Database resources of the National Center for Biotechnology Information

By Richa Agarwala, Tanya Barrett, J. Beck, Dennis A. Benson, Colleen J. Bollin, Evan E. Bolton, Devon Bourexis, J. R. Brister, Stephen H. Bryant, Kathi Canese and 63 more. 2017

5,948 citations recorded by the source corpus.

Abstract The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and retrieval operations for most of these data from 39 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. New resources released in the past year include PubMed Data Management, RefSeq Functional Elements, genome data download, variation services API, Magic-BLAST, QuickBLASTp, and Identical Protein Groups. Resources that were updated in the past year include the genome data viewer, a human genome resources page, Gene, virus variation, OSIRIS, and PubChem. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Subfields: Molecular Biology

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Citations in the corpus

PubChem Substance and Compound databases (2015, methodology): “Entrez is the search and retrieval system used for PubChem’s three primary databases and other major NCBI databases (6), including PubMed, Nucleotide and Protein Sequences, Protein Structures, Genome, Taxonomy, BioSystems, Gene Expression Omnibus (GEO) and many others.”
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life (2017, background): “Ignavibacteriae (29) Calditrichaeota (5) Marinimicrobia (46), UBP11 (1) Fibrobacteres (17), Gemmatimonadetes (39)”
Integrated interactions database: tissue-specific view of the human and model organism interactomes (2015, methodology): “Orthologs were downloaded from Homolo-Gene (32) build 68.”
Network-based approach to prediction and population-based validation of in silico drug repurposing (2018, methodology): “gene Entrez ID, chromosomal location, and the official gene symbols from the National Center for Biotechnology Information (NCBI) database (74).”
Applying and improving AlphaFold at CASP14 (2021, background): “We found that an extra five sequences from BLAST-NR 17 — searched with Jackhmmer and deduplicated to have an edit distance of at least 3, to give a total of 24 aligned sequences — gave the best improvement.”
The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses (2016, methodology): “Finally, human Ensembl (Cunningham et al., 2015) records are compared to this gene list via our GeneLoc’s exon-based uniﬁcation al-gorithm (Rosen et al., 2003); those not found to be equivalent to others in the list are included as novel Ensembl-based GeneCards gene entries.”