Major Databases AMERICA

Curation of AMERICA — major databases in this region (see the Major databases hub).

Summary Table

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NAME	REGION	URL
National Center for Biotechnology Information	United States	https://www.ncbi.nlm.nih.gov/
NCI Genomic Data Commons	United States	https://portal.gdc.cancer.gov/
CGEn	Canada	https://www.cgen.ca/

National Center for Biotechnology Information (NCBI)

Database

DESCRIPTION

The U.S. National Center for Biotechnology Information is NIH’s primary bioinformatics hub: literature (PubMed), reference sequences (RefSeq, GenBank), analysis tools, and major data archives. As an INSDC partner it exchanges nucleotide data with ENA and DDBJ. SRA stores raw sequencing reads; dbGaP provides controlled access to participant-level genotype and phenotype data; GEO archives functional genomics; ClinVar aggregates variant interpretations for clinical and research use. Datasets routinely cross-link to PubMed and Gene records.

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PubMed

https://pubmed.ncbi.nlm.nih.gov/

Bibliographic index of biomedical literature with abstracts and links to full text where available; central entry point for citations tied to NCBI sequence and GEO records.

GenBank

https://www.ncbi.nlm.nih.gov/genbank/

Annotated nucleotide sequence database and INSDC exchange partner—deposits receive accessions mirrored with ENA and DDBJ.

SRA

https://www.ncbi.nlm.nih.gov/sra/

Sequence Read Archive—high-volume store for raw sequencing output (reads, run metadata) with INSDC exchange alongside ENA and DDBJ.

RefSeq

https://www.ncbi.nlm.nih.gov/refseq/

Non-redundant reference sequences (genomes, transcripts, proteins) used for annotation, variant reporting, and stable NM_/NP_ accessions in clinical and research workflows.

ClinVar

https://www.ncbi.nlm.nih.gov/clinvar/

Archive of genomic variant interpretations (pathogenicity, drug response) aggregated from submitters; integrates with dbSNP and clinical testing pipelines.

dbGaP

https://www.ncbi.nlm.nih.gov/gap/

Database of Genotypes and Phenotypes—study-level portal for controlled-access participant genotype, phenotype, and omics under NIH data-use agreements.

GEO

https://www.ncbi.nlm.nih.gov/geo/

Gene Expression Omnibus—curated submissions of array- and sequencing-based functional genomics and expression profiling, with series and sample records.

URL

https://www.ncbi.nlm.nih.gov/