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Found 43 result(s)

ExPASy Bioinformatics Resource Portal

SIB Bioinformatics Resource Portal

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Swiss Institute of Bioinformatics (SIB) coordinates research and education in bioinformatics throughout Switzerland and provides bioinformatics services to the national and international research community. ExPASy gives access to numerous repositories and databases of SIB. For example: array map, MetaNetX, SWISS-MODEL and World-2DPAGE, and many others see a list here http://www.expasy.org/resources

Ningaloo Atlas

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The Ningaloo Atlas was created in response to the need for more comprehensive and accessible information on environmental and socio-economic data on the greater Ningaloo region. As such, the Ningaloo Atlas is a web portal to not only access and share information, but to celebrate and promote the biodiversity, heritage, value, and way of life of the greater Ningaloo region.

NONCODE

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NONCODE is an integrated knowledge database dedicated to non-coding RNAs (excluding tRNAs and rRNAs). Now, there are 16 species in NONCODE(human, mouse, cow, rat, chicken, fruitfly, zebrafish, celegans, yeast, Arabidopsis, chimpanzee, gorilla, orangutan, rhesus macaque, opossum and platypus).The source of NONCODE includes literature and other public databases. We searched PubMed using key words ‘ncrna’, ‘noncoding’, ‘non-coding’,‘no code’, ‘non-code’, ‘lncrna’ or ‘lincrna. We retrieved the new identified lncRNAs and their annotation from the Supplementary Material or web site of these articles. Together with the newest data from Ensembl , RefSeq, lncRNAdb and GENCODE were processed through a standard pipeline for each species.

NCBI Structure

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The Structure database provides three-dimensional structures of macromolecules for a variety of research purposes and allows the user to retrieve structures for specific molecule types as well as structures for genes and proteins of interest. Three main databases comprise Structure-The Molecular Modeling Database; Conserved Domains and Protein Classification; and the BioSystems Database. Structure also links to the PubChem databases to connect biological activity data to the macromolecular structures. Users can locate structural templates for proteins and interactively view structures and sequence data to closely examine sequence-structure relationships.

Ensembl Metazoa

e!EnsemblMetazoa

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Ensembl Metazoa is a genome-centric portal for metazoan species of scientific interest.

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.

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)

Genomic Observatories MetaDatabase

GEOME

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The Genomic Observatories Meta-Database (GEOME) is a web-based database that captures the who, what, where, and when of biological samples and associated genetic sequences. GEOME helps users with the following goals: ensure the metadata from your biological samples is findable, accessible, interoperable, and reusable; improve the quality of your data and comply with global data standards; and integrate with R, ease publication to NCBI's sequence read archive, and work with an associated LIMS. The initial use case for GEOME came from the Diversity of the Indo-Pacific Network (DIPnet) resource.

Data Repository for the University of Minnesota

DRUM

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Open access repository for digital research created at the University of Minnesota. U of M researchers may deposit data to the Libraries’ Data Repository for U of M (DRUM), subject to our collection policies. All data is publicly accessible. Data sets submitted to the Data Repository are reviewed by data curation staff to ensure that data is in a format and structure that best facilitates long-term access, discovery, and reuse.

Oral Cancer Gene Database

OrCGDB

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Oral Cancer Gene Database is an initiative of the Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai. The present database, version II, consists of 374 genes. It is developed as a user friendly site that would provide the scientist, information and external links from one place. The database is accessed through a list of all genes, and Keyword Search using gene name or gene symbol, chromosomal location, CGH (in %), and molecular weight. Interaction Network shows the interaction between genes for particular biological processes and molecular functions.

TriTrypDB

kinetoplastid genomics resource

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TriTrypDB is an integrated genomic and functional genomic database for pathogens of the family Trypanosomatidae, including organisms in both Leishmania and Trypanosoma genera. TriTrypDB and its continued development are possible through the collaborative efforts between EuPathDB, GeneDB and colleagues at the Seattle Biomedical Research Institute (SBRI).

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.

The National Map

TNM

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As one of the cornerstones of the U.S. Geological Survey's (USGS) National Geospatial Program, The National Map is a collaborative effort among the USGS and other Federal, State, and local partners to improve and deliver topographic information for the Nation. It has many uses ranging from recreation to scientific analysis to emergency response. The National Map is easily accessible for display on the Web, as products and services, and as downloadable data. The geographic information available from The National Map includes orthoimagery (aerial photographs), elevation, geographic names, hydrography, boundaries, transportation, structures, and land cover. Other types of geographic information can be added within the viewer or brought in with The National Map data into a Geographic Information System to create specific types of maps or map views.

