IG: phenopackets/phenomics-exchange-ig, ref: master run_id: 638342431…

…6, run_number: 17, run_attempt: 1 with branch SHA: 11997d7 and merge SHA:
HL7 · Oct 2, 2023 · 22bdcce · 22bdcce
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diff --git a/IG_BUILDS.md b/IG_BUILDS.md
@@ -1,6 +1,6 @@
 # IG Builds  
 [ig/branch/dev](https://phenopackets.github.io/core-ig/ig/branch/dev/index.html?version=a08265f2813ba85e43ca78061c3fadf00e6296d4)  
-[ig/branch/master](https://phenopackets.github.io/core-ig/ig/branch/master/index.html?version=893ec9034884526eb12ca35d06e8c2c067d5542a)  
+[ig/branch/master](https://phenopackets.github.io/phenomics-exchange-ig/ig/branch/master/index.html?version=11997d7d5e3abfb2b9ed715427a90f8084deee3a)  
 [ig/pull/89_FROM_ShahimEssaid_core-ig_shahim-test-branch_TO_master](https://phenopackets.github.io/core-ig/ig/pull/89_FROM_ShahimEssaid_core-ig_shahim-test-branch_TO_master/index.html?version=028998923d9f4ea9ca47fbec858a8bd1d569d279)  
 [ig/pull/90_FROM_ShahimEssaid_core-ig_pr-demo_TO_master](https://phenopackets.github.io/core-ig/ig/pull/90_FROM_ShahimEssaid_core-ig_pr-demo_TO_master/index.html?version=25d92694c4e5f3a3fabb5212aff37a367b556479)  
 [ig/pull/90_FROM_ShahimEssaid_core-ig_pr-demo_TO_master_MERGED](https://phenopackets.github.io/core-ig/ig/pull/90_FROM_ShahimEssaid_core-ig_pr-demo_TO_master_MERGED/index.html?version=0074a55ee17c46dacd8c9996e0733e537f8a951d)  

diff --git a/ig/branch/master/Bundle-PhenopacketsBundleExample01.change.history.html b/ig/branch/master/Bundle-PhenopacketsBundleExample01.change.history.html
@@ -7,7 +7,7 @@
 <html xml:lang="en" xmlns="http://www.w3.org/1999/xhtml" lang="en">
   <head>
     <meta content="text/html;charset=utf-8" http-equiv="Content-Type"/>
-    <title>HL7.FHIR.US.GA4GH.PHENOPACKET\ - FHIR v4.0.1</title>
+    <title> - GA4GH Phenopacket (version 2) FHIR Implementation Guide v0.1.0</title>
 
     <meta name="viewport" content="width=device-width, initial-scale=1.0"/>
     <meta name="author" content="http://hl7.org/fhir"/>
@@ -33,10 +33,10 @@
     <![endif]-->
 
     <!-- Favicons -->
-    <link rel="apple-touch-icon-precomposed" sizes="144x144" href="assets/ico/apple-touch-icon-144-precomposed.png"/>
-    <link rel="apple-touch-icon-precomposed" sizes="114x114" href="assets/ico/apple-touch-icon-114-precomposed.png"/>
-    <link rel="apple-touch-icon-precomposed" sizes="72x72" href="assets/ico/apple-touch-icon-72-precomposed.png"/>
-    <link rel="apple-touch-icon-precomposed" href="assets/ico/apple-touch-icon-57-precomposed.png"/>
+    <link rel="fhir-logo" sizes="144x144" href="assets/ico/icon-fhir-144.png"/>
+    <link rel="fhir-logo" sizes="114x114" href="assets/ico/icon-fhir-114.png"/>
+    <link rel="fhir-logo" sizes="72x72" href="assets/ico/icon-fhir-72.png"/>
+    <link rel="fhir-logo" href="assets/ico/icon-fhir-57.png"/>
     <link rel="shortcut icon" href="assets/ico/favicon.png"/>
   </head>
   <body onload="document.body.style.opacity='1'">
@@ -289,7 +289,7 @@ <h2 id="root">: Bundle/PhenopacketsBundleExample01 - Change History</h2>
 
