{ "cells": [ { "cell_type": "markdown", "id": "6b02705f-9e8d-4a9f-a83b-a8275206f95d", "metadata": {}, "source": [ "# BDI-Viz Demo\n", "\n", "## Contents\n", "\n", "- [Problem](#Problem)\n", "- [Challenges](#Challenges)\n", "- [Prerequisites](#Prerequisites)\n", " - [Installation](#Installation)\n", " - [Dataset](#Access-to-Source-and-Target-Data)\n", "- [BDI-Viz Heatmap](#BDI-Viz-Heatmap)\n", "- [Passing to BDI-Kit](#Passing-Curated-Results-to-BDI-Kit)\n", "- [Groundtruth Lookups](#Groundtruth-Lookups)\n", "\n", "## Problem\n", "_[Fenyo Lab Use Case 1](https://docs.google.com/document/d/1bQpw9QJI30xlxyOR1OQjN8V62TGGyPAvBYetPg_FnCs/edit?tab=t.0)_\n", "\n", "In biomedical research, datasets from diverse studies often need to be integrated into a unified schema, such as the Genomic Data Commons (GDC). However, schema matching is time-consuming, error-prone, and requires expert domain knowledge, especially given the complexity and scale of biomedical datasets.\n", "\n", "## Challenges\n", "- Manual schema matching processes, commonly used by researchers, are slow and struggle to scale with large datasets. \n", "- Automatic methods often lack the precision required, leading to errors and inconsistencies that demand expert intervention. Some biomedical schemas are very similar and will be nearly impossible to infer even for state-of-the-art matching methods.\n", "\n", "## Prerequisites\n", "\n", "### Installation\n", "\n", "Before starting this demo, ensure that the [bdi-viz package](https://pypi.org/project/bdi-viz/) is installed from PyPI. You can do this by running the following command:\n", "\n", "```\n", "pip install bdi-viz\n", "```\n", "\n", "---" ] }, { "cell_type": "code", "execution_count": 1, "id": "dc14a006-0cfb-40cc-b139-33c006465931", "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true }, "scrolled": true }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/ext3/miniconda3/lib/python3.9/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", " from .autonotebook import tqdm as notebook_tqdm\n" ] }, { "data": { "application/javascript": [ "(function(root) {\n", " function now() {\n", " return new Date();\n", " }\n", "\n", " var force = true;\n", " var py_version = '3.4.3'.replace('rc', '-rc.').replace('.dev', '-dev.');\n", " var reloading = false;\n", " var Bokeh = root.Bokeh;\n", "\n", " if (typeof (root._bokeh_timeout) === \"undefined\" || force) {\n", " root._bokeh_timeout = Date.now() + 5000;\n", " root._bokeh_failed_load = false;\n", " }\n", "\n", " function run_callbacks() {\n", " try {\n", " root._bokeh_onload_callbacks.forEach(function(callback) {\n", " if (callback != null)\n", " callback();\n", " });\n", " } finally {\n", " delete root._bokeh_onload_callbacks;\n", " }\n", " console.debug(\"Bokeh: all callbacks have finished\");\n", " }\n", "\n", " function load_libs(css_urls, js_urls, js_modules, js_exports, callback) {\n", " if (css_urls == 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i = 0; i < js_modules.length; i++) {\n", " var url = js_modules[i];\n", " if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n", "\tif (!window.requirejs) {\n", "\t on_load();\n", "\t}\n", "\tcontinue;\n", " }\n", " var element = document.createElement('script');\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.src = url;\n", " element.type = \"module\";\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " document.head.appendChild(element);\n", " }\n", " for (const name in js_exports) {\n", " var url = js_exports[name];\n", " if (skip.indexOf(url) >= 0 || root[name] != null) {\n", "\tif (!window.requirejs) {\n", "\t on_load();\n", "\t}\n", "\tcontinue;\n", " }\n", " var element = document.createElement('script');\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.type = \"module\";\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " element.textContent = `\n", " import ${name} from \"${url}\"\n", " window.${name} = ${name}\n", " window._bokeh_on_load()\n", " `\n", " document.head.appendChild(element);\n", " }\n", " if (!js_urls.length && !js_modules.length) {\n", " on_load()\n", " }\n", " };\n", "\n", " function inject_raw_css(css) {\n", " const element = document.createElement(\"style\");\n", " element.appendChild(document.createTextNode(css));\n", " document.body.appendChild(element);\n", " }\n", "\n", " var js_urls = [\"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/tabulator-tables@5.5.0/dist/js/tabulator.min.js\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/luxon/build/global/luxon.min.js\"];\n", " var js_modules = [];\n", " var js_exports = {};\n", " var css_urls = [\"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/tabulator-tables@5.5.0/dist/css/tabulator_simple.min.css?v=1.4.5\"];\n", " var inline_js = [ function(Bokeh) {\n", " Bokeh.set_log_level(\"info\");\n", " },\n", "function(Bokeh) {} // ensure no trailing comma for IE\n", " ];\n", "\n", " function run_inline_js() {\n", " if ((root.Bokeh !== undefined) || (force === true)) {\n", " for (var i = 0; i < inline_js.length; i++) {\n", "\ttry {\n", " inline_js[i].call(root, root.Bokeh);\n", "\t} catch(e) {\n", "\t if (!reloading) {\n", "\t throw e;\n", "\t }\n", "\t}\n", " }\n", " // Cache old bokeh versions\n", " if (Bokeh != undefined && !reloading) {\n", "\tvar NewBokeh = root.Bokeh;\n", "\tif (Bokeh.versions === undefined) {\n", "\t Bokeh.versions = new Map();\n", "\t}\n", "\tif (NewBokeh.version !== Bokeh.version) {\n", "\t Bokeh.versions.set(NewBokeh.version, NewBokeh)\n", "\t}\n", "\troot.Bokeh = Bokeh;\n", " }} else if (Date.now() < root._bokeh_timeout) {\n", " setTimeout(run_inline_js, 100);\n", " } else if (!root._bokeh_failed_load) {\n", " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", " root._bokeh_failed_load = true;\n", " }\n", " root._bokeh_is_initializing = false\n", " }\n", "\n", " function load_or_wait() {\n", " // Implement a backoff loop that tries to ensure we do not load multiple\n", " // versions of Bokeh and its dependencies at the same time.\n", " // In recent versions we use the root._bokeh_is_initializing flag\n", " // to determine whether there is an ongoing attempt to initialize\n", " // bokeh, however for backward compatibility we also try to ensure\n", " // that we do not start loading a newer (Panel>=1.0 and Bokeh>3) version\n", " // before older versions are fully initialized.\n", " if (root._bokeh_is_initializing && Date.now() > root._bokeh_timeout) {\n", " root._bokeh_is_initializing = false;\n", " root._bokeh_onload_callbacks = undefined;\n", " console.log(\"Bokeh: BokehJS was loaded multiple times but one version failed to initialize.\");\n", " load_or_wait();\n", " } else if (root._bokeh_is_initializing || (typeof root._bokeh_is_initializing === \"undefined\" && root._bokeh_onload_callbacks !== undefined)) {\n", " setTimeout(load_or_wait, 100);\n", " } else {\n", " root._bokeh_is_initializing = true\n", " root._bokeh_onload_callbacks = []\n", " var bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n", " if (!reloading && !bokeh_loaded) {\n", "\troot.Bokeh = undefined;\n", " }\n", " load_libs(css_urls, js_urls, js_modules, js_exports, function() {\n", "\tconsole.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", "\trun_inline_js();\n", " });\n", " }\n", " }\n", " // Give older versions of the autoload script a head-start to ensure\n", " // they initialize before we start loading newer version.\n", " setTimeout(load_or_wait, 100)\n", "}(window));" ], "application/vnd.holoviews_load.v0+json": "(function(root) {\n function now() {\n return new Date();\n }\n\n var force = true;\n var py_version = '3.4.3'.replace('rc', '-rc.').replace('.dev', '-dev.');\n var reloading = true;\n var Bokeh = root.Bokeh;\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks;\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, js_modules, js_exports, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n if (js_modules == null) js_modules = [];\n if (js_exports == null) js_exports = {};\n\n root._bokeh_onload_callbacks.push(callback);\n\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls.length === 0 && js_modules.length === 0 && Object.keys(js_exports).length === 0) {\n run_callbacks();\n return null;\n }\n if (!reloading) {\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n }\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n window._bokeh_on_load = on_load\n\n function on_error() {\n console.error(\"failed to load \" + url);\n }\n\n var skip = [];\n if (window.requirejs) {\n window.requirejs.config({'packages': {}, 'paths': {'tabulator': 'https://cdn.jsdelivr.net/npm/tabulator-tables@5.5.0/dist/js/tabulator.min', 'moment': 'https://cdn.jsdelivr.net/npm/luxon/build/global/luxon.min'}, 'shim': {}});\n require([\"tabulator\"], function(Tabulator) {\n\twindow.Tabulator = Tabulator\n\ton_load()\n })\n require([\"moment\"], function(moment) {\n\twindow.moment = moment\n\ton_load()\n })\n root._bokeh_is_loading = css_urls.length + 2;\n } else {\n root._bokeh_is_loading = 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['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/tabulator-tables@5.5.0/dist/js/tabulator.min.