paragraph stubs

[ci skip]

This build is based on
f146adf.

This commit was created by the following CI build and job:
https://github.com/plantbreeding/BrAPI-Manuscript2/commit/f146adfafed11799c83fd5af034fc05cce37885c/checks
https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/7994283657

README.md

@@ -1,7 +1,7 @@
 # Output directory containing the formatted manuscript
 
 The [`gh-pages`](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/gh-pages) branch hosts the contents of this directory at <https://plantbreeding.github.io/BrAPI-Manuscript2/>.
-The permalink for this webpage version is <https://plantbreeding.github.io/BrAPI-Manuscript2/v/c3012d7de55f8ca84d7e5e9ea3aeb8c1d431b821/>.
+The permalink for this webpage version is <https://plantbreeding.github.io/BrAPI-Manuscript2/v/f146adfafed11799c83fd5af034fc05cce37885c/>.
 To redirect to the permalink for the latest manuscript version at anytime, use the link <https://plantbreeding.github.io/BrAPI-Manuscript2/v/freeze/>.
 
 ## Files
@@ -35,4 +35,4 @@ Verifying timestamps with the `ots verify` command requires running a local bitc
 ## Source
 
 The manuscripts in this directory were built from
-[`c3012d7de55f8ca84d7e5e9ea3aeb8c1d431b821`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/c3012d7de55f8ca84d7e5e9ea3aeb8c1d431b821).
+[`f146adfafed11799c83fd5af034fc05cce37885c`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/f146adfafed11799c83fd5af034fc05cce37885c).

index.html

@@ -60,8 +60,8 @@
   <meta name="dc.date" content="2024-02-21" />
   <meta name="citation_publication_date" content="2024-02-21" />
   <meta property="article:published_time" content="2024-02-21" />
-  <meta name="dc.modified" content="2024-02-21T17:20:18+00:00" />
-  <meta property="article:modified_time" content="2024-02-21T17:20:18+00:00" />
+  <meta name="dc.modified" content="2024-02-21T19:10:37+00:00" />
+  <meta property="article:modified_time" content="2024-02-21T19:10:37+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -76,7 +76,6 @@
   <meta name="citation_author_orcid" content="0000-0002-5974-6523" />
   <meta name="citation_author" content="Khaled Al-Shamaa" />
   <meta name="citation_author_institution" content="ICARDA" />
-  <meta name="citation_author_orcid" content="" />
   <meta name="citation_author" content="Isabelle Alic" />
   <meta name="citation_author_institution" content="INRAE" />
   <meta name="citation_author_orcid" content="0000-0002-8961-6068" />
@@ -97,9 +96,9 @@
   <meta name="citation_fulltext_html_url" content="https://plantbreeding.github.io/BrAPI-Manuscript2/" />
   <meta name="citation_pdf_url" content="https://plantbreeding.github.io/BrAPI-Manuscript2/manuscript.pdf" />
   <link rel="alternate" type="application/pdf" href="https://plantbreeding.github.io/BrAPI-Manuscript2/manuscript.pdf" />
-  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/c3012d7de55f8ca84d7e5e9ea3aeb8c1d431b821/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/c3012d7de55f8ca84d7e5e9ea3aeb8c1d431b821/" />
-  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/c3012d7de55f8ca84d7e5e9ea3aeb8c1d431b821/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/f146adfafed11799c83fd5af034fc05cce37885c/" />
+  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/f146adfafed11799c83fd5af034fc05cce37885c/" />
+  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/f146adfafed11799c83fd5af034fc05cce37885c/manuscript.pdf" />
   <meta property="og:type" content="article" />
   <meta property="twitter:card" content="summary_large_image" />
   <link rel="icon" type="image/png" sizes="192x192" href="https://manubot.org/favicon-192x192.png" />
@@ -116,9 +115,9 @@ <h1 class="title">BrAPI Success Stories</h1>
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/c3012d7de55f8ca84d7e5e9ea3aeb8c1d431b821/">permalink</a>)
+(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/f146adfafed11799c83fd5af034fc05cce37885c/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/c3012d7de55f8ca84d7e5e9ea3aeb8c1d431b821">plantbreeding/BrAPI-Manuscript2@c3012d7</a>
+from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/f146adfafed11799c83fd5af034fc05cce37885c">plantbreeding/BrAPI-Manuscript2@f146adf</a>
 on February 21, 2024.
 </em></small></p>
 <h2 id="authors">Authors</h2>
@@ -146,8 +145,6 @@ <h2 id="authors">Authors</h2>
 </small></p></li>
 <li><p><strong>Khaled Al-Shamaa</strong>
 <br>
-<img src="images/orcid.svg" class="inline_icon" width="16" height="16" alt="ORCID icon" />
-<a href="https://orcid.org/"></a>
 · <img src="images/github.svg" class="inline_icon" width="16" height="16" alt="GitHub icon" />
 <a href="https://github.com/khaled-alshamaa">khaled-alshamaa</a>
 <br>
@@ -300,7 +297,7 @@ <h4 id="breedbase">Breedbase</h4>
 <p>Since the inception of BrAPI in 2014, the Breedbase group has been a heavy contributor to the BrAPI community.</p>
 <h4 id="bims">BIMS</h4>
 <!-- Peter S: Stub paragraph to stimulate the writing process. Please edit, rewrite, or delete as needed. -->
-<p>BIMS is relatively new to the BrPAI community, with their primary focus being a link to the Field Book mobile data collection app.</p>
+<p>BIMS is relatively new to the BrAPI community, with their primary focus being a link to the Field Book mobile data collection app.</p>
 <h4 id="germinate">Germinate</h4>
 <!-- Peter S: Stub paragraph to stimulate the writing process. Please edit, rewrite, or delete as needed. -->
 <p>Germinate is a combination breeding database and germplasm management database.</p>
@@ -371,6 +368,9 @@ <h4 id="mgis">MGIS</h4>
 <h4 id="gigwa">GIGWA</h4>
 <!-- Peter S: Stub paragraph to stimulate the writing process. Please edit, rewrite, or delete as needed. -->
 <p>GIGWA is an efficient storage system for genotype variant data. GIGWA uses BrAPI to query specific variant data out of the database. This allows for more efficient data transfer and analysis. Instead of transferring whole massive files, specific pieces, samples, markers, or chunks of data can be retrieved.</p>
+<h4 id="phg">PHG</h4>
+<!-- Peter S: Stub paragraph to stimulate the writing process. Please edit, rewrite, or delete as needed. -->
+<p>The Practical Haplotype Graph (PHG) project allows the review and analysis of genotype data in a different format. The data stored in the PHG system is accessible through BrAPI, making it compatible with older existing analysis pipelines.</p>
 <h3 id="data-portal">Data Portal</h3>
 <!-- * General use case description(s)
 * Specific tool examples