1212 lines
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1212 lines
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/* latin */
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/* latin */
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/* cyrillic */
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/* vietnamese */
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/* latin-ext */
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/* latin */
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/* vietnamese */
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/* latin-ext */
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/* latin */
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<a href="https://ncbiinsights.ncbi.nlm.nih.gov/" class="site-logo-link" rel="home" itemprop="url"></a> <h1 class="site-title"><a href="https://ncbiinsights.ncbi.nlm.nih.gov/" rel="home">NCBI Insights</a></h1>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2017/01/'> January 2017 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2016/05/'> May 2016 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2016/03/'> March 2016 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2016/02/'> February 2016 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2015/09/'> September 2015 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2015/08/'> August 2015 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2015/04/'> April 2015 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2015/03/'> March 2015 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2015/02/'> February 2015 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2014/12/'> December 2014 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2014/10/'> October 2014 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2014/08/'> August 2014 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2014/06/'> June 2014 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2014/05/'> May 2014 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2014/04/'> April 2014 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2014/03/'> March 2014 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2014/01/'> January 2014 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2013/12/'> December 2013 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2013/11/'> November 2013 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2013/10/'> October 2013 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2013/09/'> September 2013 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2013/07/'> July 2013 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2013/06/'> June 2013 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2013/05/'> May 2013 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2013/04/'> April 2013 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2013/03/'> March 2013 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2013/02/'> February 2013 </option>
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<option value='https://ncbiinsights.ncbi.nlm.nih.gov/2013/01/'> January 2013 </option>
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<article id="post-14062" class="post-14062 post type-post status-publish format-standard has-post-thumbnail hentry category-whats-new tag-pubmed-central-pmc">
|
||
<div class="post-image-link"><a rel="bookmark" href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/21/pubmed-central-updated-website/"><img width="1108" height="627" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/PMC_Website_Updates-e1729099367886.png?resize=1100%2C575&ssl=1" class="attachment-post-thumbnail size-post-thumbnail wp-post-image" alt="PubMed Central (PMC) Transitions to Updated Website" decoding="async" fetchpriority="high" data-attachment-id="14064" data-permalink="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/21/pubmed-central-updated-website/pmc_website_updates/" data-orig-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/PMC_Website_Updates-e1729099367886.png?fit=1100%2C575&ssl=1" data-orig-size="1100,575" data-comments-opened="1" data-image-meta="{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}" data-image-title="PMC_Website_Updates" data-image-description="" data-image-caption="" data-medium-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/PMC_Website_Updates-e1729099367886.png?fit=300%2C157&ssl=1" data-large-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/PMC_Website_Updates-e1729099367886.png?fit=1024%2C535&ssl=1" /></a></div><!-- .post-image-link -->
|
||
<header class="entry-header">
|
||
<h1 class="entry-title"><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/21/pubmed-central-updated-website/" rel="bookmark">PubMed Central (PMC) Transitions to Updated Website</a></h1> </header><!-- .entry-header -->
|
||
|
||
<div class="entry-content">
|
||
<h3><b><i><span data-contrast="none">The next step in the modernization of PMC</span></i></b><span data-ccp-props="{"134233117":true,"134233118":true,"201341983":0,"335559740":240}"> </span></h3>
|
||
<p><span data-contrast="auto">As </span><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/03/14/preview-pmc-improvements/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=pmc-modernization-20241021"><span data-contrast="none">previously announced</span></a><span data-contrast="auto">, NLM’s NCBI transitioned to an updated </span><a href="https://pmc.ncbi.nlm.nih.gov/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=pmc-modernization-20241021"><span data-contrast="none">PubMed Central (PMC)</span></a><span data-contrast="auto"> website, representing the next step in ongoing efforts to modernize NLM’s products and services. </span><span data-contrast="none">As part of this update, the primary URL for the PMC website has changed from ncbi.nlm.nih.gov/pmc to </span><a href="https://pmc.ncbi.nlm.nih.gov/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=pmc-modernization-20241021"><span data-contrast="none">pmc.ncbi.nlm.nih.gov</span></a><span data-contrast="none">. In addition, you’ll notice a new </span><span data-contrast="auto">look, feel, and organization of PMC article pages and the PMC Journal List. </span><span data-ccp-props="{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559740":240}"> </span></p>
|
||
