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Found 75 result(s)

Open Tree of Life

Tree of Life - Evolution

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The tree of life links all biodiversity through a shared evolutionary history. This project will produce the first online, comprehensive first-draft tree of all 1.8 million named species, accessible to both the public and scientific communities. Assembly of the tree will incorporate previously-published results, with strong collaborations between computational and empirical biologists to develop, test and improve methods of data synthesis. This initial tree of life will not be static; instead, we will develop tools for scientists to update and revise the tree as new data come in. Early release of the tree and tools will motivate data sharing and facilitate ongoing synthesis of knowledge.

SilkPathDB

Silkworm Pathogen Database

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Silkworm Pathogen Database (SilkPathDB) is a comprehensive resource for studying on pathogens of silkworm, including microsporidia, fungi, bacteria and virus. SilkPathDB provides access to not only genomic data including functional annotation of genes and gene products, but also extensive biological information for gene expression data and corresponding researches. SilkPathDB will be help with researches on pathogens of silkworm as well as other Lepidoptera insects.

RAMEDIS

Rare Metabolic Diseases Database

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The RAMEDIS system is a platform independent, web-based information system for rare metabolic diseases based on filed case reports. It was developed in close cooperation with clinical partners to allow them to collect information on rare metabolic diseases with extensive details, e.g. about occurring symptoms, laboratory findings, therapy and molecular data.

JenAge Ageing Factor Database

AgeFactDB

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The JenAge Ageing Factor Database AgeFactDB is aimed at the collection and integration of ageing phenotype and lifespan data. Ageing factors are genes, chemical compounds or other factors such as dietary restriction, for example. In a first step ageing-related data are primarily taken from existing databases. In addition, new ageing-related information is included both by manual and automatic information extraction from the scientific literature. Based on a homology analysis, AgeFactDB also includes genes that are homologous to known ageing-related genes. These homologs are considered as candidate or putative ageing-related genes.

ARS

Antibiotika-Resistenz-Surveillance

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With ARS - Antimicrobial Resistance Surveillance in Germany - the infrastructure for a nationwide surveillance of antimicrobial resistance has been established, which covers both the inpatient medical care and the ambulatory care sector. This is intended to reliable data on the epidemiology of antimicrobial resistance in Germany and differential statements provided by structural features of the health care and by region are possible. ARS is designed as a laboratory-based surveillance system for continuous collection of resistance data from routine for the full range of clinically relevant bacterial pathogens. Project participants and thus data suppliers are laboratories that analyze samples of medical facilities and doctors' offices microbiologically.

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.

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.

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.

GeoReM

Geological and Environmental Reference Materials

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GeoReM is a Max Planck Institute database for reference materials of geological and environmental interest, such as rock powders, synthetic and natural glasses as well as mineral, isotopic, biological, river water and seawater reference materials. GeoReM contains published analytical data and compilation values (major and trace element concentrations and mass fractions, radiogenic and stable isotope ratios). GeoReM contains all important metadata about the analytical values such as uncertainty, analytical method and laboratory. Sample information and references are also included. GeoReM complements the three earthchem databases: GEOROC, NAVDAT and PETDB.

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.

Pseudobase

A Pseudoknot Database

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Since the first discovery of RNA pseudoknots more and many more pseudoknots have been found. However, not all of those pseudoknot data are easy to trace. Sometimes the information is hidden in a publication where the title gives no hint that pseudoknot information is there. This was the first reason that we thought that a general accessible information source for pseudoknots would be handy.

DataBasin

Data Basin

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Data Basin is a science-based mapping and analysis platform that supports learning, research, and sustainable environmental stewardship.

Cancer GenomeAtlas Data Portal

Cancer Genome Atlas Data Portal

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The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The Data Coordinating Center (DCC) is the central provider of TCGA data. The DCC standardizes data formats and validates submitted data.

Virus Pathogen Resource

ViPR

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<<<!!!<<< This repository is no longer available. >>>!!!>>> Migration of the data, tools, and services from IRD and ViPR to BV-BRC is complete! We are now in the sunsetting phase of the transition. Starting on October 31, 2022, launching the IRD or ViPR home pages will redirect you to the new BV-BRC home page. The current plan is to completely shut down IRD and ViPR by the end of this calendar year. Although it will still be possible to use those sites until shutdown, we strongly encourage you to start using BV-BRC now.

National Harvest Survey

NHS

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Surveys provide annual information on the total, seasonal and spatial harvest of ducks, geese and other game birds in Canada, on the ecological characteristics of waterfowl harvested in Canada and the hunter activity associated with that harvest. The survey covers all of Canada divided into 23 zones and has been carried out annually since 1966. The bilingual database currently contains 9,000,000+ records.

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.

CASRdb

Calcium Sensing Receptor Database

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<<<!!!<<< This repository is no longer available. >>>!!!>>> Message since 2018-06: This virtual host is being reconstructed.

SilkDB 3.0

Silkworm Genome Database

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SilkDB is a database of the integrated genome resource for the silkworm, Bombyx mori. This database provides access to not only genomic data including functional annotation of genes, gene products and chromosomal mapping, but also extensive biological information such as microarray expression data, ESTs and corresponding references. SilkDB will be useful for the silkworm research community as well as comparative genomics

Human Autophagy Database

HADb

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HADb provides a complete and an up-to-date list of human genes and proteins involved directly or indirectly in autophagy as described in literature.

Mouse Models of Human Cancer database

MMHCdb

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The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by providing electronic access to: Information on endogenous spontaneous and induced tumors in mice, including tumor frequency & latency data, Information on genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice) in which tumors arise, Information on genetic factors associated with tumor susceptibility in mice and somatic genetic-mutations observed in the tumors, Tumor pathology reports and images, References, supporting MTB data and Links to other online resources for cancer.

The Cell Image Library

The Cell

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This library is a public and easily accessible resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. The Cell Image Library has been merged with "Cell Centered Database" in 2017. The purpose of the database is to advance research on cellular activity, with the ultimate goal of improving human health.

Rat Genome Database

RGD

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The Rat Genome Database is a collaborative effort between leading research institutions involved in rat genetic and genomic research. Its goal, as stated in RFA: HL-99-013 is the establishment of a Rat Genome Database, to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community. A secondary, but critical goal is to provide curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data.

NCBI Probe

Probe

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<<<!!!<<< NCBI has retired the Probe Database >>>!!!>>>

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.