The 2020 Nucleic Acids Research database issue features papers from NCBI staff on GenBank, ClinVar and more. These papers are also available on PubMed. To read an article, click on the PMID number listed below.
“Database resources of the National Center for Biotechnology Information”
by Eric W Sayers, Jeff Beck, J Rodney Brister, Evan E Bolton, Kathi Canese et al. (PMID: 31602479)
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 38 distinct databases. This article provides a brief overview of the NCBI Entrez system of databases, followed by a summary of resources that were either introduced or significantly updated in the past year, including PubMed, PMC, Bookshelf, BLAST databases and more!
“GenBank”
by Eric W Sayers, Mark Cavanaugh, Karen Clark, James Ostell, Kim D Pruitt, and Ilene Karsch-Mizrachi (PMID: 31665464)
GenBank® is a comprehensive database that contains over 1.6 billion publicly available nucleotide sequences for 450,000 formally described species. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. This paper describes the recent updates to GenBank®, including a new version of Genome Workbench that supports GenBank® submissions, new submission wizards for viral genomes, enhancements to BankIt and improved handling of taxonomy for sequences from pathogens.
“CDD/SPARCLE: the conserved domain database in 2020”
by Shennan Lu, Jiyao Wang, Farideh Chitsaz, Myra K Derbyshire, Renata C Geer et al. (PMID: 31777944)
As NLM’s Conserved Domain Database (CDD) enters its 20th year of operations as a publicly available resource, CDD curation staff continues to develop hierarchical classifications of widely distributed protein domain families, and to record conserved sites associated with molecular function, so that they can be mapped onto user queries in support of hypothesis-driven biomolecular research. CDD offers both an archive of pre-computed domain annotations as well as live search services for both single protein or nucleotide queries and larger sets of protein query sequences. CDD staff has continued to characterize protein families via conserved domain architectures and has built up a significant corpus of curated domain architectures in support of naming bacterial proteins in RefSeq, available via SPARCLE, the Subfamily Protein Architecture Labeling Engine.
“ClinVar: improvements to accessing data”
by Melissa J Landrum, Shanmuga Chitipiralla, Garth R Brown, Chao Chen, Baoshan Gu et al. (PMID: 29165669)
ClinVar is a freely available, public archive of human genetic variants and interpretations of their relationships to diseases and other conditions, maintained at the National Institutes of Health (NIH). This article describes updates to the ClinVar website and E-utilities.