{"id":184,"date":"2022-02-20T21:09:04","date_gmt":"2022-02-20T21:09:04","guid":{"rendered":"http:\/\/localhost\/kpv\/?p=184"},"modified":"2025-02-14T17:29:34","modified_gmt":"2025-02-14T17:29:34","slug":"solving-forks","status":"publish","type":"post","link":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/solving-forks\/","title":{"rendered":"Solving forks"},"content":{"rendered":"\n<p>To address the challenge of representing <strong>gReactions<\/strong> with multiple substrates or products, the following rules are applied to the network edges:<\/p>\n\n\n\n<div class=\"wp-block-media-text alignwide has-media-on-the-right is-stacked-on-mobile\" style=\"grid-template-columns:auto 20%\"><div class=\"wp-block-media-text__content\">\n<ul class=\"wp-block-list\">\n<li><strong>Case 1: Multiple substrates, single product<\/strong> \u2013 A virtual intermediate compound is introduced, serving as an intermediary between the reaction\u2019s multiple substrates and its final product. In the first phase, this virtual compound is generated by connecting all substrates, and in the second phase, it links to the actual reaction product.<\/li>\n<\/ul>\n<\/div><figure class=\"wp-block-media-text__media\"><img loading=\"lazy\" decoding=\"async\" width=\"290\" height=\"191\" src=\"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/2S1P-1.png\" alt=\"\" class=\"wp-image-222 size-full\"\/><\/figure><\/div>\n\n\n\n<div class=\"wp-block-media-text alignwide has-media-on-the-right is-stacked-on-mobile\" style=\"grid-template-columns:auto 20%\"><div class=\"wp-block-media-text__content\">\n<ul class=\"wp-block-list\">\n<li><strong>Case 2: Single substrate, multiple products<\/strong> \u2013 A virtual compound is created and connected to the initial substrate, subsequently linking to all reaction products.<\/li>\n<\/ul>\n<\/div><figure class=\"wp-block-media-text__media\"><img loading=\"lazy\" decoding=\"async\" width=\"288\" height=\"191\" src=\"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/1S2P-1.png\" alt=\"\" class=\"wp-image-221 size-full\"\/><\/figure><\/div>\n\n\n\n<div class=\"wp-block-media-text alignwide has-media-on-the-right is-stacked-on-mobile\" style=\"grid-template-columns:auto 25%\"><div class=\"wp-block-media-text__content\">\n<ul class=\"wp-block-list\">\n<li><strong>Case 3: Multiple substrates and multiple products<\/strong> \u2013 Two virtual compounds are introduced: one connected to all substrates and the other to all products. These two intermediates are then linked, effectively creating an additional edge to maintain network continuity.<\/li>\n<\/ul>\n<\/div><figure class=\"wp-block-media-text__media\"><img loading=\"lazy\" decoding=\"async\" width=\"393\" height=\"191\" src=\"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/2S2P-1.png\" alt=\"\" class=\"wp-image-223 size-full\" srcset=\"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/2S2P-1.png 393w, https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/2S2P-1-300x146.png 300w\" sizes=\"auto, (max-width: 393px) 100vw, 393px\" \/><\/figure><\/div>\n\n\n\n<p>To ensure consistency, all newly generated edges retain the same name and reference as the original <strong>gReaction<\/strong>.<\/p>\n\n\n\n<p>This process, illustrated in <strong>Figure H<\/strong>, may appear redundant; however, it is essential for streamlining the conversion of the <strong>primary graph G<\/strong> into its <strong>line graph L(G)<\/strong>. Upon transformation, all redundant elements are systematically removed. Specifically, after generating L(G), the complete list of its edges is examined, and any instances where the origin and destination nodes are identical are eliminated. The refined version of <strong>L(G)<\/strong> is then reconstructed based on this optimized edge list, as demonstrated in <strong>Figures I and J<\/strong>.<\/p>\n\n\n\n<figure class=\"wp-block-image size-large is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"317\" src=\"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/kegg4-1-1024x317.png\" alt=\"\" class=\"wp-image-227\" style=\"width:768px;height:238px\" srcset=\"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/kegg4-1-1024x317.png 1024w, https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/kegg4-1-300x93.png 300w, https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/kegg4-1-768x238.png 768w, https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/kegg4-1-1536x476.png 1536w, https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/kegg4-1-2048x635.png 2048w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><figcaption class=\"wp-element-caption\"><sub><sup><strong>Resolution of Bifurcated Edges and Transformation into a Line Graph.<\/strong> H) Graph representation (G) incorporating virtual compounds (<strong>FC1, FC2, FC3<\/strong>) to resolve bifurcations. Cyan circles denote actual compounds, red circles indicate artificial nodes introduced for network restructuring, blue arrows represent real edges, and red arrows depict additional edges connecting the fake nodes. Numbers over the arrows correspond to the respective <strong>gReactions<\/strong>. I) Edge list generated after transforming <strong>G<\/strong> into its line graph <strong>L(G)<\/strong>. Red lines indicate redundant edges, which are removed due to having identical origin and destination nodes. J) Final representation of <strong>L(G)<\/strong> for the corresponding KEGG pathway segment. The reactions <strong>X, Y, and Z<\/strong> represent neighboring reactions within the KEGG map.<\/sup><\/sub><\/figcaption><\/figure>\n","protected":false},"excerpt":{"rendered":"<p>To address the challenge of representing gReactions with multiple substrates or products, the following rules are applied to the network edges: To ensure consistency, all&#8230;<\/p>\n<div class=\"more-link-wrapper\"><a class=\"more-link\" href=\"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/solving-forks\/\">Continue reading<span class=\"screen-reader-text\">Solving forks<\/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-184","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\/184","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=184"}],"version-history":[{"count":5,"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/posts\/184\/revisions"}],"predecessor-version":[{"id":340,"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/posts\/184\/revisions\/340"}],"wp:attachment":[{"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/media?parent=184"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/categories?post=184"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/tags?post=184"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}