94 lines
58 KiB
HTML
94 lines
58 KiB
HTML
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/*# sourceURL=/css/ampshared.css*/</style><meta property="og:locale" content="en_US"><meta property="og:type" content="article"><meta property="og:title" content="Read About NCBI Resources in 2023 Nucleic Acids Research Database Issue - NCBI Insights"><meta property="og:description" content="The 2023 Nucleic Acids Research Database Issue features papers from NCBI staff on GenBank, Conserved Domain Database, and more. The citations are available in PubMed with full-text available in PubMed Central (PMC). To read an article, click on the PMCID number listed below. Database resources of the National Center for Biotechnology Information in 2023 PMCID: PMC9825438 NCBI … Continue reading Read About NCBI Resources in 2023 Nucleic Acids Research Database Issue →"><meta property="og:url" content="https://ncbiinsights.ncbi.nlm.nih.gov/2023/03/15/ncbi-resources-nucleic-acids-research-database-issue/"><meta property="og:site_name" content="NCBI Insights"><meta property="article:publisher" content="https://www.facebook.com/ncbi.nlm"><meta property="article:published_time" content="2023-03-15T15:46:30+00:00"><meta property="og:image" content="https://ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/Nucleic_Acids_Research_2023-1-e1678892126923.png"><meta property="og:image:width" content="1100"><meta property="og:image:height" content="575"><meta property="og:image:type" content="image/png"><meta name="author" content="NCBI Staff"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@NCBI"><meta 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<h1 class="amp-wp-title">Read About NCBI Resources in 2023 Nucleic Acids Research Database Issue</h1>
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<time datetime="2023-03-15T15:46:30+00:00">
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2 years ago </time>
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<amp-img width="1024" height="535" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/Nucleic_Acids_Research_2023-1-e1678892126923.png?fit=1024%2C535&ssl=1" class="attachment-large size-large wp-post-image amp-wp-enforced-sizes i-amphtml-layout-intrinsic i-amphtml-layout-size-defined" alt="" srcset="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/Nucleic_Acids_Research_2023-1-e1678892126923.png?w=1100&ssl=1 1100w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/Nucleic_Acids_Research_2023-1-e1678892126923.png?resize=300%2C157&ssl=1 300w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/Nucleic_Acids_Research_2023-1-e1678892126923.png?resize=1024%2C535&ssl=1 1024w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/Nucleic_Acids_Research_2023-1-e1678892126923.png?resize=150%2C78&ssl=1 150w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/Nucleic_Acids_Research_2023-1-e1678892126923.png?resize=768%2C401&ssl=1 768w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/Nucleic_Acids_Research_2023-1-e1678892126923.png?resize=270%2C141&ssl=1 270w" sizes="auto, (max-width: 1024px) 100vw, 1024px" data-hero-candidate="" layout="intrinsic" disable-inline-width="" data-hero i-amphtml-ssr i-amphtml-layout="intrinsic"><i-amphtml-sizer slot="i-amphtml-svc" class="i-amphtml-sizer"><img alt="" aria-hidden="true" class="i-amphtml-intrinsic-sizer" role="presentation" src="data:image/svg+xml;base64,PHN2ZyBoZWlnaHQ9IjUzNSIgd2lkdGg9IjEwMjQiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgdmVyc2lvbj0iMS4xIi8+"></i-amphtml-sizer><img class="i-amphtml-fill-content i-amphtml-replaced-content" decoding="async" loading="lazy" alt="" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/Nucleic_Acids_Research_2023-1-e1678892126923.png?fit=1024%2C535&ssl=1" srcset="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/Nucleic_Acids_Research_2023-1-e1678892126923.png?w=1100&ssl=1 1100w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/Nucleic_Acids_Research_2023-1-e1678892126923.png?resize=300%2C157&ssl=1 300w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/Nucleic_Acids_Research_2023-1-e1678892126923.png?resize=1024%2C535&ssl=1 1024w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/Nucleic_Acids_Research_2023-1-e1678892126923.png?resize=150%2C78&ssl=1 150w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/Nucleic_Acids_Research_2023-1-e1678892126923.png?resize=768%2C401&ssl=1 768w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/Nucleic_Acids_Research_2023-1-e1678892126923.png?resize=270%2C141&ssl=1 270w" sizes="auto, (max-width: 1024px) 100vw, 1024px"></amp-img> </figure>
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<div class="amp-wp-article-content">
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<p><span data-contrast="none">The </span><a href="https://academic.oup.com/nar/issue/51/D1"><span data-contrast="none">202</span><span data-contrast="none">3</span> <i><span data-contrast="none">Nucleic Acids Research</span></i><span data-contrast="none"> Database Issue</span></a><span data-contrast="none"> features papers from NCBI staff on GenBank, Conserved Domain Database, and more. The citations are available in PubMed with full-text available in PubMed Central (PMC). To read an article, click on the PMCID number listed below.</span><span data-ccp-props='{"201341983":0,"335559739":0,"335559740":240}'> </span></p>
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<h6>Database resources of the National Center for Biotechnology Information in 2023</h6>
|
||
<p><b><span data-contrast="none">PMCID: </span></b><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/pmc9825438/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=nucleic-acid-database-issue-20230315"><b><span data-contrast="none">PMC9825438</span></b></a><span data-ccp-props='{"201341983":0,"335559739":0,"335559740":240}'> </span></p>
|
||