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window.moment !== undefined) && (!(window.moment instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/luxon/build/global/luxon.min.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } var existing_scripts = []\n var scripts = document.getElementsByTagName('script')\n for (var i = 0; i < scripts.length; i++) {\n var script = scripts[i]\n if (script.src != null) {\n\texisting_scripts.push(script.src)\n }\n }\n for (var i = 0; i < js_urls.length; i++) {\n var url = js_urls[i];\n if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n for (var i = 0; i < js_modules.length; i++) {\n var url = js_modules[i];\n if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n element.type = \"module\";\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n for (const name in js_exports) {\n var url = js_exports[name];\n if (skip.indexOf(url) >= 0 || root[name] != null) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onerror = on_error;\n element.async = false;\n element.type = \"module\";\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n element.textContent = `\n import ${name} from \"${url}\"\n window.${name} = ${name}\n window._bokeh_on_load()\n `\n document.head.appendChild(element);\n }\n if (!js_urls.length && !js_modules.length) {\n on_load()\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n var js_urls = [\"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/tabulator-tables@5.5.0/dist/js/tabulator.min.js\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/luxon/build/global/luxon.min.js\"];\n var js_modules = [];\n var js_exports = {};\n var css_urls = [\"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/tabulator-tables@5.5.0/dist/css/tabulator_simple.min.css?v=1.4.5\"];\n var inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {} // ensure no trailing comma for IE\n ];\n\n function run_inline_js() {\n if ((root.Bokeh !== undefined) || (force === true)) {\n for (var i = 0; i < inline_js.length; i++) {\n\ttry {\n inline_js[i].call(root, root.Bokeh);\n\t} catch(e) {\n\t if (!reloading) {\n\t throw e;\n\t }\n\t}\n }\n // Cache old bokeh versions\n if (Bokeh != undefined && !reloading) {\n\tvar NewBokeh = root.Bokeh;\n\tif (Bokeh.versions === undefined) {\n\t Bokeh.versions = new Map();\n\t}\n\tif (NewBokeh.version !== Bokeh.version) {\n\t Bokeh.versions.set(NewBokeh.version, NewBokeh)\n\t}\n\troot.Bokeh = Bokeh;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n }\n root._bokeh_is_initializing = false\n }\n\n function load_or_wait() {\n // Implement a backoff loop that tries to ensure we do not load multiple\n // versions of Bokeh and its dependencies at the same time.\n // In recent versions we use the root._bokeh_is_initializing flag\n // to determine whether there is an ongoing attempt to initialize\n // bokeh, however for backward compatibility we also try to ensure\n // that we do not start loading a newer (Panel>=1.0 and Bokeh>3) version\n // before older versions are fully initialized.\n if (root._bokeh_is_initializing && Date.now() > root._bokeh_timeout) {\n root._bokeh_is_initializing = false;\n root._bokeh_onload_callbacks = undefined;\n console.log(\"Bokeh: BokehJS was loaded multiple times but one version failed to initialize.\");\n load_or_wait();\n } else if (root._bokeh_is_initializing || (typeof root._bokeh_is_initializing === \"undefined\" && root._bokeh_onload_callbacks !== undefined)) {\n setTimeout(load_or_wait, 100);\n } else {\n root._bokeh_is_initializing = true\n root._bokeh_onload_callbacks = []\n var bokeh_loaded = Bokeh != null && 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output.data[JS_MIME_TYPE];\n", " }\n", " output_area._hv_plot_id = id;\n", " if ((window.Bokeh !== undefined) && (id in Bokeh.index)) {\n", " window.PyViz.plot_index[id] = Bokeh.index[id];\n", " } else {\n", " window.PyViz.plot_index[id] = null;\n", " }\n", " } else if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", " var bk_div = document.createElement(\"div\");\n", " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", " var script_attrs = bk_div.children[0].attributes;\n", " for (var i = 0; i < script_attrs.length; i++) {\n", " toinsert[toinsert.length - 1].childNodes[1].setAttribute(script_attrs[i].name, script_attrs[i].value);\n", " }\n", " // store reference to server id on output_area\n", " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", " }\n", "}\n", "\n", "/**\n", " * Handle when an output is cleared or removed\n", " */\n", "function handle_clear_output(event, handle) {\n", " var id = 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'//cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-AMS_HTML'}, 'shim': {'mathjax': {'exports': 'MathJax'}}});\n", " require([\"tabulator\"], function(Tabulator) {\n", "\twindow.Tabulator = Tabulator\n", "\ton_load()\n", " })\n", " require([\"moment\"], function(moment) {\n", "\twindow.moment = moment\n", "\ton_load()\n", " })\n", " require([\"mathjax\"], function() {\n", "\ton_load()\n", " })\n", " root._bokeh_is_loading = css_urls.length + 3;\n", " } else {\n", " root._bokeh_is_loading = css_urls.length + js_urls.length + js_modules.length + Object.keys(js_exports).length;\n", " }\n", "\n", " var existing_stylesheets = []\n", " var links = document.getElementsByTagName('link')\n", " for (var i = 0; i < links.length; i++) {\n", " var link = links[i]\n", " if (link.href != null) {\n", "\texisting_stylesheets.push(link.href)\n", " }\n", " }\n", " for (var i = 0; i < css_urls.length; i++) {\n", " var url = css_urls[i];\n", " if (existing_stylesheets.indexOf(url) !== -1) {\n", "\ton_load()\n", "\tcontinue;\n", " }\n", " const element = document.createElement(\"link\");\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.rel = \"stylesheet\";\n", " element.type = \"text/css\";\n", " element.href = url;\n", " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", " document.body.appendChild(element);\n", " } if (((window.Tabulator !== undefined) && (!(window.Tabulator instanceof HTMLElement))) || window.requirejs) {\n", " var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/tabulator-tables@5.5.0/dist/js/tabulator.min.js'];\n", " for (var i = 0; i < urls.length; i++) {\n", " skip.push(urls[i])\n", " }\n", " } if (((window.moment !== undefined) && (!(window.moment instanceof HTMLElement))) || window.requirejs) {\n", " var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/luxon/build/global/luxon.min.js'];\n", " for (var i = 0; i < urls.length; i++) {\n", " skip.push(urls[i])\n", " }\n", " } if (((window.MathJax !== undefined) && (!