docs: Bring documentation (fully) up to date

public/docs/mavedb/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: ad4296d0777365c695d333cc4f10b8f1
+config: e35d92ec77efec5540951c13e48841cc
 tags: 645f666f9bcd5a90fca523b33c5a78b7

public/docs/mavedb/_sources/index.rst.txt

@@ -13,8 +13,7 @@ To report issues or request new features, please use the `MaveDB issue tracker`_
 .. toctree::
    :maxdepth: 2
 
-   .. getting_started
-
+   getting_started
    accounts
    record_types/index
    targets
@@ -29,6 +28,7 @@ To report issues or request new features, please use the `MaveDB issue tracker`_
    output_formats
    collections
    assay_facts
+   mavemd/index
    visualizations
    api/index
    external_integrations

public/docs/mavedb/accession_numbers.html

@@ -173,7 +173,7 @@ <h3>Navigation</h3>
       </ul>
     </div>
     <div class="footer" role="contentinfo">
-    &#169; Copyright 2017-2025, MaveDB Developers.
+    &#169; Copyright 2017-2026, MaveDB Developers.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
     </div>
   </body>

public/docs/mavedb/accounts.html

@@ -16,7 +16,7 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="Record types" href="record_types/index.html" />
-    <link rel="prev" title="Getting started with MaveDB" href="getting_started.html" />
+    <link rel="prev" title="Evaluating functional assays" href="mavemd/evaluating_functional_assays.html" />
 <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Neuton&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
 <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Nobile:regular,italic,bold,bolditalic&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
 <!--[if lte IE 6]>
@@ -35,7 +35,7 @@ <h3>Navigation</h3>
           <a href="record_types/index.html" title="Record types"
              accesskey="N">next</a> |</li>
         <li class="right" >
-          <a href="getting_started.html" title="Getting started with MaveDB"
+          <a href="mavemd/evaluating_functional_assays.html" title="Evaluating functional assays"
              accesskey="P">previous</a> |</li>
         <li class="nav-item nav-item-0"><a href="index.html">MaveDB 2025.5.2 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">User account management</a></li> 
@@ -91,8 +91,8 @@ <h3><a href="index.html">Table of Contents</a></h3>
   </div>
   <div>
     <h4>Previous topic</h4>
-    <p class="topless"><a href="getting_started.html"
-                          title="previous chapter">Getting started with MaveDB</a></p>
+    <p class="topless"><a href="mavemd/evaluating_functional_assays.html"
+                          title="previous chapter">Evaluating functional assays</a></p>
   </div>
   <div>
     <h4>Next topic</h4>
@@ -130,14 +130,14 @@ <h3>Navigation</h3>
           <a href="record_types/index.html" title="Record types"
              >next</a> |</li>
         <li class="right" >
-          <a href="getting_started.html" title="Getting started with MaveDB"
+          <a href="mavemd/evaluating_functional_assays.html" title="Evaluating functional assays"
              >previous</a> |</li>
         <li class="nav-item nav-item-0"><a href="index.html">MaveDB 2025.5.2 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">User account management</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
-    &#169; Copyright 2017-2025, MaveDB Developers.
+    &#169; Copyright 2017-2026, MaveDB Developers.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
     </div>
   </body>

public/docs/mavedb/api/index.html

@@ -108,7 +108,7 @@ <h3>Navigation</h3>
       </ul>
     </div>
     <div class="footer" role="contentinfo">
-    &#169; Copyright 2017-2025, MaveDB Developers.
+    &#169; Copyright 2017-2026, MaveDB Developers.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
     </div>
   </body>

public/docs/mavedb/assay_facts.html

@@ -15,7 +15,7 @@
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="Visualizations" href="visualizations.html" />
+    <link rel="next" title="MaveMD" href="mavemd/index.html" />
     <link rel="prev" title="Data set collections" href="collections.html" />
 <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Neuton&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
 <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Nobile:regular,italic,bold,bolditalic&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
@@ -32,7 +32,7 @@ <h3>Navigation</h3>
           <a href="genindex.html" title="General Index"
              accesskey="I">index</a></li>
         <li class="right" >
-          <a href="visualizations.html" title="Visualizations"
+          <a href="mavemd/index.html" title="MaveMD"
              accesskey="N">next</a> |</li>
         <li class="right" >
           <a href="collections.html" title="Data set collections"
@@ -118,8 +118,8 @@ <h4>Previous topic</h4>
   </div>
   <div>
     <h4>Next topic</h4>
-    <p class="topless"><a href="visualizations.html"
-                          title="next chapter">Visualizations</a></p>
+    <p class="topless"><a href="mavemd/index.html"
+                          title="next chapter">MaveMD</a></p>
   </div>
   <div role="note" aria-label="source link">
     <h3>This Page</h3>
@@ -149,7 +149,7 @@ <h3>Navigation</h3>
           <a href="genindex.html" title="General Index"
              >index</a></li>
         <li class="right" >
-          <a href="visualizations.html" title="Visualizations"
+          <a href="mavemd/index.html" title="MaveMD"
              >next</a> |</li>
         <li class="right" >
           <a href="collections.html" title="Data set collections"
@@ -159,7 +159,7 @@ <h3>Navigation</h3>
       </ul>
     </div>
     <div class="footer" role="contentinfo">
-    &#169; Copyright 2017-2025, MaveDB Developers.
+    &#169; Copyright 2017-2026, MaveDB Developers.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
     </div>
   </body>

public/docs/mavedb/bulk_downloads.html

@@ -128,7 +128,7 @@ <h3>Navigation</h3>
       </ul>
     </div>
     <div class="footer" role="contentinfo">
-    &#169; Copyright 2017-2025, MaveDB Developers.
+    &#169; Copyright 2017-2026, MaveDB Developers.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
     </div>
   </body>

public/docs/mavedb/citation.html

@@ -114,7 +114,7 @@ <h3>Navigation</h3>
       </ul>
     </div>
     <div class="footer" role="contentinfo">
-    &#169; Copyright 2017-2025, MaveDB Developers.
+    &#169; Copyright 2017-2026, MaveDB Developers.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
     </div>
   </body>

public/docs/mavedb/collections.html

@@ -184,7 +184,7 @@ <h3>Navigation</h3>
       </ul>
     </div>
     <div class="footer" role="contentinfo">
-    &#169; Copyright 2017-2025, MaveDB Developers.
+    &#169; Copyright 2017-2026, MaveDB Developers.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
     </div>
   </body>

public/docs/mavedb/controlled_vocabulary.html

@@ -287,7 +287,7 @@ <h3>Navigation</h3>
       </ul>
     </div>
     <div class="footer" role="contentinfo">
-    &#169; Copyright 2017-2025, MaveDB Developers.
+    &#169; Copyright 2017-2026, MaveDB Developers.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
     </div>
   </body>

public/docs/mavedb/data_formats.html

@@ -466,7 +466,7 @@ <h3>Navigation</h3>
       </ul>
     </div>
     <div class="footer" role="contentinfo">
-    &#169; Copyright 2017-2025, MaveDB Developers.
+    &#169; Copyright 2017-2026, MaveDB Developers.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
     </div>
   </body>

public/docs/mavedb/data_set_search.html

@@ -143,7 +143,7 @@ <h3>Navigation</h3>
       </ul>
     </div>
     <div class="footer" role="contentinfo">
-    &#169; Copyright 2017-2025, MaveDB Developers.
+    &#169; Copyright 2017-2026, MaveDB Developers.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
     </div>
   </body>

public/docs/mavedb/external_integrations.html

@@ -146,7 +146,7 @@ <h3>Navigation</h3>
       </ul>
     </div>
     <div class="footer" role="contentinfo">
-    &#169; Copyright 2017-2025, MaveDB Developers.
+    &#169; Copyright 2017-2026, MaveDB Developers.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
     </div>
   </body>

public/docs/mavedb/faqs.html

@@ -123,7 +123,7 @@ <h3>Navigation</h3>
       </ul>
     </div>
     <div class="footer" role="contentinfo">
-    &#169; Copyright 2017-2025, MaveDB Developers.
+    &#169; Copyright 2017-2026, MaveDB Developers.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
     </div>
   </body>

public/docs/mavedb/genindex.html

@@ -77,7 +77,7 @@ <h3>Navigation</h3>
       </ul>
     </div>
     <div class="footer" role="contentinfo">
-    &#169; Copyright 2017-2025, MaveDB Developers.
+    &#169; Copyright 2017-2026, MaveDB Developers.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
     </div>
   </body>

public/docs/mavedb/getting_started.html

@@ -15,6 +15,8 @@
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
+    <link rel="next" title="Variant Search" href="mavemd/variant_search.html" />
+    <link rel="prev" title="MaveDB documentation" href="index.html" />
 <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Neuton&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
 <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Nobile:regular,italic,bold,bolditalic&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
 <!--[if lte IE 6]>
@@ -29,6 +31,12 @@ <h3>Navigation</h3>
         <li class="right" style="margin-right: 10px">
           <a href="genindex.html" title="General Index"
              accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="mavemd/variant_search.html" title="Variant Search"
+             accesskey="N">next</a> |</li>
+        <li class="right" >
+          <a href="index.html" title="MaveDB documentation"
+             accesskey="P">previous</a> |</li>
         <li class="nav-item nav-item-0"><a href="index.html">MaveDB 2025.5.2 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Getting started with MaveDB</a></li> 
       </ul>
@@ -95,6 +103,16 @@ <h3><a href="index.html">Table of Contents</a></h3>
 </ul>
 