<p><span data-contrast="none">The </span><span data-contrast="none">updated website</span><span data-contrast="none"> runs on cloud services to ensure the website’s long-term sustainability and reliability. It also incorporates </span><a href="https://designsystem.digital.gov/"><span data-contrast="none">U.S. Web Design System (USWDS) </span></a><span data-contrast="none">components and design principles to improve PMC’s readability and accessibility, whether </span><span data-contrast="none">you are </span><span data-contrast="none">visiting on </span><span data-contrast="none">a </span><span data-contrast="none">desktop computer, mobile device, or accessing its content using assistive technology.</span><span data-ccp-props="{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559740":240}"> </span> <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/21/pubmed-central-updated-website/#more-14062" class="more-link">Continue reading <span class="screen-reader-text">“PubMed Central (PMC) Transitions to Updated Website”</span> <span class="meta-nav">→</span></a></p>
|
||
|
||
</div><!-- .entry-content -->
|
||
|
||
<footer class="entry-footer">
|
||
<ul class="post-meta"><li class="author vcard"><a class="url fn n" href="https://ncbiinsights.ncbi.nlm.nih.gov/author/ncbiinsights/">NCBI Staff</a></li><li class="posted-on"><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/21/pubmed-central-updated-website/" rel="bookmark"><time class="entry-date published updated" datetime="2024-10-21T10:18:29-04:00">October 21, 2024</time></a></li></ul><!-- .post-metadata --> <div class="meta-wrapper">
|
||
<ul class="post-tags"><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/pubmed-central-pmc/" rel="tag">PubMed Central (PMC)</a></li></ul><!-- .post-tags --> </div><!-- .meta-wrapper -->
|
||
</footer><!-- .entry-footer -->
|
||
</article><!-- #post-## -->
|
||
|
||
|
||
<article id="post-14054" class="post-14054 post type-post status-publish format-standard has-post-thumbnail hentry category-whats-new tag-cdart tag-conserved-domains-database-cdd">
|
||
<div class="post-image-link"><a rel="bookmark" href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/17/cdart-proteins-domain-architecture/"><img width="1108" height="600" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/CDART_Blog-e1729095032693.png?resize=1100%2C550&ssl=1" class="attachment-post-thumbnail size-post-thumbnail wp-post-image" alt="CDART: Find Proteins with Similar Domain Architecture" decoding="async" data-attachment-id="14059" data-permalink="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/17/cdart-proteins-domain-architecture/cdart_blog/" data-orig-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/CDART_Blog-e1729095032693.png?fit=1100%2C550&ssl=1" data-orig-size="1100,550" data-comments-opened="1" data-image-meta="{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}" data-image-title="CDART_Blog" data-image-description="" data-image-caption="" data-medium-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/CDART_Blog-e1729095032693.png?fit=300%2C150&ssl=1" data-large-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/CDART_Blog-e1729095032693.png?fit=1024%2C512&ssl=1" /></a></div><!-- .post-image-link -->
|
||
<header class="entry-header">
|
||
<h1 class="entry-title"><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/17/cdart-proteins-domain-architecture/" rel="bookmark">CDART: Find Proteins with Similar Domain Architecture</a></h1> </header><!-- .entry-header -->
|
||
|
||
<div class="entry-content">
|
||
<p><span data-contrast="auto">Are you interested in comparing gene families or exploring the evolution of domain architecture? Try our </span><a href="https://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=cdart-proteins-20241017"><span data-contrast="none">Conserved Domain Architecture Retrieval Tool (</span><span data-contrast="none">CDART)</span></a><span data-contrast="auto"> to retrieve sets of proteins that share the same or similar domain superfamily architecture with your query. We recently updated CDART so it’s faster and more streamlined with simplified navigation and result filtering. </span></p>
|
||
<p><b><span data-contrast="auto">Check out this example:</span></b><span data-ccp-props="{}"> </span> <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/17/cdart-proteins-domain-architecture/#more-14054" class="more-link">Continue reading <span class="screen-reader-text">“CDART: Find Proteins with Similar Domain Architecture”</span> <span class="meta-nav">→</span></a></p>
|
||
|
||
</div><!-- .entry-content -->
|
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|
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<footer class="entry-footer">
|
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<ul class="post-meta"><li class="author vcard"><a class="url fn n" href="https://ncbiinsights.ncbi.nlm.nih.gov/author/ncbiinsights/">NCBI Staff</a></li><li class="posted-on"><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/17/cdart-proteins-domain-architecture/" rel="bookmark"><time class="entry-date published updated" datetime="2024-10-17T09:34:05-04:00">October 17, 2024</time></a></li></ul><!-- .post-metadata --> <div class="meta-wrapper">
|
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<ul class="post-tags"><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/cdart/" rel="tag">CDART</a></li><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/conserved-domains-database-cdd/" rel="tag">Conserved Domains Database (CDD)</a></li></ul><!-- .post-tags --> </div><!-- .meta-wrapper -->
|
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</footer><!-- .entry-footer -->
|
||
</article><!-- #post-## -->
|
||
|
||
|
||
<article id="post-14049" class="post-14049 post type-post status-publish format-standard has-post-thumbnail hentry category-whats-new tag-cloud-computing tag-sra">
|
||
<div class="post-image-link"><a rel="bookmark" href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/16/changes-sra-data-access-aws-gcp/"><img width="1108" height="627" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/SRA_AWS_GCP-e1729087575694.png?resize=1100%2C575&ssl=1" class="attachment-post-thumbnail size-post-thumbnail wp-post-image" alt="Changes to SRA Data Access on Amazon Web Services (AWS) and Google Cloud Platform (GCP)" decoding="async" data-attachment-id="14052" data-permalink="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/16/changes-sra-data-access-aws-gcp/sra_aws_gcp/" data-orig-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/SRA_AWS_GCP-e1729087575694.png?fit=1100%2C575&ssl=1" data-orig-size="1100,575" data-comments-opened="1" data-image-meta="{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}" data-image-title="SRA_AWS_GCP" data-image-description="" data-image-caption="" data-medium-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/SRA_AWS_GCP-e1729087575694.png?fit=300%2C157&ssl=1" data-large-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/SRA_AWS_GCP-e1729087575694.png?fit=1024%2C535&ssl=1" /></a></div><!-- .post-image-link -->