(window.MathJax instanceof HTMLElement))) || window.requirejs) {\n", " var urls = ['https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML'];\n", " for (var i = 0; i < urls.length; i++) {\n", " skip.push(urls[i])\n", " }\n", " } var existing_scripts = []\n", " var scripts = document.getElementsByTagName('script')\n", " for (var i = 0; i < scripts.length; i++) {\n", " var script = scripts[i]\n", " if (script.src != null) {\n", "\texisting_scripts.push(script.src)\n", " }\n", " }\n", " for (var i = 0; i < js_urls.length; i++) {\n", " var url = js_urls[i];\n", " if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n", "\tif (!window.requirejs) {\n", "\t on_load();\n", "\t}\n", "\tcontinue;\n", " }\n", " var element = document.createElement('script');\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.src = url;\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " document.head.appendChild(element);\n", " }\n", " for (var i = 0; i < js_modules.length; i++) {\n", " var url = js_modules[i];\n", " if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n", "\tif (!window.requirejs) {\n", "\t on_load();\n", "\t}\n", "\tcontinue;\n", " }\n", " var element = document.createElement('script');\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.src = url;\n", " element.type = \"module\";\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " document.head.appendChild(element);\n", " }\n", " for (const name in js_exports) {\n", " var url = js_exports[name];\n", " if (skip.indexOf(url) >= 0 || root[name] != null) {\n", "\tif (!window.requirejs) {\n", "\t on_load();\n", "\t}\n", "\tcontinue;\n", " }\n", " var element = document.createElement('script');\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.type = \"module\";\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " element.textContent = `\n", " import ${name} from \"${url}\"\n", " window.${name} = ${name}\n", " window._bokeh_on_load()\n", " `\n", " document.head.appendChild(element);\n", " }\n", " if (!js_urls.length && !js_modules.length) {\n", " on_load()\n", " }\n", " };\n", "\n", " function inject_raw_css(css) {\n", " const element = document.createElement(\"style\");\n", " element.appendChild(document.createTextNode(css));\n", " document.body.appendChild(element);\n", " }\n", "\n", " var js_urls = [\"https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/tabulator-tables@5.5.0/dist/js/tabulator.min.js\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/luxon/build/global/luxon.min.js\"];\n", " var js_modules = [];\n", " var js_exports = {};\n", " var css_urls = [\"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/tabulator-tables@5.5.0/dist/css/tabulator_simple.min.css?v=1.4.5\"];\n", " var inline_js = [ function(Bokeh) {\n", " Bokeh.set_log_level(\"info\");\n", " },\n", "function(Bokeh) {} // ensure no trailing comma for IE\n", " ];\n", "\n", " function run_inline_js() {\n", " if ((root.Bokeh !== undefined) || (force === true)) {\n", " for (var i = 0; i < inline_js.length; i++) {\n", "\ttry {\n", " inline_js[i].call(root, root.Bokeh);\n", "\t} catch(e) {\n", "\t if (!reloading) {\n", "\t throw e;\n", "\t }\n", "\t}\n", " }\n", " // Cache old bokeh versions\n", " if (Bokeh != undefined && !reloading) {\n", "\tvar NewBokeh = root.Bokeh;\n", "\tif (Bokeh.versions === undefined) {\n", "\t Bokeh.versions = new Map();\n", "\t}\n", "\tif (NewBokeh.version !== Bokeh.version) {\n", "\t Bokeh.versions.set(NewBokeh.version, NewBokeh)\n", "\t}\n", "\troot.Bokeh = Bokeh;\n", " 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undefined;\n", " console.log(\"Bokeh: BokehJS was loaded multiple times but one version failed to initialize.\");\n", " load_or_wait();\n", " } else if (root._bokeh_is_initializing || (typeof root._bokeh_is_initializing === \"undefined\" && root._bokeh_onload_callbacks !== undefined)) {\n", " setTimeout(load_or_wait, 100);\n", " } else {\n", " root._bokeh_is_initializing = true\n", " root._bokeh_onload_callbacks = []\n", " var bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n", " if (!reloading && !bokeh_loaded) {\n", "\troot.Bokeh = undefined;\n", " }\n", " load_libs(css_urls, js_urls, js_modules, js_exports, function() {\n", "\tconsole.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", "\trun_inline_js();\n", " });\n", " }\n", " }\n", " // Give older versions of the autoload script a head-start to ensure\n", " // they initialize before we start loading newer version.\n", " 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element.rel = \"stylesheet\";\n", " element.type = \"text/css\";\n", " element.href = url;\n", " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", " document.body.appendChild(element);\n", " } if (((window.Tabulator !== undefined) && (!(window.Tabulator instanceof HTMLElement))) || window.requirejs) {\n", " var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/tabulator-tables@5.5.0/dist/js/tabulator.min.js'];\n", " for (var i = 0; i < urls.length; i++) {\n", " skip.push(urls[i])\n", " }\n", " } if (((window.moment !== undefined) && (!(window.moment instanceof HTMLElement))) || window.requirejs) {\n", " var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/luxon/build/global/luxon.min.js'];\n", " for (var i = 0; i < urls.length; i++) {\n", " skip.push(urls[i])\n", " }\n", " } if (((window.MathJax !== undefined) && (!(window.MathJax instanceof HTMLElement))) || window.requirejs) {\n", " var urls = 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skip.push(urls[i])\n", " }\n", " } if (((window.jsPanel !== undefined) && (!(window.jsPanel instanceof HTMLElement))) || window.requirejs) {\n", " var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/jspanel.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/dock/jspanel.dock.js'];\n", " for (var i = 0; i < urls.length; i++) {\n", " skip.push(urls[i])\n", " }\n", " } var existing_scripts = []\n", " var scripts = document.getElementsByTagName('script')\n", " for (var i = 0; i < scripts.length; i++) {\n", " var script = scripts[i]\n", " if (script.src != null) {\n", "\texisting_scripts.push(script.src)\n", " }\n", " }\n", " for (var i = 0; i < js_urls.length; i++) {\n", " var url = js_urls[i];\n", " if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n", "\tif (!window.requirejs) {\n", "\t on_load();\n", "\t}\n", "\tcontinue;\n", " }\n", " var element = document.createElement('script');\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.src = url;\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " document.head.appendChild(element);\n", " }\n", " for (var i = 0; i < js_modules.length; i++) {\n", " var url = js_modules[i];\n", " if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n", "\tif (!window.requirejs) {\n", "\t on_load();\n", "\t}\n", "\tcontinue;\n", " }\n", " var element = document.createElement('script');\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.src = url;\n", " element.type = \"module\";\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " document.head.appendChild(element);\n", " }\n", " for (const name in js_exports) {\n", " var url = js_exports[name];\n", " if (skip.indexOf(url) >= 0 || root[name] != null) {\n", "\tif (!window.requirejs) {\n", "\t on_load();\n", "\t}\n", "\tcontinue;\n", " }\n", " var element = document.createElement('script');\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.type = \"module\";\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " element.textContent = `\n", " import ${name} from \"${url}\"\n", " window.${name} = ${name}\n", " window._bokeh_on_load()\n", " `\n", " document.head.appendChild(element);\n", " }\n", " if (!js_urls.length && !js_modules.length) {\n", " on_load()\n", " }\n", " };\n", "\n", " function inject_raw_css(css) {\n", " const element = document.createElement(\"style\");\n", " element.appendChild(document.createTextNode(css));\n", " document.body.appendChild(element);\n", " }\n", "\n", " var js_urls = [\"https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/tabulator-tables@5.5.0/dist/js/tabulator.min.js\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/luxon/build/global/luxon.min.js\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/vegaplot/vega@5\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/vegaplot/vega-lite@5\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/vegaplot/vega-embed@6\", 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[\"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/tabulator-tables@5.5.0/dist/css/tabulator_simple.min.css?v=1.4.5\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/jspanel.css?v=1.4.5\"];\n", " var inline_js = [ function(Bokeh) {\n", " Bokeh.set_log_level(\"info\");\n", " },\n", "function(Bokeh) {} // ensure no trailing comma for IE\n", " ];\n", "\n", " function run_inline_js() {\n", " if ((root.Bokeh !== undefined) || (force === true)) {\n", " for (var i = 0; i < inline_js.length; i++) {\n", "\ttry {\n", " inline_js[i].call(root, root.Bokeh);\n", "\t} catch(e) {\n", "\t if (!reloading) {\n", "\t throw e;\n", "\t }\n", "\t}\n", " }\n", " // Cache old bokeh versions\n", " if (Bokeh != undefined && !reloading) {\n", "\tvar NewBokeh = root.Bokeh;\n", "\tif (Bokeh.versions === undefined) {\n", "\t Bokeh.versions = new Map();\n", "\t}\n", "\tif (NewBokeh.version !