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EdgeNormalization

Introduction

The Biolink Model defines allowed predicates in the Translator ecosystem. Ingesting data from arbitrary sources requires mapping predicates in those sources to Translator predicates.

The Biolink Lookup Service can find predicates if they have an exact mapping in the model. The EdgeNormalization service takes this a step further, and attempts to find the best match to a Biolink predicate, even if there is not an explicit mapping.

Most users will use the public service, but instructions for deploying a new instance are given below.

Examples of calling the service are given in the examples notebook.

Installation

Create a virtual environment and activate.

python -m venv venv
source venv/bin/activate

Install dependencies

pip install -r requirements.txt

Run web server.

python main.py --host 0.0.0.0 --port 8145

Docker

Build image locally

docker build --tag edgenormalization .

Launch

docker run -it \ -p <port>:8145 \ edgenormalization

Usage

http://"host name or IP":"port"/apidocs

Kubernetes

Deployment files for Kubernetes are available in the \kubernetes directory.

About

A service for producing relationships compliant with the biolink model

Topics

ncats-translatorshared-utility

Resources

Readme
MIT license
Activity
Custom properties

Stars

0 stars

Watchers

1 watching

Forks

1 fork
Report repository

Releases

Packages

Used by

Contributors

Languages

, '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" + '

Skip to content
BranchesTags
Repository files navigation
Build Status
EdgeNormalization
Introduction
The Biolink Model defines allowed predicates in the Translator ecosystem. Ingesting data from arbitrary sources requires mapping predicates in those sources to Translator predicates.
The Biolink Lookup Service can find predicates if they have an exact mapping in the model. The EdgeNormalization service takes this a step further, and attempts to find the best match to a Biolink predicate, even if there is not an explicit mapping.
Most users will use the public service, but instructions for deploying a new instance are given below.
Examples of calling the service are given in the examples notebook.
Installation
Create a virtual environment and activate.
python -m venv venv
source venv/bin/activate

Install dependencies
pip install -r requirements.txt

Run web server.
python main.py --host 0.0.0.0 --port 8145 
Docker
Build image locally
docker build --tag edgenormalization .

Launch
docker run -it \ -p <port>:8145 \ edgenormalization 
Usage
http://"host name or IP":"port"/apidocs
Kubernetes
Deployment files for Kubernetes are available in the \kubernetes directory.
About
A service for producing relationships compliant with the biolink model
Topics
ncats-translatorshared-utility
Resources
Readme
MIT license
Activity
Custom properties
Stars
0 stars
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
Build Status
EdgeNormalization
Introduction
The Biolink Model defines allowed predicates in the Translator ecosystem. Ingesting data from arbitrary sources requires mapping predicates in those sources to Translator predicates.
The Biolink Lookup Service can find predicates if they have an exact mapping in the model. The EdgeNormalization service takes this a step further, and attempts to find the best match to a Biolink predicate, even if there is not an explicit mapping.
Most users will use the public service, but instructions for deploying a new instance are given below.
Examples of calling the service are given in the examples notebook.
Installation
Create a virtual environment and activate.
python -m venv venv
source venv/bin/activate

Install dependencies
pip install -r requirements.txt

Run web server.
python main.py --host 0.0.0.0 --port 8145 
Docker
Build image locally
docker build --tag edgenormalization .

Launch
docker run -it \ -p <port>:8145 \ edgenormalization 
Usage
http://"host name or IP":"port"/apidocs
Kubernetes
Deployment files for Kubernetes are available in the \kubernetes directory.
About
A service for producing relationships compliant with the biolink model
Topics
ncats-translatorshared-utility
Resources
Readme
MIT license
Activity
Custom properties
Stars
0 stars
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
Build Status
EdgeNormalization
Introduction
The Biolink Model defines allowed predicates in the Translator ecosystem. Ingesting data from arbitrary sources requires mapping predicates in those sources to Translator predicates.
The Biolink Lookup Service can find predicates if they have an exact mapping in the model. The EdgeNormalization service takes this a step further, and attempts to find the best match to a Biolink predicate, even if there is not an explicit mapping.
Most users will use the public service, but instructions for deploying a new instance are given below.
Examples of calling the service are given in the examples notebook.
Installation
Create a virtual environment and activate.
python -m venv venv
source venv/bin/activate

Install dependencies
pip install -r requirements.txt

Run web server.
python main.py --host 0.0.0.0 --port 8145 
Docker
Build image locally
docker build --tag edgenormalization .