|
||
<header class="entry-header">
|
||
<h1 class="entry-title"><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/16/changes-sra-data-access-aws-gcp/" rel="bookmark">Changes to SRA Data Access on Amazon Web Services (AWS) and Google Cloud Platform (GCP)</a></h1> </header><!-- .entry-header -->
|
||
|
||
<div class="entry-content">
|
||
<p><span data-contrast="none">Important note! The storage tier for </span><a href="https://www.ncbi.nlm.nih.gov/sra?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=sra-data-access-20241016"><span data-contrast="none">Sequence Read Archive (SRA)</span></a><span data-contrast="none"> data available through Amazon Web Services (AWS) commercial buckets is transitioning to </span><a href="https://aws.amazon.com/s3/storage-classes/"><span data-contrast="none">Glacier Instant retrieval</span></a><span data-contrast="none"> and </span><span data-contrast="auto">Google Cloud Platform (GCP)</span><span data-contrast="none"> is transitioning to </span><a href="https://cloud.google.com/storage/docs/storage-classes"><span data-contrast="none">Coldline</span></a><span data-contrast="none">. This change is projected to be complete by the end of October 2024. To mitigate the cost impact of this change, we recommend adjusting your data access workflow to utilize the SRA Toolkit for accessing SRA data from </span><a href="https://www.ncbi.nlm.nih.gov/sra/docs/sra-aws-download/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=sra-data-access-20241016#installing-the-sra-toolkit-in-yo"><span data-contrast="none">AWS</span></a><span data-contrast="none"> or </span><a href="https://www.ncbi.nlm.nih.gov/sra/docs/SRA-Google-Cloud/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=sra-data-access-20241016#installing-the-sra-toolkit-in-yo"><span data-contrast="none">GCP</span></a><span data-contrast="none">. </span><span data-ccp-props="{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559740":240}"> </span></p>
|
||
<p><span data-contrast="none">Please note this change does not impact SRA data access from </span><a href="https://www.ncbi.nlm.nih.gov/sra/docs/sradownload?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=sra-data-access-20241016"><span data-contrast="none">NCBI servers</span></a> <span data-contrast="auto">or </span><a href="https://aws.amazon.com/opendata/open-data-sponsorship-program/"><span data-contrast="none">AWS Open Data Program</span></a><span data-contrast="none">. </span><span data-ccp-props="{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559740":240}"> </span> <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/16/changes-sra-data-access-aws-gcp/#more-14049" class="more-link">Continue reading <span class="screen-reader-text">“Changes to SRA Data Access on Amazon Web Services (AWS) and Google Cloud Platform (GCP)”</span> <span class="meta-nav">→</span></a></p>
|
||
|
||
</div><!-- .entry-content -->
|
||
|
||
<footer class="entry-footer">
|
||
<ul class="post-meta"><li class="author vcard"><a class="url fn n" href="https://ncbiinsights.ncbi.nlm.nih.gov/author/ncbiinsights/">NCBI Staff</a></li><li class="posted-on"><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/16/changes-sra-data-access-aws-gcp/" rel="bookmark"><time class="entry-date published updated" datetime="2024-10-16T10:33:50-04:00">October 16, 2024</time></a></li></ul><!-- .post-metadata --> <div class="meta-wrapper">
|
||
<ul class="post-tags"><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/cloud-computing/" rel="tag">Cloud computing</a></li><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/sra/" rel="tag">Sequence Read Archive (SRA)</a></li></ul><!-- .post-tags --> </div><!-- .meta-wrapper -->
|
||
</footer><!-- .entry-footer -->
|
||
</article><!-- #post-## -->
|
||
|
||
|
||
<article id="post-14038" class="post-14038 post type-post status-publish format-standard has-post-thumbnail hentry category-whats-new tag-antimicrobial-resistance tag-codeathon">
|
||
<div class="post-image-link"><a rel="bookmark" href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/10/successful-ncbi-niaid-codeathon-antimicrobial-resistance/"><img width="1108" height="627" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/AMR_Codeathon-6-e1728585802312.png?resize=1100%2C575&ssl=1" class="attachment-post-thumbnail size-post-thumbnail wp-post-image" alt="Successful NCBI-NIAID Codeathon Collaborating on Antimicrobial Resistance Data Analysis Projects" decoding="async" loading="lazy" data-attachment-id="14041" data-permalink="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/10/successful-ncbi-niaid-codeathon-antimicrobial-resistance/amr_codeathon-6/" data-orig-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/AMR_Codeathon-6-e1728585802312.png?fit=1100%2C575&ssl=1" data-orig-size="1100,575" data-comments-opened="1" data-image-meta="{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}" data-image-title="AMR_Codeathon (6)" data-image-description="" data-image-caption="" data-medium-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/AMR_Codeathon-6-e1728585802312.png?fit=300%2C157&ssl=1" data-large-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/AMR_Codeathon-6-e1728585802312.png?fit=1024%2C535&ssl=1" /></a></div><!-- .post-image-link -->
|
||
<header class="entry-header">
|
||
<h1 class="entry-title"><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/10/successful-ncbi-niaid-codeathon-antimicrobial-resistance/" rel="bookmark">Successful NCBI-NIAID Codeathon Collaborating on Antimicrobial Resistance Data Analysis Projects</a></h1> </header><!-- .entry-header -->
|
||
|
||
<div class="entry-content">
|
||
<p>With support from the <a href="https://www.niaid.nih.gov/">National Institute of Allergy and Infectious Diseases (NIAID)’s</a> Office of Genomics and Advanced Technologies and the <a href="https://ncbi.nlm.nih.gov/pathogens/about/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=codathon-amr-20241010">NCBI Pathogen Detection Project Team</a>, NCBI hosted a successful virtual event, <a href="https://www.nlm.nih.gov/ncbi/workshops/2024-09_AMR-Codeathon/codeathon-details.html?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=codathon-amr-20241010"><em>Resistance is Futile: A codeathon to combat antimicrobial resistance</em></a>. This codeathon took place September 23-27, 2024, and brought together experts in the field of antimicrobial resistance and those with bioinformatic, data science skills from around the world.</p>
|
||
<p>Because infections caused by antimicrobial-resistant bacteria do not always respond to routinely prescribed antibiotics, they can be difficult for healthcare providers to treat. Unfortunately, this is becoming an increasingly frequent worldwide problem. This codeathon examined the association of antimicrobial resistance (AMR) with genetic sequence adaptations, mutations in bacterial receptors and efflux pumps, and emergence of mobile genetic elements in common and difficult-to-treat bacterial pathogens. <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/10/successful-ncbi-niaid-codeathon-antimicrobial-resistance/#more-14038" class="more-link">Continue reading <span class="screen-reader-text">“Successful NCBI-NIAID Codeathon Collaborating on Antimicrobial Resistance Data Analysis Projects”</span> <span class="meta-nav">→</span></a></p>
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<ul class="post-meta"><li class="author vcard"><a class="url fn n" href="https://ncbiinsights.ncbi.nlm.nih.gov/author/ncbiinsights/">NCBI Staff</a></li><li class="posted-on"><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/10/successful-ncbi-niaid-codeathon-antimicrobial-resistance/" rel="bookmark"><time class="entry-date published updated" datetime="2024-10-10T15:32:12-04:00">October 10, 2024</time></a></li></ul><!-- .post-metadata --> <div class="meta-wrapper">
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<ul class="post-tags"><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/antimicrobial-resistance/" rel="tag">Antimicrobial resistance</a></li><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/codeathon/" rel="tag">Codeathon</a></li></ul><!-- .post-tags --> </div><!-- .meta-wrapper -->
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<article id="post-14031" class="post-14031 post type-post status-publish format-standard has-post-thumbnail hentry category-whats-new tag-api tag-ncbi-datasets">
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<div class="post-image-link"><a rel="bookmark" href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/08/new-api-key-system-coming-ncbi-datasets/"><img width="1108" height="627" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/Datasets_API-5-e1728408562805.png?resize=1100%2C575&ssl=1" class="attachment-post-thumbnail size-post-thumbnail wp-post-image" alt="New API Key System Coming Soon to NCBI Datasets" decoding="async" loading="lazy" data-attachment-id="14034" data-permalink="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/08/new-api-key-system-coming-ncbi-datasets/datasets_api-5/" data-orig-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/Datasets_API-5-e1728408562805.png?fit=1100%2C575&ssl=1" data-orig-size="1100,575" data-comments-opened="1" data-image-meta="{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}" data-image-title="Datasets_API (5)" data-image-description="" data-image-caption="" data-medium-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/Datasets_API-5-e1728408562805.png?fit=300%2C157&ssl=1" data-large-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/Datasets_API-5-e1728408562805.png?fit=1024%2C535&ssl=1" /></a></div><!-- .post-image-link -->
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<header class="entry-header">
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<h1 class="entry-title"><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/08/new-api-key-system-coming-ncbi-datasets/" rel="bookmark">New API Key System Coming Soon to NCBI Datasets</a></h1> </header><!-- .entry-header -->
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<div class="entry-content">
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<h3><i><span data-contrast="auto">Increased flexibility, efficiency, and reliability</span></i><span data-ccp-props="{}"> </span></h3>
|
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<p><span data-contrast="auto">Do you use the </span><a href="https://www.ncbi.nlm.nih.gov/datasets/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=datasets-api-key-20241008"><span data-contrast="auto">NCBI Datasets</span></a> <a href="https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=datasets-api-key-20241008"><span data-contrast="none">command-line tools</span></a><span data-contrast="auto"> or API? As of January 2025, you will have the option to use an API key to increase your rate of access. This update will provide you more flexibility and efficiency, while still maintaining robust access for everyone. Note that these changes will not affect web users.</span><span data-ccp-props="{"134233117":false,"134233118":false,"201341983":0,"335557856":16777215,"335559738":150,"335559739":0,"335559740":240}"> </span></p>
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<h5><b><span data-contrast="auto">What to expect?</span></b></h5>
|
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<p><b><span data-contrast="auto">Without an API Key</span></b><span data-contrast="auto">: You will be limited to 5 requests per second. </span><span data-ccp-props="{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559738":150,"335559739":0,"335559740":240}"> </span></p>
|
||
<p><b><span data-contrast="auto">With an API Key</span></b><span data-contrast="auto">: You will be able to make 10 requests per second.</span><span data-ccp-props="{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559738":150,"335559739":0,"335559740":240}"> </span> <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/08/new-api-key-system-coming-ncbi-datasets/#more-14031" class="more-link">Continue reading <span class="screen-reader-text">“New API Key System Coming Soon to NCBI Datasets”</span> <span class="meta-nav">→</span></a></p>
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</div><!-- .entry-content -->
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<footer class="entry-footer">
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<ul class="post-meta"><li class="author vcard"><a class="url fn n" href="https://ncbiinsights.ncbi.nlm.nih.gov/author/ncbiinsights/">NCBI Staff</a></li><li class="posted-on"><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/08/new-api-key-system-coming-ncbi-datasets/" rel="bookmark"><time class="entry-date published updated" datetime="2024-10-08T13:57:49-04:00">October 8, 2024</time></a></li></ul><!-- .post-metadata --> <div class="meta-wrapper">
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<ul class="post-tags"><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/api/" rel="tag">API</a></li><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/ncbi-datasets/" rel="tag">NCBI Datasets</a></li></ul><!-- .post-tags --> </div><!-- .meta-wrapper -->
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<article id="post-14017" class="post-14017 post type-post status-publish format-standard has-post-thumbnail hentry category-whats-new tag-ncbi-datasets tag-taxonomy">
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<div class="post-image-link"><a rel="bookmark" href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/02/ncbi-taxonomy-updates-prokaryotes/"><img width="1108" height="627" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/Proks_NCBI-Taxonomy-2-e1727879532293.png?resize=1100%2C575&ssl=1" class="attachment-post-thumbnail size-post-thumbnail wp-post-image" alt="NCBI Taxonomy Updates to Prokaryotes" decoding="async" loading="lazy" data-attachment-id="14021" data-permalink="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/02/ncbi-taxonomy-updates-prokaryotes/proks_ncbi-taxonomy-2/" data-orig-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/Proks_NCBI-Taxonomy-2-e1727879532293.png?fit=1100%2C575&ssl=1" data-orig-size="1100,575" data-comments-opened="1" data-image-meta="{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}" data-image-title="Proks_NCBI Taxonomy (2)" data-image-description="" data-image-caption="" data-medium-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/Proks_NCBI-Taxonomy-2-e1727879532293.png?fit=300%2C157&ssl=1" data-large-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/10/Proks_NCBI-Taxonomy-2-e1727879532293.png?fit=1024%2C535&ssl=1" /></a></div><!-- .post-image-link -->
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<header class="entry-header">
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<h1 class="entry-title"><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/02/ncbi-taxonomy-updates-prokaryotes/" rel="bookmark">NCBI Taxonomy Updates to Prokaryotes</a></h1> </header><!-- .entry-header -->
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|
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<div class="entry-content">
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<p><span data-contrast="auto">As </span><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/06/04/changes-ncbi-taxonomy-classifications/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=taxonomy-prokaryotes-20241002"><span data-contrast="none">previously announced</span></a><span data-contrast="none">, NCBI is continuing to improve our </span><a href="https://www.ncbi.nlm.nih.gov/taxonomy?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=taxonomy-prokaryotes-20241002"><span data-contrast="none">Taxonomy resource</span></a>.<span data-contrast="none"> </span><span data-contrast="none">The </span><a href="https://the-icsp.org/index.php/code-of-nomenclatur"><span data-contrast="none">International Code of Nomenclature of Prokaryotes (ICNP)</span></a><span data-contrast="none"> recently introduced changes to the code of nomenclature that governs naming of prokaryotes. Following these changes, </span><span data-contrast="none">we are updating the higher-level classification of prokaryotes with the introduction </span><span data-contrast="none">of rank ‘kingdom’ and other changes for this group. The changes will first appear both in our </span><a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2&utm_source=ncbi_insights&utm_medium=referral&utm_campaign=taxonomy-prokaryotes-20241002"><span data-contrast="none">legacy</span></a> <span data-contrast="none">and new </span><a href="https://www.ncbi.nlm.nih.gov/datasets/taxonomy/2/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=taxonomy-prokaryotes-20241002"><span data-contrast="none">NCBI Datasets taxonomy browsers</span></a><span data-contrast="none">, followed by data records. This update affects every prokaryotic record and may impact some pipelines and tools using lineage and/or name recognition. </span><span data-ccp-props="{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559740":240}"> </span> <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/02/ncbi-taxonomy-updates-prokaryotes/#more-14017" class="more-link">Continue reading <span class="screen-reader-text">“NCBI Taxonomy Updates to Prokaryotes”</span> <span class="meta-nav">→</span></a></p>
|
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</div><!-- .entry-content -->
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|
||
<footer class="entry-footer">
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<ul class="post-meta"><li class="author vcard"><a class="url fn n" href="https://ncbiinsights.ncbi.nlm.nih.gov/author/ncbiinsights/">NCBI Staff</a></li><li class="posted-on"><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/10/02/ncbi-taxonomy-updates-prokaryotes/" rel="bookmark"><time class="entry-date published" datetime="2024-10-02T10:59:11-04:00">October 2, 2024</time><time class="updated" datetime="2024-10-02T14:11:05-04:00">October 2, 2024</time></a></li></ul><!-- .post-metadata --> <div class="meta-wrapper">
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<ul class="post-tags"><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/ncbi-datasets/" rel="tag">NCBI Datasets</a></li><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/taxonomy/" rel="tag">NCBI Taxonomy</a></li></ul><!-- .post-tags --> </div><!-- .meta-wrapper -->
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||
</footer><!-- .entry-footer -->
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||
</article><!-- #post-## -->
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|
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<article id="post-13960" class="post-13960 post type-post status-publish format-standard has-post-thumbnail hentry category-whats-new tag-icn3d">
|
||
<div class="post-image-link"><a rel="bookmark" href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/30/ligand-protein-interactions-icn3d/"><img width="1108" height="627" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/09/icn3d_ligand-protein-1-e1727704778923.png?resize=1100%2C575&ssl=1" class="attachment-post-thumbnail size-post-thumbnail wp-post-image" alt="Viewing Ligand-Protein Interactions in iCn3D" decoding="async" loading="lazy" data-attachment-id="13992" data-permalink="https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/30/ligand-protein-interactions-icn3d/icn3d_ligand-protein-1/" data-orig-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/09/icn3d_ligand-protein-1-e1727704778923.png?fit=1100%2C575&ssl=1" data-orig-size="1100,575" data-comments-opened="1" data-image-meta="{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}" data-image-title="icn3d_ligand-protein (1)" data-image-description="" data-image-caption="" data-medium-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/09/icn3d_ligand-protein-1-e1727704778923.png?fit=300%2C157&ssl=1" data-large-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/09/icn3d_ligand-protein-1-e1727704778923.png?fit=1024%2C535&ssl=1" /></a></div><!-- .post-image-link -->
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<header class="entry-header">
|
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<h1 class="entry-title"><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/30/ligand-protein-interactions-icn3d/" rel="bookmark">Viewing Ligand-Protein Interactions in iCn3D</a></h1> </header><!-- .entry-header -->
|
||
|
||
<div class="entry-content">
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||
<p><span data-contrast="auto">Are you interested in viewing how a protein interacts with a ligand? </span><a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=icn3d-ligand-protein-20240930"><span data-contrast="none">iCn3D</span></a><span data-contrast="none">, </span><span data-contrast="auto">our </span><span data-contrast="none">3D molecular structure viewer, now offers improved displays of these interactions at an atomic level. </span><span data-ccp-props="{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559740":240}"> </span></p>
|
||
<p><b><span data-contrast="none">Check out this example:</span></b><span data-ccp-props="{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559740":240}"> </span></p>
|
||
<p><span data-contrast="none">You are now able to see the interactions of an embedded ligand (such as the drug </span><a href="https://www.ncbi.nlm.nih.gov/Structure/pdb/3GVU?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=icn3d-ligand-protein-20240930"><span data-contrast="none">Gleevec in the protein ABL2</span></a>)<span data-contrast="none"> within iCn3D. In the image below, the left panel shows Gleevec colored by atom type and the interacting ABL2 protein residues colored in magenta. The right panel displays Gleevec as a 2D structure with interacting protein residues shown as magenta rectangles. In both panels, the dashed lines represent individual interactions, color-coded by interaction type as explained in the “Color Legend.” Hovering over a dashed lines will display the interaction type and length.</span><span data-ccp-props="{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559740":240}"> </span> <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/30/ligand-protein-interactions-icn3d/#more-13960" class="more-link">Continue reading <span class="screen-reader-text">“Viewing Ligand-Protein Interactions in iCn3D”</span> <span class="meta-nav">→</span></a></p>
|
||
|
||
</div><!-- .entry-content -->
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||
<footer class="entry-footer">
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<ul class="post-meta"><li class="author vcard"><a class="url fn n" href="https://ncbiinsights.ncbi.nlm.nih.gov/author/ncbiinsights/">NCBI Staff</a></li><li class="posted-on"><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/30/ligand-protein-interactions-icn3d/" rel="bookmark"><time class="entry-date published" datetime="2024-09-30T10:43:26-04:00">September 30, 2024</time><time class="updated" datetime="2024-09-30T12:53:11-04:00">September 30, 2024</time></a></li></ul><!-- .post-metadata --> <div class="meta-wrapper">
|
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<ul class="post-tags"><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/icn3d/" rel="tag">iCn3D</a></li></ul><!-- .post-tags --> </div><!-- .meta-wrapper -->
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<article id="post-13973" class="post-13973 post type-post status-publish format-standard has-post-thumbnail hentry category-whats-new tag-genbank tag-ncbi-datasets tag-reference-genome tag-refseq tag-representative-genome">
|
||
<div class="post-image-link"><a rel="bookmark" href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/25/updated-terminology-reference-genome/"><img width="1108" height="627" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/09/Reference_Genome_blog-e1727188417870.png?resize=1100%2C575&ssl=1" class="attachment-post-thumbnail size-post-thumbnail wp-post-image" alt="Updated Genomes Terminology! “Representative Genome” is Replaced with “Reference Genome”" decoding="async" loading="lazy" data-attachment-id="13977" data-permalink="https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/25/updated-terminology-reference-genome/reference_genome_blog/" data-orig-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/09/Reference_Genome_blog-e1727188417870.png?fit=1100%2C575&ssl=1" data-orig-size="1100,575" data-comments-opened="1" data-image-meta="{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}" data-image-title="Reference_Genome_blog" data-image-description="" data-image-caption="" data-medium-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/09/Reference_Genome_blog-e1727188417870.png?fit=300%2C157&ssl=1" data-large-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/09/Reference_Genome_blog-e1727188417870.png?fit=1024%2C535&ssl=1" /></a></div><!-- .post-image-link -->
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<header class="entry-header">
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||
<h1 class="entry-title"><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/25/updated-terminology-reference-genome/" rel="bookmark">Updated Genomes Terminology! “Representative Genome” is Replaced with “Reference Genome”</a></h1> </header><!-- .entry-header -->
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<div class="entry-content">
|
||
<p><span data-contrast="none">NCBI is streamlining the terminology around our reference genomes. We currently have a small set of genomes collectively called representatives and an even smaller set called references. We have slowly converged on the term reference to refer to both sets. </span><span data-ccp-props="{"201341983":0,"335557856":16777215,"335559739":0,"335559740":240}"> </span></p>
|
||
<p><span data-contrast="none">A genome is labeled reference if it is deemed to be the best available genome for the species based on assembly, annotation metrics (when available), and, in a small number of cases, curatorial review. The set of eukaryotic reference assemblies is updated continuously as new assemblies are submitted to </span><a href="https://www.ncbi.nlm.nih.gov/genbank/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=terminology-reference-genome-20240925"><span data-contrast="none">GenBank</span></a><span data-contrast="none">. The set of prokaryotic references are recalculated three times a year. </span><span data-ccp-props="{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559740":240}"> </span></p>
