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monarch-initiative · Nov 15, 2023 · 6745daf · 6745daf
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diff --git a/docs/404.html b/docs/404.html
@@ -9,7 +9,7 @@
 
 
       <link rel="icon" href="/monarch-ingest/images/favicon.ico">
-      <meta name="generator" content="mkdocs-1.5.2, mkdocs-material-8.5.10">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-8.5.10">
 
 
 
@@ -649,7 +649,7 @@
 
 
     <li class="md-nav__item">
-      <a href="/monarch-ingest/Sources/phenio/" class="md-nav__link">
+      <a href="/monarch-ingest/Sources/phenio.md" class="md-nav__link">
         Phenio
       </a>
     </li>

diff --git a/docs/CLI/index.html b/docs/CLI/index.html
@@ -11,7 +11,7 @@
         <link rel="canonical" href="https://monarch-initiative.github.io/monarch-ingest/CLI/">
 
       <link rel="icon" href="../images/favicon.ico">
-      <meta name="generator" content="mkdocs-1.5.2, mkdocs-material-8.5.10">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-8.5.10">
 
 
 
@@ -388,6 +388,13 @@
     ingest download
   </a>
 
+</li>
+
+        <li class="md-nav__item">
+  <a href="#ingest-export" class="md-nav__link">
+    ingest export
+  </a>
+
 </li>
 
         <li class="md-nav__item">
@@ -748,7 +755,7 @@
 
 
     <li class="md-nav__item">
-      <a href="../Sources/phenio/" class="md-nav__link">
+      <a href="../Sources/phenio.md" class="md-nav__link">
         Phenio
       </a>
     </li>
@@ -856,6 +863,13 @@
     ingest download
   </a>
 
+</li>
+
+        <li class="md-nav__item">
+  <a href="#ingest-export" class="md-nav__link">
+    ingest export
+  </a>
+
 </li>
 
         <li class="md-nav__item">
@@ -935,6 +949,7 @@ <h1 id="ingest"><code>ingest</code></h1>
 <ul>
 <li><code>closure</code></li>
 <li><code>download</code>: Downloads data defined in download.yaml</li>
+<li><code>export</code></li>
 <li><code>jsonl</code></li>
 <li><code>merge</code>: Merge nodes and edges into kg</li>
 <li><code>release</code>: Copy data to Monarch GCP data buckets</li>
@@ -961,6 +976,14 @@ <h2 id="ingest-download"><code>ingest download</code></h2>
 <li><code>--all / --no-all</code>: Download all ingest datasets  [default: no-all]</li>
 <li><code>--help</code>: Show this message and exit.</li>
 </ul>
+<h2 id="ingest-export"><code>ingest export</code></h2>
+<p><strong>Usage</strong>:</p>
+<div class="highlight"><pre><span></span><code><span class="gp">$ </span>ingest<span class="w"> </span><span class="nb">export</span><span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span>
+</code></pre></div>
+<p><strong>Options</strong>:</p>
+<ul>
+<li><code>--help</code>: Show this message and exit.</li>
+</ul>
 <h2 id="ingest-jsonl"><code>ingest jsonl</code></h2>
 <p><strong>Usage</strong>:</p>
 <div class="highlight"><pre><span></span><code><span class="gp">$ </span>ingest<span class="w"> </span>jsonl<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span>

diff --git a/docs/Create-an-Ingest/1. Propose/index.html b/docs/Create-an-Ingest/1. Propose/index.html
@@ -11,7 +11,7 @@
         <link rel="canonical" href="https://monarch-initiative.github.io/monarch-ingest/Create-an-Ingest/1.%20Propose/">
 
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-      <meta name="generator" content="mkdocs-1.5.2, mkdocs-material-8.5.10">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-8.5.10">
 
 
 
@@ -670,7 +670,7 @@
 
 
     <li class="md-nav__item">
-      <a href="../../Sources/phenio/" class="md-nav__link">
+      <a href="../../Sources/phenio.md" class="md-nav__link">
         Phenio
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     </li>

diff --git a/docs/Create-an-Ingest/2. Configure/index.html b/docs/Create-an-Ingest/2. Configure/index.html
@@ -11,7 +11,7 @@
         <link rel="canonical" href="https://monarch-initiative.github.io/monarch-ingest/Create-an-Ingest/2.%20Configure/">
 