== Bokeh.version) {\n", "\t Bokeh.versions.set(NewBokeh.version, 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root._bokeh_is_initializing = false;\n", " root._bokeh_onload_callbacks = undefined;\n", " console.log(\"Bokeh: BokehJS was loaded multiple times but one version failed to initialize.\");\n", " load_or_wait();\n", " } else if (root._bokeh_is_initializing || (typeof root._bokeh_is_initializing === \"undefined\" && root._bokeh_onload_callbacks !== undefined)) {\n", " setTimeout(load_or_wait, 100);\n", " } else {\n", " root._bokeh_is_initializing = true\n", " root._bokeh_onload_callbacks = []\n", " var bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n", " if (!reloading && !bokeh_loaded) {\n", "\troot.Bokeh = undefined;\n", " }\n", " load_libs(css_urls, js_urls, js_modules, js_exports, function() {\n", "\tconsole.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", "\trun_inline_js();\n", " });\n", " }\n", " }\n", " // Give older versions of the autoload script a head-start to ensure\n", " // they initialize before we start loading newer version.\n", " setTimeout(load_or_wait, 100)\n", "}(window));" ], "application/vnd.holoviews_load.v0+json": "(function(root) {\n function now() {\n return new Date();\n }\n\n var force = true;\n var py_version = '3.4.3'.replace('rc', '-rc.').replace('.dev', '-dev.');\n var reloading = true;\n var Bokeh = root.Bokeh;\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks;\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, js_modules, js_exports, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n if (js_modules == null) js_modules = [];\n if (js_exports == null) 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'https://cdn.jsdelivr.net/npm/luxon/build/global/luxon.min', 'mathjax': '//cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-AMS_HTML', 'vega-embed': 'https://cdn.jsdelivr.net/npm/vega-embed@6/build/vega-embed.min', 'vega-lite': 'https://cdn.jsdelivr.net/npm/vega-lite@5/build/vega-lite.min', 'vega': 'https://cdn.jsdelivr.net/npm/vega@5/build/vega.min', 'jspanel': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/jspanel', 'jspanel-modal': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal', 'jspanel-tooltip': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip', 'jspanel-hint': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint', 'jspanel-layout': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout', 'jspanel-contextmenu': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu', 'jspanel-dock': 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{\n\ton_load()\n })\n require([\"jspanel-contextmenu\"], function() {\n\ton_load()\n })\n require([\"jspanel-dock\"], function() {\n\ton_load()\n })\n root._bokeh_is_loading = css_urls.length + 13;\n } else {\n root._bokeh_is_loading = css_urls.length + js_urls.length + js_modules.length + Object.keys(js_exports).length;\n }\n\n var existing_stylesheets = []\n var links = document.getElementsByTagName('link')\n for (var i = 0; i < links.length; i++) {\n var link = links[i]\n if (link.href != null) {\n\texisting_stylesheets.push(link.href)\n }\n }\n for (var i = 0; i < css_urls.length; i++) {\n var url = css_urls[i];\n if (existing_stylesheets.indexOf(url) !== -1) {\n\ton_load()\n\tcontinue;\n }\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error;\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n } if (((window.Tabulator !== undefined) && (!(window.Tabulator instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/tabulator-tables@5.5.0/dist/js/tabulator.min.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window.moment !== undefined) && (!(window.moment instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/luxon/build/global/luxon.min.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window.MathJax !== undefined) && (!(window.MathJax instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window.vega !== undefined) && (!(window.vega instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/vegaplot/vega@5'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window.vegaLite !== undefined) && (!(window.vegaLite instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/vegaplot/vega-lite@5'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window.vegaEmbed !== undefined) && (!(window.vegaEmbed instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/vegaplot/vega-embed@6'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window.jsPanel !== undefined) && (!(window.jsPanel instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/jspanel.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/dock/jspanel.dock.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } var existing_scripts = []\n var scripts = document.getElementsByTagName('script')\n for (var i = 0; i < scripts.length; i++) {\n var script = scripts[i]\n if (script.src != null) 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(var i = 0; i < urls.length; i++) {\n", " skip.push(urls[i])\n", " }\n", " } if (((window.vega !== undefined) && (!(window.vega instanceof HTMLElement))) || window.requirejs) {\n", " var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/vegaplot/vega@5'];\n", " for (var i = 0; i < urls.length; i++) {\n", " skip.push(urls[i])\n", " }\n", " } if (((window.vegaLite !== undefined) && (!(window.vegaLite instanceof HTMLElement))) || window.requirejs) {\n", " var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/vegaplot/vega-lite@5'];\n", " for (var i = 0; i < urls.length; i++) {\n", " skip.push(urls[i])\n", " }\n", " } if (((window.vegaEmbed !== undefined) && (!(window.vegaEmbed instanceof HTMLElement))) || window.requirejs) {\n", " var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/vegaplot/vega-embed@6'];\n", " for (var i = 0; i < urls.length; i++) {\n", " skip.push(urls[i])\n", " }\n", " } if (((window.JSONEditor !== undefined) && (!(window.JSONEditor instanceof HTMLElement))) || window.requirejs) {\n", " var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/jsoneditor/jsoneditor@10.0.1/dist/jsoneditor.min.js'];\n", " for (var i = 0; i < urls.length; i++) {\n", " skip.push(urls[i])\n", " }\n", " } if (((window.jsPanel !== undefined) && (!(window.jsPanel instanceof HTMLElement))) || window.requirejs) {\n", " var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/jspanel.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/dock/jspanel.dock.js'];\n", " for (var i = 0; i < urls.length; i++) {\n", " skip.push(urls[i])\n", " }\n", " } var existing_scripts = []\n", " var scripts = document.getElementsByTagName('script')\n", " for (var i = 0; i < scripts.length; i++) {\n", " var script = scripts[i]\n", " if (script.src != null) {\n", "\texisting_scripts.push(script.src)\n", " }\n", " }\n", " for (var i = 0; i < js_urls.length; i++) {\n", " var url = js_urls[i];\n", " if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n", "\tif (!window.requirejs) {\n", "\t on_load();\n", "\t}\n", "\tcontinue;\n", " }\n", " var element = document.createElement('script');\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.src = url;\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " document.head.appendChild(element);\n", " }\n", " for (var i = 0; i < js_modules.length; i++) {\n", " var url = js_modules[i];\n", " if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n", "\tif (!window.requirejs) {\n", "\t on_load();\n", "\t}\n", "\tcontinue;\n", " }\n", " var element = document.createElement('script');\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.src = url;\n", " element.type = \"module\";\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " document.head.appendChild(element);\n", " }\n", " for (const name in js_exports) {\n", " var url = js_exports[name];\n", " if (skip.indexOf(url) >= 0 || root[name] != null) {\n", "\tif (!window.requirejs) {\n", "\t on_load();\n", "\t}\n", "\tcontinue;\n", " }\n", " var element = document.createElement('script');\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.type = \"module\";\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " element.textContent = `\n", " import ${name} from \"${url}\"\n", " window.