{"id":172,"date":"2022-02-20T20:50:10","date_gmt":"2022-02-20T20:50:10","guid":{"rendered":"http:\/\/localhost\/kpv\/?p=172"},"modified":"2025-02-14T17:23:58","modified_gmt":"2025-02-14T17:23:58","slug":"forked-edges","status":"publish","type":"post","link":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/forked-edges\/","title":{"rendered":"Forked edges"},"content":{"rendered":"\n<p>The KEGG database does not inherently support direct graph generation due to its use of bifurcated edges in certain pathway representations. To illustrate this challenge, we analyze another segment of the <a href=\"https:\/\/www.kegg.jp\/pathway\/map00010\" target=\"_blank\" rel=\"noreferrer noopener\"><em>Glycolysis\/Gluconeogenesis<\/em> pathway (KEGG map 00010)<\/a>, as depicted in <strong>Figure F<\/strong>.<\/p>\n\n\n\n<p>When a <strong>gReaction<\/strong> involves multiple substrates or products, it cannot be accurately represented using a single edge, as these interactions result in bifurcations within the network structure (<strong>Figure G<\/strong>). To address this issue and enable the construction of both the <strong>primary graph G<\/strong> and its <strong>corresponding line graph L(G)<\/strong>, we decompose these complex reactions into a sequence of multiple virtual reactions, ensuring a structured and computationally manageable representation of metabolic pathways.<\/p>\n\n\n\n<figure class=\"wp-block-image size-large is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"249\" src=\"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/kegg3-1-1024x249.png\" alt=\"\" class=\"wp-image-226\" style=\"width:512px;height:125px\" srcset=\"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/kegg3-1-1024x249.png 1024w, https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/kegg3-1-300x73.png 300w, https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/kegg3-1-768x186.png 768w, https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/kegg3-1-1536x373.png 1536w, https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/kegg3-1-2048x497.png 2048w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><figcaption class=\"wp-element-caption\"><sub><sup><strong>Representation of Forked Edges and Their Resolution Approach.<\/strong> A) Segment of the <em>Glycolysis\/Gluconeogenesis<\/em> pathway (KEGG) displaying two forked edges. B) Schematic representation of the segment, where yellow rectangles denote enzymes, and cyan circles represent compounds involved in the reactions. Arrows indicate the direction of enzymatic reactions, with red arrows highlighting the bifurcations. The reactions <strong>X, Y, and Z<\/strong> represent neighboring reactions within the KEGG pathway.<\/sup><\/sub><\/figcaption><\/figure>\n","protected":false},"excerpt":{"rendered":"<p>The KEGG database does not inherently support direct graph generation due to its use of bifurcated edges in certain pathway representations. To illustrate this challenge,&#8230;<\/p>\n<div class=\"more-link-wrapper\"><a class=\"more-link\" href=\"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/forked-edges\/\">Continue reading<span class=\"screen-reader-text\">Forked edges<\/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-172","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\/172","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=172"}],"version-history":[{"count":3,"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/posts\/172\/revisions"}],"predecessor-version":[{"id":337,"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/posts\/172\/revisions\/337"}],"wp:attachment":[{"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/media?parent=172"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/categories?post=172"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/tags?post=172"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}