{"id":4663,"date":"2026-03-21T13:26:22","date_gmt":"2026-03-21T02:26:22","guid":{"rendered":"https:\/\/bornfree.life\/learn\/?page_id=4663"},"modified":"2026-03-23T15:30:30","modified_gmt":"2026-03-23T04:30:30","slug":"metabolic-pathway-overlay","status":"publish","type":"page","link":"https:\/\/bornfree.life\/learn\/metabolic-pathway-overlay\/","title":{"rendered":"Metabolic Pathway Overlay"},"content":{"rendered":"\n\n\n<div class=\"mpo-app\" data-mpo-app>\n    <header class=\"mpo-toolbar\">\n        <div class=\"mpo-toolbar-copy\">\n            <p class=\"mpo-eyebrow\">Launcher Mode<\/p>\n              <h2>Metabolic Pathway Overlay<\/h2>\n              <p class=\"mpo-subtitle\">\n                Add raw PDF reports or CSV output files generated by Born Free tools for\n                <a href=\"https:\/\/bornfree.life\/learn\/oligoscan-tool\/\" target=\"_blank\" rel=\"noopener noreferrer\">Oligoscan<\/a>,\n                <a href=\"https:\/\/bornfree.life\/learn\/mosaicdx-tool\/\" target=\"_blank\" rel=\"noopener noreferrer\">MosaicDX OAT<\/a>\n                or\n                <a href=\"https:\/\/bornfree.life\/learn\/theriome-tool\/\" target=\"_blank\" rel=\"noopener noreferrer\">Theriome Aristotle<\/a>\n                reports, then click \"Open Viewer\".\n              <\/p>\n        <\/div>\n        <div class=\"mpo-toolbar-actions\">\n            <label class=\"mpo-file-button\">\n                <input type=\"file\" accept=\".csv,text\/csv,.pdf,application\/pdf\" multiple data-mpo-file-input>\n                <span>Add Lab Files<\/span>\n            <\/label>\n            <button type=\"button\" class=\"mpo-secondary-button\" data-mpo-clear-files>Clear Files<\/button>\n            <button type=\"button\" class=\"mpo-primary-button\" data-mpo-open-viewer disabled>Open Viewer<\/button>\n        <\/div>\n    <\/header>\n\n    <div class=\"mpo-banner\" data-mpo-notice>\n        Tool overview: Files you select will be cached client-side and be used to create a diagram overlay. You can re-order the data-sources to prioritise the highlighting of matched markers, by dragging the lab tests up or down in \"Data Source Priority\".\n    <\/div>\n\n    <section class=\"mpo-file-strip\">\n        <div>\n            <strong>Selected lab files<\/strong>\n            <p class=\"mpo-stage-status\" data-mpo-stage-status>Choose one or more lab files to populate this session summary.<\/p>\n        <\/div>\n        <div class=\"mpo-file-list\" data-mpo-file-list>\n            <span class=\"mpo-chip mpo-chip-muted\">No files loaded yet<\/span>\n        <\/div>\n    <\/section>\n\n    <div class=\"mpo-layout mpo-layout-launcher\">\n        <aside class=\"mpo-sidebar\">\n            <div class=\"mpo-panel\">\n                <h3>Diagram<\/h3>\n                <ul class=\"mpo-facts\">\n                    <li>\n                        <span>Configured file<\/span>\n                        <strong data-mpo-diagram-name>Mito-ComplexMapv2.drawio<\/strong>\n                    <\/li>\n                    <li>\n                        <span>Lab sources<\/span>\n                        <strong data-mpo-source-count>0<\/strong>\n                    <\/li>\n                    <li>\n                        <span>Matched markers<\/span>\n                        <strong data-mpo-match-count>0<\/strong>\n                    <\/li>\n                <\/ul>\n            <\/div>\n\n            <div class=\"mpo-panel mpo-panel-priority\">\n                <h3>Data Source Priority<\/h3>\n                <div class=\"mpo-priority-panel\">\n                    <label class=\"mpo-toggle mpo-inferred-toggle\">\n                        <input type=\"checkbox\" data-mpo-include-inferred checked>\n                        <span>Include inferred deficiency rows<\/span>\n                    <\/label>\n                    <p class=\"mpo-empty-copy mpo-priority-copy\" data-mpo-priority-copy>Load more than one data source to choose which source wins overlay highlighting.<\/p>\n                    <div class=\"mpo-priority-list\" data-mpo-source-priority><\/div>\n                <\/div>\n            <\/div>\n\n            <div class=\"mpo-panel\">\n                <h3>Session Summary<\/h3>\n                <div class=\"mpo-session-list\" data-mpo-session-list>\n                    <p class=\"mpo-empty-copy\">Choose one or more lab files to populate this session summary.<\/p>\n                <\/div>\n            <\/div>\n        <\/aside>\n    <\/div>\n\n    <div class=\"mpo-viewer\" data-mpo-viewer hidden>\n        <div class=\"mpo-viewer-topbar\">\n            <div class=\"mpo-viewer-copy\">\n                <div class=\"mpo-viewer-title-row\">\n                    <p class=\"mpo-eyebrow\">Viewer Mode<\/p>\n                    <h3 data-mpo-diagram-name>Mito-ComplexMapv2.drawio<\/h3>\n                <\/div>\n                <div class=\"mpo-viewer-meta\">\n                    <p data-mpo-viewer-status>Preparing full-screen viewer...