Launch
docker run -it \ -p <port>:8145 \ edgenormalization 
Usage
http://"host name or IP":"port"/apidocs
Kubernetes
Deployment files for Kubernetes are available in the \kubernetes directory.
About
A service for producing relationships compliant with the biolink model
Topics
ncats-translatorshared-utility
Resources
Readme
MIT license
Activity
Custom properties
Stars
0 stars
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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" + '

Skip to content
BranchesTags
Repository files navigation
Build Status
EdgeNormalization
Introduction
The Biolink Model defines allowed predicates in the Translator ecosystem. Ingesting data from arbitrary sources requires mapping predicates in those sources to Translator predicates.
The Biolink Lookup Service can find predicates if they have an exact mapping in the model. The EdgeNormalization service takes this a step further, and attempts to find the best match to a Biolink predicate, even if there is not an explicit mapping.
Most users will use the public service, but instructions for deploying a new instance are given below.
Examples of calling the service are given in the examples notebook.
Installation
Create a virtual environment and activate.
python -m venv venv
source venv/bin/activate

Install dependencies
pip install -r requirements.txt

Run web server.
python main.py --host 0.0.0.0 --port 8145 
Docker
Build image locally
docker build --tag edgenormalization .

Launch
docker run -it \ -p <port>:8145 \ edgenormalization 
Usage
http://"host name or IP":"port"/apidocs
Kubernetes
Deployment files for Kubernetes are available in the \kubernetes directory.
About
A service for producing relationships compliant with the biolink model
Topics
ncats-translatorshared-utility
Resources
Readme
MIT license
Activity
Custom properties
Stars
0 stars
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
Build Status
EdgeNormalization
Introduction
The Biolink Model defines allowed predicates in the Translator ecosystem. Ingesting data from arbitrary sources requires mapping predicates in those sources to Translator predicates.
The Biolink Lookup Service can find predicates if they have an exact mapping in the model. The EdgeNormalization service takes this a step further, and attempts to find the best match to a Biolink predicate, even if there is not an explicit mapping.
Most users will use the public service, but instructions for deploying a new instance are given below.
Examples of calling the service are given in the examples notebook.
Installation
Create a virtual environment and activate.
python -m venv venv
source venv/bin/activate

Install dependencies
pip install -r requirements.txt

Run web server.
python main.py --host 0.0.0.0 --port 8145 
Docker
Build image locally
docker build --tag edgenormalization .

Launch
docker run -it \ -p <port>:8145 \ edgenormalization 
Usage
http://"host name or IP":"port"/apidocs
Kubernetes
Deployment files for Kubernetes are available in the \kubernetes directory.
About
A service for producing relationships compliant with the biolink model
Topics
ncats-translatorshared-utility
Resources
Readme
MIT license
Activity
Custom properties
Stars
0 stars
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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
BranchesTags
Repository files navigation
Build Status
EdgeNormalization
Introduction
The Biolink Model defines allowed predicates in the Translator ecosystem. Ingesting data from arbitrary sources requires mapping predicates in those sources to Translator predicates.
The Biolink Lookup Service can find predicates if they have an exact mapping in the model. The EdgeNormalization service takes this a step further, and attempts to find the best match to a Biolink predicate, even if there is not an explicit mapping.
Most users will use the public service, but instructions for deploying a new instance are given below.
Examples of calling the service are given in the examples notebook.
Installation
Create a virtual environment and activate.
python -m venv venv
source venv/bin/activate

Install dependencies
pip install -r requirements.txt

Run web server.
python main.py --host 0.0.0.0 --port 8145 
Docker
Build image locally
docker build --tag edgenormalization .

Launch
docker run -it \ -p <port>:8145 \ edgenormalization 
Usage
http://"host name or IP":"port"/apidocs
Kubernetes
Deployment files for Kubernetes are available in the \kubernetes directory.
About
A service for producing relationships compliant with the biolink model
Topics
ncats-translatorshared-utility
Resources
Readme
MIT license
Activity
Custom properties
Stars
0 stars
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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); }
})();
})();

Skip to content
BranchesTags
Repository files navigation
Build Status
EdgeNormalization
Introduction
The Biolink Model defines allowed predicates in the Translator ecosystem. Ingesting data from arbitrary sources requires mapping predicates in those sources to Translator predicates.
The Biolink Lookup Service can find predicates if they have an exact mapping in the model. The EdgeNormalization service takes this a step further, and attempts to find the best match to a Biolink predicate, even if there is not an explicit mapping.
Most users will use the public service, but instructions for deploying a new instance are given below.
Examples of calling the service are given in the examples notebook.
Installation
Create a virtual environment and activate.
python -m venv venv
source venv/bin/activate

Install dependencies
pip install -r requirements.txt

Run web server.
python main.py --host 0.0.0.0 --port 8145 
Docker
Build image locally
docker build --tag edgenormalization .

Launch
docker run -it \ -p <port>:8145 \ edgenormalization 
Usage
http://"host name or IP":"port"/apidocs
Kubernetes
Deployment files for Kubernetes are available in the \kubernetes directory.
About
A service for producing relationships compliant with the biolink model
Topics
ncats-translatorshared-utility
Resources
Readme
MIT license
Activity
Custom properties
Stars
0 stars
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages