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 35 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, a sequence database search and a gene orthologs page. Additional resources that were updated in the past year include PMC, Bookshelf, My Bibliography, Assembly, RefSeq, viral genomes, the prokaryotic genome annotation pipeline, Genome Workbench, dbSNP, BLAST, Primer-BLAST, IgBLAST and PubChem. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

[1]  Jian Zhang,et al.  PUG-View: programmatic access to chemical annotations integrated in PubChem , 2019, Journal of Cheminformatics.

[2]  Lon Phan,et al.  SPDI: Data Model for Variants and Applications at NCBI , 2019, bioRxiv.

[3]  Thomas M. Keane,et al.  The European Nucleotide Archive in 2018 , 2018, Nucleic Acids Res..

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

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

[6]  Osamu Ogasawara,et al.  DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data , 2018, Nucleic Acids Res..

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

[8]  G. Cochrane,et al.  The international nucleotide sequence database collaboration , 2017, Nucleic Acids Res..

[9]  Wen J. Li,et al.  RefSeq: an update on prokaryotic genome annotation and curation , 2017, Nucleic Acids Res..

[10]  Alejandro A. Schäffer,et al.  Virus Variation Resource – improved response to emergent viral outbreaks , 2016, Nucleic Acids Res..

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

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

[13]  Deanna M. Church,et al.  Assembly: a resource for assembled genomes at NCBI , 2015, Nucleic Acids Res..

[14]  Wen J. Li,et al.  Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation , 2015, Nucleic Acids Res..

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

[16]  Yiming Bao,et al.  NCBI Viral Genomes Resource , 2014, Nucleic Acids Res..

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

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

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

[20]  Ying Cheng,et al.  The European Nucleotide Archive , 2010, Nucleic Acids Res..

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

[22]  Erik L. L. Sonnhammer,et al.  Kalign – an accurate and fast multiple sequence alignment algorithm , 2005, BMC Bioinformatics.

[23]  K. Katoh,et al.  MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.

[24]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[25]  Elizabeth M. Smigielski,et al.  dbSNP: a database of single nucleotide polymorphisms , 2000, Nucleic Acids Res..

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