<p><span data-contrast="none">NCBI provides online information resources for biology, including the GenBank® nucleic acid sequence database and the PubMed® database of citations and abstracts published in life science journals. NCBI provides search and retrieval operations for most of these data from 35 distinct databases. The E-utilities serve as the programming interface for most of these databases. New resources include the Comparative Genome Resource (CGR) and the BLAST ClusteredNR database. Resources receiving significant updates in the past year include PubMed, PMC, Bookshelf, IgBLAST, GDV, RefSeq, NCBI Virus, GenBank type assemblies, iCn3D, ClinVar, GTR, dbGaP, ALFA, ClinicalTrials.gov, Pathogen Detection, antimicrobial resistance resources, and PubChem. </span><a href="https://www.ncbi.nlm.nih.gov/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=nucleic-acid-database-issue-20230315"><span data-contrast="none">Access NCBI resources</span></a><span data-contrast="none">! </span><span data-ccp-props='{"201341983":0,"335559739":0,"335559740":240}'> </span></p>
|
||
<h6>GenBank 2023 update</h6>
|
||
<p><b><span data-contrast="none">PMCID</span></b><span data-contrast="none">: </span><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/pmc9825519/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=nucleic-acid-database-issue-20230315"><b><span data-contrast="none">PMC9825519</span></b></a><span data-ccp-props='{"201341983":0,"335559739":0,"335559740":240}'> </span></p>
|
||
<p><a href="https://www.ncbi.nlm.nih.gov/genbank/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=nucleic-acid-database-issue-20230315"><span data-contrast="none">GenBank</span></a><span data-contrast="none">® is a comprehensive, public database that contains 19.6 trillion base pairs from over 2.9 billion nucleotide sequences for 504,000 formally described species. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. Recent updates include resources for data from the SARS-CoV-2 virus, NCBI Datasets, BLAST ClusteredNR, the Submission Portal, table2asn, a Foreign Contamination Screening tool and BioSample.</span><span data-ccp-props='{"201341983":0,"335559739":0,"335559740":240}'> </span></p>
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<h6>The conserved domain database in 2023</h6>
|
||
<p><b><span data-contrast="none">PMCID: </span></b><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825596/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=nucleic-acid-database-issue-20230315"><b><span data-contrast="none">PMC9825596</span></b></a><span data-ccp-props='{"201341983":0,"335559739":0,"335559740":240}'> </span><span data-ccp-props='{"201341983":0,"335559739":0,"335559740":240}'> </span></p>
|
||
<p><span data-contrast="none">NLM’s </span><a href="https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=nucleic-acid-database-issue-20230315"><span data-contrast="none">conserved domain database (CDD)</span></a><span data-contrast="none"> is a collection of protein domain and protein family models constructed as multiple sequence alignments. Its main purpose is to provide annotation for protein and translated nucleotide sequences with the location of domain footprints and associated functional sites, and to define protein domain architecture as a basis for assigning gene product names and putative/predicted function. CDD has been available publicly for over 20 years and has grown substantially during that time. Maintaining an archive of pre-computed annotation continues to be a challenge and has slowed down the cadence of CDD releases. CDD curation staff builds hierarchical classifications of large protein domain families, adds models for novel domain families via surveillance of the protein ‘dark matter’ that currently lacks annotation, and now spends considerable effort on providing names and attribution for conserved domain architectures. </span><span data-ccp-props='{"201341983":0,"335559739":0,"335559740":240}'> </span></p>
|
||
<h6>PubChem 2023 update</h6>
|
||
<p><b><span data-contrast="none">PMCID: </span></b><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/pmc9825602/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=nucleic-acid-database-issue-20230315"><b><span data-contrast="none">PMC9825602</span></b></a><b><span data-contrast="auto"> </span></b><span data-ccp-props='{"201341983":0,"335559739":0,"335559740":240}'> </span><span data-ccp-props='{"201341983":0,"335559739":0,"335559740":240}'> </span></p>
|
||
<p><a href="https://pubchem.ncbi.nlm.nih.gov/"><span data-contrast="none">PubChem</span></a><span data-contrast="none"> is a popular chemical information resource that serves a wide range of use cases. In the past two years, a number of changes were made to PubChem. Data from more than 120 data sources was added to PubChem. Some major highlights include: the integration of Google Patents data into PubChem, which greatly expanded the coverage of the PubChem Patent data collection; the creation of the Cell Line and Taxonomy data collections, which provide quick and easy access to chemical information for a given cell line and taxon, respectively; and the update of the bioassay data model. In addition, new functionalities were added to the PubChem programmatic access protocols, PUG-REST and PUG-View, including support for target-centric data download for a given protein, gene, pathway, cell line, and taxon and the addition of the ‘standardize’ option to PUG-REST, which returns the standardized form of an input chemical structure. A significant update was also made to PubChemRDF. The present paper provides an overview of these changes.</span><span data-ccp-props='{"201341983":0,"335559739":0,"335559740":240}'> </span></p>
|
||
<h6>Stay up to date</h6>
|
||
<p><span data-contrast="none">Follow us on Twitter </span><a href="https://twitter.com/ncbi"><span data-contrast="none">@NCBI</span></a><span data-contrast="none"> and </span><a href="https://public.govdelivery.com/accounts/USNLMOCPL/subscriber/new?topic_id=USNLMOCPL_52"><span data-contrast="none">join our mailing list</span></a><span data-contrast="none"> to keep up to date with NCBI news.</span><span data-ccp-props='{"201341983":0,"335559739":0,"335559740":240}'> </span></p>
|
||
<h6>Questions?</h6>
|
||
<p><span data-contrast="auto">If you have questions or would like to provide feedback about NCBI products or tools, please reach out to us at </span><a href="mailto:info@ncbi.nlm.nih.gov"><span data-contrast="none">info@ncbi.nlm.nih.gov</span></a><span data-contrast="auto">. </span><span data-ccp-props='{"201341983":0,"335559739":0,"335559740":240}'> </span></p>
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