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Found 69 result(s)

DOE Data Explorer

DDE

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The DOE Data Explorer (DDE) is an information tool to help you locate DOE's collections of data and non-text information and, at the same time, retrieve individual datasets within some of those collections. It includes collection citations prepared by the Office of Scientific and Technical Information, as well as citations for individual datasets submitted from DOE Data Centers and other organizations.

FungiDB

The Fungal and Oomycete Genomics Resource

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FungiDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for the kingdom Fungi. FungiDB was first released in early 2011 as a collaborative project between EuPathDB and the group of Jason Stajich (University of California, Riverside). At the end of 2015, FungiDB was integrated into the EuPathDB bioinformatic resource center. FungiDB integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes comparative genomics, analysis of gene expression, and supplemental bioinformatics analyses and a web interface for data-mining.

ENCODE

Encyclopedia of DNA Elements

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The ENCODE Encyclopedia organizes the most salient analysis products into annotations, and provides tools to search and visualize them. The Encyclopedia has two levels of annotations: Integrative-level annotations integrate multiple types of experimental data and ground level annotations. Ground-level annotations are derived directly from the experimental data, typically produced by uniform processing pipelines.

JASPAR

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JASPAR is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors and other proteins interacting with DNA in a sequence-specific manner.

City of Brantford Open Data Catalogue

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This catalogue allows users to search, browse, and download open data about the City of Brantford.

Copernicus

The European Earth Observation Pogramme

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Copernicus is a European system for monitoring the Earth. Copernicus consists of a complex set of systems which collect data from multiple sources: earth observation satellites and in situ sensors such as ground stations, airborne and sea-borne sensors. It processes these data and provides users with reliable and up-to-date information through a set of services related to environmental and security issues. The services address six thematic areas: land monitoring, marine monitoring, atmosphere monitoring, climate change, emergency management and security. The main users of Copernicus services are policymakers and public authorities who need the information to develop environmental legislation and policies or to take critical decisions in the event of an emergency, such as a natural disaster or a humanitarian crisis. Based on the Copernicus services and on the data collected through the Sentinels and the contributing missions , many value-added services can be tailored to specific public or commercial needs, resulting in new business opportunities. In fact, several economic studies have already demonstrated a huge potential for job creation, innovation and growth.

Bugwood Image Database System

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bugwood.org is the host website of the Center for Invasive Species and Ecosystem Health at the University of Georgia (Formerly: Bugwood Network). The Center aims to develop, consolidate and disseminate information and programmes focused on invasive species, forest health, natural resources and agricultural management through technology development, programmes implementation, training, applied research and public awareness at state, regional, national and international levels. The site gives details of its products (Bugwood Image Database; Early Detection and Distribution Mapping and Bugwoodwiki). Details of its projects, services and personnel are provided. Users can also access image databases on Forestry, Insects, IPM, Invasive Species, Forest Pests, weed and Bark Beetle.

UniProtKB

UniProtKnowledgebase

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The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and clear indications of the quality of annotation in the form of evidence attribution of experimental and computational data. The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc). The UniProt Metagenomic and Environmental Sequences (UniMES) database is a repository specifically developed for metagenomic and environmental data. The UniProt Knowledgebase,is an expertly and richly curated protein database, consisting of two sections called UniProtKB/Swiss-Prot and UniProtKB/TrEMBL.

The Universal Protein Resource

UniProt

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The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc).

International Mouse Phenotyping Consortium

IMPC

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The IMPC is a confederation of international mouse phenotyping projects working towards the agreed goals of the consortium: To undertake the phenotyping of 20,000 mouse mutants over a ten year period, providing the first functional annotation of a mammalian genome. Maintain and expand a world-wide consortium of institutions with capacity and expertise to produce germ line transmission of targeted knockout mutations in embryonic stem cells for 20,000 known and predicted mouse genes. Test each mutant mouse line through a broad based primary phenotyping pipeline in all the major adult organ systems and most areas of major human disease. Through this activity and employing data annotation tools, systematically aim to discover and ascribe biological function to each gene, driving new ideas and underpinning future research into biological systems; Maintain and expand collaborative “networks” with specialist phenotyping consortia or laboratories, providing standardized secondary level phenotyping that enriches the primary dataset, and end-user, project specific tertiary level phenotyping that adds value to the mammalian gene functional annotation and fosters hypothesis driven research; and Provide a centralized data centre and portal for free, unrestricted access to primary and secondary data by the scientific community, promoting sharing of data, genotype-phenotype annotation, standard operating protocols, and the development of open source data analysis tools. Members of the IMPC may include research centers, funding organizations and corporations.

PubChem

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Pubchem contains 3 databases. 1. PubChem BioAssay: The PubChem BioAssay Database contains bioactivity screens of chemical substances described in PubChem Substance. It provides searchable descriptions of each bioassay, including descriptions of the conditions and readouts specific to that screening procedure. 2. PubChem Compound: The PubChem Compound Database contains validated chemical depiction information provided to describe substances in PubChem Substance. Structures stored within PubChem Compounds are pre-clustered and cross-referenced by identity and similarity groups. 3. PubChem Substance. The PubChem Substance Database contains descriptions of samples, from a variety of sources, and links to biological screening results that are available in PubChem BioAssay. If the chemical contents of a sample are known, the description includes links to PubChem Compound.

Deep Blue Data

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The Deep Blue Data repository is a means for University of Michigan researchers to make their research data openly accessible to anyone in the world, provided they meet collections criteria. Submitted data sets undergo a curation review by librarians to support discovery, understanding, and reuse of the data.

