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Found 37 result(s)

National Contaminants Information System

NCIS

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>>>!!!<<< 2021-03-19: The repository is no longer available >>>!!!<<< The National Contaminants Information System was begun as part of the Department's Green Plan. The NCIS is a computerized warehouse of information on toxic chemicals in fish, other aquatic life and their habitats. It was built to help manage the growing base of data and information.

Smithsonian National Museum of Natural History

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Museum explorers travel to ocean depths, the peaks of the Andes, Africa's Rift Valley, the rainforests of South America, and the deserts of Central Asia. Perhaps even to a field site or research institution in your own state, territory or country. In each area, researchers collect specimens: fossils, minerals, and rocks, plants and animals, tools and artworks. Collections care professionals have meticulously preserved, labeled, cataloged, and organized items of this kind for more than 150 years. Taken together, the NMNH collections form the largest, most comprehensive natural history collection in the world. By comparing items gathered in different eras and regions, scientists learn how our world has varied across time and space.

Biodiversity Exploratories Information System

BExIS

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BExIS is the online data repository and information system of the Biodiversity Exploratories Project (BE). The BE is a German network of biodiversity related working groups from areas such as vegetation and soil science, zoology and forestry. Up to three years after data acquisition, the data use is restricted to members of the BE. Thereafter, the data is usually public available (https://www.bexis.uni-jena.de/ddm/publicsearch/index).

bonndata

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bonndata is the institutional, FAIR-aligned and curated, cross-disciplinary research data repository for the publication of research data for all researchers at the University of Bonn. The repository is fully embedded into the University IT and Data Center and curated by the Research Data Service Center (https://www.forschungsdaten.uni-bonn.de/en). The software that bonndata is based on is the open source software Dataverse (https://dataverse.org)

NCBI Datasets

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NCBI Datasets is a continually evolving platform designed to provide easy and intuitive access to NCBI’s sequence data and metadata. NCBI Datasets is part of the NIH Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses for all eukaryotic organisms through an NCBI Toolkit and community collaboration.

NGEE Tropics

Next-Generation Ecosystem Experiments - Tropics

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The future of tropical forests matter to future climate. NGEE-Tropics is advancing model predictions of tropical forest carbon cycle responses to a changing climate over the 21st Century.

Environmental Information Data Centre

EIDC

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The Environmental Information Data Centre (EIDC) is part of the Natural Environment Research Council's (NERC) Environmental Data Service and is hosted by the UK Centre for Ecology & Hydrology (UKCEH). We manage nationally-important datasets concerned with the terrestrial and freshwater sciences.

NCBI Genome

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<<<!!!<<< Effective May 2024, NCBI's Genome resource will no longer be available. NCBI Genome data can now be found on the NCBI Datasets taxonomy pages. https://www.re3data.org/repository/r3d100014298 >>>!!!>>> The Genome database contains annotations and analysis of eukaryotic and prokaryotic genomes, as well as tools that allow users to compare genomes and gene sequences from humans, microbes, plants, viruses and organelles. Users can browse by organism, and view genome maps and protein clusters.

MaizeGDB

Maize Genetics and Genomics Database

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The Maize Genetics and Genomics Database focuses on collecting data related to the crop plant and model organism Zea mays. The project's goals are to synthesize, display, and provide access to maize genomics and genetics data, prioritizing mutant and phenotype data and tools, structural and genetic map sets, and gene models. MaizeGDB also aims to make the Maize Newsletter available, and provide support services to the community of maize researchers. MaizeGDB is working with the Schnable lab, the Panzea project, The Genome Reference Consortium, and iPlant Collaborative to create a plan for archiving, dessiminating, visualizing, and analyzing diversity data. MMaizeGDB is short for Maize Genetics/Genomics Database. It is a USDA/ARS funded project to integrate the data found in MaizeDB and ZmDB into a single schema, develop an effective interface to access this data, and develop additional tools to make data analysis easier. Our goal in the long term is a true next-generation online maize database.aize genetics and genomics database.

The Paleobiology Database

PaleoDB

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The Paleobiology Database (PaleoBioDB) is a non-governmental, non-profit public resource for paleontological data. It has been organized and operated by a multi-disciplinary, multi-institutional, international group of paleobiological researchers. Its purpose is to provide global, collection-based occurrence and taxonomic data for organisms of all geological ages, as well data services to allow easy access to data for independent development of analytical tools, visualization software, and applications of all types. The Database’s broader goal is to encourage and enable data-driven collaborative efforts that address large-scale paleobiological questions.

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.

