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Public Health

Research databases: Human genetics

NCBI (National Center for Biotechnology Information): All resources

 

DNA & RNA

  • Assembly
    • A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data.
  • BioCollections
    • A curated set of metadata for culture collections, museums, herbaria and other natural history collections. The records display collection codes, information about the collections' home institutions, and links to relevant data at NCBI. 
  • BioProject (formerly Genome Project) 
    • A collection of genomics, functional genomics, and genetics studies and links to their resulting datasets. This resource describes project scope, material, and objectives and provides a mechanism to retrieve datasets that are often difficult to find due to inconsistent annotation, multiple independent submissions, and the varied nature of diverse data types which are often stored in different databases.
  • BioSample
    • The BioSample database contains descriptions of biological source materials used in experimental assays.
  • Consensus CDS (CCDS)
    • A collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality.
  • Database of Short Genetic Variations (dbSNP)
    • Includes single nucleotide variations, microsatellites, and small-scale insertions and deletions. dbSNP contains population-specific frequency and genotype data, experimental conditions, molecular context, and mapping information for both neutral variations and clinical mutations.
  • GenBank
    • GenBank is an NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. These three organizations exchange data on a daily basis. GenBank consists of several divisions, most of which can be accessed through the Nucleotide database. The exceptions are the EST and GSS divisions, which are accessed through the Nucleotide EST and Nucleotide GSS databases, respectively.
  • Influenza Virus
    • A compilation of data from the NIAID Influenza Genome Sequencing Project and GenBank.  It provides tools for flu sequence analysis, annotation and submission to GenBank. This resource also has links to other flu sequence resources, and publications and general information about flu viruses
  • NCBI Pathogen Detection Project
    • A project involving the collection and analysis of bacterial pathogen genomic sequences originating from food, environmental and patient isolates. Currently, an automated pipeline clusters and identifies sequences supplied primarily by public health laboratories to assist in the investigation of foodborne disease outbreaks and discover potential sources of food contamination.
  • Nucleotide Database
    • A collection of nucleotide sequences from several sources, including GenBank, RefSeq, the Third Party Annotation (TPA) database, and PDB. Searching the Nucleotide Database will yield available results from each of its component databases.
  • PopSet
    • Database of related DNA sequences that originate from comparative studies: phylogenetic, population, environmental and, to a lesser degree, mutational. Each record in the database is a set of DNA sequences. For example, a population set provides information on genetic variation within an organism, while a phylogenetic set may contain sequences, and their alignment, of a single gene obtained from several related organisms.
  • Probe
    • A public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.
  • RefSeqGene
    • A collection of human gene-specific reference genomic sequences. RefSeq gene is a subset of  NCBI’s RefSeq database, and are defined based on review from curators of locus-specific databases and the genetic testing community. They form a stable foundation for reporting mutations, for establishing consistent intron and exon numbering conventions, and for defining the coordinates of other biologically significant variation. RefSeqGene is a part of the Locus Reference Genomic (LRG) Collaboration.
  • Reference Sequence (RefSeq)
    • A collection of curated, non-redundant genomic DNA, transcript (RNA), and protein sequences produced by NCBI. RefSeqs provide a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. The RefSeq collection is accessed through the Nucleotide and Protein databases.
  • Sequence Read Archive (SRA)
    • The Sequence Read Archive (SRA) stores sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome Analyzer®, Life Technologies AB SOLiD System®, Helicos Biosciences Heliscope®, Complete Genomics®, and Pacific Biosciences SMRT®.
  • Third Party Annotation (TPA) Database
    • A database that contains sequences built from the existing primary sequence data in GenBank. The sequences and corresponding annotations are experimentally supported and have been published in a peer-reviewed scientific journal. TPA records are retrieved through the Nucleotide Database.

 

