{"id":147,"date":"2022-02-20T19:22:56","date_gmt":"2022-02-20T19:22:56","guid":{"rendered":"http:\/\/localhost\/kpv\/?p=147"},"modified":"2025-02-13T12:56:07","modified_gmt":"2025-02-13T12:56:07","slug":"greaction-names","status":"publish","type":"post","link":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/greaction-names\/","title":{"rendered":"gReaction names"},"content":{"rendered":"\n<p>To enhance the accuracy and efficiency of metabolic network representation, we introduce a new entity, called <strong>gReaction<\/strong>, to serve as the edges in graph G. The classification of all reactions and enzymes reported in KEGG follows the criteria outlined below:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>If a set of reactions or enzymes utilize the same primary substrates and products and share the same reversibility properties, they are collectively classified as a single <strong>gReaction<\/strong>.<\/li>\n\n\n\n<li>If only one reaction or enzyme is present within a <strong>gReaction<\/strong> definition, it retains the exact name of the enzyme. For example, in our dataset, the enzymes <strong>3.1.3.9<\/strong> and <strong>5.1.3.3<\/strong> each correspond to a unique <strong>gReaction<\/strong>.<\/li>\n\n\n\n<li>If multiple reactions or enzymes fall under the same <strong>gReaction<\/strong> definition, the entity is named after the first enzyme in the group, followed by a \u201c+\u201d sign. For instance, the enzyme set {<strong>2.7.1.1, 2.7.1.2, 2.7.1.63, 2.7.1.147<\/strong>} is designated as <strong>2.7.1.1+<\/strong>.<\/li>\n\n\n\n<li>If a single enzyme participates in multiple reactions, the <strong>gReaction<\/strong> name consists of the enzyme name appended with \u201c_N,\u201d where <strong>N<\/strong> represents a sequential identifier. For example, the enzyme <strong>ec:1.3.1.3<\/strong> mediates <strong>eight distinct reactions<\/strong> (rn:R04823, rn:R04817, rn:R03713, rn:R02219, rn:R02841, rn:R02893, rn:R01835, rn:R02498). Consequently, the corresponding <strong>gReactions<\/strong> are assigned sequential aliases: <strong>{ec:1.3.1.3, ec:1.3.1.3_1, &#8230;, ec:1.3.1.3_6, ec:1.3.1.3_7}<\/strong>.<\/li>\n<\/ul>\n\n\n\n<figure class=\"wp-block-image size-large is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"324\" src=\"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/kegg2-1-1024x324.png\" alt=\"\" class=\"wp-image-225\" style=\"width:512px;height:162px\" srcset=\"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/kegg2-1-1024x324.png 1024w, https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/kegg2-1-300x95.png 300w, https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/kegg2-1-768x243.png 768w, https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/kegg2-1.png 1412w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><figcaption class=\"wp-element-caption\"><sub><sup><strong>Optimization of Graph Representation Using gReactions<\/strong>. D) Refined structure of graph G G, illustrating a reduction in redundant edges through the incorporation of <strong>gReactions<\/strong> as nodes. Two groups of alternative reactions collapse into a single representative node each (<strong>2.7.1.1+<\/strong>, <strong>2.7.1.1+_1<\/strong>). E) Final representation of the line graph L(G) after the complete processing pipeline.<\/sup><\/sub><\/figcaption><\/figure>\n","protected":false},"excerpt":{"rendered":"<p>To enhance the accuracy and efficiency of metabolic network representation, we introduce a new entity, called gReaction, to serve as the edges in graph G.&#8230;<\/p>\n<div class=\"more-link-wrapper\"><a class=\"more-link\" href=\"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/greaction-names\/\">Continue reading<span class=\"screen-reader-text\">gReaction names<\/span><\/a><\/div>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[2],"tags":[],"class_list":["post-147","post","type-post","status-publish","format-standard","hentry","category-how-it-works","entry"],"_links":{"self":[{"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/posts\/147","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/comments?post=147"}],"version-history":[{"count":5,"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/posts\/147\/revisions"}],"predecessor-version":[{"id":335,"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/posts\/147\/revisions\/335"}],"wp:attachment":[{"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/media?parent=147"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/categories?post=147"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/tags?post=147"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}