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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 Handbook

NCBI Help Manual

NCBI Education 

 

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

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.

NCBI's annotated genetic sequence database. See information on submitting data.
 
NCBI's functional genomics data repository, including array- and sequenced-based MIAME-compliant data. See information on submitting data.
 

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. It's  official home is omim.org

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.

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.
 
NCBI's database of single nucleotide polymorphisms (SNPs) and multiple small-scale variations that include insertions/deletions, microsatellites, and non-polymorphic variants.
 
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

Omics

Structural Databases

Taxonomic and Species Diversity

Biomedical Sciences

General and/or Cross-Disciplinary

Other Data Resources

  • UVA-licensed datasets- Data Sources purchased by the UVa Library
  • Selected health sciences datasets - Publicly available health and medical data sources from U.S. government and other providers
  • DataCite a registry of datasets that searchers across many disciplinary repositories
  • DataMed - Biomedical data search engine, to discover data sets across repositories. 
  • Science.gov is home to the federal governments' collection of scientific, engineering, and R&D research, including data.
  • JSTOR Data for Research includes datasets from JSTOR collections for text mining research and teaching
  • Mendeley Data - A free cloud-based service run by Elsevier. 
     
     

    PMC is now aggregating data citations, data availability statements and supplementary materials, as available, in an Associated Data box. This box will only display on articles that have one or more of these features in the article. To limit your search to records with an Associated Data box, you can use the new "Associated Data" facet on the search results page

     

 

Open Access Data

There are a number of multidisciplinary open source data archives. 

  • Awesome Public Datasets: List maintained on GitHub
  • OAISTER: Contains over 25 million records, harvest metadata from world-wide library repositories.
  • CODATA: International Council for Science: Committee on Data for Science and Technology

 

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