Database resources of the National Center for Biotechnology Information

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 published in life science journals. The Entrez system provides search and retrieval operations for most of these data from 34 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Custom implementations of the BLAST program provide sequence-based searching of many specialized datasets. New resources released in the past year include a new PubMed interface and NCBI datasets. Additional resources that were updated in the past year include PMC, Bookshelf, Genome Data Viewer, SRA, ClinVar, dbSNP, dbVar, Pathogen Detection, BLAST, Primer-BLAST, IgBLAST, iCn3D and PubChem. All of these resources can be accessed through the NCBI home page at https://www.ncbi.nlm.nih.gov.

[1]  Zhiyong Lu,et al.  Better synonyms for enriching biomedical search , 2020, J. Am. Medical Informatics Assoc..

[2]  Takatomo Fujisawa,et al.  DDBJ Database updates and computational infrastructure enhancement , 2019, Nucleic Acids Res..

[3]  Guy Cochrane,et al.  The European Nucleotide Archive in 2019 , 2019, Nucleic Acids Res..

[4]  Thomas L. Madden,et al.  Database resources of the National Center for Biotechnology Information. , 2019, Nucleic acids research.

[5]  Ryan Shean,et al.  NCBI’s Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements , 2019, Genes.

[6]  Shaohua Zhao,et al.  Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates , 2019, Antimicrobial Agents and Chemotherapy.

[7]  Jiyao Wang,et al.  iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures , 2019, Bioinform..

[8]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information , 2018, Nucleic acids research.

[9]  Evan Bolton,et al.  PubChem 2019 update: improved access to chemical data , 2018, Nucleic Acids Res..

[10]  Zhiyong Lu,et al.  Best Match: New relevance search for PubMed , 2018, PLoS biology.

[11]  Abhinav Nellore,et al.  Cloud computing for genomic data analysis and collaboration , 2018, Nature Reviews Genetics.

[12]  Guy Cochrane,et al.  The International Nucleotide Sequence Database Collaboration , 2010, Nucleic Acids Res..

[13]  Evan Bolton,et al.  Database resources of the National Center for Biotechnology Information , 2017, Nucleic Acids Res..

[14]  E. Yaschenko,et al.  Database Resources of the National Center for Biotechnology Information , 2016, Nucleic Acids Res..

[15]  Sunghwan Kim,et al.  Getting the most out of PubChem for virtual screening , 2016, Expert opinion on drug discovery.

[16]  Eric P. Nawrocki,et al.  NCBI prokaryotic genome annotation pipeline , 2016, Nucleic acids research.

[17]  Gang Fu,et al.  PubChem Substance and Compound databases , 2015, Nucleic Acids Res..

[18]  Wanli Liu,et al.  Author Name Disambiguation for PubMed , 2013, J. Assoc. Inf. Sci. Technol..

[19]  Ning Ma,et al.  IgBLAST: an immunoglobulin variable domain sequence analysis tool , 2013, Nucleic Acids Res..

[20]  Ning Ma,et al.  BLAST: a more efficient report with usability improvements , 2013, Nucleic Acids Res..

[21]  Jian Ye,et al.  Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction , 2012, BMC Bioinformatics.

[22]  Lin Li,et al.  DelPhi: a comprehensive suite for DelPhi software and associated resources , 2012, BMC biophysics.

[23]  Hyeon Joo,et al.  OPM database and PPM web server: resources for positioning of proteins in membranes , 2011, Nucleic Acids Res..

[24]  G. Cochrane,et al.  The International Nucleotide Sequence Database Collaboration , 2011, Nucleic Acids Res..

[25]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[26]  G. Schuler,et al.  Entrez: molecular biology database and retrieval system. , 1996, Methods in enzymology.