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-      <meta name="generator" content="mkdocs-1.5.2, mkdocs-material-8.5.10">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-8.5.10">
 
 
 
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     <li class="md-nav__item">
-      <a href="../../Sources/phenio/" class="md-nav__link">
+      <a href="../../Sources/phenio.md" class="md-nav__link">
         Phenio
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     </li>

diff --git a/docs/Create-an-Ingest/3. Document/index.html b/docs/Create-an-Ingest/3. Document/index.html
@@ -11,7 +11,7 @@
         <link rel="canonical" href="https://monarch-initiative.github.io/monarch-ingest/Create-an-Ingest/3.%20Document/">
 
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     <li class="md-nav__item">
-      <a href="../../Sources/phenio/" class="md-nav__link">
+      <a href="../../Sources/phenio.md" class="md-nav__link">
         Phenio
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     </li>

diff --git a/docs/Create-an-Ingest/4. Implement/index.html b/docs/Create-an-Ingest/4. Implement/index.html
@@ -11,7 +11,7 @@
         <link rel="canonical" href="https://monarch-initiative.github.io/monarch-ingest/Create-an-Ingest/4.%20Implement/">
 
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-      <meta name="generator" content="mkdocs-1.5.2, mkdocs-material-8.5.10">
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     <li class="md-nav__item">
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+      <a href="../../Sources/phenio.md" class="md-nav__link">
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     </li>

diff --git a/docs/Create-an-Ingest/5. Test/index.html b/docs/Create-an-Ingest/5. Test/index.html
@@ -11,7 +11,7 @@
         <link rel="canonical" href="https://monarch-initiative.github.io/monarch-ingest/Create-an-Ingest/5.%20Test/">
 
       <link rel="icon" href="../../images/favicon.ico">
-      <meta name="generator" content="mkdocs-1.5.2, mkdocs-material-8.5.10">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-8.5.10">
 
 
 
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     <li class="md-nav__item">
-      <a href="../../Sources/phenio/" class="md-nav__link">
+      <a href="../../Sources/phenio.md" class="md-nav__link">
         Phenio
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     </li>

diff --git a/docs/Create-an-Ingest/index.html b/docs/Create-an-Ingest/index.html
@@ -11,7 +11,7 @@
         <link rel="canonical" href="https://monarch-initiative.github.io/monarch-ingest/Create-an-Ingest/">
 
       <link rel="icon" href="../images/favicon.ico">
-      <meta name="generator" content="mkdocs-1.5.2, mkdocs-material-8.5.10">
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@@ -670,7 +670,7 @@
 
 
     <li class="md-nav__item">
-      <a href="../Sources/phenio/" class="md-nav__link">
+      <a href="../Sources/phenio.md" class="md-nav__link">
         Phenio
       </a>
     </li>

diff --git a/docs/KG-Build-Process/kg-build-process/index.html b/docs/KG-Build-Process/kg-build-process/index.html
@@ -11,7 +11,7 @@
         <link rel="canonical" href="https://monarch-initiative.github.io/monarch-ingest/KG-Build-Process/kg-build-process/">
 
       <link rel="icon" href="../../images/favicon.ico">
-      <meta name="generator" content="mkdocs-1.5.2, mkdocs-material-8.5.10">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-8.5.10">
 
 
 
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     <li class="md-nav__item">
-      <a href="../../Sources/phenio/" class="md-nav__link">
+      <a href="../../Sources/phenio.md" class="md-nav__link">
         Phenio
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diff --git a/docs/Principles/modeling-principles/index.html b/docs/Principles/modeling-principles/index.html
@@ -11,7 +11,7 @@
         <link rel="canonical" href="https://monarch-initiative.github.io/monarch-ingest/Principles/modeling-principles/">
 
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-      <meta name="generator" content="mkdocs-1.5.2, mkdocs-material-8.5.10">
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     <li class="md-nav__item">
-      <a href="../../Sources/phenio/" class="md-nav__link">
+      <a href="../../Sources/phenio.md" class="md-nav__link">
         Phenio
       </a>
     </li>