       <div class="inner-wrapper">
         <p>
-          IG &#169; 2021+ <a style="color:var(--footer-hyperlink-text-color)" href="https://www.ga4gh.org/work_stream/clinical-phenotypic-data-capture-2/">Global Alliance for Genomics and Health - Clinical and Phenotypic Data Capture Work Stream</a>.  Package hl7.fhir.us.ga4gh.phenopacket#0.1.0 based on <a style="color: var(--footer-hyperlink-text-color)" href="http://hl7.org/fhir/R4/">FHIR 4.0.1</a>. Generated <span title="Fri, Jan 27, 2023 19:24+0000">2023-01-27</span>
+          IG &#169; 2021+ <a style="color:var(--footer-hyperlink-text-color)" href="https://www.ga4gh.org/work_stream/clinical-phenotypic-data-capture-2/">Global Alliance for Genomics and Health - Clinical and Phenotypic Data Capture Work Stream</a>.  Package hl7.fhir.us.ga4gh.phenopacket#0.1.0 based on <a style="color: var(--footer-hyperlink-text-color)" href="http://hl7.org/fhir/R4/">FHIR 4.0.1</a>. Generated <span title="Mon, Oct 2, 2023 17:28+0000">2023-10-02</span>
           <br/>
           <span style="color: var(--footer-highlight-text-color)">
                       Links: <a style="color: var(--footer-hyperlink-text-color)" href="toc.html">Table of Contents</a> |

diff --git a/ig/branch/master/Bundle-PhenopacketsBundleExample01.html b/ig/branch/master/Bundle-PhenopacketsBundleExample01.html
diff --git a/ig/branch/master/Bundle-PhenopacketsBundleExample01.json b/ig/branch/master/Bundle-PhenopacketsBundleExample01.json
diff --git a/ig/branch/master/Bundle-PhenopacketsBundleExample01.json.html b/ig/branch/master/Bundle-PhenopacketsBundleExample01.json.html
diff --git a/ig/branch/master/Bundle-PhenopacketsBundleExample01.ttl b/ig/branch/master/Bundle-PhenopacketsBundleExample01.ttl
diff --git a/ig/branch/master/Bundle-PhenopacketsBundleExample01.ttl.html b/ig/branch/master/Bundle-PhenopacketsBundleExample01.ttl.html
diff --git a/ig/branch/master/Bundle-PhenopacketsBundleExample01.xml b/ig/branch/master/Bundle-PhenopacketsBundleExample01.xml
diff --git a/ig/branch/master/Bundle-PhenopacketsBundleExample01.xml.html b/ig/branch/master/Bundle-PhenopacketsBundleExample01.xml.html
diff --git a/ig/branch/master/CodeSystem-HtsFormat-testing.html b/ig/branch/master/CodeSystem-HtsFormat-testing.html
@@ -3,7 +3,7 @@
 <html xml:lang="en" xmlns="http://www.w3.org/1999/xhtml" lang="en">
   <head>
     <meta content="text/html;charset=utf-8" http-equiv="Content-Type"/>
-    <title>HL7.FHIR.US.GA4GH.PHENOPACKET\HTS Format - Testing - FHIR v4.0.1</title>
+    <title>HTS Format - Testing - GA4GH Phenopacket (version 2) FHIR Implementation Guide v0.1.0</title>
 
     <meta name="viewport" content="width=device-width, initial-scale=1.0"/>
     <meta name="author" content="http://hl7.org/fhir"/>
@@ -29,10 +29,10 @@
     <![endif]-->
 