${name} = ${name}\n", " window._bokeh_on_load()\n", " `\n", " document.head.appendChild(element);\n", " }\n", " if (!js_urls.length && !js_modules.length) {\n", " on_load()\n", " }\n", " };\n", "\n", " function inject_raw_css(css) {\n", " const element = document.createElement(\"style\");\n", " element.appendChild(document.createTextNode(css));\n", " document.body.appendChild(element);\n", " }\n", "\n", " var js_urls = [\"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/jsoneditor/jsoneditor@10.0.1/dist/jsoneditor.min.js\", \"https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/tabulator-tables@5.5.0/dist/js/tabulator.min.js\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/luxon/build/global/luxon.min.js\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/vegaplot/vega@5\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/vegaplot/vega-lite@5\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/vegaplot/vega-embed@6\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/jspanel.js\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal.js\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip.js\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint.js\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout.js\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu.js\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/dock/jspanel.dock.js\"];\n", " var js_modules = [];\n", " var js_exports = {};\n", " var css_urls = [\"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/jsoneditor/jsoneditor@10.0.1/dist/jsoneditor.min.css?v=1.4.5\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/tabulator-tables@5.5.0/dist/css/tabulator_simple.min.css?v=1.4.5\", \"https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/jspanel.css?v=1.4.5\"];\n", " var inline_js = [ function(Bokeh) {\n", " Bokeh.set_log_level(\"info\");\n", " },\n", "function(Bokeh) {} // ensure no trailing comma for IE\n", " ];\n", "\n", " function run_inline_js() {\n", " if ((root.Bokeh !== undefined) || (force === true)) {\n", " for (var i = 0; i < inline_js.length; i++) {\n", "\ttry {\n", " inline_js[i].call(root, root.Bokeh);\n", "\t} catch(e) {\n", "\t if (!reloading) {\n", "\t throw e;\n", "\t }\n", "\t}\n", " }\n", " // Cache old bokeh versions\n", " if (Bokeh != undefined && !reloading) {\n", "\tvar NewBokeh = root.Bokeh;\n", "\tif (Bokeh.versions === undefined) {\n", "\t Bokeh.versions = new Map();\n", "\t}\n", "\tif (NewBokeh.version !== Bokeh.version) {\n", "\t Bokeh.versions.set(NewBokeh.version, NewBokeh)\n", "\t}\n", "\troot.Bokeh = Bokeh;\n", " }} else if (Date.now() < root._bokeh_timeout) {\n", " setTimeout(run_inline_js, 100);\n", " } else if (!root._bokeh_failed_load) {\n", " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", " root._bokeh_failed_load = true;\n", " }\n", " root._bokeh_is_initializing = false\n", " }\n", "\n", " function load_or_wait() {\n", " // Implement a backoff loop that tries to ensure we do not load multiple\n", " // versions of Bokeh and its dependencies at the same time.\n", " // In recent versions we use the root._bokeh_is_initializing flag\n", " // to determine whether there is an ongoing attempt to initialize\n", " // bokeh, however for backward compatibility we also try to ensure\n", " // that we do not start loading a newer (Panel>=1.0 and Bokeh>3) version\n", " // before older versions are fully initialized.\n", " if (root._bokeh_is_initializing && Date.now() > root._bokeh_timeout) {\n", " root._bokeh_is_initializing = false;\n", " root._bokeh_onload_callbacks = undefined;\n", " console.log(\"Bokeh: BokehJS was loaded multiple times but one version failed to initialize.\");\n", " load_or_wait();\n", " } else if (root._bokeh_is_initializing || (typeof root._bokeh_is_initializing === \"undefined\" && root._bokeh_onload_callbacks !== undefined)) {\n", " setTimeout(load_or_wait, 100);\n", " } else {\n", " root._bokeh_is_initializing = true\n", " root._bokeh_onload_callbacks = []\n", " var bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n", " if (!reloading && !bokeh_loaded) {\n", "\troot.Bokeh = undefined;\n", " }\n", " load_libs(css_urls, js_urls, js_modules, js_exports, function() {\n", "\tconsole.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", "\trun_inline_js();\n", " });\n", " }\n", " }\n", " // Give older versions of the autoload script a head-start to ensure\n", " // they initialize before we start loading newer version.\n", " setTimeout(load_or_wait, 100)\n", "}(window));" ], "application/vnd.holoviews_load.v0+json": "(function(root) {\n function now() {\n return new Date();\n }\n\n var force = true;\n var py_version = '3.4.3'.replace('rc', '-rc.').replace('.dev', '-dev.');\n var reloading = true;\n var Bokeh = root.Bokeh;\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks;\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, js_modules, js_exports, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n if (js_modules == null) js_modules = [];\n if (js_exports == null) js_exports = {};\n\n root._bokeh_onload_callbacks.push(callback);\n\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls.length === 0 && js_modules.length === 0 && Object.keys(js_exports).length === 0) {\n run_callbacks();\n return null;\n }\n if (!reloading) {\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n }\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n window._bokeh_on_load = on_load\n\n function on_error() {\n console.error(\"failed to load \" + url);\n }\n\n var skip = [];\n if (window.requirejs) {\n window.requirejs.config({'packages': {}, 'paths': {'tabulator': 'https://cdn.jsdelivr.net/npm/tabulator-tables@5.5.0/dist/js/tabulator.min', 'moment': 'https://cdn.jsdelivr.net/npm/luxon/build/global/luxon.min', 'mathjax': '//cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-AMS_HTML', 'vega-embed': 'https://cdn.jsdelivr.net/npm/vega-embed@6/build/vega-embed.min', 'vega-lite': 'https://cdn.jsdelivr.net/npm/vega-lite@5/build/vega-lite.min', 'vega': 'https://cdn.jsdelivr.net/npm/vega@5/build/vega.min', 'jsoneditor': '//cdn.jsdelivr.net/npm/jsoneditor@10.0.1/dist/jsoneditor.min', 'jspanel': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/jspanel', 'jspanel-modal': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal', 'jspanel-tooltip': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip', 'jspanel-hint': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint', 'jspanel-layout': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout', 'jspanel-contextmenu': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu', 'jspanel-dock': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/dock/jspanel.dock'}, 'shim': {'mathjax': {'exports': 'MathJax'}, 'jsoneditor': {'exports': 'JSONEditor'}, 'jspanel': {'exports': 'jsPanel'}}});\n require([\"tabulator\"], function(Tabulator) {\n\twindow.Tabulator = Tabulator\n\ton_load()\n })\n require([\"moment\"], function(moment) {\n\twindow.moment = moment\n\ton_load()\n })\n require([\"mathjax\"], function() {\n\ton_load()\n })\n require([\"vega-embed\"], function(vegaEmbed) {\n\twindow.vegaEmbed = vegaEmbed\n\ton_load()\n })\n require([\"vega-lite\"], function(vl) {\n\twindow.vl = vl\n\ton_load()\n })\n require([\"vega\"], function(vega) {\n\twindow.vega = vega\n\ton_load()\n })\n require([\"jsoneditor\"], function(JSONEditor) {\n\twindow.JSONEditor = JSONEditor\n\ton_load()\n })\n require([\"jspanel\"], function(jsPanel) {\n\twindow.jsPanel = jsPanel\n\ton_load()\n })\n require([\"jspanel-modal\"], function() {\n\ton_load()\n })\n require([\"jspanel-tooltip\"], function() {\n\ton_load()\n })\n require([\"jspanel-hint\"], function() {\n\ton_load()\n })\n require([\"jspanel-layout\"], function() {\n\ton_load()\n })\n require([\"jspanel-contextmenu\"], function() {\n\ton_load()\n })\n require([\"jspanel-dock\"], function() {\n\ton_load()\n })\n root._bokeh_is_loading = css_urls.length + 14;\n } else {\n root._bokeh_is_loading = css_urls.length + js_urls.length + js_modules.length + Object.keys(js_exports).length;\n }\n\n var existing_stylesheets = []\n var links = document.getElementsByTagName('link')\n for (var i = 0; i < links.length; i++) {\n var link = links[i]\n if (link.href != null) {\n\texisting_stylesheets.push(link.href)\n }\n }\n for (var i = 0; i < css_urls.length; i++) {\n var url = css_urls[i];\n if (existing_stylesheets.indexOf(url) !== -1) {\n\ton_load()\n\tcontinue;\n }\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error;\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n } if (((window.Tabulator !== undefined) && (!(window.Tabulator instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/tabulator-tables@5.5.0/dist/js/tabulator.min.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window.moment !== undefined) && (!(window.moment instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/datatabulator/luxon/build/global/luxon.min.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window.MathJax !== undefined) && (!(window.MathJax instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window.vega !== undefined) && (!(window.vega instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/vegaplot/vega@5'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window.vegaLite !== undefined) && (!(window.vegaLite instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/vegaplot/vega-lite@5'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window.vegaEmbed !== undefined) && (!(window.vegaEmbed instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/vegaplot/vega-embed@6'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window.JSONEditor !== undefined) && (!(window.JSONEditor instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/jsoneditor/jsoneditor@10.0.1/dist/jsoneditor.min.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window.jsPanel !== undefined) && (!(window.jsPanel instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/jspanel.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu.js', 'https://cdn.holoviz.org/panel/1.4.5/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/dock/jspanel.dock.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } var existing_scripts = []\n var scripts = document.getElementsByTagName('script')\n for (var i = 0; i < scripts.length; i++) {\n var script = scripts[i]\n if (script.src != null) {\n\texisting_scripts.push(script.src)\n }\n }\n for (var i = 0; i < js_urls.length; i++) {\n var url = js_urls[i];\n if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n for (var i = 0; i < js_modules.length; i++) {\n var url = js_modules[i];\n if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n element.type = \"module\";\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", 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reference to server id on output_area\n output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n }\n}\n\n/**\n * Handle when an output is cleared or removed\n */\nfunction handle_clear_output(event, handle) {\n var id = handle.cell.output_area._hv_plot_id;\n var server_id = handle.cell.output_area._bokeh_server_id;\n if (((id === undefined) || !(id in PyViz.plot_index)) && (server_id !== undefined)) { return; }\n var comm = window.PyViz.comm_manager.get_client_comm(\"hv-extension-comm\", \"hv-extension-comm\", function () {});\n if (server_id !== null) {\n comm.send({event_type: 'server_delete', 'id': server_id});\n return;\n } else if (comm !== null) {\n comm.send({event_type: 'delete', 'id': id});\n }\n delete PyViz.plot_index[id];\n if ((window.Bokeh !== undefined) & (id in window.Bokeh.index)) {\n var doc = window.Bokeh.index[id].model.document\n doc.clear();\n const i = window.Bokeh.documents.indexOf(doc);\n if (i > -1) {\n window.Bokeh.documents.splice(i, 1);\n }\n }\n}\n\n/**\n * Handle kernel restart event\n */\nfunction handle_kernel_cleanup(event, handle) {\n delete PyViz.comms[\"hv-extension-comm\"];\n window.PyViz.plot_index = {}\n}\n\n/**\n * Handle update_display_data messages\n */\nfunction handle_update_output(event, handle) {\n handle_clear_output(event, {cell: {output_area: handle.output_area}})\n handle_add_output(event, handle)\n}\n\nfunction register_renderer(events, OutputArea) {\n function append_mime(data, metadata, element) {\n // create a DOM node to render to\n var toinsert = this.create_output_subarea(\n metadata,\n CLASS_NAME,\n EXEC_MIME_TYPE\n );\n this.keyboard_manager.register_events(toinsert);\n // Render to node\n var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n render(props, toinsert[0]);\n element.append(toinsert);\n return toinsert\n }\n\n events.on('output_added.OutputArea', handle_add_output);\n events.on('output_updated.OutputArea', handle_update_output);\n events.on('clear_output.CodeCell', handle_clear_output);\n events.on('delete.Cell', handle_clear_output);\n events.on('kernel_ready.Kernel', handle_kernel_cleanup);\n\n OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n safe: true,\n index: 0\n });\n}\n\nif (window.Jupyter !== undefined) {\n try {\n var events = require('base/js/events');\n var OutputArea = require('notebook/js/outputarea').OutputArea;\n if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n register_renderer(events, OutputArea);\n }\n } catch(err) {\n }\n}\n" }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "import pandas as pd\n", "\n", "from bdiviz import BDISchemaMatchingHeatMap\n", "from bdikit import match_schema\n", "from bdikit.mapping_algorithms.column_mapping.algorithms import TwoPhaseSchemaMatcher" ] }, { "cell_type": "markdown", "id": "3d8a3bb1-2dbe-4efb-acd9-f4c52a78745e", "metadata": {}, "source": [ "### Access to Source and Target Data\n", "\n", "**GDC Metadata Validation Services:**\n", "https://docs.gdc.cancer.gov/Data_Dictionary/gdcmvs/ \n", " \n", "**Data Dictionary Viewer:**\n", "https://docs.gdc.cancer.gov/Data_Dictionary/viewer/\n", "\n", "---\n", " \n", "**Dataset:** [link](https://drive.google.com/file/d/1dbVo2gBGD8hOIsCblCDujGEnhHtidQCf/view?usp=drive_link) \n", "**Paper:** [link](https://www.sciencedirect.com/science/article/pii/S0092867420301070)\n", "\n", "\n", "_**Proteogenomic Characterization of Endometrial Carcinoma**_ \n", "\n", "_Dou et. al_\n", "\n", "We undertook a comprehensive proteogenomic characterization of 95 prospectively collected endometrial carcinomas, comprising 83 endometrioid and 12 serous tumors. This analysis revealed possible new consequences of perturbations to the p53 and Wnt/β-catenin pathways, identified a potential role for circRNAs in the epithelial-mesenchymal transition, and provided new information about proteomic markers of clinical and genomic tumor subgroups, including relationships to known druggable pathways. An extensive genome-wide acetylation survey yielded insights into regulatory mechanisms linking Wnt signaling and histone acetylation. We also characterized aspects of the tumor immune landscape, including immunogenic alterations, neoantigens, common cancer/testis antigens, and the immune microenvironment, all of which can inform immunotherapy decisions. Collectively, our multi-omic analyses provide a valuable resource for researchers and clinicians, identify new molecular associations of potential mechanistic significance in the development of endometrial cancers, and suggest novel approaches for identifying potential therapeutic targets." ] }, { "cell_type": "code", "execution_count": 2, "id": "f12f8e81-4a90-445d-a3bb-0352cbe7f7b7", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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CountryBMIGenderEthnicityRaceTumor_FocalityFIGO_stageAgeHistologic_Grade_FIGOPath_Stage_Primary_Tumor-pTPath_Stage_Reg_Lymph_Nodes-pNClin_Stage_Dist_Mets-cMPath_Stage_Dist_Mets-pMtumor_Stage-PathologicalHistologic_typeTumor_SiteTumor_Size_cm
0United States38.88FemaleNot-Hispanic or LatinoWhiteUnifocalIA64.0FIGO grade 1pT1a (FIGO IA)pN0cM0Staging IncompleteStage IEndometrioidAnterior endometrium2.9
1United States39.76FemaleNot-Hispanic or LatinoWhiteUnifocalIA58.0FIGO grade 1pT1a (FIGO IA)pNXcM0Staging IncompleteStage IVEndometrioidPosterior endometrium3.5
2United States51.19FemaleNot-Hispanic or LatinoWhiteUnifocalIA50.0FIGO grade 2pT1a (FIGO IA)pN0cM0Staging IncompleteStage IEndometrioidOther, specify4.5
3NaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNCarcinosarcomaNaNNaN
4United States32.69FemaleNot-Hispanic or LatinoWhiteUnifocalIA75.0FIGO grade 2pT1a (FIGO IA)pNXcM0No pathologic evidence of distant metastasisStage IEndometrioidOther, specify3.5
......................................................
