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Found 34 result(s)

Pombase

The scientific resource for fission yeast

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PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets.

Avibase

the world bird database

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Avibase is an extensive database information system about all birds of the world, containing over 60 million records about 10,000 species and 22,000 subspecies of birds, including distribution information, taxonomy, synonyms in several languages and more. This site is managed by Denis Lepage and hosted by Bird Studies Canada, the Canadian copartner of Birdlife International. Avibase has been a work in progress since 1992 and I am now pleased to offer it as a service to the bird-watching and scientific community.

Human Genetic Variation Repository

HGVD

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The Human Genetic Variation Database (HGVD) aims to provide a central resource to archive and display Japanese genetic variation and association between the variation and transcription level of genes. The database currently contains genetic variations determined by exome sequencing of 1,208 individuals and genotyping data of common variations obtained from a cohort of 3,248 individuals.

The Monarch Initiative

Monarch Initiative

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As with most biomedical databases, the first step is to identify relevant data from the research community. The Monarch Initiative is focused primarily on phenotype-related resources. We bring in data associated with those phenotypes so that our users can begin to make connections among other biological entities of interest. We import data from a variety of data sources. With many resources integrated into a single database, we can join across the various data sources to produce integrated views. We have started with the big players including ClinVar and OMIM, but are equally interested in boutique databases. You can learn more about the sources of data that populate our system from our data sources page https://monarchinitiative.org/about/sources.

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.

Natural History Museum, Data Portal

Explore and download the Natural History Museum’s research and collections data

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The Museum is committed to open access and open science, and has launched the Data Portal to make its research and collections datasets available online. It allows anyone to explore, download and reuse the data for their own research. Our natural history collection is one of the most important in the world, documenting 4.5 billion years of life, the Earth and the solar system. Almost all animal, plant, mineral and fossil groups are represented. These datasets will increase exponentially. Under the Museum's ambitious digital collections programme we aim to have 20 million specimens digitised in the next five years.

JGI MycoCosm

MycoCosm - the fungal genomics resource

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MycoCosm, the DOE JGI’s web-based fungal genomics resource, which integrates fungal genomics data and analytical tools for fungal biologists. It provides navigation through sequenced genomes, genome analysis in context of comparative genomics and genome-centric view. MycoCosm promotes user community participation in data submission, annotation and analysis.

Flora von Bayern: Wiki and Data Portal

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The "Flora of Bavaria" initiative with its data portal (14 million occurrence data) and Wiki representation is primarily a citizen science project. Efforts to describe and monitor the flora of Bavaria have been ongoing for 100 years. The goal of these efforts is to record all vascular plants, including newcomers, and to document threatened or former local occurrences. Being geographically largest state of Germany with a broad range of habitats, Bavaria has a special responsibility for documenting and maintaining its plant diversity . About 85% of all German vascular plant species occur in Bavaria, and in addition it has about 50 endemic taxa, only known from Bavaria (most of them occur in the Alps). The Wiki is collaboration of volunteers and local and regional Bavarian botanical societies. Everybody is welcome to contribute, especially with photos or reports of local changes in the flora. The Flora of Bavaria project is providing access to a research data repository for occurrence data powered by the Diversity Workbench database framework.

GeneCards

The Human Gene Database

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GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. It automatically integrates gene-centric data from ~125 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information.

NITRC

Neuroimaging Informatics Tools and Resources Clearinghouse

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Neuroimaging Tools and Resources Collaboratory (NITRC) is currently a free one-stop-shop environment for science researchers that need resources such as neuroimaging analysis software, publicly available data sets, and computing power. Since its debut in 2007, NITRC has helped the neuroscience community to use software and data produced from research that, before NITRC, was routinely lost or disregarded, to make further discoveries. NITRC provides free access to data and enables pay-per-use cloud-based access to unlimited computing power, enabling worldwide scientific collaboration with minimal startup and cost. With NITRC and its components—the Resources Registry (NITRC-R), Image Repository (NITRC-IR), and Computational Environment (NITRC-CE)—a researcher can obtain pilot or proof-of-concept data to validate a hypothesis for a few dollars.

Mammalian Transcriptomic Database

MTD

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MTD is focused on mammalian transcriptomes with a current version that contains data from humans, mice, rats and pigs. Regarding the core features, the MTD browses genes based on their neighboring genomic coordinates or joint KEGG pathway and provides expression information on exons, transcripts, and genes by integrating them into a genome browser. We developed a novel nomenclature for each transcript that considers its genomic position and transcriptional features.

DSPR

The Drosophila Synthetic Population Resource

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The Drosophila Synthetic Population Resource (DSPR) consists of a new panel of over 1700 recombinant inbred lines (RILs) of Drosophila melanogaster, derived from two highly recombined synthetic populations, each created by intercrossing a different set of 8 inbred founder lines (with one founder line common to both populations). Complete genome sequence data for the founder lines are available, and in addition, there is a high resolution genetic map for each RIL. The DSPR has been developed as a community resource for high-resolution QTL mapping and is intended to be used widely by the Drosophila community.