VertNet

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VertNet is a NSF-funded collaborative project that makes biodiversity data free and available on the web. VertNet is a tool designed to help people discover, capture, and publish biodiversity data. It is also the core of a collaboration between hundreds of biocollections that contribute biodiversity data and work together to improve it. VertNet is an engine for training current and future professionals to use and build upon best practices in data quality, curation, research, and data publishing. Yet, VertNet is still the aggregate of all of the information that it mobilizes. To us, VertNet is all of these things and more.

STOREDB

Sustaining access to Tissues and data frOm Radiobiological Experiments

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STOREDB is a platform for the archiving and sharing of primary data and outputs of all kinds, including epidemiological and experimental data, from research on the effects of radiation. It also provides a directory of bioresources and databases containing information and materials that investigators are willing to share. STORE supports the creation of a radiation research commons.

doRiNA

database of RNA interactions in post-transcriptional regulation

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doRiNA is a database of transcriptome-wide binding site data for RNA binding proteins and microRNAs

Universal PBM Resource for Oligonucleotide Binding Evaluation

UniPROBE

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The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the in vitro DNA binding specificities of proteins. This initial release of the UniPROBE database provides a centralized resource for accessing comprehensive data on the preferences of proteins for all possible sequence variants ('words') of length k ('k-mers'), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. In total, the database currently hosts DNA binding data for 406 nonredundant proteins from a diverse collection of organisms, including the prokaryote Vibrio harveyi, the eukaryotic malarial parasite Plasmodium falciparum, the parasitic Apicomplexan Cryptosporidium parvum, the yeast Saccharomyces cerevisiae, the worm Caenorhabditis elegans, mouse, and human. The database's web tools (on the right) include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences

GUDMAP

GenitoUrinary Development Molecular Anatomy Project

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The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research. The key components are: (1) a molecular atlas of gene expression for the developing organs of the GenitoUrinary (GU) tract; (2) a high resolution molecular anatomy that highlights development of the GU system; (3) mouse strains to facilitate developmental and functional studies within the GU system; (4) tutorials describing GU organogenesis; and (5) rapid access to primary data via the GUDMAP database.

Sextant

Infrastructure de Données Géographiques (IDG) marines et littorales

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Sextant is a marine and coastal geographic data infrastructure. It is operated by Scientific Information Systems for the Sea (SISMER) of Ifremer (https://www.ifremer.fr/). Sextant aims to document, disseminate and promote a catalog of data related to the marine environment. For Ifremer's laboratories and partners, as well as for national and European actors working in the marine and coastal field, Sextant provides tools that promote and facilitate the archiving, consultation and availability of these geographical data. Data published by Sextant are available free or restricted. They can be used in accordance with the terms of the Creative Commons license selected by the author of data. Sextant infrastructure and the technologies used are in line with the implementation of the INSPIRE Directive and make it possible to follow the Open Data approach. Some data set published by Sextant has a DOI which enables it to be cited in a publication in a reliable and sustainable way. The long-term preservation of data filed in Sextant is ensured by Ifremer infrastructure.

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.

ScholarsArchive@OSU

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ScholarsArchive@OSU is Oregon State University's digital service for gathering, indexing, making available and storing the scholarly work of the Oregon State University community. It also includes materials from outside the institution in support of the university's land, sun, sea and space grant missions and other research interests.

Electron Microscopy Data Bank

EMDB

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The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography.

GigaDB

GigaScience Database

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GigaDB primarily serves as a repository to host data and tools associated with articles published by GigaScience Press; GigaScience and GigaByte (both are online, open-access journals). GigaDB defines a dataset as a group of files (e.g., sequencing data, analyses, imaging files, software programs) that are related to and support a unit-of-work (article or study). GigaDB allows the integration of manuscript publication with supporting data and tools.

Ensembl Bacteria

e!EnsemblBacteria

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This site provides access to complete, annotated genomes from bacteria and archaea (present in the European Nucleotide Archive) through the Ensembl graphical user interface (genome browser). Ensembl Bacteria contains genomes from annotated INSDC records that are loaded into Ensembl multi-species databases, using the INSDC annotation import pipeline.

Ensembl Protists

e!EnsemblProtists

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EnsemblProtists is a genome-centric portal for protists species.