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Found 186 result(s)

IMEx

The International Molecular Exchange Consortium

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The IMEx consortium is an international collaboration between a group of major public interaction data providers who have agreed to share curation effort and develop and work to a single set of curation rules when capturing data from both directly deposited interaction data or from publications in peer-reviewed journals, capture full details of an interaction in a “deep” curation model, perform a complete curation of all protein-protein interactions experimentally demonstrated within a publication, make these interaction available in a single search interface on a common website, provide the data in standards compliant download formats, make all IMEx records freely accessible under the Creative Commons Attribution License

Expression Atlas

Gene Expression Atlas

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The Expression Atlas provides information on gene expression patterns under different biological conditions such as a gene knock out, a plant treated with a compound, or in a particular organism part or cell. It includes both microarray and RNA-seq data. The data is re-analysed in-house to detect interesting expression patterns under the conditions of the original experiment. There are two components to the Expression Atlas, the Baseline Atlas and the Differential Atlas. The Baseline Atlas displays information about which gene products are present (and at what abundance) in "normal" conditions (e.g. tissue, cell type). It aims to answer questions such as "which genes are specifically expressed in human kidney?". This component of the Expression Atlas consists of highly-curated and quality-checked RNA-seq experiments from ArrayExpress. It has data for many different animal and plant species. New experiments are added as they become available. The Differential Atlas allows users to identify genes that are up- or down-regulated in a wide variety of different experimental conditions such as yeast mutants, cadmium treated plants, cystic fibrosis or the effect on gene expression of mind-body practice. Both microarray and RNA-seq experiments are included in the Differential Atlas. Experiments are selected from ArrayExpress and groups of samples are manually identified for comparison e.g. those with wild type genotype compared to those with a gene knock out. Each experiment is processed through our in-house differential expression statistical analysis pipeline to identify genes with a high probability of differential expression.

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.

European Nucleotide Archive

ENA

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The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources. These include submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centres and routine and comprehensive exchange with our partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature.

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.

Ensembl Bacteria

e!EnsemblBacteria

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This site provides access to complete, annotated genomes from bacteria and archaea (present in the European Nucleotide Archive) through the Ensembl graphical user interface (genome browser). Ensembl Bacteria contains genomes from annotated INSDC records that are loaded into Ensembl multi-species databases, using the INSDC annotation import pipeline.

Virus Pathogen Resource

ViPR

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<<<!!!<<< This repository is no longer available. >>>!!!>>> Migration of the data, tools, and services from IRD and ViPR to BV-BRC is complete! We are now in the sunsetting phase of the transition. Starting on October 31, 2022, launching the IRD or ViPR home pages will redirect you to the new BV-BRC home page. The current plan is to completely shut down IRD and ViPR by the end of this calendar year. Although it will still be possible to use those sites until shutdown, we strongly encourage you to start using BV-BRC now.

Protein Data Bank in Europe

PDBe

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PDBe is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - we work to collate, maintain and provide access to the global repository of macromolecular structure data. We develop tools, services and resources to make structure-related data more accessible to the biomedical community.

Australian Drosophila Ecology and Evolution Resource

ADEER

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The Australian Drosophila Ecology and Evolution Resource (ADEER) from the Hoffmann lab and other contributors is a nationally significant life science collection. The Drosophila Clinal Data Collection contains data on populations along the eastern coast of Australia. It remains an excellent resource for understanding past and future evolutionary responses to climate change. The Drosophila Genomic Data Collection hosts Drosophila genomes sequenced as part of the Genomic Basis for Adaptation to Climate Change Project. 23 genomes have been sequenced as part of this project. Currently assemblies and annotations are available for Drosophila birchii, D. bunnanda, D. hydei, and D. repleta. The Drosophila Species Distribution Data Collection contains distribution data of nine drosophilid species that have been collected in Australia by the Hoffmann lab and other research groups between 1924 and 2005. More than 300 drosophilid species have been identified in the tropical and temperate forests located on the east coast of Australia. Many species are restricted to the tropics, a few are temperate specialists, and some have broad distributions across climatic regions. Their varied distribution along the tropical - temperate cline provide a powerful tool for studying climate adaptation and species distribution limits.

Rhea

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Rhea is a freely available and comprehensive resource of expert-curated biochemical reactions. It has been designed to provide a non-redundant set of chemical transformations for applications such as the functional annotation of enzymes, pathway inference and metabolic network reconstruction. There are three types of reaction participants (reactants and products): Small molecules, Rhea polymers, Generic compounds. All three types of reaction participants are linked to the ChEBI database (Chemical Entities of Biological Interest) which provides detailed information about structure, formula and charge. Rhea provides built-in validations that ensure both mass and charge balance of the reactions. We have populated the database with the reactions found in the enzyme classification (i.e. in the IntEnz and ENZYME databases), extending it with additional known reactions of biological interest. While the main focus of Rhea is enzyme-catalysed reactions, other biochemical reactions (including those that are often termed "spontaneous") also are included.

BioMemory

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BioMemory is the network of biological collections of the Department of Biology, Agriculture and Food Sciences (DiSBA) of the National Research Council of Italy (CNR) for bio-monitoring, biodiversity conservation, agri-food and environmental sustainability, and human well-being. The project is aimed to create a network of biobanks (i.e., scientific research collections) where data and metadata associated to biological samples of different nature are collected and stored in a systematic and well-organized way. Maintaining the existing collections will allow their future use for a number of purposes, from the genetic improvement of organisms to face environmental changes (climate-ready organisms) to the fight against epidemics and pandemics affecting humans, animals and plants.