     <!-- Favicons -->
-    <link rel="apple-touch-icon-precomposed" sizes="144x144" href="assets/ico/apple-touch-icon-144-precomposed.png"/>
-    <link rel="apple-touch-icon-precomposed" sizes="114x114" href="assets/ico/apple-touch-icon-114-precomposed.png"/>
-    <link rel="apple-touch-icon-precomposed" sizes="72x72" href="assets/ico/apple-touch-icon-72-precomposed.png"/>
-    <link rel="apple-touch-icon-precomposed" href="assets/ico/apple-touch-icon-57-precomposed.png"/>
+    <link rel="fhir-logo" sizes="144x144" href="assets/ico/icon-fhir-144.png"/>
+    <link rel="fhir-logo" sizes="114x114" href="assets/ico/icon-fhir-114.png"/>
+    <link rel="fhir-logo" sizes="72x72" href="assets/ico/icon-fhir-72.png"/>
+    <link rel="fhir-logo" href="assets/ico/icon-fhir-57.png"/>
     <link rel="shortcut icon" href="assets/ico/favicon.png"/>
   </head>
   <body onload="document.body.style.opacity='1'">
@@ -236,6 +236,7 @@ <h2 id="root">CodeSystem: HTS Format - Testing
 
   </h2>
 
+
   <table class="colsi">
     <tr>
 
@@ -254,7 +255,19 @@ <h2 id="root">CodeSystem: HTS Format - Testing
 
 
 
-  <p><b>No TestScripts are currently available for the  CodeSystem.</b></p>
+<!-- insert intro if present -->
+
+
+
+
+<h3>Test Plans</h3>
+
+  <p><b>No test plans are currently available for the  CodeSystem.</b></p>
+
+
+<h3>Test Scripts</h3>
+
+  <p><b>No test scripts are currently available for the  CodeSystem.</b></p>
 
 
 <!-- insert notes if present -->
@@ -286,7 +299,7 @@ <h2 id="root">CodeSystem: HTS Format - Testing
 
       <div class="inner-wrapper">
         <p>
-          IG &#169; 2021+ <a style="color:var(--footer-hyperlink-text-color)" href="https://www.ga4gh.org/work_stream/clinical-phenotypic-data-capture-2/">Global Alliance for Genomics and Health - Clinical and Phenotypic Data Capture Work Stream</a>.  Package hl7.fhir.us.ga4gh.phenopacket#0.1.0 based on <a style="color: var(--footer-hyperlink-text-color)" href="http://hl7.org/fhir/R4/">FHIR 4.0.1</a>. Generated <span title="Fri, Jan 27, 2023 19:24+0000">2023-01-27</span>
+          IG &#169; 2021+ <a style="color:var(--footer-hyperlink-text-color)" href="https://www.ga4gh.org/work_stream/clinical-phenotypic-data-capture-2/">Global Alliance for Genomics and Health - Clinical and Phenotypic Data Capture Work Stream</a>.  Package hl7.fhir.us.ga4gh.phenopacket#0.1.0 based on <a style="color: var(--footer-hyperlink-text-color)" href="http://hl7.org/fhir/R4/">FHIR 4.0.1</a>. Generated <span title="Mon, Oct 2, 2023 17:28+0000">2023-10-02</span>
           <br/>
           <span style="color: var(--footer-highlight-text-color)">
                       Links: <a style="color: var(--footer-hyperlink-text-color)" href="toc.html">Table of Contents</a> |

diff --git a/ig/branch/master/CodeSystem-HtsFormat.change.history.html b/ig/branch/master/CodeSystem-HtsFormat.change.history.html
@@ -7,7 +7,7 @@
 <html xml:lang="en" xmlns="http://www.w3.org/1999/xhtml" lang="en">
   <head>
     <meta content="text/html;charset=utf-8" http-equiv="Content-Type"/>
-    <title>HL7.FHIR.US.GA4GH.PHENOPACKET\ - FHIR v4.0.1</title>
+    <title> - GA4GH Phenopacket (version 2) FHIR Implementation Guide v0.1.0</title>
 
     <meta name="viewport" content="width=device-width, initial-scale=1.0"/>
     <meta name="author" content="http://hl7.org/fhir"/>
@@ -33,10 +33,10 @@
     <![endif]-->
 
