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Found 28 result(s)

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.

HAGR

Human Ageing Genomic Resources

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The Human Ageing Genomic Resources (HAGR) is a collection of databases and tools designed to help researchers study the genetics of human ageing using modern approaches such as functional genomics, network analyses, systems biology and evolutionary analyses.

Barcode of Life Data Systems

BOLD Systems

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The Barcode of Life Data Systems (BOLD) provides DNA barcode data. BOLD's online workbench supports data validation, annotation, and publication for specimen, distributional, and molecular data. The platform consists of four main modules: a data portal, a database of barcode clusters, an educational portal, and a data collection workbench. BOLD is the go-to site for DNA-based identification. As the central informatics platform for DNA barcoding, BOLD plays a crucial role in assimilating and organizing data gathered by the international barcode research community. Two iBOL (International Barcode of Life) Working Groups are supporting the ongoing development of BOLD.

Biomedical Informatics Research Network

BIRN

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>>>!!!<<< As stated 2017-05-16 The BIRN project was finished a few years ago. The web portal is no longer live.>>>!!!<<< BIRN is a national initiative to advance biomedical research through data sharing and online collaboration. It supports multi-site, and/or multi-institutional, teams by enabling researchers to share significant quantities of data across geographic distance and/or incompatible computing systems. BIRN offers a library of data-sharing software tools specific to biomedical research, best practice references, expert advice and other resources.

RADAM database portal

RADiation DAMage database

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RADAM portal is an interface to the network of RADAM (RADiation DAMage) Databases collecting data on interactions of ions, electrons, positrons and photons with biomolecular systems, on radiobiological effects and relevant phenomena occurring at different time, spatial and energy scales in irradiated targets during and after the irradiation. This networking system has been created by the Consortium of COST Action MP1002 (Nano-IBCT: Nano-scale insights into Ion Beam Cancer Therapy) during 2011-2014 using the Virtual Atomic and Molecular Data Center (VAMDC) standards.

MicroScope

Microbial Genome Annotation & Analysis Platform

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The MicroScope platform is an informatics infrastructure dedicated to the annotation and comparative analysis of microbial genomes and metagenomes.

NetPath

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<<<!!!<<< This repository is no longer available. >>>!!!>>> NetPath is currently one of the largest open-source repository of human signaling pathways that is all set to become a community standard to meet the challenges in functional genomics and systems biology. Signaling networks are the key to deciphering many of the complex networks that govern the machinery inside the cell. Several signaling molecules play an important role in disease processes that are a direct result of their altered functioning and are now recognized as potential therapeutic targets. Understanding how to restore the proper functioning of these pathways that have become deregulated in disease, is needed for accelerating biomedical research. This resource is aimed at demystifying the biological pathways and highlights the key relationships and connections between them. Apart from this, pathways provide a way of reducing the dimensionality of high throughput data, by grouping thousands of genes, proteins and metabolites at functional level into just several hundreds of pathways for an experiment. Identifying the active pathways that differ between two conditions can have more explanatory power than just a simple list of differentially expressed genes and proteins.

Genome-Scale Metabolic Network DataBase

GSMNDB

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<<<!!!<<< 2019-12-23: the repository is offline >>>!!!>>> Introduction of genome-scale metabolic network: The completion of genome sequencing and subsequent functional annotation for a great number of species enables the reconstruction of genome-scale metabolic networks. These networks, together with in silico network analysis methods such as the constraint based methods (CBM) and graph theory methods, can provide us systems level understanding of cellular metabolism. Further more, they can be applied to many predictions of real biological application such as: gene essentiality analysis, drug target discovery and metabolic engineering

Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer

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The information in the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer relates cytogenetic changes and their genomic consequences, in particular gene fusions, to tumor characteristics, based either on individual cases or associations. All the data have been manually culled from the literature by Felix Mitelman in collaboration with Bertil Johansson and Fredrik Mertens.

Cancer Genome Anatomy Project

CGAP

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>>>!!!<<< Noticed 26.08.2020: The NCI CBIIT instance of the CGAP no longer exist on this website. The Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer has a new home at the NCI-funded Institute for Systems Biology Cancer Genomics Cloud available at the following location: https://mitelmandatabase.isb-cgc.org >>>!!!<<<

Woods Hole Oceanographic Institution - Data & Repositories

WHOI

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WHOI is the world's leading non-profit oceanographic research organization. WHOI maintains unparalleled depth and breadth of expertise across a range of oceanographic research areas. Institution scientists and engineers work collaboratively within and across six research departments to advance knowledge of the global ocean and its fundamental importance to other planetary systems. At the same time, they also train future generations of ocean scientists and address problems that have a direct impact in efforts to understand and manage critical marine resources.