<\/p>\n                    <p class=\"mpo-viewer-nav-hint\">Navigation: Scroll or pinch to zoom, click and drag to pan, and click a highlighted item for details.<\/p>\n                <\/div>\n            <\/div>\n            <div class=\"mpo-viewer-actions\">\n                <div class=\"mpo-zoom-controls\" data-mpo-zoom-controls=\"viewer\">\n                    <div class=\"mpo-zoom-button-row\">\n                        <button type=\"button\" class=\"mpo-secondary-button mpo-zoom-button\" data-mpo-zoom-out=\"viewer\" aria-label=\"Zoom out\">-<\/button>\n                        <button type=\"button\" class=\"mpo-secondary-button mpo-zoom-button\" data-mpo-zoom-fit=\"viewer\">Fit<\/button>\n                        <button type=\"button\" class=\"mpo-secondary-button mpo-zoom-button\" data-mpo-zoom-reset=\"viewer\">100%<\/button>\n                        <button type=\"button\" class=\"mpo-secondary-button mpo-zoom-button\" data-mpo-zoom-in=\"viewer\" aria-label=\"Zoom in\">+<\/button>\n                        <span class=\"mpo-zoom-readout\" data-mpo-zoom-readout=\"viewer\">100%<\/span>\n                    <\/div>\n                <\/div>\n                <button type=\"button\" class=\"mpo-secondary-button mpo-close-button\" data-mpo-close-viewer aria-label=\"Close viewer\">\n                    <span class=\"mpo-close-label\">Close Viewer<\/span>\n                    <span class=\"mpo-close-icon\" aria-hidden=\"true\">&times;<\/span>\n                <\/button>\n            <\/div>\n        <\/div>\n\n        <div class=\"mpo-viewer-layout\">\n            <aside class=\"mpo-viewer-sidebar\">\n                <div class=\"mpo-panel\" id=\"mpo-viewer-details-panel\" data-mpo-viewer-details-panel>\n                    <h3>Session<\/h3>\n                    <ul class=\"mpo-facts\">\n                        <li>\n                            <span>Diagram<\/span>\n                            <strong data-mpo-diagram-name>Mito-ComplexMapv2.drawio<\/strong>\n                        <\/li>\n                        <li>\n                            <span>Lab sources<\/span>\n                            <strong data-mpo-source-count>0<\/strong>\n                        <\/li>\n                        <li>\n                            <span>Matched markers<\/span>\n                            <strong data-mpo-match-count>0<\/strong>\n                        <\/li>\n                    <\/ul>\n                <\/div>\n\n                <div class=\"mpo-panel\">\n                    <h3>Loaded Files<\/h3>\n                    <div class=\"mpo-session-list\" data-mpo-session-list>\n                        <p class=\"mpo-empty-copy\">Choose files in launcher mode, then reopen the viewer at any time.<\/p>\n                    <\/div>\n                <\/div>\n\n                <div class=\"mpo-panel mpo-panel-priority\">\n                    <h3>Data Source Priority<\/h3>\n                    <div class=\"mpo-priority-panel\">\n                        <label class=\"mpo-toggle mpo-inferred-toggle\">\n                            <input type=\"checkbox\" data-mpo-include-inferred checked>\n                            <span>Include inferred deficiency rows<\/span>\n                        <\/label>\n                        <p class=\"mpo-empty-copy mpo-priority-copy\" data-mpo-priority-copy>Load more than one data source to choose which source wins overlay highlighting.<\/p>\n                        <div class=\"mpo-priority-list\" data-mpo-source-priority><\/div>\n                    <\/div>\n                <\/div>\n\n                <div class=\"mpo-panel mpo-panel-matched\">\n                    <h3>Matched Markers<\/h3>\n                    <div class=\"mpo-match-summary\" data-mpo-match-summary>\n                        <p class=\"mpo-empty-copy\">Load one or more lab files to preview matched metabolites and cofactors here.<\/p>\n                    <\/div>\n                    <div class=\"mpo-match-list\" data-mpo-match-list><\/div>\n                <\/div>\n            <\/aside>\n\n            <div class=\"mpo-viewer-mobile-controls\" aria-label=\"Viewer zoom controls\">\n                <div class=\"mpo-zoom-controls mpo-zoom-controls-mobile\" data-mpo-zoom-controls=\"viewer-mobile\">\n                    <div class=\"mpo-zoom-button-row\">\n                        <button type=\"button\" class=\"mpo-secondary-button mpo-zoom-button\" data-mpo-zoom-out=\"viewer\" aria-label=\"Zoom out\">-<\/button>\n                        <button type=\"button\" class=\"mpo-secondary-button mpo-zoom-button\" data-mpo-zoom-fit=\"viewer\">Fit<\/button>\n                        <button type=\"button\" class=\"mpo-secondary-button mpo-zoom-button\" data-mpo-zoom-reset=\"viewer\">100%<\/button>\n                        <button type=\"button\" class=\"mpo-secondary-button mpo-zoom-button\" data-mpo-zoom-in=\"viewer\" aria-label=\"Zoom