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Found 119 result(s)

Addgene

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Addgene archives and distributes plasmids for researchers around the globe. They are working with thousands of laboratories to assemble a high-quality library of published plasmids for use in research and discovery. By linking plasmids with articles, scientists can always find data related to the materials they request.

Ag Data Commons

USDA’s Open Research Data

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Ag Data Commons provides access to a wide variety of open data relevant to agricultural research. We are a centralized repository for data already on the web, as well as for new data being published for the first time. While compliance with the U.S. Federal public access and open data directives is important, we aim to surpass them. Our goal is to foster innovative data re-use, integration, and visualization to support bigger, better science and policy.

Alaska Ocean Observing System

AOOS

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Alaska Ocean Observing System (AOOS) provides ocean and coastal observations data. The AOOS is governed by the Integrated Ocean Observing System (IOOS) which is a partnership among federal, regional, academic and private sector groups. The Ocean Data Explorer contains scientific and management information including real-time sensor feeds, operational oceanographic and atmospheric models, satellite observations and GIS data sets that describe the biological, chemical and physical characteristics of Alaska and its surrounding waters. This map offers many new updated features that build upon the existing data system.

Allele Frequency Net Database

AFND

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The Allele Frequency Net Database (AFND) is a public database which contains frequency information of several immune genes such as Human Leukocyte Antigens (HLA), Killer-cell Immunoglobulin-like Receptors (KIR), Major histocompatibility complex class I chain-related (MIC) genes, and a number of cytokine gene polymorphisms. The Allele Frequency Net Database (AFND) provides a central source, freely available to all, for the storage of allele frequencies from different polymorphic areas in the Human Genome. Users can contribute the results of their work into one common database and can perform database searches on information already available. We have currently collected data in allele, haplotype and genotype format. However, the success of this website will depend on you to contribute your data.

Animal QTLdb

Animal Quantitative Trait Loci

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This Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house all publicly available QTL and trait mapping data (i.e. trait and genome location association data; collectively called "QTL data" on this site) on livestock animal species for easily locating and making comparisons within and between species. New database tools are continuely added to align the QTL and association data to other types of genome information, such as annotated genes, RH / SNP markers, and human genome maps. Besides the QTL data from species listed below, the QTLdb is open to house QTL/association date from other animal species where feasible. Note that the JAS along with other journals, now require that new QTL/association data be entered into a QTL database as part of their publication requirements.

ANU Data Commons

Australian National University Data Commons

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The Australian National University undertake work to collect and publish metadata about research data held by ANU, and in the case of four discipline areas, Earth Sciences, Astronomy, Phenomics and Digital Humanities to develop pipelines and tools to enable the publication of research data using a common and repeatable approach. Aims and outcomes: To identify and describe research data held at ANU, to develop a consistent approach to the publication of metadata on the University's data holdings: Identification and curation of significant orphan data sets that might otherwise be lost or inadvertently destroyed, to develop a culture of data data sharing and data re-use.

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.

ASAP

A systematic annotation package for community analysis of genomes

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ASAP (a systematic annotation package for community analysis of genomes) is a relational database and web interface developed to store, update and distribute genome sequence data and gene expression data collected by or in collaboration with researchers at the University of Wisconsin - Madison. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments.

Atlantic Canada Conservation Data Centre

AC CDC

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The Atlantic Canada Conservation Data Centre (ACCDC) maintains comprehensive lists of plant and animal species. The Atlantic CDC has geo-located records of species occurrences and records of extremely rare to uncommon species in the Atlantic region, including New Brunswick, Nova Scotia, Prince Edward Island, Newfoundland, and Labrador. The Atlantic CDC also maintains biological and other types of data in a variety of linked databases.

Australian Antarctic Data Centre

Data management and spatial data services

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The Australian Antarctic Data Centre (AADC) provides data collection and data management services in Australia's Antarctic Science Program. The AADC manages science data from Australia's Antarctic research, maps Australia's areas of interest in the Antarctic region, manages Australia's Antarctic state of the environment reporting, and provides advice and education and a range of other products.

Beta Cell Biology Consortium Reagent and Data Resources

BCBC Reagent and Data Resources

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>>>!!!<<< Sorry.we are no longer in operation >>>!!!<<< The Beta Cell Biology Consortium (BCBC) was a team science initiative that was established by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). It was initially funded in 2001 (RFA DK-01-014), and competitively continued both in 2005 (RFAs DK-01-17, DK-01-18) and in 2009 (RFA DK-09-011). Funding for the BCBC came to an end on August 1, 2015, and with it so did our ability to maintain active websites.!!! One of the many goals of the BCBC was to develop and maintain databases of useful research resources. A total of 813 different scientific resources were generated and submitted by BCBC investigators over the 14 years it existed. Information pertaining to 495 selected resources, judged to be the most scientifically-useful, has been converted into a static catalog, as shown below. In addition, the metadata for these 495 resources have been transferred to dkNET in the form of RDF descriptors, and all genomics data have been deposited to either ArrayExpress or GEO. Please direct questions or comments to the NIDDK Division of Diabetes, Endocrinology & Metabolic Diseases (DEM).

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).

BRENDA

BRENDA Enzyme Database

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BRENDA is the main collection of enzyme functional data available to the scientific community worldwide. The enzymes are classified according to the Enzyme Commission list of enzymes. It is available free of charge for via the internet (http://www.brenda-enzymes.org/) and as an in-house database for commercial users (requests to our distributor Biobase). The enzymes are classified according to the Enzyme Commission list of enzymes. Some 5000 "different" enzymes are covered. Frequently enzymes with very different properties are included under the same EC number. BRENDA includes biochemical and molecular information on classification, nomenclature, reaction, specificity, functional parameters, occurrence, enzyme structure, application, engineering, stability, disease, isolation, and preparation. The database also provides additional information on ligands, which function as natural or in vitro substrates/products, inhibitors, activating compounds, cofactors, bound metals, and other attributes.

caArray

Array Data Management System

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>>>!!!<<< caArray Retirement Announcement >>>!!!<<< The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) instance of the caArray database was retired on March 31st, 2015. All publicly-accessible caArray data and annotations will be archived and will remain available via FTP download https://wiki.nci.nih.gov/x/UYHeDQ and is also available at GEO http://www.ncbi.nlm.nih.gov/geo/ . >>>!!!<<< While NCI will not be able to provide technical support for the caArray software after the retirement, the source code is available on GitHub https://github.com/NCIP/caarray , and we encourage continued community development. Molecular Analysis of Brain Neoplasia (Rembrandt fine-00037) gene expression data has been loaded into ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3073 >>>!!!<<< caArray is an open-source, web and programmatically accessible microarray data management system that supports the annotation of microarray data using MAGE-TAB and web-based forms. Data and annotations may be kept private to the owner, shared with user-defined collaboration groups, or made public. The NCI instance of caArray hosts many cancer-related public datasets available for download.

Canadensys repository

Database of Vascular Plants of Canada

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Biological collections are replete with taxonomic, geographic, temporal, numerical, and historical information. This information is crucial for understanding and properly managing biodiversity and ecosystems, but is often difficult to access. Canadensys, operated from the Université de Montréal Biodiversity Centre, is a Canada-wide effort to unlock the biodiversity information held in biological collections.

Canadian Open Neuroscience Platform Portal

CONP

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The CONP portal is a web interface for the Canadian Open Neuroscience Platform (CONP) to facilitate open science in the neuroscience community. CONP simplifies global researcher access and sharing of datasets and tools. The portal internalizes the cycle of a typical research project: starting with data acquisition, followed by processing using already existing/published tools, and ultimately publication of the obtained results including a link to the original dataset. From more information on CONP, please visit https://conp.ca

CancerData.org

Sharing data for cancer research

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The CancerData site is an effort of the Medical Informatics and Knowledge Engineering team (MIKE for short) of Maastro Clinic, Maastricht, The Netherlands. Our activities in the field of medical image analysis and data modelling are visible in a number of projects we are running. CancerData is offering several datasets. They are grouped in collections and can be public or private. You can search for public datasets in the NBIA (National Biomedical Imaging Archive) image archives without logging in.

