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Jason Reilly edited this page Dec 5, 2022 · 7 revisions

Welcome to the NodeNormalization wiki!

Node normalization takes a CURIE, and returns:

  • The preferred CURIE for this entity
  • All other known equivalent identifiers for the entity
  • Semantic types for the entity as defined by the Biolink Model

The data currently served by Node Normalization is created by the prototype project Babel, which attempts to find identifier equivalences, and makes sure that CURIE prefixes are BioLink Model compliant. The NodeNormalization service, however, is independent of Babel and as improved identifier equivalence tools are developed, their results can be easily incorporated.

To determine whether Node Normalization is likely to be useful, check /get_semantic_types, which lists the BioLink semantic types for which normalization has been attempted, and /get_curie_prefixes, which lists the number of times each prefix is used for a semantic type.

For examples of service usage, see the example notebook.

The Node normalization website leverages the R3 (Redis-REST with referencing) Redis data design and configuration.

Users can find the publicly available website at service.

Clone this wiki locally

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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Jason Reilly edited this page Dec 5, 2022
·
7 revisions
Welcome to the NodeNormalization wiki!
Node normalization takes a CURIE, and returns:
  • The preferred CURIE for this entity
  • All other known equivalent identifiers for the entity
  • Semantic types for the entity as defined by the Biolink Model
The data currently served by Node Normalization is created by the prototype project Babel, which attempts to find identifier equivalences, and makes sure that CURIE prefixes are BioLink Model compliant. The NodeNormalization service, however, is independent of Babel and as improved identifier equivalence tools are developed, their results can be easily incorporated.
To determine whether Node Normalization is likely to be useful, check /get_semantic_types, which lists the BioLink semantic types for which normalization has been attempted, and /get_curie_prefixes, which lists the number of times each prefix is used for a semantic type.
For examples of service usage, see the example notebook.
The Node normalization website leverages the R3 (Redis-REST with referencing) Redis data design and configuration.
Users can find the publicly available website at service.
Clone this wiki locally

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Jason Reilly edited this page Dec 5, 2022
·
7 revisions
Welcome to the NodeNormalization wiki!
Node normalization takes a CURIE, and returns:
  • The preferred CURIE for this entity
  • All other known equivalent identifiers for the entity
  • Semantic types for the entity as defined by the Biolink Model
The data currently served by Node Normalization is created by the prototype project Babel, which attempts to find identifier equivalences, and makes sure that CURIE prefixes are BioLink Model compliant. The NodeNormalization service, however, is independent of Babel and as improved identifier equivalence tools are developed, their results can be easily incorporated.
To determine whether Node Normalization is likely to be useful, check /get_semantic_types, which lists the BioLink semantic types for which normalization has been attempted, and /get_curie_prefixes, which lists the number of times each prefix is used for a semantic type.
For examples of service usage, see the example notebook.
The Node normalization website leverages the R3 (Redis-REST with referencing) Redis data design and configuration.
Users can find the publicly available website at service.
Clone this wiki locally

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Jason Reilly edited this page Dec 5, 2022
·
7 revisions
Welcome to the NodeNormalization wiki!
Node normalization takes a CURIE, and returns:
  • The preferred CURIE for this entity
  • All other known equivalent identifiers for the entity
  • Semantic types for the entity as defined by the Biolink Model
The data currently served by Node Normalization is created by the prototype project Babel, which attempts to find identifier equivalences, and makes sure that CURIE prefixes are BioLink Model compliant. The NodeNormalization service, however, is independent of Babel and as improved identifier equivalence tools are developed, their results can be easily incorporated.
To determine whether Node Normalization is likely to be useful, check /get_semantic_types, which lists the BioLink semantic types for which normalization has been attempted, and /get_curie_prefixes, which lists the number of times each prefix is used for a semantic type.
For examples of service usage, see the example notebook.
The Node normalization website leverages the R3 (Redis-REST with referencing) Redis data design and configuration.
Users can find the publicly available website at service.
Clone this wiki locally

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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Jason Reilly edited this page Dec 5, 2022
·
7 revisions
Welcome to the NodeNormalization wiki!
Node normalization takes a CURIE, and returns:
  • The preferred CURIE for this entity
  • All other known equivalent identifiers for the entity
  • Semantic types for the entity as defined by the Biolink Model
The data currently served by Node Normalization is created by the prototype project Babel, which attempts to find identifier equivalences, and makes sure that CURIE prefixes are BioLink Model compliant. The NodeNormalization service, however, is independent of Babel and as improved identifier equivalence tools are developed, their results can be easily incorporated.
To determine whether Node Normalization is likely to be useful, check /get_semantic_types, which lists the BioLink semantic types for which normalization has been attempted, and /get_curie_prefixes, which lists the number of times each prefix is used for a semantic type.
For examples of service usage, see the example notebook.
The Node normalization website leverages the R3 (Redis-REST with referencing) Redis data design and configuration.
Users can find the publicly available website at service.
Clone this wiki locally

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Jason Reilly edited this page Dec 5, 2022
·
7 revisions
Welcome to the NodeNormalization wiki!
Node normalization takes a CURIE, and returns:
  • The preferred CURIE for this entity
  • All other known equivalent identifiers for the entity
  • Semantic types for the entity as defined by the Biolink Model
The data currently served by Node Normalization is created by the prototype project Babel, which attempts to find identifier equivalences, and makes sure that CURIE prefixes are BioLink Model compliant. The NodeNormalization service, however, is independent of Babel and as improved identifier equivalence tools are developed, their results can be easily incorporated.
To determine whether Node Normalization is likely to be useful, check /get_semantic_types, which lists the BioLink semantic types for which normalization has been attempted, and /get_curie_prefixes, which lists the number of times each prefix is used for a semantic type.
For examples of service usage, see the example notebook.
The Node normalization website leverages the R3 (Redis-REST with referencing) Redis data design and configuration.
Users can find the publicly available website at service.
Clone this wiki locally

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Home
Jump to bottom

Jason Reilly edited this page Dec 5, 2022
·
7 revisions
Welcome to the NodeNormalization wiki!
Node normalization takes a CURIE, and returns:
  • The preferred CURIE for this entity
  • All other known equivalent identifiers for the entity
  • Semantic types for the entity as defined by the Biolink Model
The data currently served by Node Normalization is created by the prototype project Babel, which attempts to find identifier equivalences, and makes sure that CURIE prefixes are BioLink Model compliant. The NodeNormalization service, however, is independent of Babel and as improved identifier equivalence tools are developed, their results can be easily incorporated.
To determine whether Node Normalization is likely to be useful, check /get_semantic_types, which lists the BioLink semantic types for which normalization has been attempted, and /get_curie_prefixes, which lists the number of times each prefix is used for a semantic type.
For examples of service usage, see the example notebook.
The Node normalization website leverages the R3 (Redis-REST with referencing) Redis data design and configuration.
Users can find the publicly available website at service.
Clone this wiki locally

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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Jason Reilly edited this page Dec 5, 2022
·
7 revisions
Welcome to the NodeNormalization wiki!
Node normalization takes a CURIE, and returns:
  • The preferred CURIE for this entity
  • All other known equivalent identifiers for the entity
  • Semantic types for the entity as defined by the Biolink Model
The data currently served by Node Normalization is created by the prototype project Babel, which attempts to find identifier equivalences, and makes sure that CURIE prefixes are BioLink Model compliant. The NodeNormalization service, however, is independent of Babel and as improved identifier equivalence tools are developed, their results can be easily incorporated.
To determine whether Node Normalization is likely to be useful, check /get_semantic_types, which lists the BioLink semantic types for which normalization has been attempted, and /get_curie_prefixes, which lists the number of times each prefix is used for a semantic type.
For examples of service usage, see the example notebook.
The Node normalization website leverages the R3 (Redis-REST with referencing) Redis data design and configuration.
Users can find the publicly available website at service.
Clone this wiki locally