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Found 16 result(s)

STRING

Known and Predicted Protein-Protein Interactions

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STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources: - Genomic Context - High-throughput Experiments - (Conserved) Coexpression - Previous Knowledge STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable.

Electron Microscopy Public Image Archive

EMPIAR

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EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload, download and reprocess the thousands of raw, 2D images used to build a 3D structure. The purpose of EMPIAR is to provide an easy access to the state-of-the-art raw data to facilitate methods development and validation, which will lead to better 3D structures. It complements the Electron Microscopy Data Bank (EMDB), where 3D images are stored, and uses the fault-tolerant Aspera platform for data transfers

MGnify

formerly: EBI Metagenomics

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MGnify (formerly: EBI Metagenomics) offers an automated pipeline for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.

IntAct

IntAct Molecular Interaction Database

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IntAct provides a freely available, open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.

DisProt

Database of Protein Disorder

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The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. DisProt is a community resource annotating protein sequences for intrinsically disorder regions from the literature. It classifies intrinsic disorder based on experimental methods and three ontologies for molecular function, transition and binding partner.

Image Data Resource

IDR

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The IDR makes datasets that have never previously been accessible publicly available, allowing the community to search, view, mine and even process and analyze large, complex, multidimensional life sciences image data. Sharing data promotes the validation of experimental methods and scientific conclusions, the comparison with new data obtained by the global scientific community, and enables data reuse by developers of new analysis and processing tools.

VectorBase

Bioinformatics Resource for Invertebrate Vectors of Human Pathogens

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VectorBase provides data on arthropod vectors of human pathogens. Sequence data, gene expression data, images, population data, and insecticide resistance data for arthropod vectors are available for download. VectorBase also offers genome browser, gene expression and microarray repository, and BLAST searches for all VectorBase genomes. VectorBase Genomes include Aedes aegypti, Anopheles gambiae, Culex quinquefasciatus, Ixodes scapularis, Pediculus humanus, Rhodnius prolixus. VectorBase is one the Bioinformatics Resource Centers (BRC) projects which is funded by National Institute of Allergy and Infectious Diseases (NAID).

WikiPathways

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WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents a new model for pathway databases that enhances and complements ongoing efforts, such as KEGG, Reactome and Pathway Commons. Building on the same MediaWiki software that powers Wikipedia, we added a custom graphical pathway editing tool and integrated databases covering major gene, protein, and small-molecule systems. The familiar web-based format of WikiPathways greatly reduces the barrier to participate in pathway curation. More importantly, the open, public approach of WikiPathways allows for broader participation by the entire community, ranging from students to senior experts in each field. This approach also shifts the bulk of peer review, editorial curation, and maintenance to the community.

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.

PANDIT

Protein and Associated Nucleotide Domains with Inferred Trees

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<<<!!!<<< Efforts to obtain renewed funding after 2008 were unfortunately not successful. PANDIT has therefore been frozen since November 2008, and its data are not updated since September 2005 when version 17.0 was released (corresponding to Pfam 17.0). The existing data and website remain available from these pages, and should remain stable and, we hope, useful. >>>!!!>>> PANDIT is a collection of multiple sequence alignments and phylogenetic trees. It contains corresponding amino acid and nucleotide sequence alignments, with trees inferred from each alignment. PANDIT is based on the Pfam database (Protein families database of alignments and HMMs), and includes the seed amino acid alignments of most families in the Pfam-A database. DNA sequences for as many members of each family as possible are extracted from the EMBL Nucleotide Sequence Database and aligned according to the amino acid alignment. PANDIT also contains a further copy of the amino acid alignments, restricted to the sequences for which DNA sequences were found.

Emage

e-Mouse Atlas of Gene Expression

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EMAGE (e-Mouse Atlas of Gene Expression) is an online biological database of gene expression data in the developing mouse (Mus musculus) embryo. The data held in EMAGE is spatially annotated to a framework of 3D mouse embryo models produced by EMAP (e-Mouse Atlas Project). These spatial annotations allow users to query EMAGE by spatial pattern as well as by gene name, anatomy term or Gene Ontology (GO) term. EMAGE is a freely available web-based resource funded by the Medical Research Council (UK) and based at the MRC Human Genetics Unit in the Institute of Genetics and Molecular Medicine, Edinburgh, UK.

FAIRDOMHub

The SEEK datafiles

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The FAIRDOMHub is built upon the SEEK software suite, which is an open source web platform for sharing scientific research assets, processes and outcomes. FAIRDOM (Web Site) will establish a support and service network for European Systems Biology. It will serve projects in standardizing, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable. FAIRDOM is an initiative to develop a community, and establish an internationally sustained Data and Model Management service to the European Systems Biology community. FAIRDOM is a joint action of ERA-Net EraSysAPP and European Research Infrastructure ISBE.

InterPro

protein sequence analysis & classification

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InterPro collects information about protein sequence analysis and classification, providing access to a database of predictive protein signatures used for the classification and automatic annotation of proteins and genomes. Sequences in InterPro are classified at superfamily, family, and subfamily. InterPro predicts the occurrence of functional domains, repeats, and important sites, and adds in-depth annotation such as GO terms to the protein signatures.

PRoteomics IDEntifications Database

PRIDE

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The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. PRIDE encourages and welcomes direct user submissions of mass spectrometry data to be published in peer-reviewed publications.

Leiden Open Variation Database

LOVD

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LOVD portal provides LOVD software and access to a list of worldwide LOVD applications through Locus Specific Database list and List of Public LOVD installations. The LOVD installations that have indicated to be included in the global LOVD listing are included in the overall LOVD querying service, which is based on an API.

BBMRI-ERIC Directory

Directory of Biobanks

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BBMRI-ERIC is a European research infrastructure for biobanking. We bring together all the main players from the biobanking field – researchers, biobankers, industry, and patients – to boost biomedical research. To that end, we offer quality management services, support with ethical, legal and societal issues, and a number of online tools and software solutions. Ultimately, our goal is to make new treatments possible. The Directory is a tool to share aggregate information about the biobanks that are willing external collaboration. It is based on the MIABIS 2.0 standard, which describes the samples and data in the biobanks at an aggregated level.