|
||
<p><b><span data-contrast="none">Important Note:</span></b><span data-contrast="none"> Classification of “reference genome” is separate from inclusion in <a href="https://www.ncbi.nlm.nih.gov/refseq/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=terminology-reference-genome-20240925">RefSeq</a> – while genomes in RefSeq are preferentially used to pick the reference genome, a reference genome can also be chosen for species not included in RefSeq. </span><span data-ccp-props="{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559740":240}"> </span> <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/25/updated-terminology-reference-genome/#more-13973" class="more-link">Continue reading <span class="screen-reader-text">“Updated Genomes Terminology! “Representative Genome” is Replaced with “Reference Genome””</span> <span class="meta-nav">→</span></a></p>
|
||
|
||
</div><!-- .entry-content -->
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||
<footer class="entry-footer">
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<ul class="post-meta"><li class="author vcard"><a class="url fn n" href="https://ncbiinsights.ncbi.nlm.nih.gov/author/ncbiinsights/">NCBI Staff</a></li><li class="posted-on"><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/25/updated-terminology-reference-genome/" rel="bookmark"><time class="entry-date published" datetime="2024-09-25T10:05:14-04:00">September 25, 2024</time><time class="updated" datetime="2024-09-27T12:28:15-04:00">September 27, 2024</time></a></li></ul><!-- .post-metadata --> <div class="meta-wrapper">
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<ul class="post-tags"><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/genbank/" rel="tag">GenBank</a></li><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/ncbi-datasets/" rel="tag">NCBI Datasets</a></li><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/reference-genome/" rel="tag">Reference genome</a></li><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/refseq/" rel="tag">RefSeq</a></li><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/representative-genome/" rel="tag">Representative genome</a></li></ul><!-- .post-tags --> </div><!-- .meta-wrapper -->
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<article id="post-13909" class="post-13909 post type-post status-publish format-standard has-post-thumbnail hentry category-whats-new tag-comparative-genomics-resource-cgr tag-foreign-contamination-screen-fcs-tool tag-genbank tag-ncbi-datasets tag-refseq">
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<div class="post-image-link"><a rel="bookmark" href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/24/public-reports-fcs-tool-results/"><img width="1108" height="627" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/09/FCS_Reports_Blog-1-e1726149486303.png?resize=1100%2C575&ssl=1" class="attachment-post-thumbnail size-post-thumbnail wp-post-image" alt="Access Public Reports of Foreign Contamination Screen (FCS) Tool Results" decoding="async" loading="lazy" data-attachment-id="13911" data-permalink="https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/24/public-reports-fcs-tool-results/fcs_reports_blog-1/" data-orig-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/09/FCS_Reports_Blog-1-e1726149486303.png?fit=1100%2C575&ssl=1" data-orig-size="1100,575" data-comments-opened="1" data-image-meta="{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}" data-image-title="FCS_Reports_Blog (1)" data-image-description="" data-image-caption="" data-medium-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/09/FCS_Reports_Blog-1-e1726149486303.png?fit=300%2C157&ssl=1" data-large-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/09/FCS_Reports_Blog-1-e1726149486303.png?fit=1024%2C535&ssl=1" /></a></div><!-- .post-image-link -->
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<header class="entry-header">
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<h1 class="entry-title"><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/24/public-reports-fcs-tool-results/" rel="bookmark">Access Public Reports of Foreign Contamination Screen (FCS) Tool Results</a></h1> </header><!-- .entry-header -->
|
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<div class="entry-content">
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<p><span data-contrast="auto">Do you use genomes from NCBI and are concerned they may contain contaminant sequences? Now you can view </span><a href="https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/"><span data-contrast="none">reports</span></a><span data-contrast="auto"> generated for all prokaryotic and eukaryotic genomes with NCBI’s quality assurance tool, </span><a href="https://github.com/ncbi/fcs#readme"><span data-contrast="none">Foreign Contamination Screen (FCS)</span></a>,<span data-contrast="auto"> to better understand possible issues that may affect your studies. </span><span data-ccp-props="{}"> </span></p>
|
||
<h5><b><span data-contrast="auto">What reports are available?</span></b><span data-ccp-props="{"201341983":0,"335557856":16777215,"335559738":150,"335559739":0,"335559740":240}"> </span></h5>
|
||
<ul>
|
||
<li data-leveltext="" data-font="Symbol" data-listid="5" data-list-defn-props="{"335552541":1,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}" aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span style="font-size: 17px;">Summary reports to select better assemblies at thresholds of your choosing. </span></li>
|
||
<li data-leveltext="" data-font="Symbol" data-listid="5" data-list-defn-props="{"335552541":1,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}" aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span style="font-size: 17px;">Detailed reports to remove or mask contaminant sequences so they don’t adversely affect analyses. This is particularly useful for building k-mer databases. </span></li>
|
||
<li data-leveltext="" data-font="Symbol" data-listid="5" data-list-defn-props="{"335552541":1,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}" aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span style="font-size: 17px;">Individual assembly reports available through the FTP link located on <a href="https://www.ncbi.nlm.nih.gov/datasets/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=fcs-reports-20240924">NCBI Datasets</a> genome pages.</span></li>
|
||