Temperate Reef Base

Temperate Reef Base Portal

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TemperateReefBase is a resource for temperate reef researchers worldwide to use and contribute data. Unique in its role as a one-stop-shop for global temperate reef data, TemperateReefBase was initially established by IMAS in collaboration with the Kelp Ecology Ecosystem Network (KEEN). KEEN was instigated through a National Centre for Ecological Analysis and Synthesis (NCEAS) working group which assembled experts from around the world to examine the impacts of global change on kelp-bed ecosystem worldwide. The group has assembled significant global data for kelps, other seaweeds and associated species including fishes, and has embarked on unprecedented global experiments and surveys in which identical experiments and surveys are being conducted at sites in kelp beds around the world to determine global trends and examine the capacity of kelps to respond to disturbance in the face of climate change and other anthropogenic stressors. The TemperateReefBase Data Portal is an online discovery interface showcasing temperate reef data collected from around the globe. The portal aims to make this data freely and openly available for the benefit of marine and environmental science as a whole. The TemperateReefBase Data Portal is hosted and maintained by the Institute for Marine and Antarctic Studies at the University of Tasmania, Australia.

GabiPD

GABI Primary Database

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GABI, acronym for "Genomanalyse im biologischen System Pflanze", is the name of a large collaborative network of different plant genomic research projects. Plant data from different ‘omics’ fronts representing more than 10 different model or crop species are integrated in GabiPD.

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.

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.

DataSuds

Des données ouvertes pour une science durable au Sud

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The DataSuds data warehouse provides IRD scientists and their partners with a service to disseminate, preserve and enhance their research data by facilitating their identification and citation. It is one of the elements of the open science system for the South promoted by the IRD.

ISTA Research Explorer

ISTA REx

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ISTA Research Explorer is an online digital repository of multi-disciplinary research datasets as well as publications produced at IST Austria, hosted by the Library. ISTA researchers who have produced research data associated with an existing or forthcoming publication, or which has potential use for other researches, are invited to upload their dataset for sharing and safekeeping. A persistent identifier and suggested citation will be provided.

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.

National Ecosystem Data Bank

EcoDB

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National ecosystem data bank (EcoDB) is a public professional scientific data repository supported by the National Ecosystem Science Data Center (NESDC) for researchers in ecology and related fields, which provides long-term preservation, publication, sharing and access services of scientific data. EcoDB provides services for both individual researchers and scientific journals. Individuals can use this repository to store, manage and publish scientific data, get feedback from others on the data, and discover scientific data shared by others through this repository. Journals can use the repository to gather, manage and review the supporting data of submitted paper. At the same time, journals can timely publish these supporting data according to their own data policies.

PLEXdb

Plant Expression Database

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<<<!!!<<< 08.08.2019: Plexdb is no longer online, URLold: http://www.plexdb.org/index.php >>>!!!>>> >>>>!!!! <<<< 13.12.2018: PLEXdb is now a static site after funding stopped from NSF. We have stopped registration of new users; but past users who have data can login when needed and interact with the site. You can download data using the authentication provided at the download page. >>>>!!!!<<<< PLEXdb is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data.

KBase

KBase: The U.S. Department of Energy Systems Biology Knowledgebase

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The Department of Energy Systems Biology Knowledgebase (KBase) is a software and data platform designed to meet the grand challenge of systems biology: predicting and designing biological function. KBase integrates data and tools in a unified graphical interface so users do not need to access them from numerous sources or learn multiple systems in order to create and run sophisticated systems biology workflows. Users can perform large-scale analyses and combine multiple lines of evidence to model plant and microbial physiology and community dynamics. KBase is the first large-scale bioinformatics system that enables users to upload their own data, analyze it (along with collaborator and public data), build increasingly realistic models, and share and publish their workflows and conclusions. KBase aims to provide a knowledgebase: an integrated environment where knowledge and insights are created and multiplied.

HJ Andrews Experimental Forest

HJA

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The Andrews Forest is a place of inquiry. Our mission is to support research on forests, streams, and watersheds, and to foster strong collaboration among ecosystem science, education, natural resource management, and the humanities. Our place and our work are administered cooperatively by the USDA Forest Service's Pacific Northwest Research Station, Oregon State University, and the Willamette National Forest. First established in 1948 as an US Forest Service Experimental Forest, the H.J. Andrews is a 16,000-acre ecological research site in Oregon's beautiful western Cascades Mountains. The landscape is home to iconic Pacific Northwest old-growth forests of Cedar and Hemlock, and moss-draped ancient Douglas Firs; steep terrain; and fast, cold-running streams. In 1980 the Andrews became a charter member of the National Science Foundation's Long-Term Ecological Research (LTER) Program.

PeanutBase

Genetic and genomic data to enable more rapid crop improvement in peanut

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PeanutBase is a peanut community resource providing genetic, genomic, gene function, and germplasm data to support peanut breeding and molecular research. This includes molecular markers, genetic maps, QTL data, genome assemblies, germplasm records, and traits. Data is curated from literature and submitted directly by researchers. Funding for PeanutBase is provided by the Peanut Foundation with in-kind contributions from the USDA-ARS.

vegetweb

das Vegetationsportal für Deutschland

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Database and data handling portal for vegetation data from Germany.

Morphbank

Morphbank :: Biological Imaging

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Morphbank :: Biological Imaging is a continuously growing database of images that scientists use for international collaboration, research and education. Images deposited in Morphbank :: Biological Imaging document a wide variety of research including: specimen-based research in comparative anatomy, morphological phylogenetics, taxonomy and related fields focused on increasing our knowledge about biodiversity.