   </div>
+  <div>
+    <h4>Previous topic</h4>
+    <p class="topless"><a href="index.html"
+                          title="previous chapter">MaveDB documentation</a></p>
+  </div>
+  <div>
+    <h4>Next topic</h4>
+    <p class="topless"><a href="mavemd/variant_search.html"
+                          title="next chapter">Variant Search</a></p>
+  </div>
   <div role="note" aria-label="source link">
     <h3>This Page</h3>
     <ul class="this-page-menu">
@@ -122,12 +140,18 @@ <h3>Navigation</h3>
         <li class="right" style="margin-right: 10px">
           <a href="genindex.html" title="General Index"
              >index</a></li>
+        <li class="right" >
+          <a href="mavemd/variant_search.html" title="Variant Search"
+             >next</a> |</li>
+        <li class="right" >
+          <a href="index.html" title="MaveDB documentation"
+             >previous</a> |</li>
         <li class="nav-item nav-item-0"><a href="index.html">MaveDB 2025.5.2 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Getting started with MaveDB</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
-    &#169; Copyright 2017-2025, MaveDB Developers.
+    &#169; Copyright 2017-2026, MaveDB Developers.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
     </div>
   </body>

public/docs/mavedb/index.html

@@ -15,7 +15,7 @@
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="User account management" href="accounts.html" />
+    <link rel="next" title="Getting started with MaveDB" href="getting_started.html" />
 <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Neuton&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
 <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Nobile:regular,italic,bold,bolditalic&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
 <!--[if lte IE 6]>
@@ -31,7 +31,7 @@ <h3>Navigation</h3>
           <a href="genindex.html" title="General Index"
              accesskey="I">index</a></li>
         <li class="right" >
-          <a href="accounts.html" title="User account management"
+          <a href="getting_started.html" title="Getting started with MaveDB"
              accesskey="N">next</a> |</li>
         <li class="nav-item nav-item-0"><a href="#">MaveDB 2025.5.2 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">MaveDB documentation</a></li> 
@@ -52,6 +52,10 @@ <h1>MaveDB documentation<a class="headerlink" href="#mavedb-documentation" title
 To report issues or request new features, please use the <a class="reference external" href="https://github.com/VariantEffect/mavedb-api/issues">MaveDB issue tracker</a>.</p>
 <div class="toctree-wrapper compound" id="index">
 <ul>
+<li class="toctree-l1"><a class="reference internal" href="getting_started.html">Getting started with MaveDB</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="getting_started.html#what-is-mavedb">What is MaveDB?</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="accounts.html">User account management</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="accounts.html#setting-an-email-address">Setting an email address</a></li>
 <li class="toctree-l2"><a class="reference internal" href="accounts.html#api-access-tokens">API access tokens</a></li>
@@ -131,6 +135,13 @@ <h1>MaveDB documentation<a class="headerlink" href="#mavedb-documentation" title
 <li class="toctree-l2"><a class="reference internal" href="assay_facts.html#assay-fact-sheet-properties">Assay fact sheet properties</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="mavemd/index.html">MaveMD</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="mavemd/variant_search.html">Variant Search</a></li>
+<li class="toctree-l2"><a class="reference internal" href="mavemd/curation.html">Data Set Curation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="mavemd/clinical_view.html">Variant Clinical View</a></li>
+<li class="toctree-l2"><a class="reference internal" href="mavemd/evaluating_functional_assays.html">Evaluating functional assays</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="visualizations.html">Visualizations</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="visualizations.html#histogram">Histogram</a></li>
 <li class="toctree-l2"><a class="reference internal" href="visualizations.html#heatmap">Heatmap</a></li>
@@ -169,8 +180,8 @@ <h1>MaveDB documentation<a class="headerlink" href="#mavedb-documentation" title
         <div class="sphinxsidebarwrapper">
   <div>
     <h4>Next topic</h4>
-    <p class="topless"><a href="accounts.html"
-                          title="next chapter">User account management</a></p>
+    <p class="topless"><a href="getting_started.html"
+                          title="next chapter">Getting started with MaveDB</a></p>
   </div>
   <div role="note" aria-label="source link">
     <h3>This Page</h3>
@@ -200,14 +211,14 @@ <h3>Navigation</h3>
           <a href="genindex.html" title="General Index"
              >index</a></li>
         <li class="right" >
-          <a href="accounts.html" title="User account management"
+          <a href="getting_started.html" title="Getting started with MaveDB"
              >next</a> |</li>
         <li class="nav-item nav-item-0"><a href="#">MaveDB 2025.5.2 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">MaveDB documentation</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
-    &#169; Copyright 2017-2025, MaveDB Developers.
+    &#169; Copyright 2017-2026, MaveDB Developers.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
     </div>
   </body>