Genes & Expression

  • BioProject (formerly Genome Project) 
    • A collection of genomics, functional genomics, and genetics studies and links to their resulting datasets. This resource describes project scope, material, and objectives and provides a mechanism to retrieve datasets that are often difficult to find due to inconsistent annotation, multiple independent submissions, and the varied nature of diverse data types which are often stored in different databases.
  • ClinVar
    • A resource to provide a public, tracked record of reported relationships between human variation and observed health status with supporting evidence. Related information in the NIH Genetic Testing Registry (GTR)MedGenGeneOMIMPubMed and other sources is accessible through hyperlinks on the records.
  • Consensus CDS (CCDS)
    • A collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality.
  • Database of Genotypes and Phenotypes (dbGaP)
    • An archive and distribution center for the description and results of studies which investigate the interaction of genotype and phenotype. These studies include genome-wide association (GWAS), medical resequencing, molecular diagnostic assays, as well as association between genotype and non-clinical traits. 
  • Gene
    • A searchable database of genes, focusing on genomes that have been completely sequenced and that have an active research community to contribute gene-specific data. Information includes nomenclature, chromosomal localization, gene products and their attributes (e.g., protein interactions), associated markers, phenotypes, interactions, and links to citations, sequences, variation details, maps, expression reports, homologs, protein domain content, and external databases.
  • Gene Expression Omnibus (GEO) Database
    • A public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted and tools are provided to help users query and download experiments and curated gene expression profiles.
  • Gene Expression Omnibus (GEO) Datasets
    • Stores curated gene expression and molecular abundance DataSets assembled from the Gene Expression Omnibus (GEO) repository. DataSet records contain additional resources, including cluster tools and differential expression queries.
  • Gene Expression Omnibus (GEO) Profiles
    • Stores individual gene expression and molecular abundance Profiles assembled from the Gene Expression Omnibus (GEO) repository. Search for specific profiles of interest based on gene annotation or pre-computed profile characteristics.
  • Genes and Disease
    • Summaries of information for selected genetic disorders with discussions of the underlying mutation(s) and clinical features, as well as links to related databases and organizations.
  • Genetic Testing Registry (GTR)
    • A voluntary registry of genetic tests and laboratories, with detailed information about the tests such as what is measured and analytic and clinical validity.  GTR also is a nexus for information about genetic conditions and provides context-specific links to a variety of resources, including practice guidelines, published literature, and genetic data/information. The initial scope of GTR includes single gene tests for Mendelian disorders, as well as arrays, panels and pharmacogenetic tests.
  • Online Mendelian Inheritance in Man (OMIM)
    • A database of  human genes and genetic disorders. NCBI maintains current content and continues to support its searching and integration with other NCBI databases.  However, OMIM now has a new home at omim.org, and users are directed to this site for full record displays.
  • RefSeqGene
    • A collection of human gene-specific reference genomic sequences. RefSeq gene is a subset of  NCBI’s RefSeq database, and are defined based on review from curators of locus-specific databases and the genetic testing community. They form a stable foundation for reporting mutations, for establishing consistent intron and exon numbering conventions, and for defining the coordinates of other biologically significant variation. RefSeqGene is a part of the Locus Reference Genomic (LRG) Collaboration.