99Ukraine29.40FemaleNaNNaNUnifocalIA75.0FIGO grade 3pT1a (FIGO IA)pNXcM0Staging IncompleteStage IEndometrioidOther, specify4.2
100Ukraine35.42FemaleNaNNaNUnifocalII74.0FIGO grade 2pT2 (FIGO II)pN0cM0Staging IncompleteStage IIEndometrioidOther, specify1.5
101United States24.32FemaleNot-Hispanic or LatinoBlack or African AmericanUnifocalII85.0NaNpT2 (FIGO II)pN0Staging IncompleteStaging IncompleteStage IISerousOther, specify3.8
102Ukraine34.06FemaleNaNNaNUnifocalIA70.0NaNpT1a (FIGO IA)pN0cM0Staging IncompleteStage ISerousOther, specify5.0
103UkraineNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNSerousNaNNaN
\n", "

104 rows × 17 columns

\n", "
" ], "text/plain": [ " Country BMI Gender Ethnicity \\\n", "0 United States 38.88 Female Not-Hispanic or Latino \n", "1 United States 39.76 Female Not-Hispanic or Latino \n", "2 United States 51.19 Female Not-Hispanic or Latino \n", "3 NaN NaN NaN NaN \n", "4 United States 32.69 Female Not-Hispanic or Latino \n", ".. ... ... ... ... \n", "99 Ukraine 29.40 Female NaN \n", "100 Ukraine 35.42 Female NaN \n", "101 United States 24.32 Female Not-Hispanic or Latino \n", "102 Ukraine 34.06 Female NaN \n", "103 Ukraine NaN NaN NaN \n", "\n", " Race Tumor_Focality FIGO_stage Age \\\n", "0 White Unifocal IA 64.0 \n", "1 White Unifocal IA 58.0 \n", "2 White Unifocal IA 50.0 \n", "3 NaN NaN NaN NaN \n", "4 White Unifocal IA 75.0 \n", ".. ... ... ... ... \n", "99 NaN Unifocal IA 75.0 \n", "100 NaN Unifocal II 74.0 \n", "101 Black or African American Unifocal II 85.0 \n", "102 NaN Unifocal IA 70.0 \n", "103 NaN NaN NaN NaN \n", "\n", " Histologic_Grade_FIGO Path_Stage_Primary_Tumor-pT \\\n", "0 FIGO grade 1 pT1a (FIGO IA) \n", "1 FIGO grade 1 pT1a (FIGO IA) \n", "2 FIGO grade 2 pT1a (FIGO IA) \n", "3 NaN NaN \n", "4 FIGO grade 2 pT1a (FIGO IA) \n", ".. ... ... \n", "99 FIGO grade 3 pT1a (FIGO IA) \n", "100 FIGO grade 2 pT2 (FIGO II) \n", "101 NaN pT2 (FIGO II) \n", "102 NaN pT1a (FIGO IA) \n", "103 NaN NaN \n", "\n", " Path_Stage_Reg_Lymph_Nodes-pN Clin_Stage_Dist_Mets-cM \\\n", "0 pN0 cM0 \n", "1 pNX cM0 \n", "2 pN0 cM0 \n", "3 NaN NaN \n", "4 pNX cM0 \n", ".. ... ... \n", "99 pNX cM0 \n", "100 pN0 cM0 \n", "101 pN0 Staging Incomplete \n", "102 pN0 cM0 \n", "103 NaN NaN \n", "\n", " Path_Stage_Dist_Mets-pM tumor_Stage-Pathological \\\n", "0 Staging Incomplete Stage I \n", "1 Staging Incomplete Stage IV \n", "2 Staging Incomplete Stage I \n", "3 NaN NaN \n", "4 No pathologic evidence of distant metastasis Stage I \n", ".. ... ... \n", "99 Staging Incomplete Stage I \n", "100 Staging Incomplete Stage II \n", "101 Staging Incomplete Stage II \n", "102 Staging Incomplete Stage I \n", "103 NaN NaN \n", "\n", " Histologic_type Tumor_Site Tumor_Size_cm \n", "0 Endometrioid Anterior endometrium 2.9 \n", "1 Endometrioid Posterior endometrium 3.5 \n", "2 Endometrioid Other, specify 4.5 \n", "3 Carcinosarcoma NaN NaN \n", "4 Endometrioid Other, specify 3.5 \n", ".. ... ... ... \n", "99 Endometrioid Other, specify 4.2 \n", "100 Endometrioid Other, specify 1.5 \n", "101 Serous Other, specify 3.8 \n", "102 Serous Other, specify 5.0 \n", "103 Serous NaN NaN \n", "\n", "[104 rows x 17 columns]" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "source = pd.read_csv(\"dou_bdiviz.csv\")\n", "target = \"gdc\"\n", "\n", "source" ] }, { "cell_type": "markdown", "id": "74b20f0c-1ad0-435d-af77-09bbd3b259f2", "metadata": {}, "source": [ "## BDI-Viz Heatmap\n", "\n", "\n", "#### Spotlighted Features\n", "\n", "- **Interactive Heatmap**: Click on a heatmap cell to select candidates.\n", "- **Candidate Manipulation**:\n", " - Use the **Accept Match**, **Reject Match**, and **Discard Column** buttons to manage matching candidates.\n", " - Undo or redo actions with the **Undo** and **Redo** buttons.\n", "- **Value Comparisons**: Explore similar candidate values in detail.\n", "- **Detailed Analysis**: Examine value distributions and schema descriptions for selected attributes.\n", "- **Filtering Options**:\n", " - Filter by candidate data type using the **Candidate Type Selector**.\n", " - Identify similar source columns with the **Similar Sources Slider** (based on embeddings).\n", " - Adjust threshold values with the **Candidate Threshold Slider** to refine matches.\n", "\n", "\n", "**Note:** This result is generated by a finetuned language model, BDI-Viz can also be used with other matching methods as long as we have the top-k candidates." ] }, { "cell_type": "code", "execution_count": 3, "id": "023d3808-5d51-437d-aefc-d946b0fb974b", "metadata": {}, "outputs": [ { "data": {}, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.holoviews_exec.v0+json": "", "text/html": [ "
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\n", "" ], "text/plain": [ "Column(scroll=True)\n", " [0] Row(styles={'background': '...