GenBank submissions procedure (via BankIt or Sequin), even if part of the sequence is already in dbEST. dbEST is reserved for single-pass reads. Assembled sequences should not be submitted to dbEST. GenBank will accept assembled EST submissions for the forthcoming TSA (Transcriptome Shotgun Assembly) division. The individual reads which make up the assembly should be submitted to dbEST, the Trace archive or the Short Read Archive (SRA) prior to the submission of the assemblies.
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CBS offers Comprehensive public databases of DNA- and protein sequences, macromolecular structure, g ene and protein expression levels, pathway organization and cell signalling, have been established to optimise scientific exploitation of the explosion of data within biology. Unlike many other groups in the field of biomolecular informatics, Center for Biological Sequence Analysis directs its research primarily towards topics related to the elucidation of the functional aspects of complex biological mechanisms. Among contemporary bioinformatics concerns are reliable computational interpretation of a wide range of experimental data, and the detailed understanding of the molecular apparatus behind cellular mechanisms of sequence information. By exploiting available experimental data and evidence in the design of algorithms, sequence correlations and other features of biological significance can be inferred. In addition to the computational research the center also has experimental efforts in gene expression analysis using DNA chips and data generation in relation to the physical and structural properties of DNA. In the last decade, the Center for Biological Sequence Analysis has produced a large number of computational methods, which are offered to others via WWW servers.
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Species included in PlantTFDB 4.0 covers the main lineages of green plants. Therefore, PlantTFDB provides genomic TF repertoires across Viridiplantae. To provide comprehensive information for the TF family, a brief introduction and key references are presented for each family. Comprehensive annotations are made for each identified TF, including functional domains, 3D structures, gene ontology (GO), plant ontology (PO), expression information, expert-curated functional description, regulation information, interaction, conserved elements, references, and annotations in various databases such as UniProt, RefSeq, TransFac, STRING, and VISTA. By inferring orthologous groups and constructing phylogenetic trees, evolutionary relationships among identified TFs were inferred. In addition, PlantTFDB has a simple and user-friendly interface to allow users to query based on combined conditions or make sequence similarity search using BLAST.
The European Bioinformatics Institute (EBI) has a long-standing mission to collect, organise and make available databases for biomolecular science. It makes available a collection of databases along with tools to search, download and analyse their content. These databases include DNA and protein sequences and structures, genome annotation, gene expression information, molecular interactions and pathways. Connected to these are linking and descriptive data resources such as protein motifs, ontologies and many others. In many of these efforts, the EBI is a European node in global data-sharing agreements involving, for example, the USA and Japan.
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China National GeneBank DataBase (CNGBdb) is a unified platform built for biological big data sharing and application services to the research community. Based on the big data and cloud computing technologies, it provides data services such as archive, analysis, knowledge search, management authorization, and visualization. At present, CNGBdb has integrated large amounts of internal and external molecular data and other information from CNGB, NCBI, EBI, DDBJ, etc., indexed by search, covering 12 data structures. Moreover, CNGBdb correlates living sources, biological samples and bioinformatic data to realize the traceability of comprehensive data.
The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by providing electronic access to: Information on endogenous spontaneous and induced tumors in mice, including tumor frequency & latency data, Information on genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice) in which tumors arise, Information on genetic factors associated with tumor susceptibility in mice and somatic genetic-mutations observed in the tumors, Tumor pathology reports and images, References, supporting MTB data and Links to other online resources for cancer.
IntEnz contains the recommendation of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalyzed reactions. Users can browse by enzyme classification or use advanced search options to search enzymes by class, subclass and sub-subclass information.
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The Taenia solium genome project is a whole genome sequencing project of the parasite Taenia solium, the causal agent of human and porcine cysticercosis; a disease that is still a public health problem of relevance in Mexico. It is being carried out by a consortium of scientists belonging to diverse institutions of the Universidad Nacional Autónoma de México (UNAM, the National Autonomous University of Mexico).
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GSA is a data repository specialized for archiving raw sequence reads. It supports data generated from a variety of sequencing platforms ranging from Sanger sequencing machines to single-cell sequencing machines and provides data storing and sharing services free of charge for worldwide scientific communities. In addition to raw sequencing data, GSA also accommodates secondary analyzed files in acceptable formats (like BAM, VCF). Its user-friendly web interfaces simplify data entry and submitted data are roughly organized as two parts, viz., Metadata and File, where the former can be further assorted into BioProject, BioSample, Experiment and Run, and the latter contains raw sequence reads.
The ProteomeXchange consortium has been set up to provide a single point of submission of MS proteomics data to the main existing proteomics repositories, and to encourage the data exchange between them for optimal data dissemination. Current members accepting submissions are: The PRIDE PRoteomics IDEntifications database at the European Bioinformatics Institute focusing mainly on shotgun mass spectrometry proteomics data PeptideAtlas/PASSEL focusing on SRM/MRM datasets.
GenBank® is a comprehensive database that contains publicly available nucleotide sequences for almost 260 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP.
TPA is a database that contains sequences built from the existing primary sequence data in GenBank. TPA records are retrieved through the Nucleotide Database and feature information on the sequence, how it was cataloged, and proper way to cite the sequence information.
The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.
With the creation of the Metabolomics Data Repository managed by Data Repository and Coordination Center (DRCC), the NIH acknowledges the importance of data sharing for metabolomics. Metabolomics represents the systematic study of low molecular weight molecules found in a biological sample, providing a "snapshot" of the current and actual state of the cell or organism at a specific point in time. Thus, the metabolome represents the functional activity of biological systems. As with other ‘omics’, metabolites are conserved across animals, plants and microbial species, facilitating the extrapolation of research findings in laboratory animals to humans. Common technologies for measuring the metabolome include mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (NMR), which can measure hundreds to thousands of unique chemical entities. Data sharing in metabolomics will include primary raw data and the biological and analytical meta-data necessary to interpret these data. Through cooperation between investigators, metabolomics laboratories and data coordinating centers, these data sets should provide a rich resource for the research community to enhance preclinical, clinical and translational research.
The 1000 Genomes Project is an international collaboration to produce an extensive public catalog of human genetic variation, including SNPs and structural variants, and their haplotype contexts. This resource will support genome-wide association studies and other medical research studies. The genomes of about 2500 unidentified people from about 25 populations around the world will be sequenced using next-generation sequencing technologies. The results of the study will be freely and publicly accessible to researchers worldwide. The International Genome Sample Resource (IGSR) has been established at EMBL-EBI to continue supporting data generated by the 1000 Genomes Project, supplemented with new data and new analysis.
The PATRIC website provides an entry point to integrated data and tools for bacterial infectious disease research. The website is organized by data types and analysis tools. Primary access is provided through the PATRIC main menu, available at the top of the home page.
MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments.
ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data). The data is abstracted and curated from the primary scientific literature, and cover a significant fraction of the SAR and discovery of modern drugs We attempt to normalise the bioactivities into a uniform set of end-points and units where possible, and also to tag the links between a molecular target and a published assay with a set of varying confidence levels. Additional data on clinical progress of compounds is being integrated into ChEMBL at the current time.
The NCBI Nucleotide database collects sequences from such sources as GenBank, RefSeq, TPA, and PDB. Sequences collected relate to genome, gene, and transcript sequence data, and provide a foundation for research related to the biomedical field.
The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view.