Genetics & Medicine

  • Bookshelf
    • A collection of biomedical books that can be searched directly or from linked data in other NCBI databases. The collection includes genetic resources such as GeneReviews, and many other titles.
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  • ClinVar
    • A resource to provide a public, tracked record of reported relationships between human variation and observed health status with supporting evidence. Related information in the NIH Genetic Testing Registry (GTR)MedGenGeneOMIMPubMed and other sources is accessible through hyperlinks on the records.
  • ClinicalTrials.gov
    • A registry and results database of publicly- and privately-supported clinical studies of human participants conducted around the world.
  • Computational Resources from NCBI's Structure Group
    • A centralized page providing access and links to resources developed by the Structure Group of the NCBI Computational Biology Branch (CBB). These resources cover databases and tools to help in the study of macromolecular structures, conserved domains and protein classification, small molecules and their biological activity, and biological pathways and systems.
  • Conserved Domain Database (CDD)
    • A collection of sequence alignments and profiles representing protein domains conserved in molecular evolution. It also includes alignments of the domains to known 3-dimensional protein structures in the MMDB database.
  • Database of Genomic Structural Variation (dbVar)
    • The dbVar database has been developed to archive information associated with large scale genomic variation, including large insertions, deletions, translocations and inversions. In addition to archiving variation discovery, dbVar also stores associations of defined variants with phenotype information.
  • Database of Genotypes and Phenotypes (dbGaP)
    • An archive and distribution center for the description and results of studies which investigate the interaction of genotype and phenotype. These studies include genome-wide association (GWAS), medical resequencing, molecular diagnostic assays, as well as association between genotype and non-clinical traits. 
  • Gene
    • A searchable database of genes, focusing on genomes that have been completely sequenced and that have an active research community to contribute gene-specific data. Information includes nomenclature, chromosomal localization, gene products and their attributes (e.g., protein interactions), associated markers, phenotypes, interactions, and links to citations, sequences, variation details, maps, expression reports, homologs, protein domain content, and external databases.
  • Gene Expression Omnibus (GEO) Database
    • A public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted and tools are provided to help users query and download experiments and curated gene expression profiles.
  • Gene Expression Omnibus (GEO) Datasets
    • Stores curated gene expression and molecular abundance DataSets assembled from the Gene Expression Omnibus (GEO) repository. DataSet records contain additional resources, including cluster tools and differential expression queries.
  • Gene Expression Omnibus (GEO) Profiles
    • Stores individual gene expression and molecular abundance Profiles assembled from the Gene Expression Omnibus (GEO) repository. Search for specific profiles of interest based on gene annotation or pre-computed profile characteristics.
  • GeneReviews
    • A collection of expert-authored, peer-reviewed disease descriptions on the NCBI Bookshelf that apply genetic testing to the diagnosis, management, and genetic counseling of patients and families with specific inherited conditions.
  • Genes and Disease
    • Summaries of information for selected genetic disorders with discussions of the underlying mutation(s) and clinical features, as well as links to related databases and organizations.
  • Genetic Testing Registry (GTR)
    • A voluntary registry of genetic tests and laboratories, with detailed information about the tests such as what is measured and analytic and clinical validity.  GTR also is a nexus for information about genetic conditions and provides context-specific links to a variety of resources, including practice guidelines, published literature, and genetic data/information. The initial scope of GTR includes single gene tests for Mendelian disorders, as well as arrays, panels and pharmacogenetic tests.
  • Genome
    • Contains sequence and map data from the whole genomes of over 1000 organisms. The genomes represent both completely sequenced organisms and those for which sequencing is in progress. All three main domains of life (bacteria, archaea, and eukaryota) are represented, as well as many viruses, phages, viroids, plasmids, and organelles.
  • Genome Reference Consortium (GRC)
    • The Genome Reference Consortium (GRC) maintains responsibility for the human and mouse reference genomes. Members consist of The Genome Center at Washington University, the Wellcome Trust Sanger Institute, the European Bioinformatics Institute (EBI) and the National Center for Biotechnology Information (NCBI). The GRC works to correct misrepresented loci and to close remaining assembly gaps. In addition, the GRC seeks to provide alternate assemblies for complex or structurally variant genomic loci. At the GRC website (http://www.genomereference.org), the public can view genomic regions currently under review, report genome-related problems and contact the GRC.
  • Glycans
    • A centralized page providing access and links to glycoinformatics and glycobiology related resources.
  • HIV-1, Human Protein Interaction Database
    • A database of known interactions of HIV-1 proteins with proteins from human hosts. It provides annotated bibliographies of published reports of protein interactions, with links to the corresponding PubMed records and sequence data.
  • Identical Protein Groups
    • A collection of consolidated records describing proteins identified in annotated coding regions in GenBank and RefSeq, as well as SwissProt and PDB protein sequences. This resource allows investigators to obtain more targeted search results and quickly identify a protein of interest.
  • MedGen
    • A portal to information about medical genetics. MedGen includes term lists from multiple sources and organizes them into concept groupings and hierarchies. Links are also provided to information related to those concepts in the NIH Genetic Testing Registry (GTR)ClinVarGeneOMIMPubMed, and other sources
  • Online Mendelian Inheritance in Man (OMIM)
    • A database of  human genes and genetic disorders. NCBI maintains current content and continues to support its searching and integration with other NCBI databases.  However, OMIM now has a new home at omim.org, and users are directed to this site for full record displays.
  • Protein Clusters
    • A collection of related protein sequences (clusters), consisting of Reference Sequence proteins encoded by complete prokaryotic and organelle plasmids and genomes. The database provides easy access to annotation information, publications, domains, structures, external links, and analysis tools.
  • Protein Database
    • A database that includes protein sequence records from a variety of sources, including GenPept, RefSeq, Swiss-Prot, PIR, PRF, and PDB.
  • Protein Family Models
    • A database that includes a collection of models representing homologous proteins with a common function. It includes conserved domain architecture, hidden Markov models and BlastRules. A subset of these models are used by the Prokaryotic Genome Annotation Pipeline (PGAP) to assign names and other attributes to predicted proteins
  • Retrovirus Resources
    • A collection of resources specifically designed to support the research of retroviruses, including a genotyping tool that uses the BLAST algorithm to identify the genotype of a query sequence; an alignment tool for global alignment of multiple sequences; an HIV-1 automatic sequence annotation tool; and annotated maps of numerous retroviruses viewable in GenBank, FASTA, and graphic formats, with links to associated sequence records.
  • SARS CoV
    • A summary of data for the SARS coronavirus (CoV), including links to the most recent sequence data and publications, links to other SARS related resources, and a pre-computed alignment of genome sequences from various isolates.
  • Structure (Molecular Modeling Database)
    • Contains macromolecular 3D structures derived from the Protein Data Bank, as well as tools for their visualization and comparative analysis.
  • Taxonomy
    • Contains the names and phylogenetic lineages of more than 160,000 organisms that have molecular data in the NCBI databases. New taxa are added to the Taxonomy database as data are deposited for them.
  • Viral Genomes
    • A wide range of resources, including a brief summary of the biology of viruses, links to viral genome sequences in Entrez Genome, and information about viral Reference Sequences, a collection of reference sequences for thousands of viral genomes.
  • Virus Variation
    • An extension of the Influenza Virus Resource to other organisms, providing an interface to download sequence sets of selected viruses, analysis tools, including virus-specific BLAST pages, and genome annotation pipelines.