{"id":1691,"date":"2018-08-10T17:20:24","date_gmt":"2018-08-10T17:20:24","guid":{"rendered":"https:\/\/blog.lib.uiowa.edu\/science\/?p=1691"},"modified":"2018-08-10T17:20:24","modified_gmt":"2018-08-10T17:20:24","slug":"natural-language-searching-in-ncbi-databases","status":"publish","type":"post","link":"https:\/\/blog.lib.uiowa.edu\/science\/2018\/08\/10\/natural-language-searching-in-ncbi-databases\/","title":{"rendered":"Natural Language Searching in NCBI Databases"},"content":{"rendered":"<p>NCBI has improved its search functionality in the \u201call databases\u201d search to be compatible with <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2018\/07\/25\/ncbi-implements-new-natural-language-sequence-search\/\">natural language searching<\/a>. In the past, natural language searching for sequence data brought up too many results or sometimes zero results. Now you can search NCBI more intuitively than before and receive good results for genes, nucleotides, and assemblies! How do you get started with NCBI\u2019s new natural language searching?<\/p>\n<p>Go to the homepage of <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/\">NCBI<\/a>. The default search shows \u201cAll Databases\u201d in the drop-down box. Here you can try out some of the improved search queries:<\/p>\n<p><strong>Genes<\/strong><\/p>\n<ul>\n<li>[Species name] + [gene symbol]\n<ul>\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/search\/?term=Chelonia+mydas+SDHA\">Chelonia mydas SDHA<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-medium wp-image-1705\" src=\"https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-Chelonia-mydas-SDHA-300x182.png\" alt=\"Search result for Chelonia mydas SDHA\" width=\"300\" height=\"182\" srcset=\"https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-Chelonia-mydas-SDHA-300x182.png 300w, https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-Chelonia-mydas-SDHA-640x388.png 640w, https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-Chelonia-mydas-SDHA.png 643w\" sizes=\"(max-width: 300px) 100vw, 300px\" \/><\/p>\n<ul>\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/search\/?term=rat+B2M\">Rat B2M<\/a><\/li>\n<\/ul>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-medium wp-image-1716\" src=\"https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-rat-B2M-300x213.png\" alt=\"Search result for rat B2M\" width=\"300\" height=\"213\" srcset=\"https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-rat-B2M-300x213.png 300w, https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-rat-B2M.png 360w\" sizes=\"(max-width: 300px) 100vw, 300px\" \/><\/p>\n<p>&nbsp;<\/p>\n<p><strong>Nucleotide Sequences<\/strong><\/p>\n<ul>\n<li>[Species name] + [gene symbol] + mRNA\/transcript\/CDS\n<ul>\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/search\/?term=Salmo+salar+SUMO1+mRNA\">Salmo salar SUMO1 mRNA<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-medium wp-image-1712\" src=\"https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-Salmo-salar-SUMO1-mRNA-300x154.png\" alt=\"Search result for Salmo salar SUMO1 mRNA\" width=\"300\" height=\"154\" srcset=\"https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-Salmo-salar-SUMO1-mRNA-300x154.png 300w, https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-Salmo-salar-SUMO1-mRNA-640x328.png 640w, https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-Salmo-salar-SUMO1-mRNA.png 643w\" sizes=\"(max-width: 300px) 100vw, 300px\" \/><\/p>\n<ul>\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/search\/?term=Mus+musculus+Abcg2+transcript+\">Mus musculus Abcg2 transcript<\/a><\/li>\n<\/ul>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-medium wp-image-1711\" src=\"https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-Mus-musculus-Abcg2-transcript-300x161.png\" alt=\"Search result for Mus musculus Abcg2 transcript\" width=\"300\" height=\"161\" srcset=\"https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-Mus-musculus-Abcg2-transcript-300x161.png 300w, https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-Mus-musculus-Abcg2-transcript-640x343.png 640w, https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-Mus-musculus-Abcg2-transcript.png 708w\" sizes=\"(max-width: 300px) 100vw, 300px\" \/><\/p>\n<ul>\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/search\/?term=cow+CA2+CDS\">Cow CA2 CDS<\/a><\/li>\n<\/ul>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-medium wp-image-1718\" src=\"https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-CA2-cow-CDS-300x129.png\" alt=\"Search result for CA2 cow CDS\" width=\"300\" height=\"129\" srcset=\"https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-CA2-cow-CDS-300x129.png 300w, https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-CA2-cow-CDS.png 451w\" sizes=\"(max-width: 300px) 100vw, 300px\" \/><\/p>\n<p>&nbsp;<\/p>\n<p><strong>Genome Assemblies<\/strong><\/p>\n<ul>\n<li>[Assembly name]\n<ul>\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/search\/?term=GRCz11\">GRCz11<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-medium wp-image-1710\" src=\"https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-GRCz11-300x149.png\" alt=\"Search result for GRCz11\" width=\"300\" height=\"149\" srcset=\"https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-GRCz11-300x149.png 300w, https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-GRCz11-640x319.png 640w, https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-GRCz11.png 643w\" sizes=\"(max-width: 300px) 100vw, 300px\" \/><\/p>\n<ul>\n<li>[species name] + assembly\/genome\n<ul>\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/search\/?term=chicken+assembly\">Chicken assembly<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-medium wp-image-1707\" src=\"https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-chicken-assembly-300x153.png\" alt=\"Search result for chicken assembly\" width=\"300\" height=\"153\" srcset=\"https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-chicken-assembly-300x153.png 300w, https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-chicken-assembly-640x326.png 640w, https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-chicken-assembly.png 643w\" sizes=\"(max-width: 300px) 100vw, 300px\" \/><\/p>\n<ul>\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/search\/?term=Escherichia+coli+genome+\">Escherichia coli genome<\/a><\/li>\n<\/ul>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-medium wp-image-1709\" src=\"https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-Escherichia-coli-genome-300x153.png\" alt=\"Search result for Escherichia coli genome\" width=\"300\" height=\"153\" srcset=\"https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-Escherichia-coli-genome-300x153.png 300w, https:\/\/blog.lib.uiowa.edu\/science\/files\/2018\/08\/Search-result-for-Escherichia-coli-genome.png 619w\" sizes=\"(max-width: 300px) 100vw, 300px\" \/><\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>NCBI has improved its search functionality in the \u201call databases\u201d search to be compatible with natural language searching. In the past, natural language searching for sequence data brought up too many results or sometimes zero results. Now you can search NCBI more intuitively than before and receive good results for genes, nucleotides, and assemblies! How<a class=\"more-link\" href=\"https:\/\/blog.lib.uiowa.edu\/science\/2018\/08\/10\/natural-language-searching-in-ncbi-databases\/\">Continue reading <span class=\"screen-reader-text\">&#8220;Natural Language Searching in NCBI Databases&#8221;<\/span><\/a><\/p>\n","protected":false},"author":223,"featured_media":1722,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4,61],"tags":[70,63,69,68],"syndication":[41,37],"_links":{"self":[{"href":"https:\/\/blog.lib.uiowa.edu\/science\/wp-json\/wp\/v2\/posts\/1691"}],"collection":[{"href":"https:\/\/blog.lib.uiowa.edu\/science\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blog.lib.uiowa.edu\/science\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blog.lib.uiowa.edu\/science\/wp-json\/wp\/v2\/users\/223"}],"replies":[{"embeddable":true,"href":"https:\/\/blog.lib.uiowa.edu\/science\/wp-json\/wp\/v2\/comments?post=1691"}],"version-history":[{"count":11,"href":"https:\/\/blog.lib.uiowa.edu\/science\/wp-json\/wp\/v2\/posts\/1691\/revisions"}],"predecessor-version":[{"id":1721,"href":"https:\/\/blog.lib.uiowa.edu\/science\/wp-json\/wp\/v2\/posts\/1691\/revisions\/1721"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/blog.lib.uiowa.edu\/science\/wp-json\/wp\/v2\/media\/1722"}],"wp:attachment":[{"href":"https:\/\/blog.lib.uiowa.edu\/science\/wp-json\/wp\/v2\/media?parent=1691"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blog.lib.uiowa.edu\/science\/wp-json\/wp\/v2\/categories?post=1691"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blog.lib.uiowa.edu\/science\/wp-json\/wp\/v2\/tags?post=1691"},{"taxonomy":"syndication","embeddable":true,"href":"https:\/\/blog.lib.uiowa.edu\/science\/wp-json\/wp\/v2\/syndication?post=1691"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}