{"id":54,"date":"2022-02-20T14:21:44","date_gmt":"2022-02-20T14:21:44","guid":{"rendered":"http:\/\/localhost\/kpv\/?p=54"},"modified":"2025-02-12T12:40:18","modified_gmt":"2025-02-12T12:40:18","slug":"pathway-database","status":"publish","type":"post","link":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/pathway-database\/","title":{"rendered":"The pathway database"},"content":{"rendered":"\n<p>A canonical pathway KGML file typically contains three primary types of XML tags*, each serving a distinct role in the representation of metabolic pathways:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>Entry<\/strong> \u2013 Specifies entities within the pathway, such as enzymes, compounds, reactions, or maps.<\/li>\n\n\n\n<li><strong>Relation<\/strong> \u2013 Describes associations between entities, often identifying compounds that link two enzymes.<\/li>\n\n\n\n<li><strong>Reaction<\/strong> \u2013 Details enzymatic reactions, defining the substrates and products involved.<\/li>\n<\/ul>\n\n\n\n<p>The pipeline utilizes each <em>Entry<\/em> tag as an input and systematically integrates it with corresponding <em>Relation<\/em> and <em>Reaction<\/em> records. This process enables the accurate inference of relationships between enzymes, reactions, and compounds, facilitating the construction of a comprehensive network representation of the metabolic pathway.<\/p>\n\n\n\n<figure class=\"wp-block-image size-large is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"342\" src=\"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/pipeline2-3-1024x342.png\" alt=\"\" class=\"wp-image-234\" style=\"width:512px;height:171px\" srcset=\"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/pipeline2-3-1024x342.png 1024w, https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/pipeline2-3-300x100.png 300w, https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/pipeline2-3-768x256.png 768w, https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/pipeline2-3-1536x513.png 1536w, https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-content\/uploads\/2022\/02\/pipeline2-3-2048x683.png 2048w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<p>The processed information, including the inferred relationships between enzymes, reactions, and compounds, is systematically stored in a structured database. This database serves as the foundation for subsequent network analyses, enabling efficient retrieval and manipulation of metabolic pathway data for visualization, metric calculation, and articulation point detection.<\/p>\n\n\n\n<p id=\"more-information-about-kgml-tags-can-be-found-here\" style=\"font-size:10px\">* More information about KGML tags can be found <a rel=\"noreferrer noopener\" href=\"https:\/\/www.kegg.jp\/kegg\/xml\/docs\/\" data-type=\"URL\" data-id=\"https:\/\/www.kegg.jp\/kegg\/xml\/docs\/\" target=\"_blank\">here<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>A canonical pathway KGML file typically contains three primary types of XML tags*, each serving a distinct role in the representation of metabolic pathways: The&#8230;<\/p>\n<div class=\"more-link-wrapper\"><a class=\"more-link\" href=\"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/pathway-database\/\">Continue reading<span class=\"screen-reader-text\">The pathway database<\/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-54","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\/54","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=54"}],"version-history":[{"count":4,"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/posts\/54\/revisions"}],"predecessor-version":[{"id":325,"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/posts\/54\/revisions\/325"}],"wp:attachment":[{"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/media?parent=54"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/categories?post=54"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/wp-json\/wp\/v2\/tags?post=54"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}