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Found 53 result(s)

Open Forest Data

e-Puszcza

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Podlasie digital repository of natural science data

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.

EMBL-EBI

European Molecular Biology Laboratory - European Bioinformatics Institute

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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.

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.

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.

West African Vegetation

A vegetation data network for West Africa

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This is a database for vegetation data from West Africa, i.e. phytosociological and dendrometric relevés as well as floristic inventories. The West African Vegetation Database has been developed in the framework of the projects “SUN - Sustainable Use of Natural Vegetation in West Africa” and “Biodiversity Transect Analysis in Africa” (BIOTA, https://www.biota-africa.org/).

Golm Metabolome Database

GMD

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The Golm Metabolome Database (GMD) facilitates the search for and dissemination of reference mass spectra from biologically active metabolites quantified using gas chromatography (GC) coupled to mass spectrometry (MS)

Eurobarometer

Eurobaromètre

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Public Opinion in the European Union. Our surveys address major topics concerning European citizenship. The Standard Eurobarometer was established in 1973. Since 1973, the European Commission has been monitoring the evolution of public opinion in the Member States, thus helping the preparation of texts, decision-making and the evaluation of its work. Our surveys and studies address major topics concerning European citizenship: enlargement, social situation, health, culture, information technology, environment, the Euro, defence, etc. Each survey consists of approximately 1000 face-to-face interviews per country. Reports are published twice yearly. Reproduction is authorised, except for commercial purposes, provided the source is acknowledged. Special Eurobarometer reports are based on in-depth thematic studies carried out for various services of the European Commission or other EU Institutions and integrated in the Standard Eurobarometer's polling waves. Reproduction is authorised, except for commercial purposes, provided the source is acknowledged. Flash Eurobarometers are ad hoc thematic telephone interviews conducted at the request of any service of the European Commission. Flash surveys enable the Commission to obtain results relatively quickly and to focus on specific target groups, as and when required. Reproduction is authorised, except for commercial purposes, provided the source is acknowledged. The qualitative studies investigate in-depth the motivations, feelings and reactions of selected social groups towards a given subject or concept, by listening to and analysing their way of expressing themselves in discussion groups or with non-directive interviews.

ACTRIS Data Centre

ACTRIS DC

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The ACTRIS DC is designed to assist scientists with discovering and accessing atmospheric data and contains an up-to-date catalogue of available datasets in a number of databases distributed throughout the world. A site like this can never be complete, but we have aimed at including datasets from the most relevant databases to the ACTRIS project, also building on the work and experiences achieved in the EU FP6 research project Global Earth Observation and Monitoring. The focus of the web portal is validated data, but it is also possible to browse the ACTRIS data server for preliminary data (rapid delivery data) through this site. The web site allows you to search in a local metadata catalogue that contains information on actual datasets that are archived in external archives. It is set up so that you can search for data by selecting the chemical/physical variable, the data location, the database that holds the data, the type of data, the data acquisition platform, and the data matrix

AlphaFold

AlphaFold Protein Structure Database

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AlphaFold DB provides open access to protein structure predictions for the human proteome and 20 other key organisms to accelerate scientific research.

EUREF Permanent Network

EPN

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The EPN (or EUREF Permanent Network) is a voluntary organization of several European agencies and universities that pool resources and permanent GNSS station data to generate precise GNSS products. The EPN has been created under the umbrella of the International Association Geodesy and more precisely by its sub-commission EUREF. The European Terrestrial Reference System 89 (ETRS89) is used as the standard precise GPS coordinate system throughout Europe. Supported by EuroGeographics and endorsed by the EU, this reference system forms the backbone for all geographic and geodynamic projects on the European territory both on a national as on an international level.

Copernicus Contributing Missions Online

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As part of the Copernicus Space Component programme, ESA manages the coordinated access to the data procured from the various Contributing Missions and the Sentinels, in response to the Copernicus users requirements. The Data Access Portfolio documents the data offer and the access rights per user category. The CSCDA portal is the access point to all data, including Sentinel missions, for Copernicus Core Users as defined in the EU Copernicus Programme Regulation (e.g. Copernicus Services).The Copernicus Space Component (CSC) Data Access system is the interface for accessing the Earth Observation products from the Copernicus Space Component. The system overall space capacity relies on several EO missions contributing to Copernicus, and it is continuously evolving, with new missions becoming available along time and others ending and/or being replaced.