<li data-leveltext="" data-font="Symbol" data-listid="5" data-list-defn-props="{"335552541":1,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}" aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span style="font-size: 17px;">Reports are available for all eukaryotic and prokaryotic <a href="https://www.ncbi.nlm.nih.gov/genbank/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=fcs-reports-20240924">GenBank</a> and <a href="https://www.ncbi.nlm.nih.gov/refseq/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=fcs-reports-20240924">RefSeq</a> assemblies, currently covering over 2.7 million assemblies. </span></li>
|
||
<li data-leveltext="" data-font="Symbol" data-listid="5" data-list-defn-props="{"335552541":1,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}" aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span style="font-size: 17px;">A <a href="https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/README_fcs_summary_and_details.txt">README</a> to understand how to interpret and use contamination reports.</span><span data-ccp-props="{"134233117":true,"201341983":0,"335557856":16777215,"335559739":0,"335559740":240}"> </span></li>
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</ul>
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<p> <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/24/public-reports-fcs-tool-results/#more-13909" class="more-link">Continue reading <span class="screen-reader-text">“Access Public Reports of Foreign Contamination Screen (FCS) Tool Results”</span> <span class="meta-nav">→</span></a></p>
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<article id="post-13949" class="post-13949 post type-post status-publish format-standard has-post-thumbnail hentry category-whats-new tag-blast tag-ncbi-datasets tag-taxonomy tag-blastn tag-prokaryotic-genome-annotation tag-refseq">
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<div class="post-image-link"><a rel="bookmark" href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/19/updated-bacterial-archaeal-reference-genome-collection-available/"><img width="1108" height="627" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/09/Prok-5-e1726757192182.png?resize=1100%2C575&ssl=1" class="attachment-post-thumbnail size-post-thumbnail wp-post-image" alt="Updated Bacterial and Archaeal Reference Genome Collection now Available!" decoding="async" loading="lazy" data-attachment-id="13954" data-permalink="https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/19/updated-bacterial-archaeal-reference-genome-collection-available/prok-5/" data-orig-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/09/Prok-5-e1726757192182.png?fit=1100%2C575&ssl=1" data-orig-size="1100,575" data-comments-opened="1" data-image-meta="{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}" data-image-title="Prok (5)" data-image-description="" data-image-caption="" data-medium-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/09/Prok-5-e1726757192182.png?fit=300%2C157&ssl=1" data-large-file="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/09/Prok-5-e1726757192182.png?fit=1024%2C535&ssl=1" /></a></div><!-- .post-image-link -->
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<h1 class="entry-title"><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/19/updated-bacterial-archaeal-reference-genome-collection-available/" rel="bookmark">Updated Bacterial and Archaeal Reference Genome Collection now Available!</a></h1> </header><!-- .entry-header -->
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<div class="entry-content">
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<p>Download the updated <a href="https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=2%2C2157&reference_only=true&utm_source=ncbi_insights&utm_medium=referral&utm_campaign=prok-ref-genomes-20240919">bacterial and archaeal reference genome collection</a>! We built this collection of 20,403 genomes by selecting the “best” genome assembly for each species among the 350,000+ prokaryotic genomes in <a href="https://www.ncbi.nlm.nih.gov/refseq/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=prok-ref-genomes-20240919">RefSeq</a> (except for E. coli for which two assemblies were selected as reference). Changes have been made to the selection criteria including upgrades for type and complete assemblies resulting in a much larger set of changes as compared to previous updates.</p>
|
||
<h5>What’s New?</h5>
|
||
<ul>
|
||
<li><span style="font-size: 17px;">2,298 species have an updated reference </span></li>
|
||
<li><span style="font-size: 17px;">1,123 species are represented in this collection for the first time</span></li>
|
||
<li><span style="font-size: 17px;">1,125 species have a better reference assembly than in the <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/04/25/updated-bacterial-archaeal-reference-genomes-collection/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=prok-ref-genomes-20240919">April 2024 set</a></span></li>
|
||
<li><span style="font-size: 17px;">50 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment </span></li>
|
||
</ul>
|
||
<p> <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/19/updated-bacterial-archaeal-reference-genome-collection-available/#more-13949" class="more-link">Continue reading <span class="screen-reader-text">“Updated Bacterial and Archaeal Reference Genome Collection now Available!”</span> <span class="meta-nav">→</span></a></p>
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<ul class="post-meta"><li class="author vcard"><a class="url fn n" href="https://ncbiinsights.ncbi.nlm.nih.gov/author/ncbiinsights/">NCBI Staff</a></li><li class="posted-on"><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/19/updated-bacterial-archaeal-reference-genome-collection-available/" rel="bookmark"><time class="entry-date published updated" datetime="2024-09-19T11:01:45-04:00">September 19, 2024</time></a></li></ul><!-- .post-metadata --> <div class="meta-wrapper">
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<ul class="post-tags"><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/blast/" rel="tag">Basic Local Alignment Search Tool (BLAST)</a></li><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/ncbi-datasets/" rel="tag">NCBI Datasets</a></li><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/taxonomy/" rel="tag">NCBI Taxonomy</a></li><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/blastn/" rel="tag">Nucleotide BLAST (blastn)</a></li><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/prokaryotic-genome-annotation/" rel="tag">Prokaryotic genome annotation</a></li><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/refseq/" rel="tag">RefSeq</a></li></ul><!-- .post-tags --> </div><!-- .meta-wrapper -->
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