NCBI

Databases

Bookshelf

A collection of biomedical books that can be searched directly or from linked data in other NCBI databases. The collection includes biomedical textbooks, other scientific titles, genetic resources such as GeneReviews, and NCBI help manuals.

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), MedGen, Gene, OMIM, PubMed 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.

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.

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.

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.

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.

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), ClinVar, Gene, OMIM, PubMed, and other sources.

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.

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.

PubMed

A database of citations and abstracts for biomedical literature from MEDLINE and additional life science journals. Links are provided when full text versions of the articles are available via PubMed Central (described below) or other websites.

PubMed Central (PMC)

A digital archive of full-text biomedical and life sciences journal literature, including clinical medicine and public health.

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.

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.

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.

Downloads

FTP: ClinVar Data

This site provides full data extractions in XML and summary data in VCF format. It contains files with information about standard terms used in ClinVar, MedGen, and GTR.

FTP: SKY/M-Fish and CGH Data

This site contains SKY-CGH data in ASN.1, XML and EasySKYCGH formats. See the skycghreadme.txt file for more information.

FTP: dbGAP Open-Access Data

Open-access data generally include summaries of genotype/phenotype association studies, descriptions of the measured variables, and study documents, such as the protocol and questionnaires. Access to individual-level data, including phenotypic data tables and genotypes, requires varying levels of authorization.

Submissions

ClinVar Submissions

Guidelines and instructions for submitting assertions about the pathogenicity of human genetic variants. These submissions can include summary data about a variant (variant level/aggregate data); support for variants per case (case-level) is in development.

Database of Genotype and Phenotype (dbGaP) Data Submission Policies

Guidelines and requirements for submitting genotype and phenotype association data to dbGaP.

Genetic Testing Registry (GTR) Submissions

Guidelines and instructions for registering laboratories and submitting genetic test information including clinical and research tests for germline or somatic test targets. GTR welcomes registration of cytogenetic, biochemical, and molecular tests for Mendelian disorders, pharmacogenetic phenotypes and complex panels.

Submission Portal

A single entry point for submitters to link to and find information about all of the data submission processes at NCBI. Currently, this serves as an interface for the registration of BioProjects and BioSamples and submission of data for WGS and GTR. Future additions to this site are planned.

Tools

BLAST Microbial Genomes

Performs a BLAST search for similar sequences from selected complete eukaryotic and prokaryotic genomes.

BLAST RefSeqGene

Performs a BLAST search of the genomic sequences in the RefSeqGene/LRG set. The default display provides ready navigation to review alignments in the Graphics display.

Phenotype-Genotype Integrator (PheGenI)

Supports finding human phenotype/genotype relationships with queries by phenotype, chromosome location, gene, and SNP identifiers. Currently includes information from dbGaP, the NHGRI GWAS Catalog, and GTeX. Displays results on the genome, on sequence, or in tables for download.

PubMed Clinical Queries

A specialized PubMed search form targeted to clinicians and health services researchers. The page simplifies searching by clinical study category, finding systematic reviews and searching the medical genetics literature.

Sequence Viewer

Provides a configurable graphical display of a nucleotide or protein sequence and features that have been annotated on that sequence. In addition to use on NCBI sequence database pages, this viewer is available as an embeddable webpage component. Detailed documentation including an API Reference guide is available for developers wishing to embed the viewer in their own pages.

How To

• Find genes associated with a phenotype or disease
• Find human variations associated with a phenotype or disease (clinical association)
• Compare your sequence to the RefSeqGene/LRG standard
• View genotype frequency data for a gene, disease or short genetic variation