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Found 20 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.

DEG

Database of Essential Genes

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DEG hosts records of currently available essential genomic elements, such as protein-coding genes and non-coding RNAs, among bacteria, archaea and eukaryotes. Essential genes in a bacterium constitute a minimal genome, forming a set of functional modules, which play key roles in the emerging field, synthetic biology.

GiardiaDB

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Giardia lamblia is a significant, environmentally transmitted, human pathogen and an amitochondriate protist. It is a major contributor to the enormous worldwide burden of human diarrheal diseases, yet the basic biology of this parasite is not well understood. No virulence factor has been identified. The Giardia lamblia genome contains only 12 million base pairs distributed onto five chromosomes. Its analysis promises to provide insights about the origins of nuclear genome organization, the metabolic pathways used by parasitic protists, and the cellular biology of host interaction and avoidance of host immune systems. Since the divergence of Giardia lamblia lies close to the transition between eukaryotes and prokaryotes in universal ribosomal RNA phylogenies, it is a valuable, if not unique, model for gaining basic insights into genetic innovations that led to formation of eukaryotic cells. In evolutionary terms, the divergence of this organism is at least twice as ancient as the common ancestor for yeast and man. A detailed study of its genome will provide insights into an early evolutionary stage of eukaryotic chromosome organization as well as other aspects of the prokaryotic / eukaryotic divergence.

NCBI Genome

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<<<!!!<<< Effective May 2024, NCBI's Genome resource will no longer be available. NCBI Genome data can now be found on the NCBI Datasets taxonomy pages. https://www.re3data.org/repository/r3d100014298 >>>!!!>>> The Genome database contains annotations and analysis of eukaryotic and prokaryotic genomes, as well as tools that allow users to compare genomes and gene sequences from humans, microbes, plants, viruses and organelles. Users can browse by organism, and view genome maps and protein clusters.

SWISS-MODEL Repository

SMR

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The SWISS-MODEL Repository is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.

OrtholugeDB

The Ortholog Database

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OrtholugeDB contains Ortholuge-based orthology predictions for completely sequenced bacterial and archaeal genomes. It is also a resource for reciprocal best BLAST-based ortholog predictions, in-paralog predictions (recently duplicated genes) and ortholog groups in Bacteria and Archaea. The Ortholuge method improves the specificity of high-throughput orthology prediction.

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.

InTOR - Electronic Repository of Research and Scientific Papers

InTOR - Repository of the Institute “Torlak”

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InTOR is the institutional digital repository of the Institute of Virology, Vaccines and Sera “Torlak”. It provides open access to publications and other research outputs resulting from the projects implemented by the Institute of Virology, Vaccines and Sera “Torlak”. The software platform of the repository is adapted to the modern standards applied in the dissemination of scientific publications and is compatible with international infrastructure in this field.

InnateDB

A Knowlede Resource for Innate Immunity Interactions & Pathways

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InnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures an improved coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralised resource. The database can be mined as a knowledgebase or used with our integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response.

Ligand-Gated Ion Channel Database

LGICdb

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The Ligand-Gated Ion Channel database provides access to information about transmembrane proteins that exist under different conformations, with three primary subfamilies: the cys-loop superfamily, the ATP gated channels superfamily, and the glutamate activated cationic channels superfamily. The development of the Ligand-Gated Ion Channel database was started in 1994, as part of Le Novère's work on the phylogeny of those receptors' subunits. It grew into a serious data resource, that served the community at large. However, it is not actively maintained anymore. In addition, bioinformatics technology evolved a lot over the last two decades, so that scientists can now generate quickly customised databases from trustworthy primary data resources. Therefore, we decided to officialy freeze the data resource. The resource will not disappear, and all the information and links will stay there. But people should not consider it as an up-to-date trustable resource. For any new work, they should consider using alternative sources, such as UniProt, Ensembl, Protein Databank etc.

GallusReactome

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>>>!!!<<< 29.01.2020: Gallus.Reactome is offline >>>!!!<<<

German Federation for Biological Data

GFBio

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The project brings together national key players providing environmentally related biological data and services to develop the ‘German Federation for Biological Data' (GFBio). The overall goal is to provide a sustainable, service oriented, national data infrastructure facilitating data sharing and stimulating data intensive science in the fields of biological and environmental research.

HomoMINT

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

virus mentha

the interactome browser

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virus mentha archives evidence about viral interactions collected from different sources and presents these data in a complete and comprehensive way. Its data comes from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. virus mentha is a resource that offers a series of tools to analyse selected proteins in the context of a network of interactions. Protein interaction databases archive protein-protein interaction (PPI) information from published articles. However, no database alone has sufficient literature coverage to offer a complete resource to investigate "the interactome". virus mentha's approach generates every week a consistent interactome (graph). Most importantly, the procedure assigns to each interaction a reliability score that takes into account all the supporting evidence. virus mentha offers direct access to viral families such as: Orthomyxoviridae, Orthoretrovirinae and Herpesviridae plus, it offers the unique possibility of searching by host organism. The website and the graphical application are designed to make the data stored in virus mentha accessible and analysable to all users.virus mentha superseeds VirusMINT. The Source databases are: MINT, DIP, IntAct, MatrixDB, BioGRID.

FAIRDOMHub

The SEEK datafiles

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The FAIRDOMHub is built upon the SEEK software suite, which is an open source web platform for sharing scientific research assets, processes and outcomes. FAIRDOM (Web Site) will establish a support and service network for European Systems Biology. It will serve projects in standardizing, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable. FAIRDOM is an initiative to develop a community, and establish an internationally sustained Data and Model Management service to the European Systems Biology community. FAIRDOM is a joint action of ERA-Net EraSysAPP and European Research Infrastructure ISBE.

Plant and Fungal Carbohydrate Structure Database

PFCSDB

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<<<!!!<<< Bacterial (BCSDB) and Plant&Fungal (PFCSDB) carbohydrate structure databases have been merged into a single database, CSDB >>>!!!>>>

World Data Center of Microorganisms

WDCM

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WFCC-MIRCEN World Data Centre for Microorganisms (WDCM) provides a comprehensive directory of culture collections, databases on microbes and cell lines, and the gateway to biodiversity, molecular biology and genome projects.The WFCC is a Multidisciplinary Commission of the International Union of Biological Sciences (IUBS) and a Federation within the International Union of Microbiological Societies (IUMS). The WFCC is concerned with the collection, authentication, maintenance and distribution of cultures of microorganisms and cultured cells. Its aim is to promote and support the establishment of culture collections and related services, to provide liaison and set up an information network between the collections and their users, to organise workshops and conferences, publications and newsletters and work to ensure the long term perpetuation of important collections.

domino

domaine peptide interactions

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<<<!!!<<< This repository is no longer available. 2019-02-19 >>>!!!>>>

FANTOM

FANTOM DB

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FANTOM stands for 'Functional Annotation of the Mammalian Genome' and is the name of an international research consortium organized by the RIKEN Omics Science Center. The FANTOM5 project aims to build a full understanding of transcriptional regulation in a human system by generating transcriptional regulatory networks that define every human cell type.

BacDive

Bacterial Diversity Metadatabase

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BacDive is a bacterial metadatabase that provides strain-linked information about bacterial and archaeal biodiversity. The database is a resource for different kind of phenotypic data like taxonomy, morphology, physiology, environment and molecular-biology. The majority of data is manually annotated and curated. With the release in April 2019 BacDive offers information for 80,584 strains. The database is hosted by the Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH and is part of de.NBI the German Network for Bioinformatics Infrastructure.