ESA Earth Online

Earth Online

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The name Earth Online derives from ESA's Earthnet programme. Earthnet prepares and attracts new ESA Earth Observation missions by setting the international cooperation scheme, preparing the basic infrastructure, building the scientific and application Community and competency in Europe to define and set-up own European Programmes in consultation with member states. Earth Online is the entry point for scientific-technical information on Earth Observation activities by the European Space Agency (ESA). The web portal provides a vast amount of content, grown and collected over more than a decade: Detailed technical information on Earth Observation (EO) missions; Satellites and sensors; EO data products & services; Online resources such as catalogues and library; Applications of satellite data; Access to promotional satellite imagery. After 10 years of operations on distinct sites, the two principal portals of ESA Earth Observation - Earth Online (earth.esa.int) and the Principal Investigator's Portal (eopi.esa.int) have moved to a new platform. ESA's technical and scientific earth observation user communities will from now on be served from a single portal, providing a modern and easy-to-use interface to our services and data.

CATH

CATH-Gene3D

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The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in the CATH hierarchy; Class, Architecture, Topology and Homologous superfamily.

The Cancer Immunome Atlas

TCIA

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The Cancer Immunome Database (TCIA) provides results of comprehensive immunogenomic analyses of next generation sequencing data (NGS) data for 20 solid cancers from The Cancer Genome Atlas (TCGA) and other datasource. The Cancer Immunome Atlas (TCIA) was developed and is maintained at the Division of Bioinformatics (ICBI). The database can be queried for the gene expression of specific immune-related gene sets, cellular composition of immune infiltrates (characterized using gene set enrichment analyses and deconvolution), neoantigens and cancer-germline antigens, HLA types, and tumor heterogeneity (estimated from cancer cell fractions). Moreover it provides survival analyses for different types immunological parameters. TCIA will be constantly updated with new data and results.

NMDB

Neutron Monitor Database

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Real-Time Database for high-resolution Neutron Monitor measurements. NMDB provides access to Neutron Monitor measurements from stations around the world. The goal of NMDB is to provide easy access to all Neutron Monitor measurements through an easy to use interface. NMDB provides access to real-time as well as historical data.

IMGT/3Dstructure-DB and IMGT/2Dstructure-DB

International ImMunoGeneTics information system/3Dstructure-DB and IMGT/2Dstructure-DB

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IMGT/3Dstructure-DB is the IMGT three-dimensional (3D) structure database.

SIPAM

Spatial Information System of the Maritime Administration

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The main objective of the project is to digitize the data collected by the Maritime Administration and make it available for reuse by digitizing analog resources, integrating and harmonizing data and building a digital repository, and disseminating information about the resources collected in the system. The aim of the project is to make maritime administration data sets available on the Internet.

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.

ECCAD - the GEIA database

Emissions of atmospheric Compounds & Compilation of Ancillary Data

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The main goal of the ECCAD project is to provide scientific and policy users with datasets of surface emissions of atmospheric compounds, and ancillary data, i.e. data required to estimate or quantify surface emissions. The supply of ancillary data - such as maps of population density, maps of fires spots, burnt areas, land cover - could help improve and encourage the development of new emissions datasets. ECCAD offers: Access to global and regional emission inventories and ancillary data, in a standardized format Quick visualization of emission and ancillary data Rationalization of the use of input data in algorithms or emission models Analysis and comparison of emissions datasets and ancillary data Tools for the evaluation of emissions and ancillary data ECCAD is a dynamical and interactive database, providing the most up to date datasets including data used within ongoing projects. Users are welcome to add their own datasets, or have their regional masks included in order to use ECCAD tools.

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.

CESSDA Data Catalogue

CESSDA DC

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The CESSDA Data Catalogue contains the metadata of all data in the holdings of CESSDA service providers. It is a one-stop-shop for search and discovery, enabling effective access to European research data for researchers. Details of over 40, 000 data collections are listed. These are harvested from fifteen different CESSDA Service Providers.

International Ocean Discovery Program

IODP

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The International Ocean Discovery Program (IODP) is an international marine research collaboration that explores Earth's history and dynamics using ocean-going research platforms to recover data recorded in seafloor sediments and rocks and to monitor subseafloor environments. IODP depends on facilities funded by three platform providers with financial contributions from five additional partner agencies. Together, these entities represent 26 nations whose scientists are selected to staff IODP research expeditions conducted throughout the world's oceans. IODP expeditions are developed from hypothesis-driven science proposals aligned with the program's science plan Illuminating Earth's Past, Present, and Future. The science plan identifies 14 challenge questions in the four areas of climate change, deep life, planetary dynamics, and geohazards. Until 2013 under the name: International Ocean Drilling Program.