     <!-- Favicons -->
-    <link rel="apple-touch-icon-precomposed" sizes="144x144" href="assets/ico/apple-touch-icon-144-precomposed.png"/>
-    <link rel="apple-touch-icon-precomposed" sizes="114x114" href="assets/ico/apple-touch-icon-114-precomposed.png"/>
-    <link rel="apple-touch-icon-precomposed" sizes="72x72" href="assets/ico/apple-touch-icon-72-precomposed.png"/>
-    <link rel="apple-touch-icon-precomposed" href="assets/ico/apple-touch-icon-57-precomposed.png"/>
+    <link rel="fhir-logo" sizes="144x144" href="assets/ico/icon-fhir-144.png"/>
+    <link rel="fhir-logo" sizes="114x114" href="assets/ico/icon-fhir-114.png"/>
+    <link rel="fhir-logo" sizes="72x72" href="assets/ico/icon-fhir-72.png"/>
+    <link rel="fhir-logo" href="assets/ico/icon-fhir-57.png"/>
     <link rel="shortcut icon" href="assets/ico/favicon.png"/>
   </head>
   <body onload="document.body.style.opacity='1'">
@@ -289,7 +289,7 @@ <h2 id="root">: HtsFormat - Change History</h2>
 
       <div class="inner-wrapper">
         <p>
-          IG &#169; 2021+ <a style="color:var(--footer-hyperlink-text-color)" href="https://www.ga4gh.org/work_stream/clinical-phenotypic-data-capture-2/">Global Alliance for Genomics and Health - Clinical and Phenotypic Data Capture Work Stream</a>.  Package hl7.fhir.us.ga4gh.phenopacket#0.1.0 based on <a style="color: var(--footer-hyperlink-text-color)" href="http://hl7.org/fhir/R4/">FHIR 4.0.1</a>. Generated <span title="Fri, Jan 27, 2023 19:24+0000">2023-01-27</span>
+          IG &#169; 2021+ <a style="color:var(--footer-hyperlink-text-color)" href="https://www.ga4gh.org/work_stream/clinical-phenotypic-data-capture-2/">Global Alliance for Genomics and Health - Clinical and Phenotypic Data Capture Work Stream</a>.  Package hl7.fhir.us.ga4gh.phenopacket#0.1.0 based on <a style="color: var(--footer-hyperlink-text-color)" href="http://hl7.org/fhir/R4/">FHIR 4.0.1</a>. Generated <span title="Mon, Oct 2, 2023 17:28+0000">2023-10-02</span>
           <br/>
           <span style="color: var(--footer-highlight-text-color)">
                       Links: <a style="color: var(--footer-hyperlink-text-color)" href="toc.html">Table of Contents</a> |

diff --git a/ig/branch/master/CodeSystem-HtsFormat.html b/ig/branch/master/CodeSystem-HtsFormat.html
@@ -3,7 +3,7 @@
 <html xml:lang="en" xmlns="http://www.w3.org/1999/xhtml" lang="en">
   <head>
     <meta content="text/html;charset=utf-8" http-equiv="Content-Type"/>
-    <title>HL7.FHIR.US.GA4GH.PHENOPACKET\HTS Format - FHIR v4.0.1</title>
+    <title>HTS Format - GA4GH Phenopacket (version 2) FHIR Implementation Guide v0.1.0</title>
 
     <meta name="viewport" content="width=device-width, initial-scale=1.0"/>
     <meta name="author" content="http://hl7.org/fhir"/>
@@ -29,10 +29,10 @@
     <![endif]-->
 
