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Found 55 result(s)

HUGO Gene Nomenclature Committee

HGNC

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The HUGO Gene Nomenclature Committee (HGNC) assigned unique gene symbols and names to over 35,000 human loci, of which around 19,000 are protein coding. This curated online repository of HGNC-approved gene nomenclature and associated resources includes links to genomic, proteomic and phenotypic information, as well as dedicated gene family pages.

NCBI Gene

Gene

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The Gene database provides detailed information for known and predicted genes defined by nucleotide sequence or map position. Gene supplies gene-specific connections in the nexus of map, sequence, expression, structure, function, citation, and homology data. Unique identifiers are assigned to genes with defining sequences, genes with known map positions, and genes inferred from phenotypic information. These gene identifiers are used throughout NCBI's databases and tracked through updates of annotation. Gene includes genomes represented by NCBI Reference Sequences (or RefSeqs) and is integrated for indexing and query and retrieval from NCBI's Entrez and E-Utilities systems.

FlyReactome

a curated knowledgebase of drosophila melanogaster pathways

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<<<!!!<<< This repository is no longer available. This record is out dated >>>!!!>>>- eir fields, maintained by the FlyReactome staff.

Database of Genomic Variants Archive

DGVa

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<<<!!!<<< Phasing out support for the Database of Genomic Variants archive (DGVa). The submission, archiving, and presentation of structural variation services offered by the DGVa is transitioning to the European Variation Archive (EVA) https://www.re3data.org/repository/r3d100011553. All of the data shown in the DGVa website is already searchable and browsable from the EVA Study Browser. Submission of structural variation data to EVA is done using the VCF format. The VCF specification allows representing multiple types of structural variants such as insertions, deletions, duplications and copy-number variants. Other features such as symbolic alleles, breakends, confidence intervals etc., support more complex events, such as translocations at an imprecise position. >>>!!!>>>

NCBI Datasets

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NCBI Datasets is a continually evolving platform designed to provide easy and intuitive access to NCBI’s sequence data and metadata. NCBI Datasets is part of the NIH Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses for all eukaryotic organisms through an NCBI Toolkit and community collaboration.

Allen Brain Map

Data Portal

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The Allen Brain Atlas provides a unique online public resource integrating extensive gene expression data, connectivity data and neuroanatomical information with powerful search and viewing tools for the adult and developing brain in mouse, human and non-human primate

NCBI Influenza Virus Resource

NCBI Flu

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This resource allows users to search for and compare influenza virus genomes and gene sequences taken from GenBank. It also provides a virus sequence annotation tool and links to other influenza resources: NIAID project, JCVI Flu, Influenza research database, CDC Flu, Vaccine Selection and WHO Flu. NOTE: The redirects that are planned for completion by May 2024 will NOT impact the Influenza Virus Resource in any way. The Influenza Virus Resource will continue to be available, serving up data to support our Flu-research community.

NCBI Clone DB

NCBI clone registry

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<<<!!!<<< NCBI announced plans to retire the Clone DB web interface. Pursuant to this retirement, starting on May 27, 2019, all web pages associated with Clone DB and CloneFinder will redirect to this blog post https://ncbiinsights.ncbi.nlm.nih.gov/?s=clone+db. Links to Clone DB from the NCBI home page will also be going away. >>>!!!>>>

MGnify

formerly: EBI Metagenomics

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MGnify (formerly: EBI Metagenomics) offers an automated pipeline for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.

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.

Ensembl Metazoa

e!EnsemblMetazoa

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

TB Database

Tuberculosis Database

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The repository is no longer available. >>>!!!<<< 2018-08-29: no more access to TB Database >>>!!!<<<

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

CorrDB

Animal Trait Correlation Database

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CorrDB has data of cattle, relating to meat production, milk production, growth, health, and others. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies.

Cystic Fibrosis Mutation Database

CFTR1

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The Cystic Fibrosis Mutation Database (CFTR1) was initiated by the Cystic Fibrosis Genetic Analysis Consortium in 1989 to increase and facilitate communications among CF researchers, and is maintained by the Cystic Fibrosis Centre at the Hospital for Sick Children in Toronto. The specific aim of the database is to provide up to date information about individual mutations in the CFTR gene. In a major upgrade in 2010, all known CFTR mutations and sequence variants have been converted to the standard nomenclature recommended by the Human Genome Variation Society.

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

Morph·D·Base

MorphDBase

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Morph·D·Base has been developed to serve scientific research and education. It provides a platform for storing the detailed documentation of all material, methods, procedures, and concepts applied, together with the specific parameters, values, techniques, and instruments used during morphological data production. In other words, it's purpose is to provide a publicly available resource for recording and documenting morphological metadata. Moreover, it is also a repository for different types of media files that can be uploaded in order to serve as support and empirical substantiation of the results of morphological investigations. Our long-term perspective with Morph·D·Base is to provide an instrument that will enable a highly formalized and standardized way of generating morphological descriptions using a morphological ontology that will be based on the web ontology language (OWL - http://www.w3.org/TR/owl-features/). This, however, represents a project that is still in development.

Biofilms Structural Database

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The Biofilms Structural Database contains information on different protein structures involved in biofilm formation, development, and virulence.

mentha

the interactome browser

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mentha archives evidence 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. The aggregated data forms an interactome which includes many organisms. 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". 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. mentha offers eight interactomes (Homo sapiens, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Escherichia coli K12, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae) plus a global network that comprises every organism, including those not mentioned. The website and the graphical application are designed to make the data stored in mentha accessible and analysable to all users. Source databases are: MINT, IntAct, DIP, MatrixDB and BioGRID.

MG-RAST

Metagenomics analysis server

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The MG-RAST server is an open source system for annotation and comparative analysis of metagenomes. Users can upload raw sequence data in fasta format; the sequences will be normalized and processed and summaries automatically generated. The server provides several methods to access the different data types, including phylogenetic and metabolic reconstructions, and the ability to compare the metabolism and annotations of one or more metagenomes and genomes. In addition, the server offers a comprehensive search capability. Access to the data is password protected, and all data generated by the automated pipeline is available for download in a variety of common formats. MG-RAST has become an unofficial repository for metagenomic data, providing a means to make your data public so that it is available for download and viewing of the analysis without registration, as well as a static link that you can use in publications. It also requires that you include experimental metadata about your sample when it is made public to increase the usefulness to the community.

NCBI Probe

Probe

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

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.

SILVA

A comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data.

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SILVA is a comprehensive, quality-controlled web resource for up-to-date aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains alongside supplementary online services. In addition to data products, SILVA provides various online tools such as alignment and classification, phylogenetic tree calculation and viewer, probe/primer matching, and an amplicon analysis pipeline. With every full release a curated guide tree is provided that contains the latest taxonomy and nomenclature based on multiple references. SILVA is an ELIXIR Core Data Resource.

GenomeRNAi

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GenomeRNAi is a database containing phenotypes from RNA interference (RNAi) screens in Drosophila and Homo sapiens. In addition, the database provides an updated resource of RNAi reagents and their predicted quality.

NCBI HomoloGene

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The HomoloGene database provides a system for the automated detection of homologs among annotated genes of genomes across multiple species. These homologs are fully documented and organized by homology group. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences.