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{"id":7750,"date":"2022-02-24T14:36:12","date_gmt":"2022-02-24T19:36:12","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=7750"},"modified":"2022-02-24T14:36:12","modified_gmt":"2022-02-24T19:36:12","slug":"gene-ontology-refseq","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/02\/24\/gene-ontology-refseq\/","title":{"rendered":"Bacterial and archaeal genomes with GO terms in RefSeq!"},"content":{"rendered":"<p><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/refseq\/?utm_source=blog&utm_medium=referral&utm_campaign=GO-terms-RefSeq&utm_term=RefSeq&utm_content=20220224link1\">RefSeq<\/a> prokaryotic genomes and proteins are now annotated with <a href=\"http:\/\/geneontology.org\/\">Gene Ontology<\/a> (GO) terms. Over the years we have received many requests to add GO terms to the annotations we provide. We heard you!<\/p>\n<p>We are embarking on this adventure and starting to place terms from the Biological Process, Molecular Function and Cellular Component ontologies to genomes and proteins we annotate with the <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/genome\/annotation_prok\/?utm_source=blog&utm_medium=referral&utm_campaign=GO-terms-RefSeq&utm_term=PGAP&utm_content=20220224link2\">Prokaryotic Genome Annotation Pipeline<\/a> (PGAP). Because of the hierarchical nature of the Gene Ontologies, these annotations will help the comparison of gene content across genomes at variable levels of specificity and eventually allow GO term enrichment analysis. GO terms are now associated with coding sequence (CDS) features on newly-submitted genomes (See Figure 1). They will progressively appear on genomes that are already in RefSeq as these get reannotated (about once a year). We expect all RefSeq genomes to have some GO terms by the spring of 2023.<\/p>\n<p><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" data-attachment-id=\"7752\" data-permalink=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/02\/24\/gene-ontology-refseq\/go-figure-1\/\" data-orig-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/02\/GO-figure-1.png?fit=615%2C355&ssl=1\" data-orig-size=\"615,355\" 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=\"GO figure 1\" data-image-description=\"\" data-image-caption=\"\" data-medium-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/02\/GO-figure-1.png?fit=300%2C173&ssl=1\" data-large-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/02\/GO-figure-1.png?fit=615%2C355&ssl=1\" class=\"alignnone size-full wp-image-7752\" src=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/02\/GO-figure-1.png?resize=615%2C355&ssl=1\" alt=\"\" width=\"615\" height=\"355\" srcset=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/02\/GO-figure-1.png?w=615&ssl=1 615w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/02\/GO-figure-1.png?resize=300%2C173&ssl=1 300w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/02\/GO-figure-1.png?resize=150%2C87&ssl=1 150w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/02\/GO-figure-1.png?resize=270%2C156&ssl=1 270w\" sizes=\"auto, (max-width: 615px) 100vw, 615px\" \/><!--more--><\/p>\n<p><em>Figure 1: Excerpt from the RefSeq record for <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/nuccore\/NZ_CP091650.1?utm_source=blog&utm_medium=referral&utm_campaign=GO-terms-RefSeq&utm_term=NZ_CP091650.1&utm_content=20220224link3\">NZ_CP091650.1<\/a>, a Klebsiella pneumoniae genome, showing the annotation of the the katG gene, with Molecular Function GO terms <a href=\"http:\/\/amigo.geneontology.org\/amigo\/term\/GO:0004096\">GO:0004096<\/a> and <a href=\"http:\/\/amigo.geneontology.org\/amigo\/term\/GO:0004601\">GO:0004601<\/a> and Biological Process GO term <a href=\"http:\/\/amigo.geneontology.org\/amigo\/term\/GO:0006979\">GO:0006979<\/a>. In total, 41% of CDS features on this genome have at least one GO term.<\/em><\/p>\n<p>The GO terms are propagated from the <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/protfam?utm_source=blog&utm_medium=referral&utm_campaign=GO-terms-RefSeq&utm_term=Protfam&utm_content=20220224link4\">Protein Family Models<\/a> that provide the protein function (and sometimes Enzyme Commission (EC) number and gene symbols) to CDS and proteins, and are not individually assigned to each protein. The GO terms on Pfams (protein families) are derived from the <a href=\"http:\/\/current.geneontology.org\/ontology\/external2go\/pfam2go\">pfam2go mappings<\/a>, while those on <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/genome\/annotation_prok\/tigrfams\/?utm_source=blog&utm_medium=referral&utm_campaign=GO-terms-RefSeq&utm_term=TIGRFAMs&utm_content=20220224link5\">TIGRFAMs<\/a> were inherited from The Institute for Genomic Research (TIGR) and reviewed in the past 6 months, and those on NCBIFAMs and BlastRules were added manually by NCBI experts. We are working to add GO terms on more hidden Markov models (HMMs) and BlastRules as well as Conserved Domain Database (CDD) architectures, so that a larger proportion of the gene content of each genome can inherit GO terms.<\/p>\n<p>We also added GO terms to 65 million non-redundant RefSeq proteins (with the WP_ prefix) that are named after a Protein Family Model with one or more GO terms. See the KatG protein found in many Klebsiella genomes in Figure 2.<\/p>\n<p><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" data-attachment-id=\"7753\" data-permalink=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/02\/24\/gene-ontology-refseq\/go-figure-2\/\" data-orig-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/02\/GO-figure-2.png?fit=644%2C783&ssl=1\" data-orig-size=\"644,783\" 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=\"GO figure 2\" data-image-description=\"\" data-image-caption=\"\" data-medium-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/02\/GO-figure-2.png?fit=247%2C300&ssl=1\" data-large-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/02\/GO-figure-2.png?fit=644%2C783&ssl=1\" class=\"alignnone size-full wp-image-7753\" src=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/02\/GO-figure-2.png?resize=644%2C783&ssl=1\" alt=\"\" width=\"644\" height=\"783\" srcset=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/02\/GO-figure-2.png?w=644&ssl=1 644w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/02\/GO-figure-2.png?resize=247%2C300&ssl=1 247w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/02\/GO-figure-2.png?resize=123%2C150&ssl=1 123w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/02\/GO-figure-2.png?resize=222%2C270&ssl=1 222w\" sizes=\"auto, (max-width: 644px) 100vw, 644px\" \/><\/p>\n<p><em>Figure 2: Excerpt from the RefSeq record for KatG protein <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/protein\/WP_004180028.1?utm_source=blog&utm_medium=referral&utm_campaign=GO-terms-RefSeq&utm_term=WP_004180028.1&utm_content=20220224link6\">WP_004180028.1<\/a>, with Molecular Function GO terms <a href=\"http:\/\/amigo.geneontology.org\/amigo\/term\/GO:0004096\">GO:0004096<\/a> and <a href=\"http:\/\/amigo.geneontology.org\/amigo\/term\/GO:0004601\">GO:0004601<\/a> and Biological Process GO term <a href=\"http:\/\/amigo.geneontology.org\/amigo\/term\/GO:0006979\">GO:0006979<\/a> on the protein feature. These terms were derived from HMM <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/genome\/annotation_prok\/evidence\/TIGR00198\/?utm_source=blog&utm_medium=referral&utm_campaign=GO-terms-RefSeq&utm_term=TIGR00198&utm_content=20220224link7\">TIGR00198<\/a> after which the protein is named.<\/em><\/p>\n<p>We hope these new GO terms are useful to our community. As always, we welcome <a href=\"https:\/\/support.nlm.nih.gov\/support\/create-case\/\">your feedback<\/a>!<\/p>\n","protected":false},"excerpt":{"rendered":"<p>RefSeq prokaryotic genomes and proteins are now annotated with Gene Ontology (GO) terms. Over the years we have received many requests to add GO terms to the annotations we provide. We heard you! We are embarking on this adventure and starting to place terms from the Biological Process, Molecular Function and Cellular Component ontologies to … <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/02\/24\/gene-ontology-refseq\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Bacterial and archaeal genomes with GO terms in RefSeq!<\/span> <span class=\"meta-nav\">→<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_coblocks_attr":"","_coblocks_dimensions":"","_coblocks_responsive_height":"","_coblocks_accordion_ie_support":"","jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"Bacterial and archaeal genomes with GO terms in RefSeq!","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","enabled":false},"version":2}},"categories":[2248],"tags":[15779425,693060702,27739816],"table_tags":[],"class_list":["post-7750","post","type-post","status-publish","format-standard","hentry","category-whats-new","tag-pgap","tag-protein-family-model","tag-refseq"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Bacterial and archaeal genomes with GO terms in RefSeq! - NCBI Insights<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/02\/24\/gene-ontology-refseq\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Bacterial and archaeal genomes with GO terms in RefSeq! - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"RefSeq prokaryotic genomes and proteins are now annotated with Gene Ontology (GO) terms. Over the years we have received many requests to add GO terms to the annotations we provide. We heard you! 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