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Found 47 result(s)

PubChem

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Pubchem contains 3 databases. 1. PubChem BioAssay: The PubChem BioAssay Database contains bioactivity screens of chemical substances described in PubChem Substance. It provides searchable descriptions of each bioassay, including descriptions of the conditions and readouts specific to that screening procedure. 2. PubChem Compound: The PubChem Compound Database contains validated chemical depiction information provided to describe substances in PubChem Substance. Structures stored within PubChem Compounds are pre-clustered and cross-referenced by identity and similarity groups. 3. PubChem Substance. The PubChem Substance Database contains descriptions of samples, from a variety of sources, and links to biological screening results that are available in PubChem BioAssay. If the chemical contents of a sample are known, the description includes links to PubChem Compound.

Open Tree of Life

Tree of Life - Evolution

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The tree of life links all biodiversity through a shared evolutionary history. This project will produce the first online, comprehensive first-draft tree of all 1.8 million named species, accessible to both the public and scientific communities. Assembly of the tree will incorporate previously-published results, with strong collaborations between computational and empirical biologists to develop, test and improve methods of data synthesis. This initial tree of life will not be static; instead, we will develop tools for scientists to update and revise the tree as new data come in. Early release of the tree and tools will motivate data sharing and facilitate ongoing synthesis of knowledge.

DNASU plasmid repository

DNASU

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DNASU is a central repository for plasmid clones and collections. Currently we store and distribute over 200,000 plasmids including 75,000 human and mouse plasmids, full genome collections, the protein expression plasmids from the Protein Structure Initiative as the PSI: Biology Material Repository (PSI : Biology-MR), and both small and large collections from individual researchers. We are also a founding member and distributor of the ORFeome Collaboration plasmid collection.

NONCODE

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NONCODE is an integrated knowledge database dedicated to non-coding RNAs (excluding tRNAs and rRNAs). Now, there are 16 species in NONCODE(human, mouse, cow, rat, chicken, fruitfly, zebrafish, celegans, yeast, Arabidopsis, chimpanzee, gorilla, orangutan, rhesus macaque, opossum and platypus).The source of NONCODE includes literature and other public databases. We searched PubMed using key words ‘ncrna’, ‘noncoding’, ‘non-coding’,‘no code’, ‘non-code’, ‘lncrna’ or ‘lincrna. We retrieved the new identified lncRNAs and their annotation from the Supplementary Material or web site of these articles. Together with the newest data from Ensembl , RefSeq, lncRNAdb and GENCODE were processed through a standard pipeline for each species.

NCBI Gene

Gene

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The Gene database provides detailed information for known and predicted genes defined by nucleotide sequence or map position. Gene supplies gene-specific connections in the nexus of map, sequence, expression, structure, function, citation, and homology data. Unique identifiers are assigned to genes with defining sequences, genes with known map positions, and genes inferred from phenotypic information. These gene identifiers are used throughout NCBI's databases and tracked through updates of annotation. Gene includes genomes represented by NCBI Reference Sequences (or RefSeqs) and is integrated for indexing and query and retrieval from NCBI's Entrez and E-Utilities systems.

ENCODE

Encyclopedia of DNA Elements

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The ENCODE Encyclopedia organizes the most salient analysis products into annotations, and provides tools to search and visualize them. The Encyclopedia has two levels of annotations: Integrative-level annotations integrate multiple types of experimental data and ground level annotations. Ground-level annotations are derived directly from the experimental data, typically produced by uniform processing pipelines.

Human Genetic Variation Repository

HGVD

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The Human Genetic Variation Database (HGVD) aims to provide a central resource to archive and display Japanese genetic variation and association between the variation and transcription level of genes. The database currently contains genetic variations determined by exome sequencing of 1,208 individuals and genotyping data of common variations obtained from a cohort of 3,248 individuals.

Mouse Genome Informatics

MGI

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MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. The projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, MouseMine Project, MouseCyc Project at MGI

Clinical Genomic Database

CGD

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Clinical Genomic Database (CGD) is a manually curated database of conditions with known genetic causes, focusing on medically significant genetic data with available interventions.

Codex

A comprehensive and functional compendium of Next Generation Sequencing experiments.

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CODEX is a database of NGS mouse and human experiments. Although, the main focus of CODEX is Haematopoiesis and Embryonic systems, the database includes a large variety of cell types. In addition to the publically available data, CODEX also includes a private site hosting non-published data. CODEX provides access to processed and curated NGS experiments. To use CODEX: (i) select a specialized repository (HAEMCODE or ESCODE) or choose the whole compendium (CODEX), then (ii) filter by organism and (iii) choose how to explore the database.