Gene Ontology

GO

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The mission of the GO Consortium is to develop a comprehensive, computational model of biological systems, ranging from the molecular to the organism level, across the multiplicity of species in the tree of life. The Gene Ontology (GO) knowledgebase is the world’s largest source of information on the functions of genes. This knowledge is both human-readable and machine-readable, and is a foundation for computational analysis of large-scale molecular biology and genetics experiments in biomedical research.

mzCloud

Advanced mass spectral database

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mzCloud is an extensively curated database of high-resolution tandem mass spectra that are arranged into spectral trees. MS/MS and multi-stage MSn spectra were acquired at various collision energies, precursor m/z, and isolation widths using Collision-induced dissociation (CID) and Higher-energy collisional dissociation (HCD). Each raw mass spectrum was filtered and recalibrated giving rise to additional filtered and recalibrated spectral trees that are fully searchable. Besides the experimental and processed data, each database record contains the compound name with synonyms, the chemical structure, computationally and manually annotated fragments (peaks), identified adducts and multiply charged ions, molecular formulas, predicted precursor structures, detailed experimental information, peak accuracies, mass resolution, InChi, InChiKey, and other identifiers. mzCloud is a fully searchable library that allows spectra searches, tree searches, structure and substructure searches, monoisotopic mass searches, peak (m/z) searches, precursor searches, and name searches. mzCloud is free and available for public use online.

National Aquatic Biological Resource Center

国家水生生物种质资源库

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National Aquatic Biological Resource Center (NABRC), established in June 2019, is a member of National Science and Technology Resource Platform supported by the Ministry of Science and Technology and the Ministry of Finance. The NABRC consists of 6 sub-platforms. In summary, these six sub-platforms have reached leading levels at home and abroad in terms of the resource richness, the resource digitization, as well as the amount and quality of resource services. Right now, these platforms are in strong support of basic biology, basic medicine, aquatic economics, water environmental protection and other areas in China. It is an essential way to practice the "Great Yangtze River Protection" and promote the construction of ecological civilization in the Yangtze River. In the future, the platforms will further integrate different types of resources, optimize the resource configuration and improve the service systems, so as to build a high standard resource sharing platform on a global scale and promote international communication and cooperation.

LIPID MAPS

LIPID Metabolites And Pathways Strategy

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Tthe Lipidomics Gateway - a free, comprehensive website for researchers interested in lipid biology, provided by the LIPID MAPS (Lipid Metabolites and Pathways Strategy) Consortium. The LIPID MAPS Lipidomics Gateway provides a rich collection of information and resources to help you stay abreast of the latest developments in this rapidly expanding field. LIPID Metabolites And Pathways Strategy (LIPID MAPS®) is a multi-institutional effort created in 2003 to identify and quantitate, using a systems biology approach and sophisticated mass spectrometers, all of the major — and many minor — lipid species in mammalian cells, as well as to quantitate the changes in these species in response to perturbation. The ultimate goal of our research is to better understand lipid metabolism and the active role lipids play in diabetes, stroke, cancer, arthritis, Alzheimer's and other lipid-based diseases in order to facilitate development of more effective treatments. Since our inception, we have made great strides toward defining the "lipidome" (an inventory of the thousands of individual lipid molecular species) in the mouse macrophage. We have also worked to make lipid analysis easier and more accessible for the broader scientific community and to advance a robust research infrastructure for the international research community. We share new lipidomics findings and methods, hold annual meetings open to all interested investigators, and are exploring joint efforts to extend the use of these powerful new methods to new applications

European XFEL Data Portal

European XFEL Metadata Catalogue

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European XFEL Data Portal is provided by myMdC, allowing users to access the metadata of scientific data taken at the European XFEL facility. Datasets are linked to experiment proposals, annotated by data collection types, samples and are assigned DOIs to be referenced in publications. myMdC helps data management activities and allows users to find open and own proposals data based on the metadata.

GnpIS

Genetic and Genomic Information System

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GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, association genetics, markers, polymorphisms, germplasms, phenotypes and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. GnpIS is used by both large international projects and plant science departments at the French National Research Institute for Agriculture, Food and Environment. It is regularly improved and released several times per year. GnpIS is accessible through a web portal and allows to browse different types of data either independently through dedicated interfaces or simultaneously using a quick search ('google like search') or advanced search (Biomart, Galaxy, Intermine) tools.

Influenza Research Database

IRD

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<<<!!!<<< The migration of the data, tools, and services from the legacy IRD and ViPR applications to BV-BRC is now complete. All web traffic from the IRD and ViPR resources is also being forwarded to the BV-BRC home page https://www.re3data.org/repository/r3d100014100 >>>!!!>>>

Kyoto Encyclopedia of Genes and Genomes

KEGG

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KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies

TreeGenes

A forest tree genome database

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TreeGenes is a genomic, phenotypic, and environmental data resource for forest tree species. The TreeGenes database and Dendrome project provide custom informatics tools to manage the flood of information.The database contains several curated modules that support the storage of data and provide the foundation for web-based searches and visualization tools. GMOD GUI tools such as CMAP for genetic maps and GBrowse for genome and transcriptome assemblies are implemented here. A sample tracking system, known as the Forest Tree Genetic Stock Center, sits at the forefront of most large-scale projects. Barcode identifiers assigned to the trees during sample collection are maintained in the database to identify an individual through DNA extraction, resequencing, genotyping and phenotyping. DiversiTree, a user-friendly desktop-style interface, queries the TreeGenes database and is designed for bulk retrieval of resequencing data. CartograTree combines geo-referenced individuals with relevant ecological and trait databases in a user-friendly map-based interface. ---- The Conifer Genome Network (CGN) is a virtual nexus for researchers working in conifer genomics. The CGN web site is maintained by the Dendrome Project at the University of California, Davis.

DOE Joint Genome Institute Genome Portal

US Department of Energy Joint Genome Institute Genome Web Portal

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The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web. The JGI Genome Portal provides a unified access point to all JGI genomic databases and analytical tools. A user can find all DOE JGI sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms. Databases: Genome Online Database (GOLD), Integrated Microbial Genomes (IGM), MycoCosm, Phytozome

Finnish Biodiversity Information Facility

Suomen Lajitietokeskus

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FinBIF is an integral part of the global biodiversity informatics framework, dedicated to managing species information. Its mission encompasses a wide array of services, including the generation of digital data through various processes, as well as the sourcing, collation, integration, and distribution of existing digital data. Key initiatives under FinBIF include the digitization of collections, the development of data systems for collections Kotka (https://biss.pensoft.net/article/37179/) and observations (https://biss.pensoft.net/article/39150/), and the establishment of a national DNA barcode reference library. FinBIF manages data types such as verbal species descriptions (which include drawings, pictures, and other media types), biological taxonomy, scientific collection specimens, opportunistic systematic and event-based observations, and DNA barcodes. It employs a unified IT architecture to manage data flows, delivers services through a single online portal, fosters collaboration under a cohesive umbrella concept, and articulates development visions under a unified brand. The portal Laji.fi serves as the entry point to this harmonized open data ecosystem. FinBIF's portal is accessible in Finnish, Swedish, and English. Data intended for restricted use are made available to authorities through a separate portal, while open data are also shared with international systems, such as GBIF.

Earthdata powered by EOSDIS

Earth Observing System Data and Information System

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Earthdata powered by EOSDIS (Earth Observing System Data and Information System) is a key core capability in NASA’s Earth Science Data Systems Program. It provides end-to-end capabilities for managing NASA’s Earth science data from various sources – satellites, aircraft, field measurements, and various other programs. EOSDIS uses the metadata and service discovery tool Earthdata Search https://search.earthdata.nasa.gov/search. The capabilities of EOSDIS constituting the EOSDIS Science Operations are managed by NASA's Earth Science Data and Information System (ESDIS) Project. The capabilities include: generation of higher level (Level 1-4) science data products for several satellite missions; archiving and distribution of data products from Earth observation satellite missions, as well as aircraft and field measurement campaigns. The EOSDIS science operations are performed within a distributed system of many interconnected nodes - Science Investigator-led Processing Systems (SIPS), and distributed, discipline-specific, Earth science Distributed Active Archive Centers (DAACs) with specific responsibilities for production, archiving, and distribution of Earth science data products. The DAACs serve a large and diverse user community by providing capabilities to search and access science data products and specialized services.

INDEPTH Data Repository

International Network for the Demographic Evaluation of Populations and Their Health Data Repository

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INDEPTH is a global network of research centres that conduct longitudinal health and demographic evaluation of populations in low- and middle-income countries (LMICs). INDEPTH aims to strengthen global capacity for Health and Demographic Surveillance Systems (HDSSs), and to mount multi-site research to guide health priorities and policies in LMICs, based on up-to-date scientific evidence. The data collected by the INDEPTH Network members constitute a valuable resource of population and health data for LMIC countries. This repository aims to make well documented anonymised longitudinal microdata from these Centres available to data users.

Open Research Data

ZALF. Open Research Data

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Attention! Data sets are not updated anymore. Please, visit the BonaRes Repositor​ium​ for new datasets. Open Research Data provides quality assessed data and their metadata such as context information on measurement objectives, equipment, methods, testing and investigation areas. The purpose of the repository is to secure quality, integrity and long-term availability of landscape and ecosystem research data as well as to enhance accessibility of free data from ZALF long-term monitoring campaigns, landscape laboratories (Agro-ScapeLabs), field trials and experiments. The Leibniz Centre for Agricultural Landscape Research (ZALF) explores ecosystems in agricultural landscapes and the development of ecologically and economically viable land use systems. ZALF combines scientific expertise from agricultural science, geosciences, biosciences and socio-economics.