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)

BioPortal

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BioPortal is an open repository of biomedical ontologies, a service that provides access to those ontologies, and a set of tools for working with them. BioPortal provides a wide range of such tools, either directly via the BioPortal web site, or using the BioPortal web service REST API. BioPortal also includes community features for adding notes, reviews, and even mappings to specific ontologies. BioPortal has four major product components: the web application; the API services; widgets, or applets, that can be installed on your own site; and a Virtual Appliance version that is available for download or through Amazon Web Services machine instance (AMI). There is also a beta release SPARQL endpoint.

DrugBank

Open Data Drug & Drug Target Database

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The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The latest release of DrugBank (version 5.1.1, released 2018-07-03) contains 11,881 drug entries including 2,526 approved small molecule drugs, 1,184 approved biotech (protein/peptide) drugs, 129 nutraceuticals and over 5,751 experimental drugs. Additionally, 5,132 non-redundant protein (i.e. drug target/enzyme/transporter/carrier) sequences are linked to these drug entries. Each DrugCard entry contains more than 200 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data.

PharmGKB

Pharmacogenomics Knowledgebase

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PharmGKB is a comprehensive resource that curates knowledge about the impact of genetic variation on drug response for clinicians and researchers. PharmGKB brings together the relevant data in a single place and adds value by combining disparate data on the same relationship, making it easier to search and easier to view the key aspects and by interpreting the data.PharmGKB provide clinical interpretations of this data, curated pathways and VIP summaries which are not found elsewhere.

Gemma

Tools and database for meta-analysis of functional genomics data

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Gemma is a database for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. Gemma contains data from thousands of public studies, referencing thousands of published papers. Users can search, access and visualize co-expression and differential expression results.

Environmental data explorer

EDE

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<<<!!!<<< This repository is no longer available. Resource Unavailable The requested url (http://geodata.grid.unep.ch/) no longer exists, please contact info@unepgrid.ch for further information.. >>>!!!>>>

Mechanism and Catalytic Site Atlas

CSA (formerly)

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M-CSA is a database of enzyme reaction mechanisms. It provides annotation on the protein, catalytic residues, cofactors, and the reaction mechanisms of hundreds of enzymes. There are two kinds of entries in M-CSA. 'Detailed mechanism' entries are more complete and show the individual chemical steps of the mechanism as schemes with electron flow arrows. 'Catalytic Site' entries annotate the catalytic residues necessary for the reaction, but do not show the mechanism. The M-CSA (Mechanism and Catalytic Site Atlas) represents a unified resource that combines the data in both MACiE and the CSA

RCSB Protein Data Bank

RCSB PDB

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The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids. These are the molecules of life that are found in all organisms including bacteria, yeast, plants, flies, other animals, and humans. Understanding the shape of a molecule helps to understand how it works. This knowledge can be used to help deduce a structure's role in human health and disease, and in drug development. The structures in the archive range from tiny proteins and bits of DNA to complex molecular machines like the ribosome.

BioGRID ORCS

BioGRID Open Repository of CRISPR Screens

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BioGRID ORCS is an open repository of CRISPR screens compiled through comprehensive curation efforts. The current index is version 1.0.3 and searches more than 49 publications and 58,161 genes to return more than 895 CRISPR screens from 3 major model organism species and 629 cell lines. All screen data are freely provided through our search index and available via download in a wide variety of standardized formats.

European Variation Archive

EVA

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The European Variation Archive is an open-access database of all types of genetic variation data from all species. The EVA provides access to highly detailed, granular, raw variant data from human, with other species to follow. As of September 2017, EMBL-EBI will maintain reliable accessions for non-human genetic variation data through the European Variation Archive (EVA). NCBI's dbSNP database will continue to maintain stable identifiers for human genetic variation data only. This change will enable a more rapid turnaround for data sharing in this burgeoning field.

UK Polar Data Centre

UK PDC

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The UK Polar Data Centre (UK PDC) is the focal point for Arctic and Antarctic environmental data management in the UK. Part of the Natural Environmental Research Council’s (NERC) network of environmental data centres and based at the British Antarctic Survey, it coordinates the management of polar data from UK-funded research and supports researchers in complying with national and international data legislation and policy.

hPSCreg

human Pluripotent Stem Cell registry

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The human pluripotent stem cell registry (hPSCreg) is a public registry and data portal for human embryonic and induced pluripotent stem cell lines (hESC and hiPSC). The Registry provides comprehensive and standardized biological and legal information as well as tools to search and compare information from multiple hPSC sources and hence addresses a translational research need. To facilitate unambiguous identification over different resources, hPSCreg automatically creates a unique standardized name (identifier) for each cell line registered. In addition to biological information, hPSCreg stores extensive data about ethical standards regarding cell sourcing and conditions for application and privacy protection. hPSCreg is the first global registry that holds both, manually validated scientific and ethical information on hPSC lines, and provides access by means of a user-friendly, mobile-ready web application.

PAC - Archiving Platform CINES

PAC - Plateforme d'Archivage au CINES

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CINES is the French national long-term preservation service provider for Higher Education and Research: more than 20 institutions (universities, librairies, labs) archive their digital heritage at CINES so that it's preserved over time in a secure, dedicated environment. This includes documents such as PhD theses or publications, digitized ancient/rare books, satellite imagery, 3D/vidéos/image galleries, datasets, etc.