Genome Sequence Archive

GSA

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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.

STOREDB

Sustaining access to Tissues and data frOm Radiobiological Experiments

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STOREDB is a platform for the archiving and sharing of primary data and outputs of all kinds, including epidemiological and experimental data, from research on the effects of radiation. It also provides a directory of bioresources and databases containing information and materials that investigators are willing to share. STORE supports the creation of a radiation research commons.

SWISS-MODEL Repository

SMR

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The SWISS-MODEL Repository is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.

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.

The Taenia solium Genome Project

T. solium Genome Project

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>>>!!!<<< 2021-08; The repository is no longer available. >>>!!!<<< Archived page of Taenia solium genome project see https://web.archive.org/web/20160309194611/http://www.taeniasolium.unam.mx/taenia

BioVel

Biodiversity Virtual e-Laboratory

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<<<!!!<<< This repository is no longer available. >>>!!!>>> BioVeL is a virtual e-laboratory that supports research on biodiversity issues using large amounts of data from cross-disciplinary sources. BioVeL supports the development and use of workflows to process data. It offers the possibility to either use already made workflows or create own. BioVeL workflows are stored in MyExperiment - Biovel Group http://www.myexperiment.org/groups/643/content. They are underpinned by a range of analytical and data processing functions (generally provided as Web Services or R scripts) to support common biodiversity analysis tasks. You can find the Web Services catalogued in the BiodiversityCatalogue.

GUDMAP

GenitoUrinary Development Molecular Anatomy Project

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The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research. The key components are: (1) a molecular atlas of gene expression for the developing organs of the GenitoUrinary (GU) tract; (2) a high resolution molecular anatomy that highlights development of the GU system; (3) mouse strains to facilitate developmental and functional studies within the GU system; (4) tutorials describing GU organogenesis; and (5) rapid access to primary data via the GUDMAP database.

REBASE

The Restriction Enzyme Database

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The Restriction Enzyme Database is a collection of information about restriction enzymes, methylases, the microorganisms from which they have been isolated, recognition sequences, cleavage sites, methylation specificity, the commercial availability of the enzymes, and references - both published and unpublished observations (dating back to 1952). REBASE is updated daily and is constantly expanding.

Array Express

functional genomics data

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ArrayExpress is one of the major international repositories for high-throughput functional genomics data from both microarray and high-throughput sequencing studies, many of which are supported by peer-reviewed publications. Data sets are submitted directly to ArrayExpress and curated by a team of specialist biological curators. In the past (until 2018) datasets from the NCBI Gene Expression Omnibus database were imported on a weekly basis. Data is collected to MIAME and MINSEQE standards.

ProteomeXchange

PX

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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.

Electron Microscopy Data Bank

EMDB

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The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography.

PhytoPath

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<<<!!!<<< This site is no longer maintained and is provided for reference only. Some functionality or links may not work. For all enquiries please contact the Ensembl Helpdesk http://www.ensembl.org/Help/Contact >>>!!!>>> PhytoPath is a new bioinformatics resource that integrates genome-scale data from important plant pathogen species with literature-curated information about the phenotypes of host infection. Using the Ensembl Genomes browser, it provides access to complete genome assembly and gene models of priority crop and model-fungal, oomycete and bacterial phytopathogens. PhytoPath also links genes to disease progression using data from the curated PHI-base resource. PhytoPath portal is a joint project bringing together Ensembl Genomes with PHI-base, a community-curated resource describing the role of genes in pathogenic infection. PhytoPath provides access to genomic and phentoypic data from fungal and oomycete plant pathogens, and has enabled a considerable increase in the coverage of phytopathogen genomes in Ensembl Fungi and Ensembl Protists. PhytoPath also provides enhanced searching of the PHI-base resource as well as the fungi and protists in Ensembl Genomes.

The Comprehensive Resource of Mammalian protein complexes

CORUM

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CORUM is a manually curated dataset of mammalian protein complexes. Annotation of protein complexes includes protein complex composition and other valuable information such as method of purification, cellular function of complexes or involvement in diseases.

NBIS DOI repository

BILS DOI Repository (formerly)

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<<<!!!<<< The repository is inactive, please use SciLifeLab Data Repository https://www.re3data.org/repository/r3d100013347 >>>!!!>>>

Open PHACTS

Open Pharmacological Space

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<<<!!!<<< The Open PHACTS Linked Data API and associated infrastructure was closed down in March 2019 to allow the team to focus on the next phase. http://www.openphactsfoundation.org/open-phacts-platform-update-march-2019/ >>>!!!>>>