     <!-- Favicons -->
-    <link rel="apple-touch-icon-precomposed" sizes="144x144" href="assets/ico/apple-touch-icon-144-precomposed.png"/>
-    <link rel="apple-touch-icon-precomposed" sizes="114x114" href="assets/ico/apple-touch-icon-114-precomposed.png"/>
-    <link rel="apple-touch-icon-precomposed" sizes="72x72" href="assets/ico/apple-touch-icon-72-precomposed.png"/>
-    <link rel="apple-touch-icon-precomposed" href="assets/ico/apple-touch-icon-57-precomposed.png"/>
+    <link rel="fhir-logo" sizes="144x144" href="assets/ico/icon-fhir-144.png"/>
+    <link rel="fhir-logo" sizes="114x114" href="assets/ico/icon-fhir-114.png"/>
+    <link rel="fhir-logo" sizes="72x72" href="assets/ico/icon-fhir-72.png"/>
+    <link rel="fhir-logo" href="assets/ico/icon-fhir-57.png"/>
     <link rel="shortcut icon" href="assets/ico/favicon.png"/>
   </head>
   <body onload="document.body.style.opacity='1'">
@@ -293,10 +293,10 @@ <h2 id="root">CodeSystem: HTS Format
   </p>
 
 
-<p>This CodeSystem is not used here; it may be used elsewhere (e.g. specifications and/or implementations that use this content)</p>
+<ul><li>This CodeSystem is not used here; it may be used elsewhere (e.g. specifications and/or implementations that use this content)</li></ul>
 
 
-  <div xmlns="http://www.w3.org/1999/xhtml"><p>This code system <code>https://github.com/phenopackets/core-ig/CodeSystem/HtsFormat</code> defines the following codes:</p><table class="codes"><tr><td style="white-space:nowrap"><b>Code</b></td><td><b>Display</b></td></tr><tr><td style="white-space:nowrap">UNKNOWN<a name="HtsFormat-UNKNOWN"> </a></td><td>Unknown</td></tr><tr><td style="white-space:nowrap">SAM<a name="HtsFormat-SAM"> </a></td><td>SAM</td></tr><tr><td style="white-space:nowrap">BAM<a name="HtsFormat-BAM"> </a></td><td>BAM</td></tr><tr><td style="white-space:nowrap">CRAM<a name="HtsFormat-CRAM"> </a></td><td>CRAM</td></tr><tr><td style="white-space:nowrap">VCF<a name="HtsFormat-VCF"> </a></td><td>VCF</td></tr><tr><td style="white-space:nowrap">BCF<a name="HtsFormat-BCF"> </a></td><td>BCF</td></tr><tr><td style="white-space:nowrap">GVCF<a name="HtsFormat-GVCF"> </a></td><td>GVCF</td></tr></table></div>
+  <div xmlns="http://www.w3.org/1999/xhtml"><p>This  code system <code>https://github.com/phenopackets/core-ig/CodeSystem/HtsFormat</code> defines the following codes:</p><table class="codes"><tr><td style="white-space:nowrap"><b>Code</b></td><td><b>Display</b></td></tr><tr><td style="white-space:nowrap">UNKNOWN<a name="HtsFormat-UNKNOWN"> </a></td><td>Unknown</td></tr><tr><td style="white-space:nowrap">SAM<a name="HtsFormat-SAM"> </a></td><td>SAM</td></tr><tr><td style="white-space:nowrap">BAM<a name="HtsFormat-BAM"> </a></td><td>BAM</td></tr><tr><td style="white-space:nowrap">CRAM<a name="HtsFormat-CRAM"> </a></td><td>CRAM</td></tr><tr><td style="white-space:nowrap">VCF<a name="HtsFormat-VCF"> </a></td><td>VCF</td></tr><tr><td style="white-space:nowrap">BCF<a name="HtsFormat-BCF"> </a></td><td>BCF</td></tr><tr><td style="white-space:nowrap">GVCF<a name="HtsFormat-GVCF"> </a></td><td>GVCF</td></tr></table></div>
 
 
 