International HapMap Project

国际人类基因组单体型图计划

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<<<!!!<<< OFFLINE >>>!!!>>> A recent computer security audit has revealed security flaws in the legacy HapMap site that require NCBI to take it down immediately. We regret the inconvenience, but we are required to do this. That said, NCBI was planning to decommission this site in the near future anyway (although not quite so suddenly), as the 1,000 genomes (1KG) project has established itself as a research standard for population genetics and genomics. NCBI has observed a decline in usage of the HapMap dataset and website with its available resources over the past five years and it has come to the end of its useful life. The International HapMap Project is a multi-country effort to identify and catalog genetic similarities and differences in human beings. Using the information in the HapMap, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. The Project is a collaboration among scientists and funding agencies from Japan, the United Kingdom, Canada, China, Nigeria, and the United States. All of the information generated by the Project will be released into the public domain. The goal of the International HapMap Project is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. By making this information freely available, the Project will help biomedical researchers find genes involved in disease and responses to therapeutic drugs. In the initial phase of the Project, genetic data are being gathered from four populations with African, Asian, and European ancestry. Ongoing interactions with members of these populations are addressing potential ethical issues and providing valuable experience in conducting research with identified populations. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. The Project officially started with a meeting in October 2002 (https://www.genome.gov/10005336/) and is expected to take about three years.

BioVel

Biodiversity Virtual e-Laboratory

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<<<!!!<<< This repository is no longer available. >>>!!!>>> BioVeL is a virtual e-laboratory that supports research on biodiversity issues using large amounts of data from cross-disciplinary sources. BioVeL supports the development and use of workflows to process data. It offers the possibility to either use already made workflows or create own. BioVeL workflows are stored in MyExperiment - Biovel Group http://www.myexperiment.org/groups/643/content. They are underpinned by a range of analytical and data processing functions (generally provided as Web Services or R scripts) to support common biodiversity analysis tasks. You can find the Web Services catalogued in the BiodiversityCatalogue.

RUresearch Data Portal

Rutgers University Research Data Portal

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RUresearch Data Portal is a subset of RUcore (Rutgers University Community Repository), provides a platform for Rutgers researchers to share their research data and supplementary resources with the global scholarly community. This data portal leverages all the capabilities of RUcore with additional tools and services specific to research data. It provides data in different clusters (research-genre) with excellent search facility; such as experimental data, multivariate data, discrete data, continuous data, time series data, etc. However it facilitates individual research portals that include the Video Mosaic Collaborative (VMC), an NSF-funded collection of mathematics education videos for Teaching and Research. Its' mission is to maintain the significant intellectual property of Rutgers University; thereby intended to provide open access and the greatest possible impact for digital data collections in a responsible manner to promote research and learning.

PlasmoDB

Plasmodium Genomics Resource

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PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria.

Cancer Cell Line Encyclopedia

CCLE

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The Cancer Cell Line Encyclopedia project is a collaboration between the Broad Institute, and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access to genomic data, analysis and visualization for about 1000 cell lines.

UniRef

UniProt Reference Clusters

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The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view.

DEPOD

DEPhOsphorylation Database

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DEPOD - the human DEPhOsphorylation Database (version 1.1) is a manually curated database collecting human active phosphatases, their experimentally verified protein and non-protein substrates and dephosphorylation site information, and pathways in which they are involved. It also provides links to popular kinase databases and protein-protein interaction databases for these phosphatases and substrates. DEPOD aims to be a valuable resource for studying human phosphatases and their substrate specificities and molecular mechanisms; phosphatase-targeted drug discovery and development; connecting phosphatases with kinases through their common substrates; completing the human phosphorylation/dephosphorylation network.

MassBank Europe

MassBank

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Database of mass spectra of known, unknown and provisionally identified substances. MassBank is the first public repository of mass spectral data for sharing them among scientific research community. MassBank data are useful for the chemical identification and structure elucidation of chemical compounds detected by mass spectrometry.

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.

IMGT/GENE-DB

ImMunoGeneTics / Gene-DB

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IMGT/GENE-DB is the IMGT genome database for IG and TR genes from human, mouse and other vertebrates. IMGT/GENE-DB provides a full characterization of the genes and of their alleles: IMGT gene name and definition, chromosomal localization, number of alleles, and for each allele, the IMGT allele functionality, and the IMGT reference sequences and other sequences from the literature. IMGT/GENE-DB allele reference sequences are available in FASTA format (nucleotide and amino acid sequences with IMGT gaps according to the IMGT unique numbering, or without gaps).

cropPAL

Compendium of crop Proteins with Annotated Locations

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<<<!!!<<< This repository is no longer available >>>!!!>>>

PATRIC

Pathosystems Resource Integration Center

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<<<!!!<<< This repository is no longer available. >>>!!!>>> PATRIC will go offline by mid-December2022. Here is what you need to know. As announced previously, PATRIC, the bacterial BRC, and IRD / ViPR, the viral BRCs, are being merged into the new Bacterial and Viral Bioinformatics Resource Center (BV-BRC). BV-BRC combines the data, tools, and technologies from these BRCs to provide an integrated resource for bacterial and viral genomics-based infectious disease research.

PhenoGen Informatics

PhenoGen

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The PhenoGen website shares experimental data with a worldwide community of investigators and provides a flexible, integrated, multi-resolution repository of neuroscience transcriptomic genetic data for collaborative research on genomic disorders. The main development focus is on providing Hybrid Rat Diversity Panel transcriptomic data (sequencing, genome coverage, reconstructed totalRNA/smallRNA transcriptomes, quanification of the transcriptome, eQTLs, and WGCNA) and integrating additional tools to provide platform for visualization and analysis of HRDP transcriptome data.