in\">+<\/button>\n                        <span class=\"mpo-zoom-readout\" data-mpo-zoom-readout=\"viewer\">100%<\/span>\n                    <\/div>\n                <\/div>\n                <button\n                    type=\"button\"\n                    class=\"mpo-secondary-button mpo-details-toggle\"\n                    data-mpo-toggle-details\n                    aria-controls=\"mpo-viewer-details-panel\"\n                    aria-expanded=\"false\"\n                >\n                    Show details\n                <\/button>\n            <\/div>\n\n            <main class=\"mpo-viewer-stage\">\n                <div class=\"mpo-viewer-shell\">\n                    <div class=\"mpo-viewer-loading\" data-mpo-viewer-loading hidden>\n                        <div class=\"mpo-viewer-loading-card\">\n                            <span class=\"mpo-viewer-loading-spinner\" aria-hidden=\"true\"><\/span>\n                            <strong>Please wait<\/strong>\n                            <p data-mpo-viewer-loading-message>Loading the full-screen viewer...<\/p>\n                        <\/div>\n                    <\/div>\n                    <div class=\"mpo-viewer-canvas\" data-mpo-viewer-canvas><\/div>\n                <\/div>\n            <\/main>\n        <\/div>\n    <\/div>\n\n    <div class=\"mpo-modal\" data-mpo-pdf-source-modal hidden>\n        <div class=\"mpo-modal-card mpo-panel\">\n            <p class=\"mpo-eyebrow\">PDF Source<\/p>\n            <h3>Select Parser<\/h3>\n            <p data-mpo-pdf-source-description>Choose which Born Free parser should handle this PDF.<\/p>\n            <div class=\"mpo-source-choice-list\" data-mpo-pdf-source-options><\/div>\n            <div class=\"mpo-modal-actions\">\n                <button type=\"button\" class=\"mpo-secondary-button\" data-mpo-pdf-source-cancel>Cancel<\/button>\n            <\/div>\n        <\/div>\n    <\/div>\n\n    <div class=\"mpo-modal\" data-mpo-warning-modal hidden>\n        <div class=\"mpo-modal-card mpo-panel mpo-warning-modal-card\" role=\"dialog\" aria-modal=\"true\" aria-label=\"Warning details\">\n            <p class=\"mpo-eyebrow\">Import Warnings<\/p>\n            <h3 data-mpo-warning-title>Warning details<\/h3>\n            <p class=\"mpo-modal-hint\" data-mpo-warning-description>Review parser warnings for this lab file.<\/p>\n            <ul class=\"mpo-warning-list\" data-mpo-warning-list><\/ul>\n            <div class=\"mpo-modal-actions\">\n                <button type=\"button\" class=\"mpo-secondary-button\" data-mpo-warning-close>Close<\/button>\n            <\/div>\n        <\/div>\n    <\/div>\n\n<\/div>\n\n<p><strong><em><br>Disclaimer:<\/em><\/strong><em><br>Names and trademarks used are used\n nominatively to identify the compatible lab report. Born Free is not affiliated with, endorsed by, or sponsored by labs. For support with official reports, contact the vendor directly; this tool is community-built and independent.&nbsp;<br><br>Information is general and not medical advice.&nbsp;Outputs\n are experimental and may contain errors. Do not use for diagnosis or \nclinical decisions; seek advice from a qualified health professional. \nThis tool is provided for research\/education to help read report PDFs. \nIt is not intended to diagnose, treat, prevent or monitor disease, and \nis not intended for clinical decision-support. If you use software for \nsuch purposes, you are responsible for complying with applicable \nregulations.<br><br>This tool is provided \u2018as is\u2019: we don\u2019t warrant \ncompleteness or accuracy and exclude all implied warranties to the \nmaximum extent permitted by law.&nbsp;<strong><br><br>Known bugs:<\/strong><br>The diagram rendering on some mobile devices is currently producing some minor text artefacts \/ glitches.<strong><br><br>Acknowledgements:<\/strong><br>Many thanks to Zack Polizzi for the original overlay concept and excellent prior work.<\/em><\/p>\n\n\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"pagelayer_contact_templates":[],"_pagelayer_content":"","footnotes":""},"class_list":["post-4663","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/bornfree.life\/learn\/wp-json\/wp\/v2\/pages\/4663","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/bornfree.life\/learn\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/bornfree.life\/learn\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/bornfree.life\/learn\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/bornfree.life\/learn\/wp-json\/wp\/v2\/comments?post=4663"}],"version-history":[{"count":5,"href":"https:\/\/bornfree.life\/learn\/wp-json\/wp\/v2\/pages\/4663\/revisions"}],"predecessor-version":[{"id":4685,"href":"https:\/\/bornfree.life\/learn\/wp-json\/wp\/v2\/pages\/4663\/revisions\/4685"}],"wp:attachment":[{"href":"https:\/\/bornfree.life\/learn\/wp-json\/wp\/v2\/media?parent=4663"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}