}, width=1200)\n", " [0] Select(name='Source Column', options=['Country', 'BMI', ...], value='Country', width=120)\n", " [1] Select(name='Candidate Type', options=['All', 'enum', ...], value='All', width=120)\n", " [2] IntSlider(end=5, name='Similar Sources', width=150)\n", " [3] FloatSlider(name='Candidate Threshold', step=0.01, value=0.1, width=150)\n", " [4] Column\n", " [0] Button(button_type='success', name='Accept Match')\n", " [1] Button(button_type='danger', name='Reject Match')\n", " [2] Button(button_type='warning', name='Discard Column')\n", " [5] Column\n", " [0] Button(button_style='outline', button_type='warning', name='Undo')\n", " [1] Button(button_style='outline', button_type='primary', name='Redo')\n", " [6] Column\n", " [0] Button(button_type='primary', name='Show/Hide AI Assistant')\n", " [1] Button(button_type='primary', name='Show/Hide Operation Log')\n", " [1] ParamFunction(function, _pane=Str, defer_load=False)\n", " [2] Spacer(height=5)\n", " [3] Column\n", " [0] ParamFunction(function, _pane=Column, defer_load=False)" ] }, "execution_count": 3, "metadata": { "application/vnd.holoviews_exec.v0+json": { "id": "e7b05c61-427c-49e6-a60e-2dd1a0d4c74d" } }, "output_type": "execute_result" } ], "source": [ "heatmap_manager = BDISchemaMatchingHeatMap(\n", " source,\n", " target=target,\n", " top_k=20\n", ")\n", "\n", "heatmap_manager.plot_heatmap()" ] }, { "cell_type": "markdown", "id": "d7525be2-f388-4e97-a222-6a69bc806685", "metadata": {}, "source": [ "## Passing Curated Results to BDI-Kit\n", "\n", "BDI-Viz seamlessly integrates as an extension of BDI-Kit. By passing results from BDI-Viz to BDI-Kit, you can retain and utilize all manually updated candidates for further processing. \n", "\n", "If you notice that some columns are still not properly aligned, you can return to the [BDI-Viz Heatmap](#BDI-Viz-Heatmap) and continue refining the matching candidates as needed." ] }, { "cell_type": "code", "execution_count": 4, "id": "2b1c98e8-280b-429c-9aa8-f1dba5eed8f1", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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sourcetarget
0Countrycountry_of_birth
1BMIdemographics
2Gendergender
3Ethnicityethnicity
4Racerace
5Tumor_Focalitytumor_focality
6FIGO_stageirs_stage
7Ageweight
8Histologic_Grade_FIGOhistologic_progression_type
9Path_Stage_Primary_Tumor-pTmargin_distance
10Path_Stage_Reg_Lymph_Nodes-pNperipancreatic_lymph_nodes_tested
11Clin_Stage_Dist_Mets-cMinrg_stage
12Path_Stage_Dist_Mets-pMmasaoka_stage
13tumor_Stage-Pathologicalajcc_pathologic_t
14Histologic_typehistory_of_tumor_type
15Tumor_Sitetumor_shape
16Tumor_Size_cmtumor_depth
\n", "
" ], "text/plain": [ " source target\n", "0 Country country_of_birth\n", "1 BMI demographics\n", "2 Gender gender\n", "3 Ethnicity ethnicity\n", "4 Race race\n", "5 Tumor_Focality tumor_focality\n", "6 FIGO_stage irs_stage\n", "7 Age weight\n", "8 Histologic_Grade_FIGO histologic_progression_type\n", "9 Path_Stage_Primary_Tumor-pT margin_distance\n", "10 Path_Stage_Reg_Lymph_Nodes-pN peripancreatic_lymph_nodes_tested\n", "11 Clin_Stage_Dist_Mets-cM inrg_stage\n", "12 Path_Stage_Dist_Mets-pM masaoka_stage\n", "13 tumor_Stage-Pathological ajcc_pathologic_t\n", "14 Histologic_type history_of_tumor_type\n", "15 Tumor_Site tumor_shape\n", "16 Tumor_Size_cm tumor_depth" ] }, "execution_count": 4, "metadata": {}, "output_type": "execute_result" } ], "source": [ "two_phase_viz = TwoPhaseSchemaMatcher(top_k_matcher=heatmap_manager)\n", "column_mappings = match_schema(source, target=target, method=two_phase_viz)\n", "column_mappings" ] }, { "cell_type": "markdown", "id": "fa0b3aff-9db8-4592-81a2-9609e3c5c003", "metadata": {}, "source": [ "\n", "## Groundtruth Lookups\n", "\n", "| **Source Column** | **Target Column (GDC Schema)** | **Matching Type** | **Notes** |\n", "|-----------------------------|------------------------------------------|-------------------------------------------|---------------------------------------------------------------------------------------------------|\n", "| Country | country_of_birth | Exact match in values, semantically similar names | |\n", "| BMI | bmi | Exact match in name | |\n", "| Gender | gender | Exact match in name and values | |\n", "| Ethnicity | ethnicity | Exact match in name and values | |\n", "| Race | race | Exact match in name and values | |\n", "| Tumor_Focality | tumor_focality | Exact match in name and values | |\n", "| FIGO_stage | figo_stage | Exact match in name, semantically similar values | (e.g., \"IA\" to \"Stage IA\") |\n", "| Age | age_at_diagnosis / age_at_index | Semantically similar names | \"weight\" incorrectly returned as top result by matcher; unit mismatch (days vs. years) |\n", "| Histologic_Grade_FIGO | tumor_grade | Semantically similar names, values | (e.g., \"FIGO grade 1\" to \"G1\") |\n", "| Path_Stage_Primary_Tumor-pT| ajcc_pathologic_t | Semantically similar names, values | (e.g., \"pT1 (FIGO I)\" to \"T1\") |\n", "| Path_Stage_Reg_Lymph_Nodes-pN| ajcc_pathologic_n | Semantically similar names, values | (e.g., \"pNX\" to \"NX\") |\n", "| Clin_Stage_Dist_Mets-cM | ajcc_clinical_m | Semantically similar names, values | (e.g., \"cM0\" to \"cM0 (i+)\") |\n", "| Path_Stage_Dist_Mets-pM | ajcc_pathologic_m | Semantically similar names, values | (e.g., \"pM1\" to \"M1\") |\n", "| tumor_Stage-Pathological | ajcc_pathologic_stage | Semantically similar names, exact values | (e.g., \"Stage I\" to \"Stage I\"); requires knowledge of use-case-specific standards |\n", "| Histologic_type | primary_diagnosis | Unrelated names, semantically similar values | (e.g., \"Serous\" to \"Serous adenocarcinofibroma\") |\n", "| Tumor_Site | site_of_resection_or_biopsy | Unrelated names, semantically similar values | (e.g., \"Posterior endometrium\" to \"Endometrium\") |\n", "| Tumor_Size_cm | tumor_largest_dimension_diameter | Semantically similar names | |\n" ] } ], "metadata": { "kernelspec": { "display_name": "kernel_bdi_viz", "language": "python", "name": "kernel_bdi_viz" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.9.18" }, "widgets": { "application/vnd.jupyter.widget-state+json": { "state": {}, "version_major": 2, "version_minor": 0 } } }, "nbformat": 4, "nbformat_minor": 5 }