Carbohydrate Structure Database

CSDB

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This is CSDB version 1 merged from Bacterial (BCSDB) and Plant&Fungal (PFCSDB) databases. This database aims at provision of structural, bibliographic, taxonomic, NMR spectroscopic and other information on glycan and glycoconjugate structures of prokaryotic, plant and fungal origin. It has been merged from the Bacterial and Plant&Fungal Carbohydrate Structure Databases (BCSDB+PFCSDB). The key points of this service are: High coverage. The coverage for bacteria (up to 2016) and archaea (up to 2016) is above 80%. Similar coverage for plants and fungi is expected in the future. The database is close to complete up to 1998 for plants, and up to 2006 for fungi. Data quality. High data quality is achieved by manual curation using original publications which is assisted by multiple automatic procedures for error control. Errors present in publications are reported and corrected, when possible. Data from other databases are verified on import. Detailed annotations. Structural data are supplied with extended bibliography, assigned NMR spectra, taxon identification including strains and serogroups, and other information if available in the original publication. Services. CSDB serves as a platform for a number of computational services tuned for glycobiology, such as NMR simulation, automated structure elucidation, taxon clustering, 3D molecular modeling, statistical processing of data etc. Integration. CSDB is cross-linked to other glycoinformatics projects and NCBI databases. The data are exportable in various formats, including most widespread encoding schemes and records using GlycoRDF ontology. Free web access. Users can access the database for free via its web interface (see Help). The main source of data is retrospective literature analysis. About 20% of data were imported from CCSD (Carbbank, University of Georgia, Athens; structures published before 1996) with subsequent manual curation and approval. The current coverage is displayed in red on the top of the left menu. The time lag between the publication of new data and their deposition into CSDB is ca. 1 year. In the scope of bacterial carbohydrates, CSDB covers nearly all structures of this origin published up to 2016. Prokaryotic, plant and fungal means that a glycan was found in the organism(s) belonging to these taxonomic domains or was obtained by modification of those found in them. Carbohydrate means a structure composed of any residues linked by glycosidic, ester, amidic, ketal, phospho- or sulpho-diester bonds in which at least one residue is a sugar or its derivative.

ChemSpider

Search and share chemistry

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ChemSpider is a free chemical structure database providing fast access to over 58 million structures, properties and associated information. By integrating and linking compounds from more than 400 data sources, ChemSpider enables researchers to discover the most comprehensive view of freely available chemical data from a single online search. It is owned by the Royal Society of Chemistry. ChemSpider builds on the collected sources by adding additional properties, related information and links back to original data sources. ChemSpider offers text and structure searching to find compounds of interest and provides unique services to improve this data by curation and annotation and to integrate it with users’ applications.

Collaborative Research Centre Transregio 32 Database

TR32DB

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In the framework of the Collaborative Research Centre/Transregio 32 ‘Patterns in Soil-Vegetation-Atmosphere Systems: Monitoring, Modelling, and Data Assimilation’ (CRC/TR32, www.tr32.de), funded by the German Research Foundation from 2007 to 2018, a RDM system was self-designed and implemented. The so-called CRC/TR32 project database (TR32DB, www.tr32db.de) is operating online since early 2008. The TR32DB handles all data including metadata, which are created by the involved project participants from several institutions (e.g. Universities of Cologne, Bonn, Aachen, and the Research Centre Jülich) and research fields (e.g. soil and plant sciences, hydrology, geography, geophysics, meteorology, remote sensing). The data is resulting from several field measurement campaigns, meteorological monitoring, remote sensing, laboratory studies and modelling approaches. Furthermore, outcomes of the scientists such as publications, conference contributions, PhD reports and corresponding images are collected in the TR32DB.

CSIRO Data Access Portal

CSIRO DAP

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The CSIRO Data Access Portal provides access to data published by CSIRO across a range of disciplines to facilitate sharing and reuse of data held by CSIRO.

CU Scholar

University of Colorado Boulder's institutional repository

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CU Scholar is an open access institutional repository supporting the research and teaching mission of the University of Colorado Boulder. It is intended to serve as a platform for preserving the research activities of members of the CU Boulder community and for providing public access to that research. CU Scholar is maintained by the University Libraries.

Database of Genomic Variants Archive

DGVa

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<<<!!!<<< Phasing out support for the Database of Genomic Variants archive (DGVa). The submission, archiving, and presentation of structural variation services offered by the DGVa is transitioning to the European Variation Archive (EVA) https://www.re3data.org/repository/r3d100011553. All of the data shown in the DGVa website is already searchable and browsable from the EVA Study Browser. Submission of structural variation data to EVA is done using the VCF format. The VCF specification allows representing multiple types of structural variants such as insertions, deletions, duplications and copy-number variants. Other features such as symbolic alleles, breakends, confidence intervals etc., support more complex events, such as translocations at an imprecise position. >>>!!!>>>

Database of Interacting Proteins

DIP

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The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Please, check the reference page to find articles describing the DIP database in greater detail. The Database of Ligand-Receptor Partners (DLRP) is a subset of DIP (Database of Interacting Proteins). The DLRP is a database of protein ligand and protein receptor pairs that are known to interact with each other. By interact we mean that the ligand and receptor are members of a ligand-receptor complex and, unless otherwise noted, transduce a signal. In some instances the ligand and/or receptor may form a heterocomplex with other ligands/receptors in order to be functional. We have entered the majority of interactions in DLRP as full DIP entries, with links to references and additional information

DRYAD

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Dryad is an open data publishing platform and a community committed to the open availability and routine re-use of all research data. We publish data in any format and any discipline. All Dryad data undergoes a curation process and is published under a CC0 waiver to promote reuse.