@@ -329,7 +329,7 @@ <h2 id="root">CodeSystem: HTS Format
 
       <div class="inner-wrapper">
         <p>
-          IG &#169; 2021+ <a style="color:var(--footer-hyperlink-text-color)" href="https://www.ga4gh.org/work_stream/clinical-phenotypic-data-capture-2/">Global Alliance for Genomics and Health - Clinical and Phenotypic Data Capture Work Stream</a>.  Package hl7.fhir.us.ga4gh.phenopacket#0.1.0 based on <a style="color: var(--footer-hyperlink-text-color)" href="http://hl7.org/fhir/R4/">FHIR 4.0.1</a>. Generated <span title="Fri, Jan 27, 2023 19:24+0000">2023-01-27</span>
+          IG &#169; 2021+ <a style="color:var(--footer-hyperlink-text-color)" href="https://www.ga4gh.org/work_stream/clinical-phenotypic-data-capture-2/">Global Alliance for Genomics and Health - Clinical and Phenotypic Data Capture Work Stream</a>.  Package hl7.fhir.us.ga4gh.phenopacket#0.1.0 based on <a style="color: var(--footer-hyperlink-text-color)" href="http://hl7.org/fhir/R4/">FHIR 4.0.1</a>. Generated <span title="Mon, Oct 2, 2023 17:28+0000">2023-10-02</span>
           <br/>
           <span style="color: var(--footer-highlight-text-color)">
                       Links: <a style="color: var(--footer-hyperlink-text-color)" href="toc.html">Table of Contents</a> |

diff --git a/ig/branch/master/CodeSystem-HtsFormat.json b/ig/branch/master/CodeSystem-HtsFormat.json
@@ -3,7 +3,7 @@
   "id" : "HtsFormat",
   "text" : {
     "status" : "generated",
-    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p>This code system <code>https://github.com/phenopackets/core-ig/CodeSystem/HtsFormat</code> defines the following codes:</p><table class=\"codes\"><tr><td style=\"white-space:nowrap\"><b>Code</b></td><td><b>Display</b></td></tr><tr><td style=\"white-space:nowrap\">UNKNOWN<a name=\"HtsFormat-UNKNOWN\"> </a></td><td>Unknown</td></tr><tr><td style=\"white-space:nowrap\">SAM<a name=\"HtsFormat-SAM\"> </a></td><td>SAM</td></tr><tr><td style=\"white-space:nowrap\">BAM<a name=\"HtsFormat-BAM\"> </a></td><td>BAM</td></tr><tr><td style=\"white-space:nowrap\">CRAM<a name=\"HtsFormat-CRAM\"> </a></td><td>CRAM</td></tr><tr><td style=\"white-space:nowrap\">VCF<a name=\"HtsFormat-VCF\"> </a></td><td>VCF</td></tr><tr><td style=\"white-space:nowrap\">BCF<a name=\"HtsFormat-BCF\"> </a></td><td>BCF</td></tr><tr><td style=\"white-space:nowrap\">GVCF<a name=\"HtsFormat-GVCF\"> </a></td><td>GVCF</td></tr></table></div>"
+    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p>This  code system <code>https://github.com/phenopackets/core-ig/CodeSystem/HtsFormat</code> defines the following codes:</p><table class=\"codes\"><tr><td style=\"white-space:nowrap\"><b>Code</b></td><td><b>Display</b></td></tr><tr><td style=\"white-space:nowrap\">UNKNOWN<a name=\"HtsFormat-UNKNOWN\"> </a></td><td>Unknown</td></tr><tr><td style=\"white-space:nowrap\">SAM<a name=\"HtsFormat-SAM\"> </a></td><td>SAM</td></tr><tr><td style=\"white-space:nowrap\">BAM<a name=\"HtsFormat-BAM\"> </a></td><td>BAM</td></tr><tr><td style=\"white-space:nowrap\">CRAM<a name=\"HtsFormat-CRAM\"> </a></td><td>CRAM</td></tr><tr><td style=\"white-space:nowrap\">VCF<a name=\"HtsFormat-VCF\"> </a></td><td>VCF</td></tr><tr><td style=\"white-space:nowrap\">BCF<a name=\"HtsFormat-BCF\"> </a></td><td>BCF</td></tr><tr><td style=\"white-space:nowrap\">GVCF<a name=\"HtsFormat-GVCF\"> </a></td><td>GVCF</td></tr></table></div>"
   },
   "url" : "https://github.com/phenopackets/core-ig/CodeSystem/HtsFormat",
   "version" : "0.1.0",