Discovering Biomedical Data

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Discovering Genomics Data

The National Center for Biotechnology Information advances science and health by providing access to genomic and biomedical information. View the full list of NCBI resources here.

A list of educational NCBI resources:

NCBI hosts several bioinformatic databases as well as analytical resources. Below are a few of the more popular databases.

GenBank NCBI's annotated genetic sequence database. See information on submitting data.
Gene Expression Omnibus (GEO) NCBI's functional genomics data repository, including array- and sequenced-based MIAME-compliant data. See information on submitting data.
Ensembl Genome Browser - see training videos including Ensembl Browser Day1: https://youtu.be/_-VLdzc47bU Browser Day2: https://youtu.be/TleXtkwQyqw REST API Day1: https://youtu.be/2nijlNa1sSg REST API Day2: https://youtu.be/2PhNPDd9INI
Entrez: Cross Database Search Page.
Gene: Gene integrates information from a wide range of species. A record may include nomenclature, maps, RefSeqs, pathways, variants, phenotypes, and links to genome, phenotype, and locus-specific resources.
Gene Expression Omnibus Data Sets NCBI repository that contains curated gene expression DataSets, as well as original Series and Platform records in the Gene Expression Omnibus repository.
Gene Expression Omnibus Profiles: NCBI repository that contains individual gene expression profiles from curated DataSets.
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, viroids, phages, plasmids, and organelles.
NCBI OMIM A database of human genes and genetic disorders. OMIM does not contain GWAS data, only references to studies related to a specific phenotype or genotype. NCBI maintains current content and continues to support its searching and integration with other NCBI databases.
MEDGEN A database that organizes information related to human medical genetics, such as attributes of conditions with a genetic contribution. One can use MEDGEN to search for relationships between specific genes and medical conditions.
NCBI Nucleotide database is a collection of sequences from different sources including RefSeq, GenBank, the Third Party Annotation (TPA) database, and PDB. Gene and transcript sequence data are essential for biomedical research and discovery.
Database of Genotypes and Phenotypes (dbGAP) National Center for Biotechnology Information's (NCBI) database containing the results of studies that have investigated the interaction of genotype and phenotype. See information on submitting data.
Database of Short Genetic Variations (dbSNP) NCBI's database of single nucleotide polymorphisms (SNPs) and multiple small-scale variations that include insertions/deletions, microsatellites, and non-polymorphic variants.
Database of Genomic Structural Variation (dbVAR) NCBI's database of genomic structural variation including inversions, insertions, and translocations. Includes data from all species, clinical data, and both germline and somatic variants. See information on submitting data.

Subject Specific Data Repositories

External resources for identifying relevant repositories for specific types of data include the Registry of Research Data Repositories and the NIH Data Sharing Repositories

There are a number of data repositories designed for specific data types, such as:

Biochemistry

Sequencing

dbSNP
dbVar
Database of Genomic Variants archive (DGVa)
DNA DataBank of Japan (DDBJ)
European Nucleotide Archive (ENA)
GenBank
GenomeRNAi - See information on submitting data.
MGnify
miRBase
NCBI Sequence Read Archive (SRA)
NCBI Trace Archives
UniProt

Omics

Structural Databases

Taxonomic and Species Diversity

Biomedical Sciences

General and/or Cross-Disciplinary

Dryad Digital Repository - An International repository of data underlying peer-reviewed articles in the basic and applied sciences. See information on submitting data.
figshare- a free cloud-based service for researchers to upload their data for discovery and access
Open Science Framework
Zenodo - A free cloud-based service based on the European Organization for Nuclear Research (CERN's) data repository platform.
BioStudies
Harvard Data Verse Network